Decoding Human T Cell Immunity with Artificial Intelligence and Single-Cell Genomics

T cells are key mediators of adaptive immunity, yet their highly dynamic response states and immense T cell receptor (TCR) diversity pose challenges in deciphering their functional roles in human diseases. Recent advances in single-cell genomics and TCR sequencing provide unprecedented opportunities to resolve T cell heterogeneity, decode clonal response dynamics, and facilitate high-throughput antigen specificity mapping. In this review, we summarize major technological innovations that have transformed T cell research, from experimental tools for antigen-specific T cell profiling to machine learning frameworks for predicting interactions between the TCR and peptide-MHC (pMHC) and structural modeling powered by deep learning. We discuss current bottlenecks, including data limitations and model generalizability, and explore emerging strategies to guide the next generation of T cell discoveries. We argue that artificial intelligence and single-cell genomics will collectively pave the way for dissecting T cell heterogeneity, mapping TCR sequence to pMHC specificity, and interpreting these features in the context of clinical outcomes.