Multi-omic characterization of genetic variants in IBD risk loci - PROJECT SUMMARY/ABSTRACT The NIDDK IBD Genetics Consortium (IBDGC) has led Genome-wide association studies (GWAS) that have determined >250 genomic loci associated with IBD. The vast majority of these loci, which can contain hundreds of variants, are in non-coding regions enriched for regulatory elements. As a result, determining both the casual variant and the mechanism by which this variation contributes to IBD is not known for most. A primary goal of this IBDGC Ancillary RFA is to fill this gap. In line with this goal, we hypothesize that most IBD GWAS loci contribute to disease by altering activity of regulatory elements defined by accessible, chemically modified chromatin resulting in changed gene expression and cellular function. Molecular quantitative trait loci (QTL) define genetic variants associated with cellular processes such as gene expression (eQTL), alternative splicing isoform usage (sQTL), and gene regulation (chromatin accessible caQTL). These analyses have great potential to suggest the missing mechanistic link between GWAS loci and the associated disease. Large-scale molecular QTL efforts in human tissues and cells have primarily used biological material from non-diseased individuals. While QTLs have been identified for some GWAS loci, the recent Gene-Tissue Expression (GTEx) consortium showed a surprising lack of ability to comprehensively determine GWAS-linked eQTL. We hypothesize this lack of success specifically for IBD is due to three primary factors: (1) only performing eQTL and sQTL and not QTL related to gene regulation; (2) performing analyses in samples from non-IBD individuals; and (3) limited sample size. We propose to address this challenge by first focusing on analysis of IBD patient derived tissue samples, and second performing both expression-based eQTL and sQTL analyses and chromatin-based caQTL analyses to better link genetic variants to gene regulatory mechanisms. We aim to recruit a diverse patient population to ensure better generalizability of our results to all IBD patients. To better annotate regulatory region activity, we will also determine genome-wide landscapes for four histone modifications (H3K36me3, H3K27ac, H3K27me3, H3K4me3) that have been linked to IBD. Based on QTL analyses, we will identify putative casual variants in IBD GWAS loci and investigate their functional mechanisms in intestinal epithelial cells using patient derived 2D intestinal monolayer systems. The successful completion of this project will significantly increase our understanding of how genetic variation contributes to the risk of developing IBD.
