MoSAIC: Multi-Resolution Spatial Regression Analysis of Cellular Colocalizations in Cancer Imaging

Abstract: Hierarchical multiplex imaging approaches generate spatially resolved single-cell measurements across multiple, spatially organized fields of view (FOVs) within patient tumor specimens, thereby enabling systematic investigation of how the organization of the tumor microenvironment varies along biologically meaningful intratumoral gradients. Existing approaches fail to jointly address this multi-resolution data structure needed to recover true biological signals. We propose MoSAIC: multi-resolution spatial regression analysis of cell colocalizations, a hierarchical Bayesian spatial regression model designed for multi-resolution spatial data. MoSAIC decomposes the joint variation into three model components: (i) global tumor-gradient effects, (ii) patient-specific effects to capture inter-patient variability, and (iii) Gaussian process models to account for spatial dependence between FOVs within each patient tumor tissue. Simulations demonstrate MoSAIC has improved prediction and model fit compared to existing spatial and non-spatial model alternatives. Our method is motivated by and applied to a renal cell carcinoma multiplex imaging cohort to investigate immune-tumor colocalization patterns across the epithelial-to-mesenchymal transition (EMT) gradient. MoSAIC identifies increased macrophage-tumor colocalization and decreased cytotoxic T-tumor colocalization progressing across the increasing EMT gradient, consistent with EMT-associated immune suppression and spatially varying immune engagement. Overall, MoSAIC provides an interpretable, multi-resolution framework for quantifying spatial tumor-gradient effects in cancer imaging studies. Software is available on GitHub at jcaldous/MoSAIC.