Jacqueline Perrigoue

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and pathophysiology of IBD. Our model consists of individual networks constructed using molecular data generated from intestinal samples isolated from three populations of patients with IBD at different stages of disease. We performed key driver analysis to identify genes predicted to modulate network regulatory states associated with IBD, prioritizing and prospectively validating 12 of the top key drivers experimentally. This validated key driver set not only introduces new regulators of processes central to IBD but also provides the integrated circuits of genetic, molecular, and clinical traits that can be directly queried to interrogate and refine the regulatory framework defining IBD.

Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci.

OBJECTIVES:Genome-wide association studies (GWAS) have identified loci reproducibly associated with inflammatory bowel disease (IBD) and other immune-mediated diseases; however, the molecular mechanisms underlying most of genetic susceptibility remain undefined. Expressional quantitative trait loci (eQTL) of disease-relevant tissue can be employed in order to elucidate the genes and pathways affected by disease-specific genetic variance.METHODS:In this study, we derived eQTLs for human whole blood and intestine tissues of anti-tumor necrosis factor-resistant Crohn’s disease (CD) patients. We interpreted these eQTLs in the context of published IBD GWAS hits to inform on the disease process.RESULTS:At 10% false discovery rate, we discovered that 5,174 genes in blood and 2,063 genes in the intestine were controlled by a nearby single-nucleotide polymorphism (SNP) (i.e., cis-eQTL), among which 1,360 were shared between the two tissues. A large fraction of the identified eQTLs were supported by the regulomeDB database, showing that the eQTLs reside in regulatory elements (odds ratio; OR=3.44 and 3.24 for blood and intestine eQTLs, respectively) as opposed to protein-coding regions. Published IBD GWAS hits as a whole were enriched for blood and intestine eQTLs (OR=2.88 and 2.05; and P value=2.51E-9 and 0.013, respectively), thereby linking genetic susceptibility to control of gene expression in these tissues. Through a systematic search, we used eQTL data to inform 109 out of 372 IBD GWAS SNPs documented in National Human Genome Research Institute catalog, and we categorized the genes influenced by eQTLs according to their functions. Many of these genes have experimentally validated roles in specific cell types contributing to intestinal inflammation.CONCLUSIONS:The blood and intestine eQTLs described in this study represent a powerful tool to link GWAS loci to a regulatory function and thus elucidate the mechanisms underlying the genetic loci associated with IBD and related conditions. Overall, our eQTL discovery approach empirically identifies the disease-associated variants including their impact on the direction and extent of expression changes in the context of disease-relevant cellular pathways in order to infer the functional outcome of this aspect of genetic susceptibility.

Interplay of nutrients and microbial metabolites in intestinal immune homeostasis: distinct and common mechanisms of immune regulation in the small bowel and colon.

The intestinal mucosa is the largest body surface exposed to the environment. While there are common features when comparing immune responses along the intestinal mucosa, the small bowel and colon exhibit striking differences in their mechanisms driving immune regulation. The vitamin A (VA) metabolite all-trans retinoic acid (RA) signaling via RA nuclear receptors plays a key role in immune homeostasis in the small bowel, and recent work indicates that RA is required for establishing immune tolerance to dietary antigens in the upper intestinal tract by inducing α4β7(+)CCR9(+) gut-tropic TREG. In contrast, microbiota-specific TREG in the colon do not appear to require RA, but can be regulated by short-chain fatty acids (SCFA), microbial metabolites that signal through the G protein-coupled receptor GPR43. Moreover, TREG do not need CCR9 to home to the colon, but utilize another G protein-coupled receptor, GPR15, which is upregulated by SCFA. Thus, the mechanisms governing intestinal tolerance to dietary antigens in the upper digestive tract differ from those controlling tolerance to the microbiota in the colon, with RA and SCFA playing key complementary roles in their respective compartments. In addition to VA and SCFA, recent studies have highlighted the roles of other dietary and microbial metabolites that influence immune cell homeostasis across the small and large bowel including dietary ligands for aryl hydrocarbon receptor and microbiota-modified bile acids. Understanding the complex and dynamic interplay between dietary metabolites and commensal microbiota within the intestinal microenvironment could therefore inform novel strategies for the treatment of food allergies and inflammatory bowel diseases.