Human islet antigen reactive CD4+ memory T cells (IAR T cells) play a key role in the pathogenesis of autoimmune type 1 diabetes (T1D). Using single cell RNA-sequencing (scRNA-seq) to identify T cell receptors (TCRs) in IAR T cells, we identified a multi-specific class of T1D-associated T cell receptors (TCRs) that share TCR alpha chains between individuals (“public”). We isolated IAR T cells from blood of healthy, new onset and established T1D donors using multiplexed CD154 enrichment and identified paired TCR alpha/beta sequences from 2767 individual cells. More than a quarter of TCR junctions were shared between 2 or more cells (“expanded”) and 29/47 (~62%) of expanded TCRs tested showed specificity for islet antigen epitopes. Public TCRs sharing TCR alpha junctions were most prominent in new onset T1D. Public TCR sequences were more germline-like than unique or ‘private’ TCRs, and had shorter junction sequences, suggestive of fewer random nucleotide insertions. Public TCR alpha junctions were often paired with mismatched TCR beta junctions in TCRs; remarkably, a subset of these TCRs exhibited cross-reactivity towards distinct islet antigen peptides. Our findings demonstrate a prevalent population of IAR T cells with diverse specificities determined by TCRs with restricted TCR alpha junctions and germline-constrained antigen recognition properties. Since these “innate”-like TCRs differ from previously described immunodominant TCR beta chains in autoimmunity, they have implications for fundamental studies of disease drivers, as well as translational application to the identification of immune biomarkers and targets for TCR-based therapeutics. In the present proposal, we seek to extend these findings with IAR T cells in blood to spleen.
