CD4+ T cells reactive to a hybrid peptide from insulin-chromogranin A adopt a distinct effector fate and are pathogenic in autoimmune diabetes

T cell-mediated islet destruction is a hallmark of autoimmune diabetes. Here, we examined the dynamics and pathogenicity of CD4+ T cell responses to four different insulin-derived epitopes during diabetes initiation in non-obese diabetic (NOD) mice. Single-cell RNA sequencing of tetramer-sorted CD4+ T cells from the pancreas revealed that islet-antigen-specific T cells adopted a wide variety of fates and required XCR1+ dendritic cells for their activation. Hybrid-insulin C-chromogranin A (InsC-ChgA)-specific CD4+ T cells skewed toward a distinct Th1 (T helper type 1) effector phenotype, whereas the majority of insulin B chain and hybrid-insulin C-islet amyloid polypeptide-specific CD4+ T exhibited a regulatory T cell phenotype and early or weak Th1 phenotype, respectively. InsC-ChgA-specific CD4+ T cells were uniquely pathogenic upon transfer, and an anti-InsC-ChgA:IAg7 antibody prevented spontaneous diabetes. Our findings highlight the heterogeneity of T cell responses to insulin-derived epitopes in diabetes and argue for the feasibility of antigen-specific therapies that blunts the response of pathogenic CD4+ T cells causing autoimmunity. Pancreas-infiltrating CD4+ T cells from 10-week-old mice were sorted using islet-peptide-specific MHCII tetramers for InsC-ChgA, InsC-IAPP, InsBp8E, or InsB p8G. The RNA from tetramer-bound single-cells was then sequenced and cells from individual mice were identified using hashtag oligonucleotides, and antigen-specific cells were identified using unique oligonucleotide tags specific for each tetramer. The data were were analysed for gene expression levels and tetramer positivity. The dataset contains 13 HTO (mouse specific) tags and 4 TET (tetramer specific) tags.