Enhancer-based Beta Cell Dysregulation Underlying T2D Risk

The vast majority of genetic risk variants associated with T2D GWAS is in non-coding regions, suggesting that they impose risk by altering regulatory elements that control gene expression. Interpretation of identified variants from these extensive studies is currently limited because the clear identity of causative variants in regulatory elements and their regulation of the coding target genes remain unknown. To address these challenges, we are systematically identifying causal enhancer T2D variants and their dysregulated target genes. The human genome is estimated to encode ~1 million enhancer elements, with distinct sets of approximately 40,000–70,000 enhancers being active in a particular cell type. By defining the role of a specific enhancer implicated by a T2D risk association, it is possible to infer the identities of regulatory factors and environmental signals the cell is receiving that might impact T2D. The objective of this work is to identify functional enhancers altered by regulatory T2D variants and uncover their causal impact by high-throughput molecular assays in human iPS-derived beta cells. To this end, we will identify a set of candidate causal variants in enhancers that contribute to the genetic risk of T2D by computational methods that integrate a large number of diverse genomic and epigenomic annotations. We will then perform ultra-high resolution chromatin conformation capture (Tri-HiC) of iPS-derived beta cells to identify the enhancers’ target genes and perform single cell RNA-seq analysis to establish links between the causal enhancer variants and transcriptional outputs. The proposed study will identify enhancer-promoter interaction networks, elucidating whether and to what extent T2D-associated variants alter enhancer function, thereby playing a functional role in T2D genetic risk.