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Gu P, Dube S, Gellada N, Choi SY, Win S, Lee YJ, Yang S, Haritunians T, Melmed GY, Vasiliauskas EA, Bonthala N, Syal G, Yarur AJ, Ziring D, Rabizadeh S, Fleshner P, Kallman C, Devkota S, Targan SR, Li D, McGovern DPB. Pre-operative visceral adipose tissue radiodensity is a potentially novel prognostic biomarker for early endoscopic post-operative recurrence in Crohn's disease. World J Gastrointest Surg 2024; 16:740-750. [PMID: 38577075 PMCID: PMC10989343 DOI: 10.4240/wjgs.v16.i3.740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Evidence suggests inflammatory mesenteric fat is involved in post-operative recurrence (POR) of Crohn's disease (CD). However, its prognostic value is uncertain, in part, due to difficulties studying it non-invasively. AIM To evaluate the prognostic value of pre-operative radiographic mesenteric parameters for early endoscopic POR (ePOR). METHODS We conducted a retrospective cohort study of CD subjects ≥ 12 years who underwent ileocecal or small bowel resection between 1/1/2007 to 12/31/2021 with computerized tomography abdomen/pelvis ≤ 6 months pre-operatively and underwent ileocolonoscopy ≤ 15 months post-operatively. Visceral adipose tissue (VAT) volume (cm3), ratio of VAT:subcutaneous adipose tissue (SAT) volume, VAT radiodensity, and ratio of VAT:SAT radiodensity were generated semiautomatically. Mesenteric lymphadenopathy (LAD, largest lymph node > 10 mm) and severe vasa recta (VR) engorgement (diameter of the VR supplying diseased bowel ≥ 2 × VR supplying healthy bowel) were derived manually. The primary outcome was early ePOR (Rutgeert's score ≥ i2 on first endoscopy ≤ 15 months post-operatively) and the secondary outcome was ePOR severity (Rutgeert's score i0-4). Regression analyses were performed adjusting for demographic and disease-related characteristics to calculate adjusted odds ratio (aOR) and 95% confidence interval (CI). RESULTS Of the 139 subjects included, 45% of subjects developed early ePOR (n = 63). VAT radiodensity (aOR 0.59, 95%CI: 0.38-0.90) and VAT:SAT radiodensity (aOR 8.54, 95%CI: 1.48-49.28) were associated with early ePOR, whereas, VAT volume (aOR 1.23, 95%CI: 0.78-1.95), VAT:SAT volume (aOR 0.80, 95%CI: 0.53-1.20), severe VR engorgement (aOR 1.53, 95%CI: 0.64-3.66), and mesenteric LAD (aOR 1.59, 95%CI: 0.67-3.79) were not. Similar results were observed for severity of ePOR. CONCLUSION VAT radiodensity is potentially a novel non-invasive prognostic imaging marker to help risk stratify CD patients for POR.
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Affiliation(s)
- Phillip Gu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Shishir Dube
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Norman Gellada
- Department of Imaging, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - So Yung Choi
- Department of Biostatistics Shared Resource, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Susan Win
- Department of Imaging, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Yoo Jin Lee
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu 42601, South Korea
| | - Shaohong Yang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Talin Haritunians
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Gil Y Melmed
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Eric A Vasiliauskas
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Niru Bonthala
- Department of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States
| | - Gaurav Syal
- Department of Medicine, University of California at San Diego, San Diego, CA 92093, United States
| | - Andres J Yarur
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - David Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Phillip Fleshner
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Cindy Kallman
- Department of Imaging, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Suzanne Devkota
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Stephan R Targan
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dalin Li
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dermot PB McGovern
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
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Khrom M, Long M, Dube S, Robbins L, Botwin GJ, Yang S, Mengesha E, Li D, Naito T, Bonthala NN, Ha C, Melmed G, Rabizadeh S, Syal G, Vasiliauskas E, Ziring D, Brant SR, Cho J, Duerr RH, Rioux J, Schumm P, Silverberg M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Xavier RJ, Kugathasan S, Hercules D, Targan SR, Sartor RB, Haritunians T, McGovern DPB. Comprehensive Association Analyses of Extraintestinal Manifestations in Inflammatory Bowel Disease. Gastroenterology 2024:S0016-5085(24)00232-4. [PMID: 38490347 DOI: 10.1053/j.gastro.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel disease (IBD) frequently develop extraintestinal manifestations (EIMs) that contribute substantially to morbidity. We assembled the largest multicohort data set to date to investigate the clinical, serologic, and genetic factors associated with EIM complications in IBD. METHODS Data were available in 12,083 unrelated European ancestry IBD cases with presence or absence of EIMs (eg, ankylosing spondylitis [ankylosing spondylitis and sacroiliitis], primary sclerosing cholangitis [PSC], peripheral arthritis, and skin and ocular manifestations) across 4 cohorts (Cedars-Sinai Medical Center, National Institute for Diabetes and Digestive and Kidney Diseases IBD Genetics Consortium, Sinai Helmsley Alliance for Research Excellence Consortium, and Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn's Disease cohort). Clinical and serologic parameters were analyzed by means of univariable and multivariable regression analyses using a mixed-effects model. Within-case logistic regression was performed to assess genetic associations. RESULTS Most EIMs occurred more commonly in female subjects (overall EIM: P = 9.0E-05, odds ratio [OR], 1.2; 95% CI, 1.1-1.4), with CD (especially colonic disease location; P = 9.8E-09, OR, 1.7; 95% CI, 1.4-2.0), and in subjects who required surgery (both CD and UC; P = 3.6E-19, OR, 1.7; 95% CI, 1.5-1.9). Smoking increased risk of EIMs except for PSC, where there was a "protective" effect. Multiple serologic associations were observed, including with PSC (IgG and IgA, perinuclear anti-nuclear cytoplasmic antibody; anti-Saccharomyces cerevisiae antibodies; and anti-flagellin) and any EIM (IgG and IgA, perinuclear anti-nuclear cytoplasmic antibody; anti-Saccharomyces cerevisiae antibodies; and anti-Pseudomonas fluorescens-associated sequence). We identified genome-wide significant associations within major histocompatibility complex (ankylosing spondylitis and sacroiliitis, P = 1.4E-15; OR, 2.5; 95% CI, 2.0-3.1; PSC, P = 2.7E-10; OR, 2.8; 95% CI, 2.0-3.8; ocular, P = 2E-08, OR, 3.6; 95% CI, 2.3-5.6; and overall EIM, P = 8.4E-09; OR, 2.2; 95% CI, 1.7-2.9) and CPEB4 (skin, P = 2.7E-08; OR, 1.5; 95% CI, 1.3-1.8). Genetic associations implicated tumor necrosis factor, JAK-STAT, and IL6 as potential targets for EIMs. Contrary to previous reports, only 2% of our subjects had multiple EIMs and most co-occurrences were negatively correlated. CONCLUSIONS We have identified demographic, clinical, and genetic associations with EIMs that revealed underlying mechanisms and implicated novel and existing drug targets-important steps toward a more personalized approach to IBD management.
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Millie Long
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Lori Robbins
- Palmetto Digestive Health Specialists, Charleston, South Carolina
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christina Ha
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gil Melmed
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shervin Rabizadeh
- Department of Pediatrics, Pediatric Inflammatory Bowel Disease Program, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gaurav Syal
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Eric Vasiliauskas
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Ziring
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, New York
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John Rioux
- Department of Medicine, Université de Montréal and Research Center, Montreal Heart Institute, Montréal, Québec, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Mark Silverberg
- University of Toronto, Samuel Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Bana Jabri
- University of Chicago, Pritzker School of Medicine, Chicago, Illinois
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Subra Kugathasan
- Children's Healthcare of Atlanta Combined Center for Pediatric Inflammatory Bowel Disease, Atlanta, Georgia; Emory School of Medicine, Atlanta, Georgia
| | | | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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McDonald GB, Landsverk OJ, McGovern DP, Aasebø A, Paulsen V, Haritunians T, Reims HM, McLaughlin BM, Zisman T, Li D, Elholm ET, Jahnsen FL, Georges GE, Gedde-Dahl T. Allogeneic bone marrow transplantation for patients with treatment-refractory Crohn's Disease. Heliyon 2024; 10:e24026. [PMID: 38283244 PMCID: PMC10818189 DOI: 10.1016/j.heliyon.2024.e24026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
Background & aims Durable remissions of Crohn's Disease (CD) have followed myeloablative conditioning therapy and allogeneic marrow transplantation. For patients with treatment-refractory disease, we used reduced-intensity conditioning to minimize toxicity, marrow from donors with low Polygenic Risk Scores for CD as cell sources, and protracted immune suppression to lower the risk of graft-versus-host disease (GVHD). Our aim was to achieve durable CD remissions while minimizing transplant-related complications. Methods DNA from patients and their HLA-matched unrelated donors was genotyped and Polygenic Risk Scores calculated. Donor marrow was infused following non-myeloablative conditioning. Patient symptoms and endoscopic findings were documented at intervals after transplant. Results We screened 807 patients, 143 of whom met eligibility criteria; 2 patients received allografts. Patient 1 had multiple complications and died at day 332 from respiratory failure. Patient 2 had resolution of CD symptoms until day 178 when CD recurred, associated with persistent host chimerism in both peripheral blood and intestinal mucosa. Withdrawal of immune suppression was followed by dominant donor immune chimerism in peripheral blood and resolution of CD findings. Over time, mucosal T-cells became donor-dominant. At 5 years after allografting, Patient 2 remained off all medications but had mild symptoms related to a jejunal stricture that required stricturoplasty at 6 years. At 8 years, she remains stable off medications. Conclusions The kinetics of immunologic chimerism after allogeneic marrow transplantation for CD patients depends on the intensity of the conditioning regimen and the magnitude of immune suppression. One patient achieved durable improvement of her previously refractory CD only after establishing donor immunologic chimerism in intestinal mucosa. Her course provides proof-of-principal for allografting as a potential treatment for refractory CD, but an immunoablative conditioning regimen should be considered for future studies.(ClinicalTrials.gov, NCT01570348).
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Affiliation(s)
- George B. McDonald
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anders Aasebø
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Vemund Paulsen
- Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Norway
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Henrik M. Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Timothy Zisman
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elisabeth T.M.M. Elholm
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Hematology, Oslo University Hospital, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Frode L. Jahnsen
- Department of Pathology, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Norway
| | - George E. Georges
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Tobias Gedde-Dahl
- Department of Hematology, Oslo University Hospital, Norway and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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4
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Malique A, Sun S, Chandwe K, Amadi B, Haritunians T, Jain U, Muegge BD, Frein J, Sasaki Y, Foster A, Storer CE, Mengesha E, Kern J, McGovern DPB, Head RD, Kelly P, Liu TC. NAD + precursors and bile acid sequestration treat preclinical refractory environmental enteric dysfunction. Sci Transl Med 2024; 16:eabq4145. [PMID: 38170788 DOI: 10.1126/scitranslmed.abq4145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Environmental enteric dysfunction (EED) is a diffuse small bowel disorder associated with poor growth, inadequate responses to oral vaccines, and nutrient malabsorption in millions of children worldwide. We identify loss of the small intestinal Paneth and goblet cells that are critical for innate immunity, reduced villous height, increased bile acids, and dysregulated nicotinamide adenine dinucleotide (NAD+) synthesis signaling as potential mechanisms underlying EED and which also correlated with diminished length-for-age z score. Isocaloric low-protein diet (LPD) consumption in mice recapitulated EED histopathology and transcriptomic changes in a microbiota-independent manner, as well as increases in serum and fecal bile acids. Children with refractory EED harbor single-nucleotide polymorphisms in key enzymes involved in NAD+ synthesis. In mice, deletion of Nampt, the gene encoding the rate-limiting enzyme in the NAD+ salvage pathway, from intestinal epithelium also reduced Paneth cell function, a deficiency that was further aggravated by LPD. Separate supplementation with NAD+ precursors or bile acid sequestrant partially restored LPD-associated Paneth cell defects and, when combined, fully restored all histopathology defects in LPD-fed mice. Therapeutic regimens that increase protein and NAD+ contents while reducing excessive bile acids may benefit children with refractory EED.
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Affiliation(s)
- Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shengxiang Sun
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer Frein
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amanda Foster
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Justin Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
- Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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5
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Gu P, Dube S, Lee Y, Yang S, Li D, Haritunians T, Vasiliauskas E, Bonthala N, Syal G, Yarur A, Ziring D, Targan S, Rabizadeh S, Melmed GY, Fleshner P, McGovern DPB. Comparative Persistence of Non-tumor Necrosis Factor (TNF) vs. TNF Antagonists for Post-operative Prophylaxis in Crohn's Disease (CD). Dig Dis Sci 2024; 69:235-245. [PMID: 38015321 PMCID: PMC10787872 DOI: 10.1007/s10620-023-08192-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND The comparative safety and effectiveness of available biologics for post-operative prophylaxis in Crohn's disease (CD) is uncertain. Drug persistence may serve as a real-world proxy for tolerability and effectiveness. We evaluated the comparative persistence of non-TNF and TNF antagonists for post-operative prophylaxis and their comparative effectiveness for preventing early endoscopic post-operative recurrence (POR). METHODS We conducted a single-center, retrospective study of surgically naïve CD subjects undergoing ileocecal or small bowel resection between 1/1/2000 and 12/31/2021 and prescribed a biologic for post-operative prophylaxis. We compared the risk of prophylaxis failure (requiring recurrent surgery or discontinuation of therapy due to persistent POR despite optimized drug level or dose escalation, immunogenicity, and/or adverse event) and early endoscopic POR (Rutgeert's score ≥ i2 within 15 months postoperatively) between non-TNF and TNF antagonist prophylaxis using Cox proportional hazard and logistic regression, respectively, adjusting for demographic and disease characteristics. RESULTS The study included 291 subjects (81% TNF antagonists). After multivariable adjustment, non-TNF antagonist prophylaxis was associated with a significantly lower risk of prophylaxis failure than TNF antagonists (hazard ratio 0.26; 95% confidence interval (CI) [0.13-0.53]). Prophylaxis with non-TNF and TNF antagonists had similar risk of early endoscopic POR (odds ratio 0.66; 95% CI [0.32-1.36]). Stratifying the non-TNF antagonists by anti-integrin and anti-IL12/23 yielded similar results. CONCLUSION In a cohort of surgically naïve CD subjects prescribed a biologic for post-operative prophylaxis, non-TNF antagonists had greater persistence than TNF antagonists with similar risk for early endoscopic POR. If confirmed by large, prospective studies, these findings can inform post-operative management strategies in CD.
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Affiliation(s)
- Phillip Gu
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA.
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - YooJin Lee
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Eric Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Niru Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Gaurav Syal
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Andres Yarur
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - David Ziring
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Stephan Targan
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Shervin Rabizadeh
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Phillip Fleshner
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
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6
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Akhlaghpour M, Haritunians T, More SK, Thomas LS, Stamps DT, Dube S, Li D, Yang S, Landers CJ, Mengesha E, Hamade H, Murali R, Potdar AA, Wolf AJ, Botwin GJ, Khrom M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Sartor RB, Xavier RJ, Brant SR, Cho JH, Duerr RH, Lazarev MG, Rioux JD, Schumm LP, Silverberg MS, Zaghiyan K, Fleshner P, Melmed GY, Vasiliauskas EA, Ha C, Rabizadeh S, Syal G, Bonthala NN, Ziring DA, Targan SR, Long MD, McGovern DPB, Michelsen KS. Genetic coding variant in complement factor B (CFB) is associated with increased risk for perianal Crohn's disease and leads to impaired CFB cleavage and phagocytosis. Gut 2023; 72:2068-2080. [PMID: 37080587 DOI: 10.1136/gutjnl-2023-329689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 04/22/2023]
Abstract
OBJECTIVE Perianal Crohn's disease (pCD) occurs in up to 40% of patients with CD and is associated with poor quality of life, limited treatment responses and poorly understood aetiology. We performed a genetic association study comparing CD subjects with and without perianal disease and subsequently performed functional follow-up studies for a pCD associated SNP in Complement Factor B (CFB). DESIGN Immunochip-based meta-analysis on 4056 pCD and 11 088 patients with CD from three independent cohorts was performed. Serological and clinical variables were analysed by regression analyses. Risk allele of rs4151651 was introduced into human CFB plasmid by site-directed mutagenesis. Binding of recombinant G252 or S252 CFB to C3b and its cleavage was determined in cell-free assays. Macrophage phagocytosis in presence of recombinant CFB or serum from CFB risk, or protective CD or healthy subjects was assessed by flow cytometry. RESULTS Perianal complications were associated with colonic involvement, OmpC and ASCA serology, and serology quartile sum score. We identified a genetic association for pCD (rs4151651), a non-synonymous SNP (G252S) in CFB, in all three cohorts. Recombinant S252 CFB had reduced binding to C3b, its cleavage was impaired, and complement-driven phagocytosis and cytokine secretion were reduced compared with G252 CFB. Serine 252 generates a de novo glycosylation site in CFB. Serum from homozygous risk patients displayed significantly decreased macrophage phagocytosis compared with non-risk serum. CONCLUSION pCD-associated rs4151651 in CFB is a loss-of-function mutation that impairs its cleavage, activation of alternative complement pathway, and pathogen phagocytosis thus implicating the alternative complement pathway and CFB in pCD aetiology.
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Affiliation(s)
- Marzieh Akhlaghpour
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shyam K More
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa S Thomas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalton T Stamps
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carol J Landers
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Hussein Hamade
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Andrea J Wolf
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | | | - Bana Jabri
- Biological Sciences Division, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
| | - Sergio A Lira
- Immunology Institute, Mount Sinai Medical Center, New York, New York, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Washington Univ. Sch. of Medicine, Saint Louis, Missouri, USA
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Steven R Brant
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Judy H Cho
- Genetics and Genomics Sciences, Mt Sinai School of Medicine, New York, New York, USA
| | - Richard H Duerr
- Departments of Medicine and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark G Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Rioux
- Faculty of Medicine, Universite de Montreal, Montreal, Québec, Canada
| | - L Philip Schumm
- Dept of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Karen Zaghiyan
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eric A Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christina Ha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gaurav Syal
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David A Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Millie D Long
- Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathrin S Michelsen
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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7
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Liu R, Li D, Haritunians T, Ruan Y, Daly MJ, Huang H, McGovern DP. Profiling the inflammatory bowel diseases using genetics, serum biomarkers, and smoking information. iScience 2023; 26:108053. [PMID: 37841595 PMCID: PMC10568094 DOI: 10.1016/j.isci.2023.108053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/28/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are two etiologically related yet distinctive subtypes of the inflammatory bowel diseases (IBD). Differentiating CD from UC can be challenging using conventional clinical approaches in a subset of patients. We designed and evaluated a novel molecular-based prediction model aggregating genetics, serum biomarkers, and tobacco smoking information to assist the diagnosis of CD and UC in over 30,000 samples. A joint model combining genetics, serum biomarkers and smoking explains 46% (42-50%, 95% CI) of phenotypic variation. Despite modest overlaps with serum biomarkers, genetics makes unique contributions to distinguishing IBD subtypes. Smoking status only explains 1% (0-6%, 95% CI) of the phenotypic variance suggesting it may not be an effective biomarker. This study reveals that molecular-based models combining genetics, serum biomarkers, and smoking information could complement current diagnostic strategies and help classify patients based on biologic state rather than imperfect clinical parameters.
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Affiliation(s)
- Ruize Liu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yunfeng Ruan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dermot P.B. McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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8
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Khrom M, Li D, Naito T, Lee HS, Botwin GJ, Potdar AA, Boucher G, Yang S, Mengesha E, Dube S, Song K, McGovern DPB, Haritunians T. Sex-Dimorphic Analyses Identify Novel and Sex-Specific Genetic Associations in Inflammatory Bowel Disease. Inflamm Bowel Dis 2023; 29:1622-1632. [PMID: 37262302 PMCID: PMC10547236 DOI: 10.1093/ibd/izad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Sex is an integral variable often overlooked in complex disease genetics. Differences between sexes have been reported in natural history, disease complications, and age of onset in inflammatory bowel disease (IBD). While association studies have identified >230 IBD loci, there have been a limited number of studies investigating sex differences underlying these genetic associations. METHODS We report the first investigation of sex-dimorphic associations via meta-analysis of a sex-stratified association study (34 579 IBD cases, 39 125 controls). In addition, we performed chromosome (chr) X-specific analyses, considering models of X inactivation (XCI) and XCI escape. Demographic and clinical characteristics were also compared between sexes. RESULTS We identified significant differences between sexes for disease location and perianal complication in Crohn's disease and disease extent in ulcerative colitis. We observed genome-wide-significant sex-dimorphic associations (P < 5 × 10-8) at loci not previously reported in large-scale IBD genetic studies, including at chr9q22, CARMIL1, and UBASH3A. We identified variants in known IBD loci, including in chr2p15 and within the major histocompatibility complex on chr6, exhibiting sex-specific patterns of association (P < 5 × 10-7 in one sex only). We identified 3 chrX associations with IBD, including a novel Crohn's disease susceptibility locus at Xp22. CONCLUSIONS These analyses identified novel IBD loci, in addition to characterizing sex-specific patterns of associations underlying sex-dimorphic associations. By elucidating the role of sex in IBD genetics, our study will help enhance our understanding of the differences between the sexes in IBD biology and underscores a need to move beyond conventional sex-combined analyses to appreciate the genetic architecture of IBD more comprehensively.
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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9
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Mweetwa MN, Haritunians T, Dube S, Chandwe K, Amadi B, Zyambo K, Liu TC, McGovern D, Kelly P. Genetic variation in environmental enteropathy and stunting in Zambian children: A pilot genome wide association study using the H3Africa chip. PLoS One 2023; 18:e0291311. [PMID: 37756315 PMCID: PMC10529557 DOI: 10.1371/journal.pone.0291311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE Stunting is known to be heavily influenced by environmental factors, so the genetic contribution has received little attention. Here we report an exploration of genetic influences in stunted Zambian children with environmental enteropathy. METHOD Children with stunting (LAZ < -2) were enrolled and given nutritional therapy. Those that were non-responsive to therapy were designated as cases, and children with good growth (LAZ > -1) from the same community as controls. Blood and stool samples were taken to measure biomarkers of intestinal inflammation, epithelial damage, and microbial translocation. Single nucleotide polymorphism array genotyping was carried out on saliva samples using the H3Africa consortium array. RESULTS Genome wide associations were analysed in 117 cases and 41 controls. While no significant associations with stunting were observed at P<5x10-8, likely due to the small sample size, interesting associations were observed at lower thresholds. SNPs associated with stunting were in genomic regions known to modulate neuronal differentiation and fatty acid biosynthesis. SNPs associated with increased microbial translocation were associated with non-integrin membrane ECM interactions, tight junctions, hemostasis, and G-alpha signalling events. SNPs associated with increased inflammation were associated with, ECM interactions, purine metabolism, axon guidance, and cell motility. SNPs negatively associated with inflammation overlapped genes involved in semaphoring interactions. We explored the existing coeliac disease risk HLA genotypes and found present: DQ2.5 (7.5%), DQ8 (3.5%) and DQ2.2 (3.8%); however, no children were positive for coeliac antibodies. We detected HLA-DRB:1301 and HLA-C:1802 with high odds ratios and P<0.05 in stunted children compared to controls. CONCLUSION Genetic variations associated with stunting and the enteropathy underlying it, include variants associated with multiple pathways relating to gene expression, glycosylation, nerve signalling, and sensing of the nutritional and microbiological milieu.
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Affiliation(s)
- Monica N. Mweetwa
- Tropical Gastroenterology & Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
- Department of Physiology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Kanta Chandwe
- Tropical Gastroenterology & Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
- Department of Paediatrics, University of Zambia School of Medicine, Lusaka, Zambia
| | - Beatrice Amadi
- Tropical Gastroenterology & Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
- Department of Paediatrics, University of Zambia School of Medicine, Lusaka, Zambia
| | - Kanekwa Zyambo
- Tropical Gastroenterology & Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
| | - Ta-Chiang Liu
- Washington University in St. Louis (WUSTL), St. Louis, Missouri, United States of America
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Paul Kelly
- Tropical Gastroenterology & Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
- Washington University in St. Louis (WUSTL), St. Louis, Missouri, United States of America
- Blizard Institute, Queen Mary University of London, London, United Kingdom
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10
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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 2023; 14:2256. [PMID: 37080976 PMCID: PMC10119186 DOI: 10.1038/s41467-023-37849-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.
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Affiliation(s)
- Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kyle Gettler
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalin Li
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Maffucci
- Immunology Institute, Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ksenija Sabic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Adam P Levine
- Division of Medicine, University College London (UCL), London, UK
- Research Department of Pathology, University College London (UCL), London, UK
| | - Elena R Schiff
- Division of Medicine, University College London (UCL), London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony W Segal
- Division of Medicine, University College London (UCL), London, UK
| | | | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Oncology Boston Children's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Mark S Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Steven R Brant
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dermot P B McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Besa E, Tembo MJ, Mulenga C, Mweetwa M, Choudhry N, Chandwe K, Storer C, Head R, Amadi B, Haritunians T, McGovern D, Kwenda G, Peiris M, Kelly P. Potential determinants of low circulating glucagon-like peptide 2 concentrations in Zambian children with non-responsive stunting. Exp Physiol 2023; 108:568-580. [PMID: 36744850 PMCID: PMC10103869 DOI: 10.1113/ep090492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/19/2023] [Indexed: 02/07/2023]
Abstract
NEW FINDINGS What is the central question of this study? Non-responsive stunting is characterised by a progressive decline of circulating glucagon-like peptide 2: what are the possible causes of this decline? What is the main finding and its importance? In contrast with the established loss of Paneth and goblet cells in environmental enteropathy, there was no evidence of a parallel loss of enteroendocrine cells as seen by positive tissue staining for chromogranin A. Transcriptomic and genomic analyses showed evidence of genetic transcripts that could account for some of the variability seen in circulating glucagon-like peptide 2 values. ABSTRACT Nutrient sensing determines digestive and hormonal responses following nutrient ingestion. We have previously reported decreased levels of glucagon-like peptide 2 (GLP-2) in children with stunting. Here we demonstrate the presence of enteroendocrine cells in stunted children and explore potential pathways that may be involved in reduced circulating levels of GLP-2. At the time of performing diagnostic endoscopies for non-responsive stunted children, intestinal biopsies were collected for immunofluorescence staining of enteroendocrine cells and transcriptomic analysis. Circulating levels of GLP-2 were also measured and correlated with transcriptomic data. An exploratory genome-wide association study (GWAS) was conducted on DNA samples (n = 158) to assess genetic contribution to GLP-2 variability. Intestinal tissue sections collected from non-responsive stunted children stained positive for chromogranin A (88/89), alongside G-protein-coupled receptors G-protein receptor 119 (75/87), free fatty acid receptor 3 (76/89) and taste 1 receptor 1 (39/45). Transcriptomic analysis found three pathways correlated with circulating GLP-2: sugar metabolism, epithelial transport, and barrier function, which likely reflect downstream events following receptor-ligand interaction. GWAS analysis revealed potential genetic contributions to GLP-2 half-life and receptor binding. Enteroendocrine cell loss was not identified in stunted Zambian children as has been observed for goblet and Paneth cells. Transcriptomic analysis suggests that GLP-2 has pleiotrophic actions on the intestinal mucosa in malnutrition, but further work is needed to dissect pathways leading to perturbations in nutrient sensing.
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Affiliation(s)
- Ellen Besa
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Mizinga Jacqueline Tembo
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Chola Mulenga
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Monica Mweetwa
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Naheed Choudhry
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Chad Storer
- Genome Technology Access Center at McDonnell Genome InstituteWashington University in St LouisSt LouisMOUSA
| | - Richard Head
- Genome Technology Access Center at McDonnell Genome InstituteWashington University in St LouisSt LouisMOUSA
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
| | - Talin Haritunians
- Cedars‐Sinai Medical CenterInflammatory Bowel and Immunobiology Research InstituteLos AngelesCAUSA
| | - Dermot McGovern
- Cedars‐Sinai Medical CenterInflammatory Bowel and Immunobiology Research InstituteLos AngelesCAUSA
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health SciencesUniversity of ZambiaLusakaZambia
| | - Madusha Peiris
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition Group, School of MedicineUniversity of ZambiaLusakaZambia
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
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12
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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet 2022; 54:1275-1283. [PMID: 36038634 PMCID: PMC9700438 DOI: 10.1038/s41588-022-01156-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.
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Affiliation(s)
- Aleksejs Sazonovs
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christine R Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kai Yuan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandon Avila
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Abreu
- Crohn's and Colitis Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Matthieu Allez
- Hopital Saint-Louis, APHP, Universite de Paris, INSERM U1160, Paris, France
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Crohn's and Colitis Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gil Atzmon
- Department for Human Biology, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- The Institute for Aging Research, The Nathan Shock Center of Excellence in the Basic Biology of Aging and the Paul F. Glenn Center for the Biology of Human Aging Research at Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Laurent Beaugerie
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Alain Bitton
- McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Bernd Bokemeyer
- Department of Internal Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Jacques Cosnes
- Professeur Chef de Service chez APHP and Universite Paris-6, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Allan Daly
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noor Dawany
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
- University of Rome Sapienza, Rome, Italy
- IRGB - CNR, Cagliari, Italy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eva Ellinghaus
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Laura Fachal
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kyle Gettler
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Philippe Goyette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Daniel Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marc Hoeppner
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Peter Irving
- Department of Gastroenterology, Guys and Saint Thomas Hospital, London, UK
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Vivek Iyer
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Chaim Jalas
- Director of Genetic Resources and Services, Center for Rare Jewish Genetic Disorders, Bonei Olam, Brooklyn, NY, USA
| | - Judith Kelsen
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Barbara S Kirschner
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Kimmo Kontula
- Department of Medicine, Helsinki University Hospital, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Subra Kugathasan
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Chloé Lévesque
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - James D Lewis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Crohn's and Colitis Foundation, New York, NY, USA
| | | | - Britt-Sabina Loescher
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - John Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra May
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Myriam Mni
- University of Liège, ULG, Liège, Belgium
| | | | | | | | | | - David T Okou
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
- Institut National de Sante Publique (INSP), Abidjan, Côte d'Ivoire
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jean Paquette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Joel Pekow
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Natalie Prescott
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel L Rice
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Bruce Sands
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Stefan Schreiber
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Philippe Seksik
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Rasha Shawky
- IBD BioResource, NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Alison Simmons
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skeiceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Matthew Solomonson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hari Somineni
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Turner
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
- Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Andrea E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Séverine Vermeire
- University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Andre Franke
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Crohn's Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Kurt Isselbacher Professor of Medicine at Harvard Medical School, Cambridge, MA, USA
- Core Institute Member, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Immunology Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John D Rioux
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Mark J Daly
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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13
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Jacobs JP, Goudarzi M, Lagishetty V, Li D, Mak T, Tong M, Ruegger P, Haritunians T, Landers C, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih D, Targan S, Borneman J, Fornace AJ, McGovern DPB, Braun J. Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome. Genome Med 2022; 14:91. [PMID: 35971134 PMCID: PMC9377146 DOI: 10.1186/s13073-022-01099-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Crohn's disease (CD) patients demonstrate distinct intestinal microbial compositions and metabolic characteristics compared to unaffected controls. However, the impact of inflammation and underlying genetic risk on these microbial profiles and their relationship to disease phenotype are unclear. We used lavage sampling to characterize the colonic mucosal-luminal interface (MLI) microbiome of CD patients in endoscopic remission and unaffected controls relative to obesity, disease genetics, and phenotype. METHODS Cecum and sigmoid colon were sampled from 110 non-CD controls undergoing screening colonoscopy who were stratified by body mass index and 88 CD patients in endoscopic remission (396 total samples). CD polygenic risk score (GRS) was calculated using 186 known CD variants. MLI pellets were analyzed by 16S ribosomal RNA gene sequencing, and supernatants by untargeted liquid chromatography-mass spectrometry. RESULTS CD and obesity were each associated with decreased cecal and sigmoid MLI bacterial diversity and distinct bacterial composition compared to controls, including expansion of Escherichia/Shigella. Cecal and sigmoid dysbiosis indices for CD were significantly greater in obese controls than non-overweight controls. CD, but not obesity, was characterized by altered biogeographic relationship between the sigmoid and cecum. GRS was associated with select taxonomic shifts that overlapped with changes seen in CD compared to controls including Fusobacterium enrichment. Stricturing or penetrating Crohn's disease behavior was characterized by lower MLI bacterial diversity and altered composition, including reduced Faecalibacterium, compared to uncomplicated CD. Taxonomic profiles including reduced Parasutterella were associated with clinical disease progression over a mean follow-up of 3.7 years. Random forest classifiers using MLI bacterial abundances could distinguish disease state (area under the curve (AUC) 0.93), stricturing or penetrating Crohn's disease behavior (AUC 0.82), and future clinical disease progression (AUC 0.74). CD patients showed alterations in the MLI metabolome including increased cholate:deoxycholate ratio compared to controls. CONCLUSIONS Obesity, CD in endoscopic remission, and high CD genetic risk have overlapping colonic mucosal-luminal interface (MLI) microbiome features, suggesting a shared microbiome contribution to CD and obesity which may be influenced by genetic factors. Microbial profiling during endoscopic remission predicted Crohn's disease behavior and progression, supporting that MLI sampling could offer unique insight into CD pathogenesis and provide novel prognostic biomarkers.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
| | | | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Tytus Mak
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Maomeng Tong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Paul Ruegger
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Philip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Eric Vasiliauskas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Andrew Ippoliti
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, USA
| | - Gil Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - David Shih
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
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14
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Chandwe K, Zyambo K, Mulenga C, Haritunians T, Amadi B, Kosek M, Heimburger DC, McGovern D, Kelly P. Histo-Blood Group Antigens, Enteropathogen Carriage and Environmental Enteropathy in Stunted Zambian Children. J Pediatr Gastroenterol Nutr 2022; 74:529-534. [PMID: 34724448 PMCID: PMC9046470 DOI: 10.1097/mpg.0000000000003343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Stunting, the most common form of childhood undernutrition, is associated with environmental enteropathy (EE). Enteric infections are believed to play a role in the pathophysiology of EE and stunting though the exact mechanism remains undetermined. The FUT2 (secretor) and FUT3 (Lewis) genes have been shown to be associated with some symptomatic enteric infections in both children and adults. These genes are responsible for the presence of histo-blood group antigens (HBGAs) in various secretions and epithelial surfaces.We evaluated whether the secretor and Lewis status influences asymptomatic enteric infections and thus EE severity on duodenal biopsies of stunted children. METHODS In this case-control study, we used saliva samples to determine the secretor and Lewis status of stunted children (cases, n = 113) enrolled in a nutritional rehabilitation program and from their well-nourished counterparts (controls, n = 42). Where available, saliva was also collected from the mothers. Baseline stool samples were used to detect asymptomatic enteropathogen carriage. Duodenal biopsies were collected from a subgroup of stunted children (n = 77) who had an upper gastrointestinal endoscopy done as part of the evaluation process for their non-response to nutritional therapy. RESULTS The proportion of secretors was similar between the cases and the controls (82% vs 81%, P = 0.81). The stunted children had significantly higher rates of carrying multiple enteropathogens, but this was not associated with their secretor status nor that of their mothers. The secretor status was also not associated with mucosal morphometry of duodenal biopsies. CONCLUSION This case-control analysis in Zambian children does not support the hypothesis that fucosylation status determines asymptomatic enteropathogen carriage in stunting.
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Affiliation(s)
- Kanta Chandwe
- University of Zambia School of Medicine, Lusaka, Zambia
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Kanekwa Zyambo
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Chola Mulenga
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Beatrice Amadi
- University of Zambia School of Medicine, Lusaka, Zambia
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
| | | | - Douglas C. Heimburger
- University of Zambia School of Medicine, Lusaka, Zambia
- Vanderbilt University Medical Center
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Paul Kelly
- Tropical Gastroenterology & Nutrition group, Lusaka, Zambia
- Queen Mary University of London, London, UK
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15
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Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. Am J Hum Genet 2021; 108:1765-1779. [PMID: 34450030 DOI: 10.1016/j.ajhg.2021.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a transcriptional risk score (TRS). Here, we demonstrate that a measured TRS based on bulk rectal gene expression in the PROTECT inception cohort study has a positive predictive value approaching 50% for colectomy. Single-cell profiling demonstrates that the genes are active in multiple diverse cell types from both the epithelial and immune compartments. Expression quantitative trait locus (QTL) analysis identifies genes with differential effects at baseline and week 52 follow-up, but for the most part, differential expression associated with colectomy risk is independent of local genetic regulation. Nevertheless, a predicted polygenic transcriptional risk score (PPTRS) derived by summation of transcriptome-wide association study (TWAS) effects identifies UC-affected individuals at 5-fold elevated risk of colectomy with data from the UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with TWASs for stratification of risk of disease complications.
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Affiliation(s)
- Angela Mo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sini Nagpal
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kyle Gettler
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Giri
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yael Haberman
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Sheba Medical Center, Tel Hashomer, Tel Aviv University, Tel Aviv 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dalia Arafat
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nai-Yun Hsu
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Nathan Gotman
- University of North Carolina, Chapel Hill, NC 27516, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Paul A Rufo
- Harvard University-Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo, Buffalo, NY 14222, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, New Hyde Park, NY 11040, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, NJ 07960, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, ON K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University, New York City, NY 10032, USA
| | - Melvin B Heyman
- University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | | | - Judy H Cho
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Greg Gibson
- Georgia Institute of Technology, Atlanta, GA 30332, USA.
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16
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Liu TC, Kern JT, Jain U, Sonnek NM, Xiong S, Simpson KF, VanDussen KL, Winkler ES, Haritunians T, Malique A, Lu Q, Sasaki Y, Storer C, Diamond MS, Head RD, McGovern DPB, Stappenbeck TS. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host Microbe 2021; 29:988-1001.e6. [PMID: 34010595 DOI: 10.1016/j.chom.2021.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Intestinal Paneth cells modulate innate immunity and infection. In Crohn's disease, genetic mutations together with environmental triggers can disable Paneth cell function. Here, we find that a western diet (WD) similarly leads to Paneth cell dysfunction through mechanisms dependent on the microbiome and farnesoid X receptor (FXR) and type I interferon (IFN) signaling. Analysis of multiple human cohorts suggests that obesity is associated with Paneth cell dysfunction. In mouse models, consumption of a WD for as little as 4 weeks led to Paneth cell dysfunction. WD consumption in conjunction with Clostridium spp. increased the secondary bile acid deoxycholic acid levels in the ileum, which in turn inhibited Paneth cell function. The process required excess signaling of both FXR and IFN within intestinal epithelial cells. Our findings provide a mechanistic link between poor diet and inhibition of gut innate immunity and uncover an effect of FXR activation in gut inflammation.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Naomi M Sonnek
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katherine F Simpson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Talin Haritunians
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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17
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Ma C, Storer CE, Chandran U, LaFramboise WA, Petrosko P, Frank M, Hartman DJ, Pantanowitz L, Haritunians T, Head RD, Liu TC. Crohn's disease-associated ATG16L1 T300A genotype is associated with improved survival in gastric cancer. EBioMedicine 2021; 67:103347. [PMID: 33906066 PMCID: PMC8099593 DOI: 10.1016/j.ebiom.2021.103347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A non-synonymous single nucleotide polymorphism of the ATG16L1 gene, T300A, is a major Crohn's disease (CD) susceptibility allele, and is known to be associated with increased apoptosis induction in the small intestinal crypt base in CD subjects and mouse models. We hypothesized that ATG16L1 T300A genotype also correlates with increased tumor apoptosis and therefore could lead to superior clinical outcome in cancer subjects. METHODS T300A genotyping by Taqman assay was performed for gastric carcinoma subjects who underwent resection from two academic medical centers. Transcriptomic analysis was performed by RNA-seq on formalin-fixed paraffin-embedded cancerous tissue. Tumor apoptosis and autophagy were determined by cleaved caspase-3 and p62 immunohistochemistry, respectively. The subjects' genotypes were correlated with demographics, various histopathologic features, transcriptome, and clinical outcome. FINDINGS Of the 220 genotyped subjects, 163 (74%) subjects carried the T300A allele(s), including 55 (25%) homozygous and 108 (49%) heterozygous subjects. The T300A/T300A subjects had superior overall survival than the other groups. Their tumors were associated with increased CD-like lymphoid aggregates and increased tumor apoptosis without concurrent increase in tumor mitosis or defective autophagy. Transcriptomic analysis showed upregulation of WNT/β-catenin signaling and downregulation of PPAR, EGFR, and inflammatory chemokine pathways in tumors of T300A/T300A subjects. INTERPRETATION Gastric carcinoma of subjects with the T300A/T300A genotype is associated with repressed EGFR and PPAR pathways, increased tumor apoptosis, and improved overall survival. Genotyping gastric cancer subjects may provide additional insight for clinical stratification.
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Affiliation(s)
- Changqing Ma
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States.
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| | - William A LaFramboise
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Patricia Petrosko
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Madison Frank
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Ta-Chiang Liu
- Departments of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, Saint Louis, MO 63110, United States.
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18
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Chen E, Chuang LS, Giri M, Villaverde N, Hsu NY, Sabic K, Joshowitz S, Gettler K, Nayar S, Chai Z, Alter IL, Chasteau CC, Korie UM, Dzedzik S, Thin TH, Jain A, Moscati A, Bongers G, Duerr RH, Silverberg MS, Brant SR, Rioux JD, Peter I, Schumm LP, Haritunians T, McGovern DP, Itan Y, Cho JH. Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target. Gastroenterology 2021; 160:1709-1724. [PMID: 33421512 PMCID: PMC8494017 DOI: 10.1053/j.gastro.2020.12.076] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Recent literature has implicated a key role for mast cells in murine models of colonic inflammation, but their role in human ulcerative colitis (UC) is not well established. A major advance has been the identification of mrgprb2 (human orthologue, MRGPX2) as mediating IgE-independent mast cell activation. We sought to define mechanisms of mast cell activation and MRGPRX2 in human UC. METHODS Colon tissues were collected from patients with UC for bulk RNA sequencing and lamina propria cells were isolated for MRGPRX2 activation studies and single-cell RNA sequencing. Genetic association of all protein-altering G-protein coupled receptor single-nucleotide polymorphism was performed in an Ashkenazi Jewish UC case-control cohort. Variants of MRGPRX2 were transfected into Chinese hamster ovary (CHO) and human mast cell (HMC) 1.1 cells to detect genotype-dependent effects on β-arrestin recruitment, IP-1 accumulation, and phosphorylated extracellular signal-regulated kinase. RESULTS Mast cell-specific mediators and adrenomedullin (proteolytic precursor of PAMP-12, an MRGPRX2 agonist) are up-regulated in inflamed compared to uninflamed UC. MRGPRX2 stimulation induces carboxypeptidase secretion from inflamed UC. Of all protein-altering GPCR alleles, a unique variant of MRGPRX2, Asn62Ser, was most associated with and was bioinformatically predicted to alter arrestin recruitment. We validated that the UC protective serine allele enhances β-arrestin recruitment, decreases IP-1, and increases phosphorylated extracellular signal-regulated kinase with MRGPRX2 agonists. Single-cell RNA sequencing defines that adrenomedullin is expressed by activated fibroblasts and epithelial cells and that interferon gamma is a key upstream regulator of mast cell gene expression. CONCLUSION Inflamed UC regions are distinguished by MRGPRX2-mediated activation of mast cells, with decreased activation observed with a UC-protective genetic variant. These results define cell modules of UC activation and a new therapeutic target.
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Affiliation(s)
- Ernie Chen
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ling-shiang Chuang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nicole Villaverde
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nai-yun Hsu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Sari Joshowitz
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Kyle Gettler
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Zhi Chai
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Isaac L. Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Colleen C. Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ujunwa M. Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Siarhei Dzedzik
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Tin Htwe Thin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Gerardus Bongers
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Ontario, Canada, Toronto, Ontario, Canada
| | - Steven R. Brant
- Crohns and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States
| | - John D. Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada. Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Inga Peter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - L. Philip Schumm
- Department of Health Sciences, University of Chicago, Chicago, Illinois, United States
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Dermot P. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States,To whom correspondence should be addressed: Judy Cho, Hess CSM Building Floor 8th Room 118, 1470 Madison Avenue, New York, NY 10029, TEL. (212) 824-8940, FAX. (646) 537-9452,
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19
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Somineni HK, Nagpal S, Venkateswaran S, Cutler DJ, Okou DT, Haritunians T, Simpson CL, Begum F, Datta LW, Quiros AJ, Seminerio J, Mengesha E, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Iskandar H, Dryden GW, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kuemmerle JF, Lazarev M, Li E, Mannon P, Moulton DE, Newberry RD, Patel AS, Pekow J, Saeed SA, Valentine JF, Wang MH, McCauley JL, Abreu MT, Jester T, Molle-Rios Z, Palle S, Scherl EJ, Kwon J, Rioux JD, Duerr RH, Silverberg MS, Zwick ME, Stevens C, Daly MJ, Cho JH, Gibson G, McGovern DP, Brant SR, Kugathasan S. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Am J Hum Genet 2021; 108:431-445. [PMID: 33600772 PMCID: PMC8008495 DOI: 10.1016/j.ajhg.2021.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644 healthy control Americans with African ancestry (African Americans). Although no new loci for inflammatory bowel disease are discovered at genome-wide significance levels, we identify numerous instances of differential effect sizes in combination with divergent allele frequencies. For example, the major effect at PTGER4 fine maps to a single credible interval of 22 SNPs corresponding to one of four independent associations at the locus in European ancestry individuals but with an elevated odds ratio for Crohn disease in African Americans. A rare variant aggregate analysis implicates Ca2+-binding neuro-immunomodulator CALB2 in ulcerative colitis. Highly significant overall overlap of common variant risk for inflammatory bowel disease susceptibility between individuals with African and European ancestries was observed, with 41 of 241 previously known lead variants replicated and overall correlations in effect sizes of 0.68 for combined inflammatory bowel disease. Nevertheless, subtle differences influence the performance of polygenic risk scores, and we show that ancestry-appropriate weights significantly improve polygenic prediction in the highest percentiles of risk. The median amount of variance explained per locus remains the same in African and European cohorts, providing evidence for compensation of effect sizes as allele frequencies diverge, as expected under a highly polygenic model of disease.
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20
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Degenhardt F, Mayr G, Wendorff M, Boucher G, Ellinghaus E, Ellinghaus D, ElAbd H, Rosati E, Hübenthal M, Juzenas S, Abedian S, Vahedi H, Thelma BK, Yang SK, Ye BD, Cheon JH, Datta LW, Daryani NE, Ellul P, Esaki M, Fuyuno Y, McGovern DPB, Haritunians T, Hong M, Juyal G, Jung ES, Kubo M, Kugathasan S, Lenz TL, Leslie S, Malekzadeh R, Midha V, Motyer A, Ng SC, Okou DT, Raychaudhuri S, Schembri J, Schreiber S, Song K, Sood A, Takahashi A, Torres EA, Umeno J, Alizadeh BZ, Weersma RK, Wong SH, Yamazaki K, Karlsen TH, Rioux JD, Brant SR, Franke A. Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations. Hum Mol Genet 2021; 30:356-369. [PMID: 33555323 PMCID: PMC8098114 DOI: 10.1093/hmg/ddab017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabrielle Boucher
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Dermatology, Venerology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Homayon Vahedi
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi 110021, India
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naser Ebrahim Daryani
- Department of Gastroenterology, Emam Hospital, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Myhunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 351-0198, Japan
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Pediatric Institute, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Stephen Leslie
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Vandana Midha
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Allan Motyer
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - David T Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Centre for Genetics and Genomics Versus Arthritis, Division of Musculosceletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - John Schembri
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Ajit Sood
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, Riken, Yokohama, 230-0045, Japan
| | - Esther A Torres
- Department of Medicine, University of Puerto Rico Center for IBD, University of Puerto Rico School of Medicine, Rio Piedras, San Juan, PR 00936-5067, USA
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700 AB Groningen, The Netherlands
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway.,Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, 0372 Oslo, Norway
| | - John D Rioux
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Medicine, Rutgers Robert Wood Johnson School of Medicine and Department of Genetics, Rutgers University Brunswick and Piscataway, NJ 08903-0019, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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21
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Naito T, Botwin GJ, Haritunians T, Li D, Yang S, Khrom M, Braun J, Abbou L, Mengesha E, Stevens C, Masamune A, Daly M, McGovern DPB. Prevalence and Effect of Genetic Risk of Thromboembolic Disease in Inflammatory Bowel Disease. Gastroenterology 2021; 160:771-780.e4. [PMID: 33098885 DOI: 10.1053/j.gastro.2020.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS The largest cause of mortality in patients with inflammatory bowel disease (IBD) remains thromboembolic disease (TED). Recent reports have demonstrated that both monogenic and polygenic factors contribute to TED and 10% of healthy subjects are genetically at high risk for TED. Our aim was to utilize whole-exome sequencing and genome-wide genotyping to determine the proportion of IBD patients genetically at risk for TED and investigate the effect of genetic risk of TED in IBD. METHODS The TED polygenic risk score was calculated from genome-wide genotyping. Thrombophilia pathogenic variants were extracted from whole-exome sequencing. In total, 792 IBD patients had both whole-exome sequencing and genotyping data. We defined patients at genetically high risk for TED if they had a high TED polygenic risk score or carried at least 1 thrombophilia pathogenic variant. RESULTS We identified 122 of 792 IBD patients (15.4%) as genetically high risk for TED. Among 715 of 792 subjects whose documented TED status were available, 63 of the 715 patients (8.8%) had TED events. Genetic TED risk was significantly associated with increased TED event (odds ratio, 2.5; P = .0036). In addition, we confirmed an additive effect of monogenic and polygenic risk on TED (P = .0048). Patients with high TED genetic risk more frequently had thrombosis at multiple sites (78% vs 42%, odds ratio, 3.96; P = .048). CONCLUSIONS Genetic risk (both poly- and monogenic) was significantly associated with TED history. Our results suggest that genetic traits identify approximately 1 in 7 patients with IBD who will experience 2.5-fold or greater risk for TED.
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Affiliation(s)
- Takeo Naito
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California; Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Gregory J Botwin
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michelle Khrom
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Lisa Abbou
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Dermot P B McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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22
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Potdar AA, Dube S, Naito T, Li K, Botwin G, Haritunians T, Li D, Casero D, Yang S, Bilsborough J, Perrigoue JG, Denson LA, Daly M, Targan SR, Fleshner P, Braun J, Kugathasan S, Stappenbeck TS, McGovern DP. Altered Intestinal ACE2 Levels Are Associated With Inflammation, Severe Disease, and Response to Anti-Cytokine Therapy in Inflammatory Bowel Disease. Gastroenterology 2021; 160:809-822.e7. [PMID: 33160965 PMCID: PMC9671555 DOI: 10.1053/j.gastro.2020.10.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS The host receptor for severe acute respiratory syndrome coronavirus 2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small bowel (SB). Our aim was to identify factors influencing intestinal ACE2 expression in Crohn's disease (CD), ulcerative colitis (UC), and non-inflammatory bowel disease (IBD) controls. METHODS Using bulk RNA sequencing or microarray transcriptomics from tissue samples (4 SB and 2 colonic cohorts; n = 495; n = 387 UC; n = 94 non-IBD), we analyzed the relationship between ACE2 with demographics and disease activity and prognosis. We examined the outcome of anti-tumor necrosis factor and anti-interleukin-12/interleukin-23 treatment on SB and colonic ACE2 expression in 3 clinical trials. Univariate and multivariate regression models were fitted. RESULTS ACE2 levels were consistently reduced in SB CD and elevated in colonic UC compared with non-IBD controls. Elevated SB ACE2 was also associated with demographic features (age and elevated body mass index) associated with poor coronavirus disease 2019 outcomes. Within CD, SB ACE2 was reduced in patients subsequently developing complicated disease. Within UC, colonic ACE2 was elevated in active disease and in patients subsequently requiring anti-tumor necrosis factor rescue therapy. SB and colonic ACE2 expression in active CD and UC were restored by anti-cytokine therapy, most notably in responders. CONCLUSIONS Reduced SB but elevated colonic ACE2 levels in IBD are associated with inflammation and severe disease, but normalized after anti-cytokine therapy, suggesting compartmentalization of ACE2-related biology in SB and colonic inflammation. The restoration of ACE2 expression with anti-cytokine therapy might be important in the context of severe acute respiratory syndrome coronavirus 2 infection and potentially explain reports of reduced morbidity from coronavirus disease 2019 in IBD patients treated with anti-cytokines.
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Affiliation(s)
- Alka A. Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katherine Li
- Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Gregory Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Mark Daly
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California,Correspondence Address correspondence to: Dermot P. B. McGovern, MD, PhD, FRCP(Lon), F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, 8730 Alden Drive, Los Angeles, California 90048
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23
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Sunuwar L, Frkatović A, Sharapov S, Wang Q, Neu HM, Wu X, Haritunians T, Wan F, Michel S, Wu S, Donowitz M, McGovern D, Lauc G, Sears C, Melia J. Pleiotropic ZIP8 A391T implicates abnormal manganese homeostasis in complex human disease. JCI Insight 2020; 5:140978. [PMID: 32897876 PMCID: PMC7605523 DOI: 10.1172/jci.insight.140978] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
ZIP8 is a metal transporter with a role in manganese (Mn) homeostasis. A common genetic variant in ZIP8 (rs13107325; A391T) ranks in the top 10 of pleiotropic SNPs identified in GWAS; A391T has associations with an increased risk of schizophrenia, obesity, Crohn’s disease, and reduced blood Mn. Here, we used CRISPR/Cas9-mediated knockin (KI) to generate a mouse model of ZIP8 A391T (Zip8 393T-KI mice). Recapitulating the SNP association with blood Mn, blood Mn was reduced in Zip8 393T-KI mice. There was restricted abnormal tissue Mn homeostasis, with decreases in liver and kidney Mn and a reciprocal increase in biliary Mn, providing in vivo evidence of hypomorphic Zip8 function. Upon challenge in a chemically induced colitis model, male Zip8 393T-KI mice exhibited enhanced disease susceptibility. ZIP8 391-Thr associated with reduced triantennary plasma N-glycan species in a population-based cohort to define a genotype-specific glycophenotype hypothesized to be linked to Mn-dependent glycosyltransferase activity. This glycophenotype was maintained in a cohort of patients with Crohn’s disease. These data and the pleiotropic disease associations with ZIP8 391-Thr suggest underappreciated roles of Mn homeostasis in complex human disease. Abnormal manganese homeostasis is implicated by a GWAS disease-associated SNP, rs13107325 (ZIP8 A391T), studied in a knockin mouse model and human N-glycome analyses.
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Affiliation(s)
- Laxmi Sunuwar
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Sodbo Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Qinchuan Wang
- Department of Medicine, Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heather M Neu
- University of Maryland School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Xinqun Wu
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Fengyi Wan
- Department of Biochemistry and Molecular Biology and.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah Michel
- University of Maryland School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Shaoguang Wu
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Cynthia Sears
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joanna Melia
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Potdar AA, Dube S, Naito T, Botwin G, Haritunians T, Li D, Yang S, Bilsborough J, Denson LA, Daly M, Targan SR, Fleshner P, Braun J, Kugathasan S, Stappenbeck TS, McGovern DP. Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn's disease. medRxiv 2020:2020.04.19.20070995. [PMID: 32511625 PMCID: PMC7276052 DOI: 10.1101/2020.04.19.20070995] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Angiotensin-Converting Enzyme 2 ( ACE2 ) has been identified as the host receptor for SARS-coronavirus 2 (SARS-CoV-2) which has infected millions world-wide and likely caused hundreds of thousands of deaths. Utilizing transcriptomic data from four cohorts taken from Crohn's disease (CD) and non-inflammatory bowel disease (IBD) subjects, we observed evidence of increased ACE2 mRNA in ileum with demographic features that have been associated with poor outcomes in COVID-19 including age and raised BMI. ACE2 was downregulated in CD compared to controls in independent cohorts. Within CD, ACE2 expression was reduced in inflamed ileal tissue and also remarkably, from uninvolved tissue in patients with a worse prognosis in both adult and pediatric cohorts. In active CD, small bowel ACE2 expression was restored by anti-TNF therapy particularly in anti-TNF responders. Collectively our data suggest that ACE2 downregulation is associated with inflammation and worse outcomes in CD.
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Affiliation(s)
- Alka A. Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and nutrition, Department of Pediatrics, University of Cincinnati college of Medicine and the Cincinnati children’s Hospital Medical center, Cincinnati, OH, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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25
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Potdar AA, Li D, Haritunians T, VanDussen KL, Fiorino MF, Liu TC, Stappenbeck TS, Fleshner P, Targan SR, McGovern DPB, Bilsborough J. Ileal Gene Expression Data from Crohn's Disease Small Bowel Resections Indicate Distinct Clinical Subgroups. J Crohns Colitis 2019; 13:1055-1066. [PMID: 30877309 PMCID: PMC6939877 DOI: 10.1093/ecco-jcc/jjz021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Heterogeneity in Crohn's disease [CD] provides a challenge for the development of effective therapies. Our goal was to define a unique molecular signature for severe, refractory CD to enable precision therapy approaches to disease treatment and to facilitate earlier intervention in complicated disease. METHODS We analysed clinical metadata, genetics, and transcriptomics from uninvolved ileal tissue from CD patients who underwent a single small bowel resection. We determined transcriptional risk scores, cellular signatures, and mechanistic pathways that define patient subsets in refractory CD. RESULTS Within refractory CD, we found three CD patient subgroups [CD1, CD2, and CD3]. Compared with CD1, CD3 was enriched for subjects with increased disease recurrence after first surgery [OR = 6.78, p = 0.04], enhanced occurrence of second surgery [OR = 5.07, p = 0.016], and presence of perianal CD [OR = 3.61, p = 0.036]. The proportion of patients with recurrence-free survival was smaller in CD3 than in CD1 (p = 0.02, median survival time [months] in CD1 = 10 and CD3 = 6). Overlaying differential gene expression between CD1 and CD3 on CD subgroup-associated genetic polymorphisms identified 174 genes representing both genetic and biological differences between the CD subgroups. Pathway analyses using this unique gene signature indicated eukaryotic initiation factor 2 [eIF2] and cyclic adenosine monophosphate [cAMP] signalling to be dominant pathways associated with CD3. Furthermore, the severe, refractory subset, CD3, was associated with a higher transcriptional risk score and enriched with eosinophil and natural killer T [NKT] cell gene signatures. CONCLUSION We characterized a subset of severe, refractory CD patients who may need more aggressive treatment after first resection and who are likely to benefit from targeted therapy based on their genotype and tissue gene expression signature.
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Affiliation(s)
- Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Marie F Fiorino
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA,Corresponding author: Janine Bilsborough, IBD Drug Development Unit, F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, 8693 Wilshire Blvd, Beverly Hills, CA 90211, USA. Tel: 310-423-7797; Fax: 310-423-0224;
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26
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2019; 15:e1008190. [PMID: 31145742 PMCID: PMC6542503 DOI: 10.1371/journal.pgen.1008190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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27
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Han B, Akiyama M, Kim KK, Oh H, Choi H, Lee CH, Jung S, Lee HS, Kim EE, Cook S, Haritunians T, Yamazaki K, Park SH, Ye BD, McGovern DPB, Esaki M, Kawaguchi T, Khor SS, Taylor KD, Rotter JI, Suzuki Y, Matsui T, Motoya S, Bang SY, Kim TH, Momozawa Y, Kamatani Y, Tokunaga K, Kubo M, Okada Y, Yang SK, Song K. Amino acid position 37 of HLA-DRβ1 affects susceptibility to Crohn's disease in Asians. Hum Mol Genet 2019; 27:3901-3910. [PMID: 30084967 DOI: 10.1093/hmg/ddy285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are the major types of chronic inflammatory bowel disease (IBD) characterized by recurring episodes of inflammation of the gastrointestinal tract. Although it is well established that human leukocyte antigen (HLA) is a major risk factor for IBD, it is yet to be determined which HLA alleles or amino acids drive the risks of CD and UC in Asians. To define the roles of HLA for IBD in Asians, we fine-mapped HLA in 12 568 individuals from Korea and Japan (3294 patients with CD, 1522 patients with UC and 7752 controls). We identified that the amino acid position 37 of HLA-DRβ1 plays a key role in the susceptibility to CD (presence of serine being protective, P = 3.6 × 10-67, OR = 0.48 [0.45-0.52]). For UC, we confirmed the known association of the haplotype spanning HLA-C*12:02, HLA-B*52:01 and HLA-DRB1*1502 (P = 1.2 × 10-28, OR = 4.01 [3.14-5.12]).
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Affiliation(s)
- Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kyung-Kon Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea.,Convergence Medicine Research Center and Biomedical Research Center, AILS, Asan Medical Center, Seoul, Korea
| | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunchul Choi
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Emma E Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea.,Department of Chemistry, Seoul National University, Seoul, Korea
| | - Seungho Cook
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Talin Haritunians
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Keiko Yamazaki
- Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan.,Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takaaki Kawaguchi
- Division of Gastroenterology, Department of Medicine, TokyoYamate Medical Center, Tokyo, Japan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Seik-Soon Khor
- Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences,Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical CenterTorrance, CA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences,Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical CenterTorrance, CA, USA
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba, Japan
| | - Toshiyuki Matsui
- Department of Gastroenterology, Fukuoka University,Chikushi Hospital, Fukuoka, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo-Kosei General Hospital, Sapporo, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine,Sakyo-ku, Kyoto, Japan
| | - Katsushi Tokunaga
- Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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28
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Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 2019; 10:10/423/eaai7795. [PMID: 29321258 DOI: 10.1126/scitranslmed.aai7795] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/31/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Abstract
Crohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3.3 × 10-8). These variants affected CD age of onset, disease location, LRRK2 activity, and autophagy. Bayesian network analysis of CD patient intestinal tissue further implicated LRRK2 in CD pathogenesis. Analysis of the extended LRRK2 locus in 24,570 CD cases, patients with Parkinson's disease (PD), and healthy controls revealed extensive pleiotropy, with shared genetic effects between CD and PD in both Ashkenazi Jewish and non-Jewish cohorts. The LRRK2 N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. Like the G2019S mutation, the N2081D variant was associated with increased kinase activity, whereas neither N551K nor R1398H variants on the protective haplotype altered kinase activity. We also confirmed that R1398H, but not N551K, increased guanosine triphosphate binding and hydrolyzing enzyme (GTPase) activity, thereby deactivating LRRK2. The presence of shared LRRK2 alleles in CD and PD provides refined insight into disease mechanisms and may have major implications for the treatment of these two seemingly unrelated diseases.
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Affiliation(s)
- Ken Y Hui
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | | | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Schaffner
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianting Li
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manual Rivas
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Xiuliang Bao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philippe R Labrias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Talin Haritunians
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Darren Ruane
- Department of Immunology and Inflammation, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Kyle Gettler
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Ernie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dalin Li
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Elena R Schiff
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nikolas Pontikos
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nir Barzilai
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Susan Bressman
- Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Adam S Cheifetz
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark J Daly
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Seymour Katz
- New York University School of Medicine, New York City, NY 10016, USA.,North Shore University-Long Island Jewish Medical Center, Manhasset, NY, USA.,St. Francis Hospital, Roslyn, NY 11576, USA
| | - Todd Lencz
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA 02114, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Deparment of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Haydeh Payami
- Departments of Neurology and Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35805, USA
| | - Yakov Peter
- Department of Biology, Touro College, Queens, NY 10033, USA.,Department of Pulmonary Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10033, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, Quebec H1T1C8, Canada.,Faculté de Médecine, Université de Montréal, Montreal, Quebec H1T1C8, Canada
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - William K Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario M5T3L9, USA.,Department of Medicine, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Jeffery M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gil Atzmon
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Itsik Pe'er
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Yiannis Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dermot P B McGovern
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Judy H Cho
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA.,Section of Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. .,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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29
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Li D, Haritunians T, Landers C, Potdar AA, Yang S, Huang H, Schumm LP, Daly M, Targan SR, McGovern DPB. Late-Onset Crohn's Disease Is A Subgroup Distinct in Genetic and Behavioral Risk Factors With UC-Like Characteristics. Inflamm Bowel Dis 2018; 24:2413-2422. [PMID: 29860388 PMCID: PMC6195175 DOI: 10.1093/ibd/izy148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Age of onset is linked to variations in clinical phenotypes and natural history in Crohn's disease (CD). We aim to define etiologically more homogenous subgroups in CD based on ages of onset. METHODS We examined the distribution of CD polygenetic risk score (PRS) across ages of diagnosis in a Caucasian cohort of 2344 independent CD patients. We identified subgroups with a distinct distribution of PRS and compared those groups in genetics, demographic characteristics, clinical subphenotypes, and serological markers. The results were replicated in an independent cohort of 13,065 CD patients from the International Inflammatory Bowel Diseases Genetic Consortium (IIBDGC). RESULTS We identified a late-onset (LO) subgroup in CD (age at diagnosis ≥ 55 years) with significantly lower PRS compared with the intermediate group (age at diagnosis between 5 and 55 years) in both cohorts. Smoking cessation, a risk factor for ulcerative colitis (UC) and protective factor for CD, had a higher rate in this LO subgroup in comparison with the intermediate group. We also compared the LO group with the intermediate group, and, consistent with previous reports, the LO group more often had colonic CD, had less penetrating disease behavior, and had less need for surgery. Serological analysis showed that LO CD patients were more antineutrophil cytoplasmic antibody positive and less antisaccharomyces cerevisiae antibody positive compared with the intermediate group. Variance component analysis indicated that overall genetic contribution to LO CD was lower relative to the middle group, and genetic heterogeneity testing indicated that LO CD was different from the middle group in underlying genetic architecture. CONCLUSIONS Late-onset CD is subgroup distinct in genetic and behavioral risk factors with UC-like characteristics. 10.1093/ibd/izy148_video1izy148.video15791413461001.
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Affiliation(s)
- Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California,Address correspondence to: Dalin Li, PhD, 8730 Alden Drive, Thalians E216, Los Angeles, CA 90048 (); or Dermot P. B. McGovern, MD, PhD, 8730 Alden Drive, Thalians E242,Los Angeles, CA 90048 ()
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California,Address correspondence to: Dalin Li, PhD, 8730 Alden Drive, Thalians E216, Los Angeles, CA 90048 (); or Dermot P. B. McGovern, MD, PhD, 8730 Alden Drive, Thalians E242,Los Angeles, CA 90048 ()
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30
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Lee HS, Yang SK, Hong M, Jung S, Kim BM, Moon JW, Park SH, Ye BD, Oh SH, Kim KM, Yoon YS, Yu CS, Baek J, Lee CH, Han B, Liu J, Haritunians T, McGovern DPB, Song K. An Intergenic Variant rs9268877 Between HLA-DRA and HLA-DRB Contributes to the Clinical Course and Long-term Outcome of Ulcerative Colitis. J Crohns Colitis 2018; 12:1113-1121. [PMID: 29905830 DOI: 10.1093/ecco-jcc/jjy080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/30/2018] [Accepted: 06/12/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS The genetic contribution to the prognosis of ulcerative colitis [UC] is poorly understood, and most currently known susceptibility loci are not associated with prognosis. To identify genetic variants influencing the prognosis of UC, we performed an Immunochip-based study using an extreme phenotype approach. METHODS Based on the finding that the only association, Pdiscovery-meta <1 × 10-4, was located in the human leukocyte antigen [HLA], we focused our analyses on the HLA region. We performed the analysis using HLA imputation data from three independent discovery cohorts of 607 UC patients [243 poor-prognosis and 364 good-prognosis], followed by replication in 274 UC patients [145 poor-prognosis and 129 good-prognosis]. RESULTS We found that rs9268877, located between HLA-DRA and HLA-DRB, was associated with poor-prognosis of UC at genome-wide significance (odds ratio [ORdiscovery] = 1.82; ORreplication = 1.55; ORcombined-meta = 1.72, pcombined-meta = 1.04 × 10-8), with effect size [OR] increasing incrementally according to worsening of prognosis in each of the three independent discovery cohorts and the replication cohort. However, rs9268877 showed no association with UC susceptibility [ORcombined-meta = 1.07, pcombined-meta = 0.135]; rs9268877 influenced 30-year clinical outcomes, and the presence of the rs9268877 risk allele had a sensitivity of 80.0% and specificity of 38.1% for colectomy. CONCLUSIONS Our results provide new insights into prognosis-associated genetic variation in UC, which appears to be distinct from the genetic contribution to disease susceptibility. These findings could be useful in identifying poor-prognosis patients who might benefit from early aggressive therapy.
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Affiliation(s)
- Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Byoung Mok Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Won Moon
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seak Hee Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Sik Yoon
- Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang Sik Yu
- Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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31
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Burke KE, Khalili H, Garber JJ, Haritunians T, McGovern DPB, Xavier RJ, Ananthakrishnan AN. Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis. Inflamm Bowel Dis 2018; 24:1840-1848. [PMID: 29718226 PMCID: PMC6128143 DOI: 10.1093/ibd/izy083] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Despite a high nonresponse rate, predictors of response to anti-tumor necrosis factor (anti-TNF) therapy in ulcerative colitis (UC) remain limited. We aim to determine clinical and genetic predictors of primary nonresponse (PNR) and durable response (DR) to anti-TNF therapy in a large prospective UC cohort. METHODS Using the Illumina Immunochip, candidate polymorphisms associated with clinical outcomes of PNR and DR were separately evaluated and combined into weighted genetic risk scores. Combined genetic and clinical multivariable models for PNR and DR were compared with clinical predictive models using area under the receiver operating characteristic (AUROC) curves. Models were internally (DR) or externally (PNR) validated. Multivariable logistic regression was utilized to assess the association of genetic risk scores with infliximab levels and antibodies. RESULTS Of 231 patients, 28 (12%) experienced PNR and 120 (52%) experienced DR. There was no significant difference in clinical features between primary nonresponders and responders. Eight alleles were associated with PNR. A combined clinical-genetic model (AUROC, 0.87) more accurately predicted PNR compared with a clinical-only model (AUROC, 0.57; P < 0.0001). In an external cohort of 131 patients, increasing tertiles of PNR genetic risk score correlated with increased risk of PNR (P = 0.052). Twelve candidate loci were associated with DR. Genetic risk score quartiles for DR demonstrated a strong dose-response relationship in predicting treatment duration. Genetic risk scores for PNR and DR were not associated with infliximab levels or antibody formation. CONCLUSION Genetic polymorphisms enhance prediction of PNR and DR to anti-TNF therapy in patients with UC.
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Affiliation(s)
- Kristin E Burke
- Inflammatory Bowel Disease Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Hamed Khalili
- Inflammatory Bowel Disease Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - John J Garber
- Inflammatory Bowel Disease Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ramnik J Xavier
- Inflammatory Bowel Disease Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Ashwin N Ananthakrishnan
- Inflammatory Bowel Disease Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts,Address correspondence to: Ashwin N. Ananthakrishnan, Massachusetts General Hospital Crohn’s and Colitis Center, 165 Cambridge Street, Boston, MA 02114 ()
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32
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Hong M, Ye BD, Yang SK, Jung S, Lee HS, Kim BM, Lee SB, Hong J, Baek J, Park SH, Han B, Li Y, Liu W, Haritunians T, Taylor KD, Rotter JI, Bang SY, Kim TH, McGovern DPB, Liu J, Song K. Immunochip Meta-Analysis of Inflammatory Bowel Disease Identifies Three Novel Loci and Four Novel Associations in Previously Reported Loci. J Crohns Colitis 2018; 12:730-741. [PMID: 29584801 PMCID: PMC6279085 DOI: 10.1093/ecco-jcc/jjy002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/16/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Recent meta-analysis of genome-wide association studies have identified over 241 inflammatory bowel disease susceptibility loci. However, the known variants only account for a fraction of inflammatory bowel disease heritability. To identify additional susceptibility loci, we performed a trans-ethnic meta-analysis as well as an Asian-specific meta-analysis, using all published Immunochip association results of inflammatory bowel disease. METHODS An inverse-variance fixed-effects meta-analysis was carried out across Korean and East Asian Immunochip datasets of 4156 cases and 4904 controls [Asian ancestry]. A trans-ethnic meta-analysis of inflammatory bowel disease was performed together with the European datasets of 38 155 cases and 48 485 controls genotyped on the immunochip using a Bayesian approach, Meta-Analysis of Trans-ethnic Association studies [MANTRA]. RESULTS We identified seven novel associations, including three novel susceptibility loci at MYO10-BASP1, PPP2R3C/KIAA0391/PSMA6/NFKB1A and LRRK1 as well as four novel secondary associations within previously known loci at NCF4, TSPAN32, CIITA and VANGL2. The new loci further implicate alterations in B cell biology in Crohn's disease pathogenesis. The effects of five loci were universal across European and Asian ancestries, whereas the NCF4 and CIITA loci showed significant heterogeneity between European and East Asian populations. In addition, 103 previously known IBD loci showed supporting evidence of association with nominal significance [p < 0.05] in Asians. CONCLUSIONS Our findings of new loci not previously associated with IBD support the importance of studying inflammatory bowel disease genetics in diverse populations.
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Affiliation(s)
- Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan
College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan
College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Byoung Mok Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Soo Bin Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Jeonghoon Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan
College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine
& Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Yi Li
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Wenting Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute; Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles
Biomedical Research Institute and Department of Pediatrics. Harbor-UCLA Medical Center,
Torrance, California, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles
Biomedical Research Institute and Department of Pediatrics. Harbor-UCLA Medical Center,
Torrance, California, USA
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic
Diseases, Seoul, Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic
Diseases, Seoul, Korea
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute; Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College
of Medicine, Seoul, Korea,Corresponding author: Kyuyoung Song, Department of Biochemistry and
Molecular Biology, University of Ulsan College of Medicine, 88, Olympic-ro, 43-gil,
Songpa-Gu, Seoul 05505, Korea. Tel: +82-2-3010-4277; Fax: +82-2-3010-4248; E-mail:
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33
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2018; 14:e1007329. [PMID: 29795570 PMCID: PMC5967709 DOI: 10.1371/journal.pgen.1007329] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 02/05/2023] Open
Abstract
As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also available in gnomAD at http://gnomad.broadinstitute.org). We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations. As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10-100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohn's disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically attempt to evaluate whether strong acting rare alleles, particularly protein-truncating or otherwise large effect-size alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohn's disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are enriched in AJ (p < 0.005), including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC (sites VCF available via FTP at ftp.broadinstitute.org/pub/ExAC_release/release0.3/) to pinpoint genetic variation that contributes to variable disease predisposition across populations.
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Affiliation(s)
- Manuel A. Rivas
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States of America
| | - Brandon E. Avila
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jukka Koskela
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Christine Stevens
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Benjamin M. Neale
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Mitja Kurki
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Andrea Ganna
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Daniel Graham
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Benjamin Glaser
- Hadassah-Hebrew University Medical Center, Endocrinology and Metabolism Service Department of Internal Medicine, Jerusalem, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gil Atzmon
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Adam P. Levine
- Division of Medicine, University College London, London, United Kingdom
| | - Elena Schiff
- Division of Medicine, University College London, London, United Kingdom
| | - Nikolas Pontikos
- Division of Medicine, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Ben Weisburd
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Monkol Lek
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Konrad J. Karczewski
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Bloom
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Eric V. Minikel
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laurent Beaugerie
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Jacques Cosnes
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Stefan Schreiber
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Johannes Bethge
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Graham Heap
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter, United Kingdom
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Anthony W. Segal
- Division of Medicine, University College London, London, United Kingdom
| | - Stephan Targan
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paivi Saavalainen
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Martti Farkkila
- Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Kontula
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Aarno Palotie
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States of America
| | - Mark S. Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D. Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel G. MacArthur
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Chaim Jalas
- Bonei Olam, Center for Rare Jewish Genetic Disorders, Brooklyn, NY, United States of America
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Ramnik J. Xavier
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ann Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Judy H. Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, NY, United States of America
| | - Dermot P. B. McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Mark J. Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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Gu P, Kapur A, Li D, Haritunians T, Vasiliauskas E, Shih DQ, Targan SR, Spiegel BM, McGovern DP, Black JT, Melmed GY. Serological, genetic and clinical associations with increased health-care resource utilization in inflammatory bowel disease. J Dig Dis 2018; 19:15-23. [PMID: 29251413 PMCID: PMC6023617 DOI: 10.1111/1751-2980.12566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Inflammatory bowel diseases (IBD) are associated with significant morbidity and economic burden. The variable course of IBD creates a need for predictors of clinical outcomes and health resource utilization (HRU) to guide treatment decisions. We aimed to identify clinical, serological or genetic markers associated with inpatient resource utilization in patients with ulcerative colitis (UC) and Crohn's disease (CD). METHODS Patients with IBD with available genetic and serological data who had at least one emergency department visit or hospitalization in a 3-year period were included. The primary outcome measure was HRU, as measured by the All Patient Refined Diagnosis Related Group classification system. Univariate and multivariate linear and logistic regression models were used to identify the associations with HRU. RESULTS Altogether 858 (562 CD and 296 UC) patients were included. Anti-CBir1 seropositivity (P = 0.002, effect size [ES]: 0.762, 95% confidence interval [CI] 0.512-1.012) and low socioeconomic status (P = 0.005, ES: 1.620 [95% CI 1.091-2.149]) were independently associated with a high HRU. CD diagnosis (P = 0.006, ES: -0.701 [95% CI -0.959 to -0.443]) was independently associated with a low inpatient HRU. CONCLUSION In patients with IBD who required at least one emergency department visit or hospitalization, anti-CBir1 antibody status may be a useful biomarker of HRU when formulating management strategies to reduce disease complications and resource utilization.
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Affiliation(s)
- Phillip Gu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Anshika Kapur
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dalin Li
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Talin Haritunians
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Eric Vasiliauskas
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - David Q. Shih
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stephan R. Targan
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Brennan M.R. Spiegel
- Center for Outcomes Research and Education, Cedars-Sinai Health System, Los Angeles, CA
| | - Dermot P.B. McGovern
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jeanne T. Black
- Resource & Outcomes Management Department, Cedars-Sinai Health System, Los Angeles, CA
| | - Gil Y. Melmed
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
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35
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Lew D, Yoon SM, Yan X, Robbins L, Haritunians T, Liu Z, Li D, McGovern DPB. Genetic associations with adverse events from anti-tumor necrosis factor therapy in inflammatory bowel disease patients. World J Gastroenterol 2017; 23:7265-7273. [PMID: 29142473 PMCID: PMC5677193 DOI: 10.3748/wjg.v23.i40.7265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 08/25/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To study the type and frequency of adverse events associated with anti-tumor necrosis factor (TNF) therapy and evaluate for any serologic and genetic associations.
METHODS This study was a retrospective review of patients attending the inflammatory bowel disease (IBD) centers at Cedars-Sinai IBD Center from 2005-2016. Adverse events were identified via chart review. IBD serologies were measured by ELISA. DNA samples were genotyped at Cedars-Sinai using Illumina Infinium Immunochipv1 array per manufacturer’s protocol. SNPs underwent methodological review and were evaluated using several SNP statistic parameters to ensure optimal allele-calling. Standard and rigorous QC criteria were applied to the genetic data, which was generated using immunochip. Genetic association was assessed by logistic regression after correcting for population structure.
RESULTS Altogether we identified 1258 IBD subjects exposed to anti-TNF agents in whom Immunochip data were available. 269/1258 patients (21%) were found to have adverse events to an anti-TNF-α agent that required the therapy to be discontinued. 25% of women compared to 17% of men experienced an adverse event. All adverse events resolved after discontinuing the anti-TNF agent. In total: n = 66 (5%) infusion reactions; n = 49 (4%) allergic/serum sickness reactions; n = 19 (1.5%) lupus-like reactions, n = 52 (4%) rash, n = 18 (1.4%) infections. In Crohn’s disease, IgA ASCA (P = 0.04) and IgG-ASCA (P = 0.02) levels were also lower in patients with any adverse events, and anti-I2 level in ulcerative colitis was significantly associated with infusion reactions (P = 0.008). The logistic regression/human annotation and network analyses performed on the Immunochip data implicated the following five signaling pathways: JAK-STAT (Janus Kinase-signal transducer and activator of transcription), measles, IBD, cytokine-cytokine receptor interaction, and toxoplasmosis for any adverse event.
CONCLUSION Our study shows 1 in 5 IBD patients experience an adverse event to anti-TNF therapy with novel serologic, genetic , and pathways associations.
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Affiliation(s)
- Daniel Lew
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Soon Man Yoon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Xiaofei Yan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Lori Robbins
- Department of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dermot PB McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
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36
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Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KKH, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 2017; 547:173-178. [PMID: 28658209 PMCID: PMC5511510 DOI: 10.1038/nature22969] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 05/07/2017] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn's disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.
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Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Ming Fang
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Christ Church, University of Oxford, St Aldates OX1 1DP, UK
| | - Maša Umićević Mirkov
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Gabrielle Boucher
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vibeke Andersen
- Focused research unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland, Hospital of Southern Jutland, 6200 Åbenrå, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | | | - Adrian Cortes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - François Crins
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Gastrointestinal and Liver Diseases, BioDonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Valérie Deffontaine
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Julia Dmitrieva
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Elisa Docampo
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mahmoud Elansary
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Kyle Kai-How Farh
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Illumina, San Diego, California 92122, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Ann-Stephan Gori
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Philippe Goyette
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, SE-70182 Örebro, Sweden
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jo Knight
- Data Science Institute and Lancaster Medical School, Lancaster University, Lancaster LA1 4YG, UK
| | - Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco, Western Australia 6008, Australia.,Harry Perkins Institute for Medical Research, School of Medicine and Pharmacology, University of Western Australia, Murdoch, Western Australia 6150, Australia
| | - Charlie W Lees
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Edouard Louis
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Division of Gastroenterology, Centre Hospitalier Universitaire (CHU) de Liège, 4000 Liège, Belgium
| | - Rob Mariman
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Theo Meuwissen
- Institute of Livestock and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Myriam Mni
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Yukihide Momozawa
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Open Targets, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emilie Théâtre
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Gosia Trynka
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Severine Vermeire
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.,Division of Gastroenterology, University Hospital Gasthuisberg, 3000 Leuven, Belgium
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | | | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK.,Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Michel Georges
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DPB, Kugathasan S. Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:2082-2083. [PMID: 28478146 PMCID: PMC6033331 DOI: 10.1053/j.gastro.2017.02.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/17/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn’s disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10−8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10−6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide signifi-cance on conditioning), IL12B, PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee,Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, South Carolina
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, South Carolina
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | - Robert N. Baldassano
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, Maryland
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, North Carolina
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; Veterans Affairs Health Services Research and Development Service, Center for Innovations in Quality Effectiveness and Safety; Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, Louisiana
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, Ohio
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children’s Hospital, Chicago, Illinois
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, Virginia
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | | | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida, Jacksonville, Florida
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, Quebec, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute, School of Medicine and Department of Human Genetics, Graduate School of Public Health; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Personalized Medicine, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
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Liu TC, Naito T, Liu Z, VanDussen KL, Haritunians T, Li D, Endo K, Kawai Y, Nagasaki M, Kinouchi Y, McGovern DP, Shimosegawa T, Kakuta Y, Stappenbeck TS. LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn's disease patients. JCI Insight 2017; 2:e91917. [PMID: 28352666 DOI: 10.1172/jci.insight.91917] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND. Morphological patterns of Paneth cells are a prognostic biomarker in Western Crohn's disease (CD) patients, and are associated with autophagy-associated ATG16L1 and NOD2 variants. We hypothesized that genetic determinants of Paneth cell phenotype in other ethnic CD cohorts are distinct but also involved in autophagy. METHODS. We performed a hypothesis-driven analysis of 56 single nucleotide polymorphisms (SNPs) associated with CD susceptibility or known to affect Paneth cell function in 110 Japanese CD patients who underwent ileal resection. We subsequently performed a genome-wide association analysis. Paneth cell phenotype was determined by defensin-5 immunofluorescence. Selected genotype-Paneth cell defect correlations were compared to a Western CD cohort (n = 164). RESULTS. The average percentage of abnormal Paneth cells in Japanese CD was similar to Western CD (P = 0.87), and abnormal Paneth cell phenotype was also associated with early recurrence (P = 0.013). In contrast to Western CD, ATG16L1 T300A was not associated with Paneth cell defect in Japanese CD (P = 0.20). Among the 56 selected SNPs, only LRRK2 M2397T showed significant association with Paneth cell defect (P = 3.62 × 10-4), whereas in the Western CD cohort it was not (P = 0.76). Pathway analysis of LRRK2 and other candidate genes with P less than 5 × 10-4 showed connections with known CD susceptibility genes and links to autophagy and TNF-α networks. CONCLUSIONS. We found dichotomous effects of ATG16L1 and LRRK2 on Paneth cell defect between Japanese and Western CD. Genes affecting Paneth cell phenotype in Japanese CD were also associated with autophagy. Paneth cell phenotype also predicted prognosis in Japanese CD. FUNDING. Helmsley Charitable Trust, Doris Duke Foundation (grant 2014103), Japan Society for the Promotion of Science (KAKENHI grants JP15H04805 and JP15K15284), Crohn's and Colitis Foundation grant 274415, NIH (grants 1R56DK095820, K01DK109081, and UL1 TR000448).
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Zhenqiu Liu
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoshitaka Kinouchi
- Health Administration Center, Center for the Advancement of Higher Education, Tohoku University, Sendai, Japan
| | - Dermot Pb McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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39
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Thomas LS, Targan SR, Tsuda M, Yu QT, Salumbides BC, Haritunians T, Mengesha E, McGovern DPB, Michelsen KS. The TNF family member TL1A induces IL-22 secretion in committed human T h17 cells via IL-9 induction. J Leukoc Biol 2017; 101:727-737. [PMID: 27733581 PMCID: PMC6608031 DOI: 10.1189/jlb.3a0316-129r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 08/30/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022] Open
Abstract
TL1A contributes to the pathogenesis of several chronic inflammatory diseases, including those of the bowel by enhancing TH1, TH17, and TH2 responses. TL1A mediates a strong costimulation of these TH subsets, particularly of mucosal CCR9+ T cells. However, the signaling pathways that TL1A induces in different TH subsets are incompletely understood. We investigated the function of TL1A on human TH17 cells. TL1A, together with TGF-β, IL-6, and IL-23, enhanced the secretion of IL-17 and IFN-γ from human CD4+ memory T cells. TL1A induced expression of the transcription factors BATF and T-bet that correlated with the secretion of IL-17 and IFN-γ. In contrast, TL1A alone induced high levels of IL-22 in memory CD4+ T cells and committed TH17 cells. However, TL1A did not enhance expression of IL-17A in TH17 cells. Expression of the transcription factor aryl hydrocarbon receptor, which regulates the expression of IL-22 was not affected by TL1A. Transcriptome analysis of TH17 cells revealed increased expression of IL-9 in response to TL1A. Blocking IL-9 receptor antibodies abrogated TL1A-induced IL-22 secretion. Furthermore, TL1A increased IL-9 production by peripheral TH17 cells isolated from patients with Crohn's disease. These data suggest that TL1A differentially induces expression of TH17 effector cytokines IL-17, -9, and -22 and provides a potential target for therapeutic intervention in TH17-driven chronic inflammatory diseases.
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Affiliation(s)
- Lisa S Thomas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Masato Tsuda
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Qi T Yu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Brenda C Salumbides
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathrin S Michelsen
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
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40
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DP, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10-8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10-6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee
Health Science Center, Memphis, TN, 38163, USA,Computational and Statistical Genomics Branch, National Human Genome
Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, MUSC Pediatric Center for Inflammatory Bowel
Disorders, Summerville, SC, 29485, USA
| | - Jenifer Seminerio
- Department of Gastroenterology, MUSC Digestive Disease Center, Charleston,
SC, 29486, USA
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University
Health Sciences Center, Shreveport, LA, 71130, USA
| | - Robert N. Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia,
Philadelphia, PA, 19104, USA
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine &
Nursing, Baltimore, MD, 21287, USA
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, KY, 40202,
USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, NC, 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for
Innovations in Quality Effectiveness and Safety; Michael E. DeBakey VA Medical Center,
Houston, TX, 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport,
LA, 71118, USA
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel
Hill, NC, 27514, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill,
Chapel Hill, NC, 27514, USA
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas
Children's Hospital, Houston, TX, 77030, USA
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's
Hospital, Chicago, IL, 60637, USA
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus
of Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical
Center, Dallas, TX, 75390, USA
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine,
Baltimore, MD, 21205, USA
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony
Brook, NY, 11794, USA
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s
Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham,
AL, 35294, USA
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine,
St. Louis, MO, 63110, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth,
TX, 76104, USA
| | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center,
Dallas, TX, 75390, USA
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida,
Jacksonville, FL, 32224, USA
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI,
48202, USA
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the
Montreal Heart Institute Research Center, Montreal, Quebec, H1T 1C8, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute,
School of Medicine; and Department of Human Genetics, Graduate School of Public Health;
University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount
Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, M5G1X5, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles
Bronfman Institute for Personalized Medicine, New York, NY, 10029, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
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41
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Chuang LS, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Evelyn Ng SM, Zhang W, Hsu NY, Facey JA, Luong T, Fernandez-Hernandez H, Li D, Rivas M, Schiff ER, Gusev A, Schumm LP, Bowen BM, Sharma Y, Ning K, Remark R, Gnjatic S, Legnani P, George J, Sands BE, Stempak JM, Datta LW, Lipka S, Katz S, Cheifetz AS, Barzilai N, Pontikos N, Abraham C, Dubinsky MJ, Targan S, Taylor K, Rotter JI, Scherl EJ, Desnick RJ, Abreu MT, Zhao H, Atzmon G, Pe’er I, Kugathasan S, Hakonarson H, McCauley JL, Lencz T, Darvasi A, Plagnol V, Silverberg MS, Muise AM, Brant SR, Daly MJ, Segal AW, Duerr RH, Merad M, McGovern DP, Peter I, Cho JH. A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF. Gastroenterology 2016; 151:710-723.e2. [PMID: 27377463 PMCID: PMC5037012 DOI: 10.1053/j.gastro.2016.06.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Crohn's disease (CD) has the highest prevalence in Ashkenazi Jewish populations. We sought to identify rare, CD-associated frameshift variants of high functional and statistical effects. METHODS We performed exome sequencing and array-based genotype analyses of 1477 Ashkenazi Jewish individuals with CD and 2614 Ashkenazi Jewish individuals without CD (controls). To validate our findings, we performed genotype analyses of an additional 1515 CD cases and 7052 controls for frameshift mutations in the colony-stimulating factor 2-receptor β common subunit gene (CSF2RB). Intestinal tissues and blood samples were collected from patients with CD; lamina propria leukocytes were isolated and expression of CSF2RB and granulocyte-macrophage colony-stimulating factor-responsive cells were defined by adenomatous polyposis coli (APC) time-of-flight mass cytometry (CyTOF analysis). Variants of CSF2RB were transfected into HEK293 cells and the expression and functions of gene products were compared. RESULTS In the discovery cohort, we associated CD with a frameshift mutation in CSF2RB (P = 8.52 × 10(-4)); the finding was validated in the replication cohort (combined P = 3.42 × 10(-6)). Incubation of intestinal lamina propria leukocytes with granulocyte-macrophage colony-stimulating factor resulted in high levels of phosphorylation of signal transducer and activator of transcription (STAT5) and lesser increases in phosphorylation of extracellular signal-regulated kinase and AK straining transforming (AKT). Cells co-transfected with full-length and mutant forms of CSF2RB had reduced pSTAT5 after stimulation with granulocyte-macrophage colony-stimulating factor, compared with cells transfected with control CSF2RB, indicating a dominant-negative effect of the mutant gene. Monocytes from patients with CD who were heterozygous for the frameshift mutation (6% of CD cases analyzed) had reduced responses to granulocyte-macrophage colony-stimulating factor and markedly decreased activity of aldehyde dehydrogenase; activity of this enzyme has been associated with immune tolerance. CONCLUSIONS In a genetic analysis of Ashkenazi Jewish individuals, we associated CD with a frameshift mutation in CSF2RB. Intestinal monocytes from carriers of this mutation had reduced responses to granulocyte-macrophage colony-stimulating factor, providing an additional mechanism for alterations to the innate immune response in individuals with CD.
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Affiliation(s)
- Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Ken Y. Hui
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA 06520,Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Arthur Mortha
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Adeeb Rahman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Adam P. Levine
- Centre for Molecular Medicine, Division of Medicine, University College, London, UK WC1E 6JF
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 90048
| | - Sok Meng Evelyn Ng
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Wei Zhang
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Jody-Ann Facey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Tramy Luong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | | | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 90048
| | - Manuel Rivas
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA, USA 02142,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA 02114,Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics Research, University of Oxford, Oxford, UK OX3 UBN
| | - Elena R. Schiff
- Centre for Molecular Medicine, Division of Medicine, University College, London, UK WC1E 6JF
| | - Alexander Gusev
- Department of Epidemiology, Harvard University, Boston, MA, USA 02115
| | - L. Phillip Schumm
- Department of Health Studies, University of Chicago, Chicago, IL, USA 60637
| | - Beatrice M. Bowen
- Department of Genetics, Yale University, New Haven, CT, USA 06520,Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Yashoda Sharma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Kaida Ning
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520,Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA 90033
| | - Romain Remark
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Sacha Gnjatic
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Peter Legnani
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - James George
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Bruce E. Sands
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Joanne M. Stempak
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada M5T3L9,Department of Medicine, University of Toronto, Toronto, Ontario, Canada M5G1X5
| | - Lisa W. Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA 21231,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA 21231
| | - Seth Lipka
- Department of Internal Medicine, University of South Florida, Tampa, FL, USA 33606
| | - Seymour Katz
- Department of Medicine, New York University School of Medicine, New York, NY, USA10016
| | - Adam S. Cheifetz
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA 02215
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA 10461
| | - Nikolas Pontikos
- Centre for Molecular Medicine, Division of Medicine, University College, London, UK WC1E 6JF
| | - Clara Abraham
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA 06520
| | - Marla J. Dubinsky
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 90048
| | - Kent Taylor
- Institute for Translational Genomics and Population Sciences, Division of Genomic Outcomes, Harbor-UCLA Medical Center, Torrance, CA, USA 90502
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Division of Genomic Outcomes, Harbor-UCLA Medical Center, Torrance, CA, USA 90502
| | - Ellen J. Scherl
- The Division of Gastroenterology & Hepatology, Sanford I. Weill College of Cornell University—New York Presbyterian Hospital, New York, NY, USA 10021
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Maria T. Abreu
- Division of Gastroenterology, University of Miami, Miller School of Medicine, Miami, Florida, USA 33136
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, CT, USA 06520
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA 10461
| | - Itsik Pe’er
- Department of Computer Science, Columbia University, New York, NY, USA 10027
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA, USA 30322
| | - Hakon Hakonarson
- Centre for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA 19104,Division of Human Genetics, University of Pennsylvania, Philadelphia, PA, USA 19014
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA 33136,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA 33136
| | - Todd Lencz
- Feinstein Institute for Medical Research, North Shore – Long Island Jewish Health System, Manhasset, NY, USA 11030
| | - Ariel Darvasi
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel 91904
| | - Vincent Plagnol
- Genetics Institute, Division of Biosciences, University College, London, UK WC1E 6BT
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada M5T3L9,Department of Medicine, University of Toronto, Toronto, Ontario, Canada M5G1X5
| | - Aleixo M. Muise
- Inflammatory Bowel Disease Centre and Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada M5G1X8,Department of Pediatrics, University of Toronto, Toronto, ON, Canada M5G1X8
| | - Steven R. Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA 21231,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA 21231
| | - Mark J. Daly
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA, USA 02142,Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA USA 02114,Department of Genetics, Harvard Medical School, Boston, MA, USA 02115
| | - Anthony W. Segal
- Centre for Molecular Medicine, Division of Medicine, University College, London, UK WC1E 6JF
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA, 15261
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 90048
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Judy H. Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,To whom correspondence should be addressed. The corresponding author’s contact information: Judy Cho, Hess CSM Building Floor 8th Room 118, 1470 Madison Avenue, New York, NY 10029, TEL. (212) 824-8940, FAX. (646) 537-9452,
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42
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Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DPB, Duerr RH. A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition. Gastroenterology 2016; 151:724-32. [PMID: 27492617 PMCID: PMC5037008 DOI: 10.1053/j.gastro.2016.06.051] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies have identified 200 inflammatory bowel disease (IBD) loci, but the genetic architecture of Crohn's disease (CD) and ulcerative colitis remain incompletely defined. Here, we aimed to identify novel associations between IBD and functional genetic variants using the Illumina ExomeChip (San Diego, CA). METHODS Genotyping was performed in 10,523 IBD cases and 5726 non-IBD controls. There were 91,713 functional single-nucleotide polymorphism loci in coding regions analyzed. A novel identified association was replicated further in 2 independent cohorts. We further examined the association of the identified single-nucleotide polymorphism with microbiota from 338 mucosal lavage samples in the Mucosal Luminal Interface cohort measured using 16S sequencing. RESULTS We identified an association between CD and a missense variant encoding alanine or threonine at position 391 in the zinc transporter solute carrier family 39, member 8 protein (SLC39A8 alanine 391 threonine, rs13107325) and replicated the association with CD in 2 replication cohorts (combined meta-analysis P = 5.55 × 10(-13)). This variant has been associated previously with distinct phenotypes including obesity, lipid levels, blood pressure, and schizophrenia. We subsequently determined that the CD risk allele was associated with altered colonic mucosal microbiome composition in both healthy controls (P = .009) and CD cases (P = .0009). Moreover, microbes depleted in healthy carriers strongly overlap with those reduced in CD patients (P = 9.24 × 10(-16)) and overweight individuals (P = 6.73 × 10(-16)). CONCLUSIONS Our results suggest that an SLC39A8-dependent shift in the gut microbiome could explain its pleiotropic effects on multiple complex diseases including CD.
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Affiliation(s)
- Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jean-Paul Achkar
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Ken Y Hui
- Division of Gastroenterology, Department of Medicine, Yale University, New Haven, Connecticut
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Stephan Brand
- Department of Medicine II, University Hospital Munich-Grosshadern, Munich, Germany
| | - Graham Radford-Smith
- Inflammatory Bowel Diseases, Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Department of Gastroenterology, Royal Brisbane and Women's Hospital, Brisbane, Australia; School of Medicine, University of Queensland, Brisbane, Australia
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Orebro, Sweden
| | - Jan-Hendrik Niess
- Department of Internal Medicine I, University of Ulm, Ulm, Germany; Division of Visceral Surgery and Medicine, Department of Gastroenterology, Inselspital Bern, Bern, Switzerland; Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta, Atlanta, Georgia
| | - Carsten Büning
- Internal Medicine, Krankenhaus Waldfriede, Berlin, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, Biostatistical Laboratory, University of Chicago, Chicago, Illinois
| | - Lambertus Klei
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ashwin Ananthakrishnan
- Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Guy Aumais
- Université de Montréal, Montréal, Québec, Canada; Hopital Maisonneuve Rosemont, Montréal, Québec, Canada
| | - Leonard Baidoo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marla Dubinsky
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Jürgen Glas
- Department of Preventive Dentistry and Periodontology, Ludwig-Maximilians-University, Munich, Germany
| | - Raquel Milgrom
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Deborah D Proctor
- Division of Gastroenterology, Department of Medicine, Yale University, New Haven, Connecticut
| | - Miguel Regueiro
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lisa A Simms
- Inflammatory Bowel Diseases, Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Joanne M Stempak
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Leif Törkvist
- Department of Clinical Science Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Center for Digestive Disease, IBD-unit, Karolinska University Hospital, Stockholm, Sweden
| | - Yashoda Sharma
- Department of Genetic & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bernie Devlin
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ramnik J Xavier
- Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, Maryland; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - John D Rioux
- Université de Montréal, Montréal, Québec, Canada; Montreal Heart Institute, Montréal, Québec, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Judy H Cho
- Department of Genetic & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan Braun
- Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.
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43
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Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ. Characterization of candidate genes in inflammatory bowel disease-associated risk loci. JCI Insight 2016; 1:e87899. [PMID: 27668286 DOI: 10.1172/jci.insight.87899] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
GWAS have linked SNPs to risk of inflammatory bowel disease (IBD), but a systematic characterization of disease-associated genes has been lacking. Prior studies utilized microarrays that did not capture many genes encoded within risk loci or defined expression quantitative trait loci (eQTLs) using peripheral blood, which is not the target tissue in IBD. To address these gaps, we sought to characterize the expression of IBD-associated risk genes in disease-relevant tissues and in the setting of active IBD. Terminal ileal (TI) and colonic mucosal tissues were obtained from patients with Crohn's disease or ulcerative colitis and from healthy controls. We developed a NanoString code set to profile 678 genes within IBD risk loci. A subset of patients and controls were genotyped for IBD-associated risk SNPs. Analyses included differential expression and variance analysis, weighted gene coexpression network analysis, and eQTL analysis. We identified 116 genes that discriminate between healthy TI and colon samples and uncovered patterns in variance of gene expression that highlight heterogeneity of disease. We identified 107 coexpressed gene pairs for which transcriptional regulation is either conserved or reversed in an inflammation-independent or -dependent manner. We demonstrate that on average approximately 60% of disease-associated genes are differentially expressed in inflamed tissue. Last, we identified eQTLs with either genotype-only effects on expression or an interaction effect between genotype and inflammation. Our data reinforce tissue specificity of expression in disease-associated candidate genes, highlight genes and gene pairs that are regulated in disease-relevant tissue and inflammation, and provide a foundation to advance the understanding of IBD pathogenesis.
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Affiliation(s)
- Joanna M Peloquin
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Gautam Goel
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Lingjia Kong
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dermot P McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Vijay Yajnik
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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44
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Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LLE, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DPB, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun 2016; 7:12342. [PMID: 27503255 PMCID: PMC4980482 DOI: 10.1038/ncomms12342] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/24/2016] [Indexed: 01/05/2023] Open
Abstract
Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain.
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Affiliation(s)
- Manuel A. Rivas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Daniel Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Christine Stevens
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - A. Nicole Desch
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Philippe Goyette
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada H1T1C8
| | - Daniel Gudbjartsson
- deCODE Genetics, Amgen Inc., 101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics, Amgen Inc., 101 Reykjavik, Iceland
- Department of Immunology, Landspitali, the National University Hospital of Iceland, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen Inc., 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Mitja I. Kurki
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California 90048 USA
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Stockholm, Sweden
- BioCruces Health Research Institute and IKERBASQUE, Basque Foundation for Science, 48903 Bilbao, Spain
| | - Vito Annese
- Unit of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, 71013 San Giovanni Rotondo, Italy
- Strutture Organizzative Dipartimentali (SOD) Gastroenterologia 2, Azienda Ospedaliero Universitaria (AOU) Careggi, 50134 Florence, Italy
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, Translational Research in GastroIntestinal Disorders (TARGID), Katholieke Universiteit (KU) Leuven, Leuven 3000, Belgium
- Division of Gastroenterology, University Hospital Gasthuisberg, BE-3000 Leuven, Belgium
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, SE 701 82 Örebro, Sweden
| | - Paulina Paavola-Sakki
- Department of Medicine, University of Helsinki, 00100 Helsinki, Finland
- Helsinki University Hospital, 00100 Helsinki, Finland
- Clinic of Gastroenterology, Helsinki University Hospital, 00100 Helsinki, Finland
| | - Maarit Lappalainen
- Department of Medicine, University of Helsinki, 00100 Helsinki, Finland
- Helsinki University Hospital, 00100 Helsinki, Finland
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
| | - Monkol Lek
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Beryl Cummings
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Taru Tukiainen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California 90048 USA
| | - Leena Halme
- Department of Transplantation and Liver Surgery, University of Helsinki, 00100 Helsinki, Finland
| | - Lotta L. E. Koskinen
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, 00100 Helsinki, Finland
| | - Ashwin N. Ananthakrishnan
- Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Yang Luo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Graham A. Heap
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Marijn C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Daniel G. MacArthur
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Benjamin M. Neale
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter PL6 8BU, UK
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21205, USA
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Mark S. Silverberg
- Department of Medicine, Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Institute for Molecular Medicine Finland, University of Helsinki, 00100 Helsinki, Finland
- Massachusetts General Hospital, Center for Human Genetic Research, Psychiatric and Neurodevelopmental Genetics Unit, Boston, Massachusetts 02114, USA
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, 00100 Helsinki, Finland
| | - Kimmo Kontula
- Department of Medicine, University of Helsinki, 00100 Helsinki, Finland
- Helsinki University Hospital, 00100 Helsinki, Finland
| | - Martti Färkkilä
- Department of Medicine, University of Helsinki, 00100 Helsinki, Finland
- Helsinki University Hospital, 00100 Helsinki, Finland
- Clinic of Gastroenterology, Helsinki University Hospital, 00100 Helsinki, Finland
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California 90048 USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Kari Stefansson
- deCODE Genetics, Amgen Inc., 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - John D. Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada H1T1C8
- Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada H3T 1J4
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Mark J. Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - J. Barrett
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - K. de Lane
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - C. Edwards
- Department of Gastroenterology, Torbay Hospital, Devon, UK
| | - A. Hart
- Department of Medicine, St. Mark's Hospital, Middlesex, UK
| | - C. Hawkey
- Nottingham Digestive Disease Centre, Queens Medical Centre, Nottingham, UK
| | - L. Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK
- Christ Church, University of Oxford, Oxford, UK
| | - N. Kennedy
- Gastrointestinal Unit, Wester General Hospital, University of Edinburgh, Edinburgh, UK
| | - C. Lamb
- Newcastle University, Newcastle upon Tyne, UK
| | - J. Lee
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge, UK
| | - C. Lees
- Gastrointestinal Unit, Wester General Hospital, University of Edinburgh, Edinburgh, UK
| | | | - C. Mathew
- Department of Medical and Molecular Genetics, Guy's Hospital, London, UK
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, UK
| | - C. Mowatt
- Department of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - B. Newman
- Genetic Medicine, Manchester Academic Health Science Centre, Manchester, UK
- The Manchester Centre for Genomic Medicine, University of Manchester, Manchester, UK
| | - E. Nimmo
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - M. Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge, UK
| | - M. Pollard
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - N. Prescott
- Department of Medical and Molecular Genetics, Guy's Hospital, London, UK
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, UK
| | - J. Randall
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - D. Rice
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - J. Satsangi
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - A. Simmons
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - M. Tremelling
- Gastroenterology & General Medicine, Norfolk and Norwich University Hospital, Norwich, UK
| | - H. Uhlig
- Translational Gastroenterology Unit and the Department of Pediatrics, University of Oxford, Oxford, UK
| | - D. Wilson
- Pediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, Edinburgh, UK
- Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - C. Abraham
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - J. P. Achkar
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - A. Bitton
- Division of Gastroenterology, Royal Victoria Hospital, Montréal, Québec, Canada
| | - G. Boucher
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada H1T1C8
| | - K. Croitoru
- Inflammatory Bowel Disease Group, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - P. Fleshner
- Department of Transplantation and Liver Surgery, University of Helsinki, 00100 Helsinki, Finland
| | - J. Glas
- Division of Gastroenterology, Royal Victoria Hospital, Montréal, Québec, Canada
| | - S. Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - J. V. Limbergen
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Toronto, Ontario, Canada
| | - R. Milgrom
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - D. Proctor
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - M. Regueiro
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - P. L. Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA
| | - Y. Sharma
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - J. M. Stempak
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - S. R. Targan
- Department of Transplantation and Liver Surgery, University of Helsinki, 00100 Helsinki, Finland
| | - M. H. Wang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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45
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Palmer ND, Wagenknecht LE, Langefeld CD, Wang N, Buchanan TA, Xiang AH, Allayee H, Bergman RN, Raffel LJ, Chen YDI, Haritunians T, Fingerlin T, Goodarzi MO, Taylor KD, Rotter JI, Watanabe RM, Bowden DW. Improved Performance of Dynamic Measures of Insulin Response Over Surrogate Indices to Identify Genetic Contributors of Type 2 Diabetes: The GUARDIAN Consortium. Diabetes 2016; 65:2072-80. [PMID: 27207554 PMCID: PMC4915581 DOI: 10.2337/db15-1543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/09/2016] [Indexed: 01/24/2023]
Abstract
Type 2 diabetes (T2D) is a heterogeneous disorder with contributions from peripheral insulin resistance and β-cell dysfunction. For minimization of phenotypic heterogeneity, quantitative intermediate phenotypes characterizing basal glucose homeostasis (insulin resistance and HOMA of insulin resistance [HOMAIR] and of β-cell function [HOMAB]) have shown promise in relatively large samples. We investigated the utility of dynamic measures of glucose homeostasis (insulin sensitivity [SI] and acute insulin response [AIRg]) evaluating T2D-susceptibility variants (n = 57) in Hispanic Americans from the GUARDIAN Consortium (n = 2,560). Basal and dynamic measures were genetically correlated (HOMAB-AIRg: ρG = 0.28-0.73; HOMAIR-SI: ρG = -0.73 to -0.83) with increased heritability for the dynamic measure AIRg Significant association of variants with dynamic measures (P < 8.77 × 10(-4)) was observed. A pattern of superior performance of AIRg was observed for well-established loci including MTNR1B (P = 9.46 × 10(-12)), KCNQ1 (P = 1.35 × 10(-4)), and TCF7L2 (P = 5.10 × 10(-4)) with study-wise statistical significance. Notably, significant association of MTNR1B with AIRg (P < 1.38 × 10(-9)) was observed in a population one-fourteenth the size of the initial discovery cohort. These observations suggest that basal and dynamic measures provide different views and levels of sensitivity to discrete elements of glucose homeostasis. Although more costly to obtain, dynamic measures yield significant results that could be considered physiologically "closer" to causal pathways and provide insight into the discrete mechanisms of action.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Nan Wang
- Department of Preventative Medicine, Keck School of Medicine of USC, Los Angeles, CA Department of Physiology and Biophysics, Keck School of Medicine of USC, Los Angeles, CA
| | - Thomas A Buchanan
- Department of Physiology and Biophysics, Keck School of Medicine of USC, Los Angeles, CA Department of Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Anny H Xiang
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA
| | - Hooman Allayee
- Department of Preventative Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Richard N Bergman
- Department of Physiology and Biophysics, Keck School of Medicine of USC, Los Angeles, CA
| | - Leslie J Raffel
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Tasha Fingerlin
- Department of Epidemiology, University of Colorado Denver, Aurora, CO Department of Biostatistics and Informatics, University of Colorado Denver, Aurora, CO
| | - Mark O Goodarzi
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Kent D Taylor
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Richard M Watanabe
- Department of Preventative Medicine, Keck School of Medicine of USC, Los Angeles, CA Department of Physiology and Biophysics, Keck School of Medicine of USC, Los Angeles, CA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC
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Bodea C, Neale B, Ripke S, Daly M, Devlin B, Roeder K, Barclay M, Peyrin-Biroulet L, Chamaillard M, Colombel JF, Cottone M, Croft A, D’Incà R, Halfvarson J, Hanigan K, Henderson P, Hugot JP, Karban A, Kennedy N, Khan M, Lémann M, Levine A, Massey D, Milla M, Montgomery G, Ng S, Oikonomou I, Peeters H, Proctor D, Rahier JF, Roberts R, Rutgeerts P, Seibold F, Stronati L, Taylor K, Törkvist L, Ublick K, Van Limbergen J, Van Gossum A, Vatn M, Zhang H, Zhang W, Andrews J, Bampton P, Barclay M, Florin T, Gearry R, Krishnaprasad K, Lawrance I, Mahy G, Montgomery G, Radford-Smith G, Roberts R, Simms L, Amininijad L, Cleynen I, Dewit O, Franchimont D, Georges M, Laukens D, Peeters H, Rahier JF, Rutgeerts P, Theatre E, Van Gossum A, Vermeire S, Aumais G, Baidoo L, Barrie A, Beck K, Bernard EJ, Binion D, Bitton A, Brant S, Cho J, Cohen A, Croitoru K, Daly M, Datta L, Deslandres C, Duerr R, Dutridge D, Ferguson J, Fultz J, Goyette P, Greenberg G, Haritunians T, Jobin G, Katz S, Lahaie R, McGovern D, Nelson L, Ng S, Ning K, Oikonomou I, Paré P, Proctor D, Regueiro M, Rioux J, Ruggiero E, Schumm L, Schwartz M, Scott R, Sharma Y, Silverberg M, Spears D, Steinhart A, Stempak J, Swoger J, Tsagarelis C, Zhang W, Zhang C, Zhao H, Aerts J, Ahmad T, Arbury H, Attwood A, Auton A, Ball S, Balmforth A, Barnes C, Barrett J, Barroso I, Barton A, Bennett A, Bhaskar S, Blaszczyk K, Bowes J, Brand O, Braund P, Bredin F, Breen G, Brown M, Bruce I, Bull J, Burren O, Burton J, Byrnes J, Caesar S, Cardin N, Clee C, Coffey A, Connell J, Conrad D, Cooper J, Dominiczak A, Downes K, Drummond H, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans D, Evans G, Eyre S, Farmer A, Ferrier N, Flynn E, Forbes A, Forty L, Franklyn J, Frayling T, Freathy R, Giannoulatou E, Gibbs P, Gilbert P, Gordon-Smith K, Gray E, Green E, Groves C, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman G, Hocking L, Holmes C, Howard E, Howard P, Howson J, Hughes D, Hunt S, Isaacs J, Jain M, Jewell D, Johnson T, Jolley J, Jones I, Jones L, Kirov G, Langford C, Lango-Allen H, Lathrop G, Lee J, Lee K, Lees C, Lewis K, Lindgren C, Maisuria-Armer M, Maller J, Mansfield J, Marchini J, Martin P, Massey D, McArdle W, McGuffin P, McLay K, McVean G, Mentzer A, Mimmack M, Morgan A, Morris A, Mowat C, Munroe P, Myers S, Newman W, Nimmo E, O’Donovan M, Onipinla A, Ovington N, Owen M, Palin K, Palotie A, Parnell K, Pearson R, Pernet D, Perry J, Phillips A, Plagnol V, Prescott N, Prokopenko I, Quail M, Rafelt S, Rayner N, Reid D, Renwick A, Ring S, Robertson N, Robson S, Russell E, St Clair D, Sambrook J, Sanderson J, Sawcer S, Schuilenburg H, Scott C, Scott R, Seal S, Shaw-Hawkins S, Shields B, Simmonds M, Smyth D, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens H, Stirrups K, Stone M, Strachan D, Su Z, Symmons D, Thompson J, Thomson W, Tobin M, Travers M, Turnbull C, Vukcevic D, Wain L, Walker M, Walker N, Wallace C, Warren-Perry M, Watkins N, Webster J, Weedon M, Wilson A, Woodburn M, Wordsworth B, Yau C, Young A, Zeggini E, Brown M, Burton P, Caulfield M, Compston A, Farrall M, Gough S, Hall A, Hattersley A, Hill A, Mathew C, Pembrey M, Satsangi J, Stratton M, Worthington J, Hurles M, Duncanson A, Ouwehand W, Parkes M, Rahman N, Todd J, Samani N, Kwiatkowski D, McCarthy M, Craddock N, Deloukas P, Donnelly P, Blackwell J, Bramon E, Casas J, Corvin A, Jankowski J, Markus H, Palmer C, Plomin R, Rautanen A, Trembath R, Viswanathan A, Wood N, Spencer C, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson R, Strange A, Blackburn H, Bumpstead S, Dronov S, Gillman M, Jayakumar A, McCann O, Liddle J, Potter S, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies. Am J Hum Genet 2016; 98:857-868. [PMID: 27087321 DOI: 10.1016/j.ajhg.2016.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/29/2016] [Indexed: 02/08/2023] Open
Abstract
One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.
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Siegel CA, Horton H, Siegel LS, Thompson KD, Mackenzie T, Stewart SK, Rice PW, Stempak JM, Dezfoli S, Haritunians T, Levy A, Baek M, Milgrom R, Dulai PS, Targan SR, Silverberg MS, Dubinsky MC, McGovern DP. A validated web-based tool to display individualised Crohn's disease predicted outcomes based on clinical, serologic and genetic variables. Aliment Pharmacol Ther 2016; 43:262-71. [PMID: 26567467 DOI: 10.1111/apt.13460] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/25/2015] [Accepted: 10/11/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Early treatment for Crohn's disease (CD) with immunomodulators and/or anti-TNF agents improves outcomes in comparison to a slower 'step up' algorithm. However, there remains a limited ability to identify those who would benefit most from early intensive therapy. AIM To develop a validated, individualised, web-based tool for patients and clinicians to visualise individualised risks for developing Crohn's disease complications. METHODS A well-characterised cohort of adult patients with CD was analysed. Available data included: demographics; clinical characteristics; serologic immune responses; NOD2 status; time from diagnosis to complication; and medication exposure. Cox proportional analyses were performed to model the probability of developing a CD complication over time. The Cox model was validated externally in two independent CD cohorts. Using system dynamics analysis (SDA), these results were transformed into a simple graphical web-based display to show patients their individualised probability of developing a complication over a 3-year period. RESULTS Two hundered and forty three CD patients were included in the final model of which 142 experienced a complication. Significant variables in the multivariate Cox model included small bowel disease (HR 2.12, CI 1.05-4.29), left colonic disease (HR 0.73, CI 0.49-1.09), perianal disease (HR 4.12, CI 1.01-16.88), ASCA (HR 1.35, CI 1.16-1.58), Cbir (HR 1.29, CI 1.07-1.55), ANCA (HR 0.77, CI 0.62-0.95), and the NOD2 frameshift mutation/SNP13 (HR 2.13, CI 1.33-3.40). The Harrell's C (concordance index for predictive accuracy of the model) = 0.73. When applied to the two external validation cohorts (adult n = 109, pediatric n = 392), the concordance index was 0.73 and 0.75, respectively, for adult and pediatric patients. CONCLUSIONS A validated, web-based tool has been developed to display an individualised predicted outcome for adult patients with Crohn's disease based on clinical, serologic and genetic variables. This tool can be used to help providers and patients make personalised decisions about treatment options.
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Affiliation(s)
- C A Siegel
- Dartmouth-Hitchcock Inflammatory Bowel Disease Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - H Horton
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - L S Siegel
- Siegel Environmental Dynamics, Hanover, NH, USA.,Climate Interactive, Washington, DC, USA
| | - K D Thompson
- Dartmouth-Hitchcock Inflammatory Bowel Disease Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - T Mackenzie
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - S K Stewart
- Dartmouth-Hitchcock Inflammatory Bowel Disease Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - P W Rice
- Climate Interactive, Washington, DC, USA
| | - J M Stempak
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - S Dezfoli
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - T Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - A Levy
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - M Baek
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - R Milgrom
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - P S Dulai
- Dartmouth-Hitchcock Inflammatory Bowel Disease Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - S R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - M S Silverberg
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - M C Dubinsky
- Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - D P McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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48
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Taleban S, Li D, Targan SR, Ippoliti A, Brant SR, Cho JH, Duerr RH, Rioux JD, Silverberg MS, Vasiliauskas EA, Rotter JI, Haritunians T, Shih DQ, Dubinsky M, Melmed GY, McGovern DP. Ocular Manifestations in Inflammatory Bowel Disease Are Associated with Other Extra-intestinal Manifestations, Gender, and Genes Implicated in Other Immune-related Traits. J Crohns Colitis 2016; 10:43-9. [PMID: 26449790 PMCID: PMC6082592 DOI: 10.1093/ecco-jcc/jjv178] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 08/28/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND There has been considerable progress in identifying inflammatory bowel disease [IBD] susceptibility genes but little progress in examining the role of genetic variation in the development of the extra-intestinal manifestations [EIMs] of IBD. This study identified clinical, serological, and genetic factors associated with ocular EIMs [O-EIMs] in IBD. METHODS We performed a retrospective case-control study of IBD patients, comparing those with and without O-EIMs using the Cedars-Sinai IBD Research Repository and the NIDDK IBD Genetics Consortium Repository. Genotyping was performed using Illumina whole genome platforms. RESULTS In all, 124 cases and 3328 controls with available clinical data were identified; 103 cases and 2808 controls had genetic data available. Erythema nodosum and peripheral arthritis particularly were common in patients with O-EIMs [p = 2.77 x 10(-13) and p = 2.58 x 10(-13), respectively] with increasing odds ratios for O-EIMs with each additional non-ocular-EIM [for ≥ 2 EIMs, odds ratio 14.72]. Nominal association with O-EIMs was observed at several known IBD susceptibility single nuclear polymorphisms. One locus, containing RBM19, achieved genome-wide level of significance for association with O-EIMs. CONCLUSIONS In IBD, O-EIMs co-occur with musculoskeletal and skin manifestations and, in this study, are nominally associated with known IBD loci. Additional cohorts are needed to verify these results and identify additional genes.
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Affiliation(s)
- Sasha Taleban
- Department of Medicine, Division of Gastroenterology, University of Arizona College of Medicine
,
Tucson, AZ
,
USA,F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Andrew Ippoliti
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Steven R. Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Bloomberg School of Public Health, Johns Hopkins University
,
Baltimore, MD
,
USA
| | - Judy H. Cho
- Division of Gastroenterology, Mount Sinai Medical Center
,
New York, NY
,
USA
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - John D. Rioux
- Department of Medicine, University of Montreal and Montreal Heart Institute
,
Montreal, QC
,
Canada
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto
,
Toronto, ON
,
Canada
| | - Eric A. Vasiliauskas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center
,
Torrance, CA
,
USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - David Q. Shih
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Marla Dubinsky
- Department of Pediatrics, Division of Gastroenterology, Mount Sinai Medical Center
,
New York, NY
,
USA
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
| | - Dermot P.B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center
,
Los Angeles, CA
,
USA
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49
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de Vries PS, Chasman DI, Sabater-Lleal M, Chen MH, Huffman JE, Steri M, Tang W, Teumer A, Marioni RE, Grossmann V, Hottenga JJ, Trompet S, Müller-Nurasyid M, Zhao JH, Brody JA, Kleber ME, Guo X, Wang JJ, Auer PL, Attia JR, Yanek LR, Ahluwalia TS, Lahti J, Venturini C, Tanaka T, Bielak LF, Joshi PK, Rocanin-Arjo A, Kolcic I, Navarro P, Rose LM, Oldmeadow C, Riess H, Mazur J, Basu S, Goel A, Yang Q, Ghanbari M, Willemsen G, Rumley A, Fiorillo E, de Craen AJM, Grotevendt A, Scott R, Taylor KD, Delgado GE, Yao J, Kifley A, Kooperberg C, Qayyum R, Lopez LM, Berentzen TL, Räikkönen K, Mangino M, Bandinelli S, Peyser PA, Wild S, Trégouët DA, Wright AF, Marten J, Zemunik T, Morrison AC, Sennblad B, Tofler G, de Maat MPM, de Geus EJC, Lowe GD, Zoledziewska M, Sattar N, Binder H, Völker U, Waldenberger M, Khaw KT, Mcknight B, Huang J, Jenny NS, Holliday EG, Qi L, Mcevoy MG, Becker DM, Starr JM, Sarin AP, Hysi PG, Hernandez DG, Jhun MA, Campbell H, Hamsten A, Rivadeneira F, Mcardle WL, Slagboom PE, Zeller T, Koenig W, Psaty BM, Haritunians T, Liu J, Palotie A, Uitterlinden AG, Stott DJ, Hofman A, Franco OH, Polasek O, Rudan I, Morange PE, Wilson JF, Kardia SLR, Ferrucci L, Spector TD, Eriksson JG, Hansen T, Deary IJ, Becker LC, Scott RJ, Mitchell P, März W, Wareham NJ, Peters A, Greinacher A, Wild PS, Jukema JW, Boomsma DI, Hayward C, Cucca F, Tracy R, Watkins H, Reiner AP, Folsom AR, Ridker PM, O'Donnell CJ, Smith NL, Strachan DP, Dehghan A. A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration. Hum Mol Genet 2015; 25:358-70. [PMID: 26561523 DOI: 10.1093/hmg/ddv454] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have previously identified 23 genetic loci associated with circulating fibrinogen concentration. These studies used HapMap imputation and did not examine the X-chromosome. 1000 Genomes imputation provides better coverage of uncommon variants, and includes indels. We conducted a genome-wide association analysis of 34 studies imputed to the 1000 Genomes Project reference panel and including ∼120 000 participants of European ancestry (95 806 participants with data on the X-chromosome). Approximately 10.7 million single-nucleotide polymorphisms and 1.2 million indels were examined. We identified 41 genome-wide significant fibrinogen loci; of which, 18 were newly identified. There were no genome-wide significant signals on the X-chromosome. The lead variants of five significant loci were indels. We further identified six additional independent signals, including three rare variants, at two previously characterized loci: FGB and IRF1. Together the 41 loci explain 3% of the variance in plasma fibrinogen concentration.
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Affiliation(s)
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA, Harvard Medical School, Boston, MA, USA
| | - Maria Sabater-Lleal
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA, Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Jennifer E Huffman
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Weihong Tang
- Division of Epidemiology and Community Health and
| | | | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, Centre for Genomic and Experimental Medicine, Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | | | - Jouke J Hottenga
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Stella Trompet
- Department of Cardiology, Department of Gerontology and Geriatrics and
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Department of Medicine I, Ludwig-Maximilians-University Munich, Munich, Germany, DZHK (German Centre for Cardiovascular Research) and
| | - Jing Hua Zhao
- MRC Epidemiology Unit, School of Clinical Medicine and
| | | | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, CA, USA
| | - Jie Jin Wang
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John R Attia
- Public Health Stream and School of Medicine and Public Health and
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tarunveer S Ahluwalia
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences and Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, The Danish Pediatric Asthma Center, Gentofte Hospital, The Capital Region, Copenhagen, Denmark
| | - Jari Lahti
- Institute of Behavioural Sciences, Folkhälsan Research Centre, Helsinki, Finland
| | - Cristina Venturini
- Institute of Opthalmology, UCL, London, UK, Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Peter K Joshi
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Ares Rocanin-Arjo
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Paris F-75013, France, Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris F-75013, France, Institute for Cardiometabolism and Nutrition (ICAN), Paris F-75013, France
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Johanna Mazur
- Institute of Medical Biostatistics, Epidemiology and Informatics and
| | - Saonli Basu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Anuj Goel
- Cardiovascular Medicine Department/Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Qiong Yang
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mohsen Ghanbari
- Department of Epidemiology, Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Ann Rumley
- Institute of Cardiovascular and Medical Sciences and
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | | | | | - Robert Scott
- MRC Epidemiology Unit, School of Clinical Medicine and
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences and
| | - Annette Kifley
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | | | - Rehan Qayyum
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorna M Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland, University College Dublin, UCD Conway Institute, Centre for Proteome Research, UCD, Belfield, Dublin, Ireland
| | - Tina L Berentzen
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | | | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Wild
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics
| | - David-Alexandre Trégouët
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Paris F-75013, France, Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris F-75013, France, Institute for Cardiometabolism and Nutrition (ICAN), Paris F-75013, France
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Jonathan Marten
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | | | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bengt Sennblad
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Geoffrey Tofler
- Royal North Shore Hospital, Sydney University, Sydney, Australia
| | | | - Eco J C de Geus
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands, EMGO+ institute, VU University & VU Medical Center, Amsterdam
| | - Gordon D Lowe
- Institute of Cardiovascular and Medical Sciences and
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Naveed Sattar
- Faculty of Medicine, BHF Glasgow Cardiovascular Research Centre, Glasgow, UK
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics and
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics and
| | - Melanie Waldenberger
- Institute of Epidemiology II and Research Unit of Molecular Epidemiology, Helmholtz ZentrumMünchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Jie Huang
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Elizabeth G Holliday
- Public Health Stream, Hunter Medical Research Institute, School of Medicine and Public Health and
| | - Lihong Qi
- Division of Biostatistics, Department of Public Health Sciences, UC Davis, Davis, CA, USA
| | - Mark G Mcevoy
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Alzheimer Scotland Dementia Research Centre and
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM) and Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Min A Jhun
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Anders Hamsten
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and
| | - Fernando Rivadeneira
- Department of Epidemiology, Department of Internal Medicine, Erasmus MC, Wytemaweg 80, Rotterdam, The Netherlands
| | - Wendy L Mcardle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Centre, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, German Center for Cardiovascular Research (DZHK), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Wolfgang Koenig
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany, Department of Internal Medicine II - Cardiology, University of Ulm Medical Centre, Ulm, Germany, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Bruce M Psaty
- Department of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Talin Haritunians
- Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jingmin Liu
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - André G Uitterlinden
- Department of Epidemiology, Department of Internal Medicine, Erasmus MC, Wytemaweg 80, Rotterdam, The Netherlands
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, UK
| | | | | | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Department of Public Health, Faculty of Medicine, Centre for Global Health, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille F-13385, France, INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille F-13385, France, Aix-Marseille University, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille F-13385, France
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland, Folkhälsan Research Centre, Helsinki, Finland, National Institute for Health and Welfare, Helsinki, Finland, Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - Torben Hansen
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences and
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rodney J Scott
- Information based Medicine Program, Hunter Medical Research Institute, New Lambton Heights, Australia, School of Biomedical Sciences and Pharmacy, University of Newcastle, New Lambton Heights, Australia
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany, Synlab Academy, Synlab Services LLC, Mannheim, Germany, Clinical Institute of Medical, Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | | | - Annette Peters
- Institute of Epidemiology II and DZHK (German Centre for Cardiovascular Research) and
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Philipp S Wild
- Center for Thrombosis and Hemostasis (CTH), Preventive Cardiology and Preventive Medicine, Department of Medicine 2, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Mainz, Germany
| | - J Wouter Jukema
- Department of Cardiology, Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands, Interuniversity Cardiology Institute of The Netherlands, Utrecht, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Russell Tracy
- Department of Pathology and Laboratory Medicine, Center for Clinical and Translational Sciences, University of Vermont College of Medicine, Colchester, VT, USA
| | - Hugh Watkins
- Cardiovascular Medicine Department/Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alex P Reiner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA, University of Washington, Seattle, WA, USA
| | | | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA, Harvard Medical School, Boston, MA, USA
| | - Christopher J O'Donnell
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, National Heart, Lung and Blood Institute, Division of Intramural Research, Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA, Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, UK, Department of Veterans Affairs, Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA, USA and
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, UK
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Huang C, Haritunians T, Okou DT, Cutler DJ, Zwick ME, Taylor KD, Datta LW, Maranville JC, Liu Z, Ellis S, Chopra P, Alexander JS, Baldassano RN, Cross RK, Dassopoulos T, Dhere TA, Duerr RH, Hanson JS, Hou JK, Hussain SZ, Isaacs KL, Kachelries KE, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kumar A, Kwon JH, Lazarev M, Mannon P, Moulton DE, Osuntokun BO, Patel A, Rioux JD, Rotter JI, Saeed S, Scherl EJ, Silverberg MS, Silverman A, Targan SR, Valentine JF, Wang MH, Simpson CL, Bridges SL, Kimberly RP, Rich SS, Cho JH, Rienzo AD, Kao LW, McGovern DP, Brant SR, Kugathasan S. Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. Gastroenterology 2015; 149:1575-1586. [PMID: 26278503 PMCID: PMC4685036 DOI: 10.1053/j.gastro.2015.07.065] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) has familial aggregation in African Americans (AAs), but little is known about the molecular genetic susceptibility. Mapping studies using the Immunochip genotyping array expand the number of susceptibility loci for IBD in Caucasians to 163, but the contribution of the 163 loci and European admixture to IBD risk in AAs is unclear. We performed a genetic mapping study using the Immunochip to determine whether IBD susceptibility loci in Caucasians also affect risk in AAs and identify new associated loci. METHODS We recruited AAs with IBD and without IBD (controls) from 34 IBD centers in the United States; additional controls were collected from 4 other Immunochip studies. Association and admixture loci were mapped for 1088 patients with Crohn's disease, 361 with ulcerative colitis, 62 with IBD type unknown, and 1797 controls; 130,241 autosomal single-nucleotide polymorphisms (SNPs) were analyzed. RESULTS The strongest associations were observed between ulcerative colitis and HLA rs9271366 (P = 7.5 × 10(-6)), Crohn's disease and 5p13.1 rs4286721 (P = 3.5 × 10(-6)), and IBD and KAT2A rs730086 (P = 2.3 × 10(-6)). Additional suggestive associations (P < 4.2 × 10(-5)) were observed between Crohn's disease and IBD and African-specific SNPs in STAT5A and STAT3; between IBD and SNPs in IL23R, IL12B, and C2orf43; and between ulcerative colitis and SNPs near HDAC11 and near LINC00994. The latter 3 loci have not been previously associated with IBD, but require replication. Established Caucasian associations were replicated in AAs (P < 3.1 × 10(-4)) at NOD2, IL23R, 5p15.3, and IKZF3. Significant admixture (P < 3.9 × 10(-4)) was observed for 17q12-17q21.31 (IZKF3 through STAT3), 10q11.23-10q21.2, 15q22.2-15q23, and 16p12.2-16p12.1. Network analyses showed significant enrichment (false discovery rate <1 × 10(-5)) in genes that encode members of the JAK-STAT, cytokine, and chemokine signaling pathways, as well those involved in pathogenesis of measles. CONCLUSIONS In a genetic analysis of 3308 AA IBD cases and controls, we found that many variants associated with IBD in Caucasians also showed association evidence with these diseases in AAs; we also found evidence for variants and loci not previously associated with IBD. The complex genetic factors that determine risk for or protection against IBD in different populations require further study.
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Affiliation(s)
- Chengrui Huang
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,90502, USA
| | - Lisa W. Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Joseph C. Maranville
- Committee on Clinical Pharmacology and Pharmacogenomics, and the Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - Shannon Ellis
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Robert N. Baldassano
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Raymond K. Cross
- Division of Gastroenterology, University of Maryland, Baltimore, MD 21201, USA
| | | | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, PLLC, Charlotte, NC 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for Innovations in Quality, Effectiveness and Safety , Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, LA 71118, USA
| | - Kim L. Isaacs
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kelly E Kachelries
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jeffrey Katz
- Division of Gastroenterology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, TX, 77030
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - John F. Kuemmerle
- Departments of Medicine and Physiology and Biophysics, VCU Program in Enteric Neuromuscular Sciences, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond VA 23298, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John H. Kwon
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Mark Lazarev
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dedrick E. Moulton
- Division of Gastroenterology, Vanderbilt Children's Hospital, Nashville TN 37212, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Ashish Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Rioux
- Universite de Montreal and the Montreal Heart Institute, Research Center, Montreal, Quebec H1T 1C8, Canada
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences and Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,90502, USA
| | - Shehzad Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ellen J. Scherl
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mark S. Silverberg
- Departments of Medicine, Surgery, Public Health Sciences, Immunology, and Molecular and Medical Genetics, University of Toronto, Samuel Lunenfeld Research Institute and Mount Sinai Hospital, Toronto General Hospital Research Institute, Toronto, Ontario M5S 2J7, Canada
| | - Ann Silverman
- Department of Gastroenterology, Henry Ford Health System Detroit, MI 48208, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - John F. Valentine
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah, Salt Lake City, Utah
| | - Ming-Hsi Wang
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Claire L. Simpson
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - S. Louis Bridges
- Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P. Kimberly
- Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Judy H. Cho
- Department of Medicine and Genetics, Yale University, New Haven, CT 06520, USA
| | - Anna Di Rienzo
- Committee on Clinical Pharmacology and Pharmacogenomics, and the Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Linda W.H. Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - Steven R. Brant
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA, Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA, Corresponding author Steven R. Brant, M.D., Johns Hopkins University School of Medicine, Meyerhoff Inflammatory Bowel Disease Center, 1501 E. Jefferson St., B136, Baltimore, MD 21231. ; Phone: 410-955-9679; Fax: 410-502-9913
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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