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Generating counterfactual explanations of tumor spatial proteomes to discover effective strategies for enhancing immune infiltration (2211.04020v2)

Published 8 Nov 2022 in q-bio.QM, cs.LG, q-bio.GN, and q-bio.TO

Abstract: The tumor microenvironment (TME) significantly impacts cancer prognosis due to its immune composition. While therapies for altering the immune composition, including immunotherapies, have shown exciting results for treating hematological cancers, they are less effective for immunologically-cold, solid tumors. Spatial omics technologies capture the spatial organization of the TME with unprecedented molecular detail, revealing the relationship between immune cell localization and molecular signals. Here, we formulate T-cell infiltration prediction as a self-supervised machine learning problem and develop a counterfactual optimization strategy that leverages large scale spatial omics profiles of patient tumors to design tumor perturbations predicted to boost T-cell infiltration. A convolutional neural network predicts T-cell distribution based on signaling molecules in the TME provided by imaging mass cytometry. Gradient-based counterfactual generation, then, computes perturbations predicted to boost T-cell abundance. We apply our framework to melanoma, colorectal cancer liver metastases, and breast tumor data, discovering combinatorial perturbations predicted to support T-cell infiltration across tens to hundreds of patients. This work presents a paradigm for counterfactual-based prediction and design of cancer therapeutics using spatial omics data.

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References (34)
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Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Binnewies, M. et al. Understanding the tumor immune microenvironment (time) for effective therapy. Nature medicine 24 (5), 541–550 (2018) . (3) Bruni, D., Angell, H. K. & Galon, J. The immune contexture and immunoscore in cancer prognosis and therapeutic efficacy. Nature Reviews Cancer 20 (11), 662–680 (2020) . (4) Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bruni, D., Angell, H. K. & Galon, J. The immune contexture and immunoscore in cancer prognosis and therapeutic efficacy. Nature Reviews Cancer 20 (11), 662–680 (2020) . (4) Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. 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Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bruni, D., Angell, H. K. & Galon, J. The immune contexture and immunoscore in cancer prognosis and therapeutic efficacy. Nature Reviews Cancer 20 (11), 662–680 (2020) . (4) Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  3. The immune contexture and immunoscore in cancer prognosis and therapeutic efficacy. Nature Reviews Cancer 20 (11), 662–680 (2020) . (4) Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  4. Top 10 challenges in cancer immunotherapy. Immunity 52 (1), 17–35 (2020) . (5) Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Choe, J. H., Williams, J. Z. & Lim, W. A. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  5. Engineering t cells to treat cancer: the convergence of immuno-oncology and synthetic biology. Annual Review of Cancer Biology 4, 121–139 (2020) . (6) Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  6. Pitt, J. et al. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Annals of Oncology 27 (8), 1482–1492 (2016) . (7) Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Haslam, A. & Prasad, V. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. 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(24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  7. Estimation of the percentage of us patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs. JAMA network open 2 (5), e192535–e192535 (2019) . (8) Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lee, J. S. & Ruppin, E. Multiomics prediction of response rates to therapies to inhibit programmed cell death 1 and programmed cell death 1 ligand 1. JAMA oncology 5 (11), 1614–1618 (2019) . (9) Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Pittet, M. J., Michielin, O. & Migliorini, D. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. 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Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  9. Clinical relevance of tumour-associated macrophages. Nature reviews Clinical oncology 19 (6), 402–421 (2022) . (10) Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  10. Bonaventura, P. et al. Cold tumors: a therapeutic challenge for immunotherapy. Frontiers in immunology 10, 168 (2019) . (11) Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  11. Savas, P. et al. Clinical relevance of host immunity in breast cancer: from tils to the clinic. Nature reviews Clinical oncology 13 (4), 228–241 (2016) . (12) Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Tsaur, I., Brandt, M. P., Juengel, E., Manceau, C. & Ploussard, G. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  12. Immunotherapy in prostate cancer: new horizon of hurdles and hopes. World journal of urology 39, 1387–1403 (2021) . (13) Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  13. The emerging landscape of spatial profiling technologies. Nature Reviews Genetics 23 (12), 741–759 (2022) . (14) Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Lanitis, E., Dangaj, D., Irving, M. & Coukos, G. Mechanisms regulating t-cell infiltration and activity in solid tumors. Annals of Oncology 28, xii18–xii32 (2017) . (15) Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. 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(25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . 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(34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Rodriques, S. G. et al. Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science 363 (6434), 1463–1467 (2019) . (16) Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. 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(33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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(21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by rna seqfish+. Nature 568 (7751), 235–239 (2019) . (17) Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nature methods 11 (4), 417–422 (2014) . (18) Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Goltsev, Y. et al. Deep profiling of mouse splenic architecture with codex multiplexed imaging. Cell 174 (4), 968–981 (2018) . (19) Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
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Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Bhate, S. S., Barlow, G. L., Schürch, C. M. & Nolan, G. P. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  19. Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors. Cell Systems 13 (2), 109–130 (2022) . (20) Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  20. Wu, Z. et al. Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature Biomedical Engineering 1–14 (2022) . (21) Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  21. Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182 (5), 1341–1359 (2020) . (22) Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  22. Hoch, T. et al. Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology 7 (70), eabk1692 (2022) . (23) Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  23. Wang, Z. et al. Extracellular vesicles in fatty liver promote a metastatic tumor microenvironment. Cell Metabolism (2023) . (24) Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  24. Danenberg, E. et al. Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature genetics 54 (5), 660–669 (2022) . (25) Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Buda, M., Saha, A. & Mazurowski, M. A. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  25. Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm. Computers in Biology and Medicine 109 (2019). 10.1016/j.compbiomed.2019.05.002 . (26) Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Looveren, A. V. & Klaise, J. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  26. Interpretable counterfactual explanations guided by prototypes. Joint European Conference on Machine Learning and Knowledge Discovery in Databases 650–665 (2021) . (27) Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Hughes, C. E. & Nibbs, R. J. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  27. A guide to chemokines and their receptors. The FEBS journal 285 (16), 2944–2971 (2018) . (28) Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  28. Steele, M. M. et al. T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature Immunology 24 (4), 664–675 (2023) . (29) Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  29. Ghanem, I. et al. Insights on the CXCL12-CXCR4 axis in hepatocellular carcinoma carcinogenesis. American journal of translational research 6 (4), 340 (2014) . (30) Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  30. Biasci, D. et al. CXCR4 inhibition in human pancreatic and colorectal cancers induces an integrated immune response. Proceedings of the National Academy of Sciences 117 (46), 28960–28970 (2020) . (31) Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  31. Chen, Y. et al. Cxcr4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice. Hepatology 61 (5), 1591–1602 (2015) . (32) Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  32. Sullivan, K. M. et al. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 72 (2), 325–337 (2023) . (33) Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  33. Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays. Cell 185 (10), 1777–1792 (2022) . (34) Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) . Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .
  34. Paszke, A. et al. PyTorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems 32 (2019) .

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