Background: Genome-wide association studies (GWAS) have identified numerous loci for complex diseases. This success has been most notable for the inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC), where ~100 genetic risk factors have been discovered, some that are phenotype-specific and others that are common to more than one disease. But, how do disease-associated genes and their corresponding alleles exert their influence on the biology of health and disease? The genetic data indicates that IBD can emerge from the perturbations of distinct signal transduction pathways, resulting from the dysregulation of disease-causative genes. Hypothesis and specific aims: Although there has been tremendous success for identifying IBD genetic risk loci using GWAS, this approach primarily leads to the identification of common variants, most of which have modest genetic effect. We postulate that rare variants within these loci might be responsible for the effects observed. To tackle this issue, we propose to perform targeted re-sequencing of validated IBD loci to identify the causal (rare) variation. With the advent of next-generation sequencing technologies and access to well-phenotyped cohorts, we are now able to use this innovative approach, which is complementary to our previous work using GWAS, and sequence UC-associated loci to identify rare variants of greater genetic effect. These rarer, more penetrant, alleles are expected to have a more significant biological impact thus increasing the feasibility and relevance of performing allele-specific functional studies as we propose herein. Intestinal inflammation is a complex process involving an interplay genetic predisposition and environmental factors and can be the result of the dysregulation of different biological processes involving specific cell types. In an attempt to dissect this interplay between genetics and environmental factors and understand the complexity of UC pathogenesis, we will complement our genomics approach with a systematic approach to functionally characterize UC-associated genes in conjunction with different environmental stresses. Given the diverse expertise of our teams, we will combine several functional approaches, including gene-expression analysis, shRNA and allele-specific rescue experiments in different cell types to place the genes and their variants under study in functional pathways in the relevant cell type and environmental context. We anticipate that these studies will point to a subset of key pathways that are perturbed in UC to define disease-mechanism clusters and will provide a more complete picture of the complex biological networks involved in UC.
Our specific aims are:
Aim 1) To identify risk and protective alleles within UC-associated regions identified by GWAS We want to (1A) identify novel uncommon and rare variants by deep re-sequencing in samples from patients and controls and (1B) validate these novel variants by genotyping large cohorts.
Aim 2) To determine the function of UC-candidate genes We propose to take a systematic stepwise approach to place UC-associated genes within biological pathways. We will: (2A) Determine the RNA and protein expression of confirmed UC genes in primary cells and colon biopsies from UC patients and control individuals;(2B) Perform targeted over- expression and RNA interference (RNAi) screens using cell-based functional assays (2C) Determine the biological impact of selected genes (and their variants) at a cell-specific context. Impact: Understanding the mechanisms through which genetic variation contributes to UC, although challenging, offers exciting and promising advances in biomedicine, both by providing new insights into the genetic and molecular basis of UC pathophysiology and by helping to improve diagnosis and therapy. The investigation of causal genes (and their variants) linked to UC combined with our high-throughput and cell-type specific functional analysis will provide a mechanistic understanding of the role of genetic factors in UC. The identification of causal genetic variants linked to UC and their functional implications could provide new guidelines for drug dose adjustment, for changes in treatment modalities and for prevention strategies.

Public Health Relevance

Inflammatory bowel diseases (IBD) are characterized by chronic relapsing inflammation of the gastrointestinal tract. Crohn's disease and ulcerative colitis, the two main subtypes of IBD, have an important impact on health, economic and social welfare systems, as a consequence of the associated morbidity. IBD can affect anyone at any age with the majority of cases being diagnosed in adolescents and young adults;this is a crucial time of life for an individual's education, the ability to establish a stable financial footing andto launch a career and family. This proposal was triggered by the gap in the knowledge of the mechanisms underlying IBD pathophysiology and the pressing need to novel therapeutic targets and the means needed for the tailored management of individual patient care. Our recent genetic work has indicated a way in which to fill this gap. Our aims include understanding the mechanisms through which genetic differences (variations in the DNA) among individuals contribute to disease mechanisms, understand how they affect biological pathways that are perturbed in disease and then establish relevant cell models to explore mechanistic links to disease. Ultimately, our work will lead to the development of new research and clinical tools that could improve IBD detection, diagnosis and treatment.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Project (R01)
Project #
Application #
Study Section
Genetics of Health and Disease Study Section (GHD)
Program Officer
Karp, Robert W
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Montreal Heart Institute
Zip Code
H1 1-C8
Mohanan, Vishnu; Nakata, Toru; Desch, A Nicole et al. (2018) C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Science 359:1161-1166
Huang, Hailiang; Fang, Ming; Jostins, Luke et al. (2017) Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 547:173-178
Kopylov, Uri; Boucher, Gabrielle; Waterman, Matti et al. (2016) Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Inflamm Bowel Dis 22:2311-6
Rivas, Manuel A; Graham, Daniel; Sulem, Patrick et al. (2016) Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun 7:12869
Rivas, Manuel A; Graham, Daniel; Sulem, Patrick et al. (2016) A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun 7:12342
Goyette, Philippe; Boucher, Gabrielle; Mallon, Dermot et al. (2015) High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Nat Genet 47:172-9
Ananthakrishnan, Ashwin N; Huang, Hailiang; Nguyen, Deanna D et al. (2014) Differential effect of genetic burden on disease phenotypes in Crohn's disease and ulcerative colitis: analysis of a North American cohort. Am J Gastroenterol 109:395-400
Ananthakrishnan, Ashwin N; Nguyen, Deanna D; Sauk, Jenny et al. (2014) Genetic polymorphisms in metabolizing enzymes modifying the association between smoking and inflammatory bowel diseases. Inflamm Bowel Dis 20:783-9
Ananthakrishnan, A N; Oxford, E C; Nguyen, D D et al. (2013) Genetic risk factors for Clostridium difficile infection in ulcerative colitis. Aliment Pharmacol Ther 38:522-30
Smeekens, Sanne P; Ng, Aylwin; Kumar, Vinod et al. (2013) Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans. Nat Commun 4:1342

Showing the most recent 10 out of 42 publications