ProTCR: a protein language model-driven framework for decoding TCR-antigen recognition toward precision immunotherapies

The ability of T-cell receptors (TCRs) to recognize neoantigens is fundamental to the initiation and maintenance of adaptive immune responses. In TCR-based immunotherapies, elucidating the recognition patterns of TCRs for peptides and accurately identifying therapeutically relevant TCR-peptide pairs remain critical challenges. Here, we present a novel dual-pathway network model, ProTCR, which integrates the protein language model ProtT5 with deep learning methods. By incorporating both global and local feature extraction mechanisms, ProTCR enables efficient representation of amino acid sequences, thereby enhancing the model's generalizability across diverse data distributions and improving its biological interpretability. ProTCR demonstrates robust performance and broad applicability across various datasets, including neoantigens, previously unseen peptides, and MHC class II-restricted epitopes, overcoming the reliance on known peptide-TCR pairs observed in previous studies. It also offers new insights for predicting diverse classes of antigenic peptides. We applied ProTCR to several clinically relevant scenarios, including immunotherapeutic target identification in acute myeloid leukemia, neoantigen-targeted immunotherapy in solid tumours, and antigen-specific T cell recognition against pathogens such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Across these complex settings, ProTCR consistently maintained high accuracy and stability, demonstrating strong cross-task adaptability and broad potential for clinical application. This work not only provides a powerful tool for elucidating immune response mechanisms but also offers a solid computational foundation for the design of neoantigen or TCR based precision immunotherapy strategies.