Long non-coding RNAs as a novel source of beta cell autoantigens in type 1 diabetes

Abstract

Aims/hypothesisGenome-wide association studies increasingly highlight the role of non-coding regions in complex diseases such as type 1 diabetes, pointing, in particular, to long non-coding RNAs (lncRNAs) as potentially active molecular players. Emerging evidence suggests that lncRNAs may encode (small) peptides with the potential to modulate cellular processes, including immune responses. In this study, we have investigated whether these (micro)peptides translated from lncRNAs can act as neoantigens capable of activating autoreactive CD4T cells in individuals with type 1 diabetes. MethodsWe have integrated transcriptomic, proteomic and in silico data to identify a subset of lncRNAs with genuine peptide-coding potential in basal or inflamed-condition beta cells. We further assessed the suitability of those candidates to encode (micro)peptides by sequence analysis and in vitro experimentation techniques. Finally, we have predicted HLA-II epitopes within the micropeptide candidates and evaluated their immunogenicity by analyzing T cell activation responses in peripheral blood mononuclear cells from HLA matching individuals with type 1 diabetes. ResultsBy merging ribosome-bound RNA sequencing with nascent peptide mass spectrometry, we identified a total of 30 lncRNAs with potential coding capacity. We verified the peptide-coding ORF translation for three lncRNA candidates: UXT-AS1, RAPGEF4-AS1 and ENSG00000227066. After predicting potential type 1 diabetes risk-associated HLA-DRB1*03:01 and HLA-DRB1*04:01-binding epitopes within translated lncRNA (micro)peptides, we identified several peptides that elicited CD4+ T cell activation. Furthermore, several epitopes elicited T cell activation in multiple donors with type 1 diabetes. T cell lines were isolated and studied to confirm responses restricted by type 1 diabetes risk HLA alleles. ConclusionsThese results reveal a novel class of immunogenic (micro)peptides derived from lncRNAs, supporting their potential role in the autoimmune response that underlies type 1 diabetes. Our findings open new perspectives on the contribution of non-coding genomic elements to autoimmunity and highlight the need to further investigate lncRNA-encoded (micro)peptides as possible targets for future immunotherapies. RESEARCH IN CONTEXTO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIShort proteins can sometimes be translated from lncRNAs. C_LIO_LIType 1 diabetes neoepitopes arising from non-native forms of proteins and their post translational modifications have been described. C_LI What is the key question?O_LICan lncRNA-encoded peptides be recognized by the human immune system and contribute to type 1 diabetes development? C_LI What are the new findings?O_LIWe have identified three candidate lncRNAs with peptide coding capacity. C_LIO_LIEpitopes derived from these peptides drive T cell activation in PBMCs of individuals with type 1 diabetes. C_LIO_LIPresentation of some of these peptides are restricted to type 1 diabetes risk-associated HLA-DRB1*03:01 and *04:01 molecules. C_LI How might this impact on clinical practice in the foreseeable future?O_LIDiscovery of lncRNA-derived peptide reactive T cells might serve as a diagnostic or stratification indicator in the early stages of disease development, aiding the development of more personalized treatments and unlocking a new array of therapeutic targets. C_LI