Cross-reactive public TCR sequences undergo positive selection in the human thymic repertoire

We studied human T cell repertoire formation using high-throughput T cell receptor beta (TCR beta) complementarity-determining region 3 (CDR3) sequencing in immunodeficient mice receiving human hematopoietic stem cells (HSCs) and human thymus grafts. Replicate humanized mice generated diverse and highly divergent repertoires. We observed repertoire narrowing and increased CDR3 beta sharing during thymocyte selection. Whereas hydrophobicity analysis implicated self-peptides in positive selection of the overall repertoire, positive selection favored shorter shared sequences that had reduced hydrophobicity at positions 6 and 7 of CDR3 beta s, suggesting weaker interactions with self-peptides than were observed with unshared sequences, possibly allowing escape from negative selection. Sharing was similar between autologous and allogeneic thymi and occurred between different cell subsets. Shared sequences were enriched for allo-cross-reactive CDR3 beta s and for type 1 diabetes-associated autoreactive CDR3 beta s. Single-cell TCR sequencing showed increased sharing of CDR3as compared with CDR3 beta s between mice. Our data collectively implicate preferential positive selection for shared human CDR3 beta s that are highly cross-reactive. Although previous studies suggested a role for recombination bias in producing public sequences in mice, our study is the first to our knowledge to demonstrate a role for thymic selection. Our results implicate positive selection for promiscuous TCR beta sequences that probably evade negative selection, given their low affinity for self-ligands, in the abundance of public human TCR beta sequences.