1. Variant-to-Gene-Mapping Analyses Reveal a Role for the Hypothalamus in Genetic Susceptibility to Inflammatory Bowel Disease
- Author
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Diana L. Cousminer, James A. Pippin, Kenyaita M. Hodge, Claudia A. Doege, Matthew E. Johnson, Reza K. Hammond, Michelle E. Leonard, Natalie A. Terry, Matthew C. Pahl, Rudolph L. Leibel, Struan F.A. Grant, Louis R. Ghanem, Chiara Lasconi, Alessandra Chesi, Andrew D. Wells, Sumei Lu, and Chun Su
- Subjects
0301 basic medicine ,Linkage disequilibrium ,Datasets as Topic ,Disease ,Inflammatory bowel disease ,Linkage Disequilibrium ,Pathogenesis ,0302 clinical medicine ,ATAC, Assay for Transposase-Accessible Chromatin ,LDSC, linkage disequilibrium score regression ,Brain-Gut Axis ,Promoter Regions, Genetic ,Padj, adjusted P value ,Original Research ,Neurons ,Genetics ,IBD, inflammatory bowel disease ,Depression ,rg, genetic correlation ,Gastroenterology ,Chromosome Mapping ,HPA ,030211 gastroenterology & hepatology ,SNP, single-nucleotide polymorphism ,cRE, cis-regulatory element ,Hypothalamo-Hypophyseal System ,hESC, human Embryonic Stem Cell ,LD, linkage disequilibrium ,Hypothalamus ,Context (language use) ,Biology ,Stress ,Polymorphism, Single Nucleotide ,MS, multiple sclerosis ,03 medical and health sciences ,Gene mapping ,CNTF, – ,HN, hypothalamic-like neuron ,CD, Crohn’s disease ,medicine ,Genetic predisposition ,Humans ,Genetic Predisposition to Disease ,lcsh:RC799-869 ,GWAS, genome-wide association study ,Gene ,Hepatology ,Inflammatory Bowel Diseases ,medicine.disease ,CRH, corticotrophin-releasing hormone ,RHOA, ras homolog gene family, member A ,HPA, hypothalamus–pituitary–adrenal ,UC, ulcerative colitis ,PSC, primary sclerosing cholangitis ,030104 developmental biology ,Colonoids ,hESC ,Case-Control Studies ,lcsh:Diseases of the digestive system. Gastroenterology ,ACTH, adrenocorticotrophic hormone ,Stress, Psychological ,NE, norepinephrine ,Genome-Wide Association Study - Abstract
Background & Aims Inflammatory bowel disease (IBD) is a polygenic disorder characterized principally by dysregulated inflammation impacting the gastrointestinal tract. However, there also is increasing evidence for a clinical association with stress and depression. Given the role of the hypothalamus in stress responses and in the pathogenesis of depression, useful insights could be gleaned from understanding its genetic role in IBD. Methods We conducted genetic correlation analyses on publicly available genome-wide association study summary statistics for depression and IBD traits to identify genetic commonalities. We used partitioned linkage disequilibrium score regression, leveraging our ATAC sequencing and promoter-focused Capture C data, to measure enrichment of IBD single-nucleotide polymorphisms within promoter-interacting open chromatin regions of human embryonic stem cell-derived hypothalamic-like neurons (HNs). Using the same data sets, we performed variant-to-gene mapping to implicate putative IBD effector genes in HNs. To contrast these results, we similarly analyzed 3-dimensional genomic data generated in epithelium-derived colonoids from rectal biopsy specimens from donors without pathologic disease noted at the time of colonoscopy. Finally, we conducted enrichment pathway analyses on the implicated genes to identify putative IBD dysfunctional pathways. Results We found significant genetic correlations (rg) of 0.122 with an adjusted P (Padj) = 1.4 × 10-4 for IBD: rg = 0.122; Padj = 2.5 × 10-3 for ulcerative colitis and genetic correlation (rg) = 0.094; Padj = 2.5 × 10-3 for Crohn’s disease, and significant approximately 4-fold (P = .005) and approximately 7-fold (P = .03) enrichment of IBD single-nucleotide polymorphisms in HNs and colonoids, respectively. We implicated 25 associated genes in HNs, among which CREM, CNTF, and RHOA encode key regulators of stress. Seven genes also additionally were implicated in the colonoids. We observed an overall enrichment for immune and hormonal signaling pathways, and a colonoid-specific enrichment for microbiota-relevant terms. Conclusions Our results suggest that the hypothalamus warrants further study in the context of IBD pathogenesis., Graphical abstract
- Published
- 2021
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