BeAT1D

Autoimmune type 1 diabetes (T1D) is characterized by pancreatic islet inflammation (insulitis) and destruction of insulin-producing beta cells. This destruction involves the recognition of peptide-HLA Class I (pHLA-I) complexes on the beta-cell surface by autoreactive CD8+ T cells. We identified the peptides presented by beta cells using HLA peptidomics and transcriptomics strategies. Surprisingly, CD8+ T cells recognizing these known and novel beta-cell peptides circulate at a similar frequency in T1D and healthy donors and display a largely naïve phenotype (Culina et al, Sci Immunol 2018; Gonzalez-Duque et al, Cell Metab 2018). Thus, a universal state of ‘benign’ islet autoimmunity exists in all individuals, to a much larger extent than previously appreciated. Our overall objective is to understand how benign autoimmunity progresses to T1D in few persons, and not in many others. Our hypothesis is that such progression may rely on two non-mutually exclusive mechanisms: a) loss of immune ignorance toward beta-cell antigens (Ags) that are normally invisible to T cells (beta-cell-centric hypothesis); and b) loss of the immune regulation that controls autoreactive T cells (T-cell-centric hypothesis). In other words, T1D may be an autoimmune disease mediated not only by T cells, but also by the target beta cells themselves. In this context, the dialogue among T cells, Ag-presenting cells and target beta cells will be explored through an integrated strategy, which we have secured with the BeAT1D consortium. Our two Tasks mirror the beta-cell- and T-cell-driven mechanisms outlined above. Task #1. Loss of immune ignorance. We will investigate whether progression to T1D involves a higher vulnerability of beta cells in the face of a naive autoimmune repertoire that is similar across individuals. This vulnerability may be increased in T1D at two levels. First, due to inhibitory signals that are not sufficient to maintain a ‘peaceful’ dialog between beta cells and autoimmune T cells (#1A). We will define the dynamics and outcomes of these inhibitory signals and identify agents that may potentiate them. Second, due to a higher and more diversified (e.g. neo-epitopes) pHLA presentation, either locally by beta cells (#1B) or in the pancreatic lymph nodes by dendritic cells (DCs) (#1C). To address these points, we will use our HLA peptidomics pipelines to characterize the peptidome of beta cells and of DCs exposed to beta cells under resting or inflammatory stress. Task #2. Loss of immune regulation. We will focus on the immune mechanisms regulating the autoimmune T-cell repertoire that we all harbor, which may be defective in T1D. #2A. We will first test the T-cell recognition of the novel HLA-I and HLA-II peptides identified in Task #1, to verify whether the universal benign autoimmunity previously reported also applies to these novel Ags, and to CD4+ T cells. #2B. We will employ short-term in-vitro assays, flow cytometry and single-cell RNAseq to explore candidate pathways already identified by RNAseq that may drive the preferential activation of islet-reactive CD8+ T cells in T1D patients, and to simultaneously define their TCR usage, which may be indicative of in-vivo Ag-driven selection. Dominant TCR clonotypes will be re-expressed in carrier cells to define their beta-cell killing capacity and potential cross-reactivity with microbial mimotopes. This research is expected to offer a novel view of T1D as a T-cell- and beta-cell-mediated autoimmune disease. On one side, the extended panel of Ags identified will allow to quantify the overall autoimmune ‘burden’ of a given individual. On the other, the definition of the mechanisms driving the progression of benign autoimmunity toward T1D should deliver the earliest biomarkers of disease development for prognostic stratification and, possibly, novel therapeutic targets to revert autoimmunity to its benign state.