W112 - Non-canonical translation of long non-coding RNAs are a source of neo-antigens in pancreatic beta cells

Leire Bergara – University of the Basque Country UPV/EHU; Ainara Castellanos-Rubio – Biobizkaia Health Research Institute; Eddie James – Benaroya Research Institute; Izortze Santin – University of the Basque Country UPV/EHU

Abstract Text: Genome Wide Association Studies (GWAS) have revealed the presence of type 1 diabetes (T1D) risk variants in non-coding regions of the human genome, including long non-coding RNAs (lncRNAs). lncRNAs are defined as RNA molecules of more than 200 nucleotides that lack coding potential, but there is increasing evidence that short peptides can be translated from small open reading (smORFs) frames in lncRNAs. These micropeptides could affect β cell homeostasis and constitute an unexplored source of neo-antigens, possibly contributing to the perpetuation of the β cell destruction by T cells.
In this study, we aimed to identify lncRNA-derived peptides that act as autoantigens in pancreatic islets. We combined RNA sequencing of ribosome complex-bound RNA from basal and polyinosinic-polycytidylic acid (PIC)-treated human β cells (EndoC-βH1) and mass spectrometry (MS) analysis of the nascent peptides of ribosome complexes to identify candidate lncRNA-derived micropeptides. We then utilized a published algorithm to identify micropeptides likely to be bound and presented by HLA-DRB1*03:01 (a prevalent high-risk HLA-DR allele in our patient population). After confirming binding to HLA-DRB1*03:01 using an in vitro competition assay, we evaluated T cell recognition of candidate micropeptides using activation induced marker assays and HLA class II tetramer staining.
Our results validate an approach for the rapid identification of lncRNA capable of generating micropeptide translation products and suggest that such micropeptides can function as neo-epitopes that drive T cell activation. Our future work will further characterize the translation of micropeptides and the relevance of micropeptide specific T cells in individuals with T1D.