A qualitative and quantitative characterisation of CD8+ T cell targets on human beta cells in Type 1 diabetes: perspectives from a proteomic strategy

Type 1 diabetes (T1D) is a tissue specific autoimmune disease that result from the targeted destruction of the insulin-secreting beta cells in the pancreatic islets. A hallmark of T1D is the infiltration of autoimmune T cells into the islets that is predominantly composed of CD8+ T cells. The strongest genetic association with susceptibility to T1D are to the human leukocyte antigen (HLA) genes, particularly the class II, and to a lesser extent, the class I HLA genes. The class I HLA genes encode for cell surface HLA molecules that constitutively present endogenous antigenic peptides for scrutiny by incoming CD8+ T cells. Autoantigens involved in T1D have been widely characterised, however, little is known about the identities of autoantigenic peptides presented by less studied alleles and the nature of naturally processed and presented CD8+ T cell epitopes that leads to a targeted beta cell destruction as disease unfolds. In this study, the nature of bound peptide antigens (immunopeptidomes) restricted to a panel of T1D associated class I HLA allotypes (HLA-A*01:01, -A*02:01, -A*24:02, - B*08:01 and –B*18:01) were studied in depth using advanced mass spectrometry techniques. First I assessed the immunopeptidomes of C1R cell lines that were individually transfected with each HLA allotype. An extensive class I ligand dataset (up to 18 600 naturally presented peptides) was identified in this study which allowed the extension and clarification of previously reported binding motifs for these class I HLA molecules. We found no differences in the nature of peptide presentation by T1D disease predisposing and protective HLAs. Overall, features (subcellular localisation and biological functions) of source proteins for all five HLA allotypes were similar and we observed that peptide sampling was not affected by source protein masses and lengths. Next, we examined the features of naturally presented autoantigenic peptides by class I HLA allotypes on a panel of surrogate beta