Generative design of antigen-specific T-cell receptor sequences with a conditional diffusion model

Abstract

T cell receptor (TCR)-based immunotherapy holds immense potential for treating cancers, autoimmunity, and infectious diseases, where antigen-specific TCR recognition is crucial for adaptive immune responses. Engineering or de novo generation of the complementarity-determining region 3 (CDR3) loops of TCRs using artificial intelligence offers a powerful alternative to designing antigen-specific TCRs rather than laborious experimental screening. However, current in silico approaches are constrained by weak conditional guidance, limited flexibility, and a lack of rigorous functional validation. To address these limitations, we introduce TCRDiff, a generative diffusion framework for designing antigen-specific TCRs conditioned on peptide-MHC (pMHC) targets and germline-encoded TCR variable genes. By leveraging pre-trained knowledge from massive T-cell repertoires and TCR-pMHC recognition data, TCRDiff generates CDR3{beta} sequences that closely resemble native-binding TCRs via a denoising diffusion process. Furthermore, incorporating interface geometry features generated TCR-pMHC complexes with superior structural plausibility than models relying solely on sequence-based diffusion or structure-based modeling. As a proof of concept, we deployed TCRDiff in a systematic pipeline to design candidate TCRs against a clinically validated cancer antigen. In vitro activation assays validated that TCRDiff-generated TCRs efficiently recognize the MAGE-A3 epitope with minimal off-target reactivity. Thus, TCRDiff establishes a powerful, validated computational paradigm to accelerate the development of TCR-based immunotherapies.