Project Summary Crohn’s disease (CD) and ulcerative colitis (UC) affect over 2 million individuals in the United States and are associated with considerable morbidity. They develop due to a dysregulated immune response to a dysbiotic microbiome on a background of genetic susceptibility. Environmental factors play an important role in these diseases. However, the mechanisms of influence of environmental determinants is poorly understood, and consequently, insights into disease prevention cannot be inferred. Smoking is the only consistently replicated environmental determinant of IBD. It intriguingly exerts an unexplained divergent effect on CD and UC. Former and current smoking are both associated with an increased risk and greater progression of CD. In contrast, current smoking confers protection against UC and is associated with a milder disease course while former smoking triggers relapses and is associated with a two-fold increase in disease risk. The exact component within the complex exposures comprising cigarette smoke as well as the mechanisms for this divergent effect have not been established. Defining the determinants of this divergent effect will shed fundamental insights on the different biologic pathways (and consequently, differing natural history and progression) in CD and UC. Further, identifying mechanisms for the protective influence of cigarette smoke on UC activity may offer insights into novel therapeutic pathways that can be harnessed for treatment. In this propose, we present an overarching hypothesis that the effect of smoking on disease risk and progression is through its differential impact on the mucosal transcriptome and epigenome in CD and UC. We also hypothesize that this effect differs between current and former smoking. In the first two aims, we will quantify exposure to cigarette smoke by measuring serum cotinine, and examine its biologic impact on the transcriptome and epigenome through RNAseq from ileal and colonic biopsies, and DNA methylation profiles from peripheral blood. By performing pairwise comparisons, we will be able to define the differential biologic impact of smoking by disease-type, smoking history, and disease-location. In the third aim, we will define the contribution of genotype to these biologic effects by performing a novel gene-smoking interaction analysis on three, large well-characterized cohorts to identify variants on whole exome sequencing that modify effect of smoking on transcriptional and epigenetic profiles in CD or UC. The insights obtained from this innovative and exploratory proposal leveraging the strengths of large international genotyped cohorts, expertise in gene-environment interaction analysis, and comprehensive tissue immune-profiling will lay an important foundation for more robust study on the biologic effects of the environment and their translation to disease prevention in CD and UC.