tcrLM: a lightweight protein language model for predicting T cell receptor and epitope binding specificity

Abstract: The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises from the immense diversity of TCR repository. However, TCR diversity poses a significant challenge on accurately predicting antigen-TCR bindings. In this study, we introduce a lightweight masked LLM, termed tcrLM, to address this challenge. Our approach involves randomly masking segments of TCR sequences and training tcrLM to infer the masked segments, thereby enabling the extraction of expressive features from TCR sequences. To further enhance robustness, we incorporate virtual adversarial training into tcrLM. We construct the largest TCR CDR3 sequence set with more than 100 million distinct sequences, and pretrain tcrLM on these sequences. The pre-trained encoder is subsequently applied to predict TCR-antigen binding specificity. We evaluate model performance on three test datasets: independent, external, and COVID-19 test set. The results demonstrate that tcrLM not only surpasses existing TCR-antigen binding prediction methods, but also outperforms other mainstream protein LLMs. More interestingly, tcrLM effectively captures the biochemical properties and positional preference of amino acids within TCR sequences. Additionally, the predicted TCR-neoantigen binding scores indicates the immunotherapy responses and clinical outcomes in a melanoma cohort. These findings demonstrate the potential of tcrLM in predicting TCR-antigen binding specificity, with significant implications for advancing immunotherapy and personalized medicine.