Dynamic Regulation of Alternative Splicing in the Initiation and Progression of Islet Autoimmunity in The Environmental Determinants of Diabetes in the Young (TEDDY) Study

About This Grant

PROJECT SUMMARY / ABSTRACT Type 1 diabetes (T1D) is an autoimmune disease from an immune-mediated attack on the pancreatic beta cells. As ~5% of those developing T1D have a positive family history, there is little awareness of symptoms. T1D is most virulent in children, yet it affects all age and ancestry groups. The beta cell destruction in T1D is identified only through presence of islet autoantibodies to insulin (IAA), glutamic acid decarboxylase (GADA), insulinoma- associated protein 2 (IA-2A), and zinc transporter 8 (ZnT8A), although their prevalence can vary depending on age, sex, and ancestry. Genetic factors account for ~50% of T1D risk, and we (and others) have identified over 100 loci containing disease-associated variants. The vast majority of T1D variants reside in the non-coding genome and map to enhancer regions in immune-relevant cell types (e.g., CD4+ T cells). The mechanisms underlying the transition from an individual’s genetic risk to islet autoimmunity and development of T1D have not been resolved. The proposed research is an ancillary project of The Environmental Determinants of Diabetes in the Young (TEDDY) study. TEDDY is a longitudinal cohort study designed to discover triggers of islet autoimmunity by following newborns at high genetic risk with frequent follow-up and collection of samples for deep phenotyping and biological profiling. This project proposes to use TEDDY data and PBMC samples to examine an under-studied mechanism in T1D, the role of alternative splicing. Alternative splicing of pre-mRNA generates diversity in gene expression (regulation) and protein in a tissue-specific manner. Errors in alternative splicing can result in errors in gene regulation and has been shown to lead to human disease, including autoimmune diseases. Further, genetic variation also impacts proper splicing of mRNA, generating aberrant variants. We have shown that alternative splicing is associated with T1D in known T1D loci using short-read RNA sequencing. In addition, RNA-binding proteins (RBPs) with roles in alternative splicing can generate different mRNA and protein isoforms with change or loss of protein function. We have identified 12 genes in known T1D loci that encode RBPs of relevance to gene expression and T1D susceptibility. To gain a comprehensive understanding of the role of these RBP-regulated alternative splicing events on initiation and progression of islet autoimmunity leading to T1D, we propose to focus on a relevant cell type (CD4+ T cells) obtained from TEDDY participants at multiple time points during the transition periods of islet autoimmunity. We will obtain long-read RNA sequencing (for full isoform detection) and short-read RNA sequencing (for isoform abundance) to define differential alternative splicing events, construct RBP networks, and utilize deep learning time series models to map T1D risk over time. We will experimentally validate alternatively spliced genes, their RBPs, and biological mechanisms that lead to islet autoimmunity and T1D. Together, the outcome of the proposed research will enable better prediction of islet autoimmunity and T1D risk trajectory, the timing for monitoring, and novel therapeutic interventions in T1D.