Crohn?s disease and ulcerative colitis, the two major forms of idiopathic inflammatory bowel disease (IBD), are chronic disorders of the gastrointestinal tract affecting ~3.7 million Americans and Europeans, and several hundred thousand more worldwide. Intensive searches for genetic risk factors, including genome-wide association studies (GWAS) and follow-up studies by the NIDDK Inflammatory Bowel Disease Genetics Consortium and the International Inflammatory Bowel Disease Genetics Consortium have yielded significant evidence for association between IBD and >240 genetic loci, and have illuminated biological pathways such as the IL-23/T helper 17 (Th17) immune pathway, autophagy, mucosal barrier function, and immune activation of multiple integrin genes in IBD pathogenesis. While fine genetic association mapping efforts have resolved 51 association signals to a single genetic variant with >50% probability of being causal, the remaining known IBD loci have yet to be fine mapped. Access to large patient sample sizes and the multidisciplinary team science that a consortium facilitates are crucial for the momentum in dissecting the genetics of IBD to continue, and for bridging the gaps between genetic associations, mechanistic understanding, and improved therapies. Thus, in Aim 1 of this competitive renewal application we propose to continue our participation in IBDGC research efforts, and we propose specific consortium-wide projects for consideration by the Steering Committee. A major challenge in moving from genetic associations to mechanistic understanding is the fact that SNP(s) with the strongest association signal(s) in most established IBD loci lie in non-coding regions, where our knowledge of the functional effects of DNA variation pales in contrast to our understanding of the genetic code for amino acids in protein-coding regions. Additionally, genetic studies alone cannot distinguish causal variants from neighboring non-causal variants in linkage disequilibrium for many known IBD association signals. Fortunately, recent studies suggest a way forward. Comparing the locations of non-coding, disease-associated SNPs with chromatin maps in specific cell types and stimulation conditions can prioritize candidate non-coding DNA variants, specific cell types and contexts for follow-up functional studies.
In Aim 2, we will define the molecular effects of IBD-associated, non-coding, accessible chromatin region DNA variation on primary human CD4+CD45RO+CD196(CCR6)+ T cell (a subset including both Th17 and T regulatory [Treg] cells) functional responses to specific stimulation conditions. This work will build on our mapping of accessible chromatin regions in CD4+CD45RO+CD196+ T cells stimulated under two specific conditions, our identification of overlap between these accessible chromatin regions and SNPs in the credible set for each fine mapped IBD locus that is >95% likely to contain the causal variant, and our preliminary integration of chromatin accessibility, RNA-seq and genotype data in the same samples. CRISPR/cas9 genome editing in primary human T cells will be utilized to test the functional effects of accessible chromatin regions harboring IBD-associated SNPs.
Inflammatory bowel disease (IBD) has both genetic and non-genetic risk factors. Genetic variation that has been associated with this complex disorder so far explains only a modest proportion of the estimated disease heritability, so additional genetic studies are needed to more fully explain the heritability. To learn how IBD arises and progresses, we must also understand how the genetic variation associated with IBD affects human biology. We propose to continue supporting the NIDDK IBD Genetics Consortium in all its activities and to explore the effect of genetic variants associated with IBD on immune biology.
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