Germline-encoded V(D)J gene usage does not impose strict constraints on the epitope-specificity of T cell receptors

Abstract

The theoretical diversity of T cell receptors (TCRs), generated through V(D)J recombination, is enormous, yet the diversity of TCRs capable of recognizing the same epitope remains unknown. Defining this TCR solution space is essential for uncovering basic principles that govern TCR specificity. Using single-cell RNA and TCR sequencing, we generated ultra-deep (more than 4000 unique TCRs per epitope) epitope-specific TCR libraries derived from 560 immunized C57BL/6 mice, identifying over 27,000 unique epitope-reactive TCRs across three distinct CD8+ T cell epitopes presented by two major histocompatibility complex (MHC) class I alleles. Saturation analyses indicated that the solution space for all studied epitopes comprises many tens of thousands of unique TCRs. Despite highly skewed and peptide-dependent VJ-usage patterns, nearly the entire set of functional germline V/ and J/ segments was detected at least once within each epitope-specific repertoire. Therefore, diversity of epitope-specific TCRs is not limited by distinct germline combinations but rather can emerge from a near-to-complete combinatorial space of - and -chain, V and J segments paired with compatible CDR3 sequences.