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.