Autoreactive T cell receptors with shared germline-like alpha chains in type 1 diabetes

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 have identified a class of TCRs that share TCR alpha chains between individuals ("public" chains). We isolated IAR T cells from blood of healthy, new-onset T1D and established T1D donors using multiplexed CD154 enrichment and identified paired TCR alpha/beta sequences from 2767 individual cells. More than a quarter of cells shared TCR junctions between 2 or more cells ("expanded"), and 29/47 (similar to 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 expanded 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 toward 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 mechanisms. Self-reactive restricted TCR alpha chains and their associated epitopes should be considered in fundamental and translational investigations of TCRs in T1D.