Tailoring epitope specificity through TCR chain substitution 3324

Abstract Description The T cell’s ability to recognize antigens relies on the diversity of the T cell receptor (TCR) arising from V(D)J recombination of the two TCR chains, complemented by their random pairing. While it is generally recognized that both TCR chains are crucial for epitope recognition, their relative contribution remains unclear. To estimate the extent to which a single TCR chain determines epitope specificity, we introduced an exogenous TCR chain with known specificity into PBMC samples. This enabled it to pair with diverse endogenous TCR chains, determining the frequency and features of paired repertoires for MAIT, NKT, and conventional HLA class I and II epitopes. For each tested chain, we identified hundreds to thousands of novel, specific receptors showing antigen selection biases. Comparisons with existing data demonstrated that these engineered paired TCRs accurately replicate the natural repertoire. We found suitable partner chain frequencies varied greatly depending on the specific chain tested. The resulting data, including over 70,000 unique epitope-specific paired chain TCRs, broadens our understanding of each chain’s role in epitope recognition and quantifies a previously underestimated amount of single chain sharing across epitope specificities. Utilizing such comprehensive epitope-specific positive and negative data to train TCR-epitope prediction algorithms can enhance the accuracy of TCR specificity predictions. Funding Sources The work was funded by AI136514 and AI150747. Topic Categories Immune Response Regulation: Molecular Mechanisms (IRM)