Dissecting the Molecular Logic of Beta Cell Autoimmune Recognition in Type 1 Diabetes

Abstract

In type 1 diabetes (T1D), beta cells are selectively targeted by an autoreactive immune system, whereas neighboring alpha cells that share the same human leukocyte antigen (HLA) genotype are relatively spared. Although HLA-mediated presentation of self-peptides is implicated in disease, it remains unclear how endocrine identity shapes the peptides displayed on surface HLA class I (HLA-I), how canonical and noncanonical peptide species contribute to immune visibility, and how these differences influence autoreactive recognition. To address this question, we generated cell-type-resolved HLA-I immunopeptidomes from stem-cell-derived alpha and beta cells from a donor with T1D, with a healthy donor analyzed in parallel. We paired these analyses with targeted peptide quantification, peptide-HLA binding measurements, autoreactive T cell receptor (TCR) reporter assays, and single-cell transcriptomic and TCR profiling in a humanized in vivo graft model. The largest alpha-beta differences in peptide display were carried by the principal secretory hormone precursors themselves: hormone-derived peptides from each cell type were enriched in that cell type, and the two precursors differed in how their peptides were distributed across HLA-I loci. Restricting presentation to a subset of HLA-I loci attenuated recognition of a diabetic epitope by an autoreactive TCR. Beyond canonical hormone-derived peptides, beta cells and alpha cells both displayed noncanonical diabetic epitopes, but only beta cells produced non-canonical epitopes that retained precursor-like sequence features, formed productive HLA-I ligands, were detected at copy numbers within the range of established islet autoantigens, and were recognized by diabetic immune cells or an autoreactive TCR reporter. In vivo, challenge with peripheral blood mononuclear cells (PBMCs) from a matched T1D donor reduced beta-cell graft function and was associated with effector T-cell infiltration, expanded clonotypes, and greater clonotype dominance in beta-cell grafts than in alpha-cell grafts. Alpha-cell grafts remained immunologically visible but retained a larger endocrine compartment and a broader, more singleton-rich TCR repertoire, suggesting that immune visibility can be uncoupled from destructive targetability. Together, these data show that endocrine identity, HLA context, noncanonical peptide generation, and local TCR repertoire structure help determine immune visibility in T1D and provide a framework for understanding beta-cell selectivity and for designing replacement cells with reduced immune recognition.