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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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2
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Cristian HR, Walshe M, Birch S, Sabic K, Korie U, Chasteau C, Miladinova VM, Sabol WB, Mengesha E, Hanna M, Pozdnyakova V, Datta L, Kohen R, Milgrom R, Stempak JM, Bitton A, Brant SR, Rioux JD, McGovern DPB, Duerr RH, Cho JH, Schumm PL, Silverberg MS, Lazarev M. Clinical predictors of early and late endoscopic recurrence following ileocolonic resection in Crohn's disease. J Crohns Colitis 2023:jjad186. [PMID: 37976264 DOI: 10.1093/ecco-jcc/jjad186] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIM Multiple factors are suggested to place Crohn's disease patients at risk of recurrence after ileocolic resection with conflicting associations. We aimed to identify clinical predictors of recurrence at first (early) and further (late) postoperative colonoscopy. METHODS Crohn's disease patients undergoing ileocolic resection were prospectively recruited at six North American centers. Clinical data was collected and endoscopic recurrence was defined as Rutgeerts score ≥i2. A multivariable model was fitted to analyze variables independently associated with recurrence. RESULTS A total of 365 patients undergoing 674 postoperative colonoscopies were included with a median age of 32 years, 189 (51.8%) were male and 37 (10.1%) non-Whites. Postoperatively, 133 (36.4%) used anti-TNF and 30 (8.2%) were smokers. At first colonoscopy, 109 (29.9%) had recurrence. Male gender (OR = 1.95, 95% CI 1.12 - 3.40), non-White ethnicity (OR = 2.48, 95% CI 1.09 - 5.63), longer interval between surgery and colonoscopy (OR = 1.09, 95% CI 1.002 - 1.18), and postoperative smoking (OR = 2.78, 95% CI 1.16 - 6.67) were associated with recurrence, while prophylactic anti-TNF reduced the risk (OR = 0.28, 95% CI 0.14 - 0.55). Postoperative anti-TNF prophylaxis had a protective effect on anti-TNF experienced patients but not on anti-TNF naïve patients. Among patients without recurrence at first colonoscopy, Rutgeerts score i1 was associated with subsequent recurrence (OR = 4.43, 95% CI 1.73 - 11.35). CONCLUSIONS We identified independent clinical predictors of early and late Crohn's disease postoperative endoscopic recurrence. Clinical factors traditionally used for risk stratification failed to predict recurrence and need to be revised.
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Affiliation(s)
- Hernandez-Rocha Cristian
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Sondra Birch
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Colleen Chasteau
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vessela M Miladinova
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - William B Sabol
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Mary Hanna
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Datta
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
| | - Rita Kohen
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Raquel Milgrom
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Joanne M Stempak
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Alain Bitton
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Steven R Brant
- Crohn's and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Dermot P B McGovern
- 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, University of Pittsburgh, Pittsburgh, PA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Phil L Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Mark Lazarev
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
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3
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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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4
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Ferru-Clément R, Boucher G, Forest A, Bouchard B, Bitton A, Lesage S, Schumm P, Lazarev M, Brant S, Duerr RH, McGovern DPB, Silverberg M, Cho JH, Ananthakrishnan A, Xavier RJ, Rioux JD, Des Rosiers C. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease. Inflamm Bowel Dis 2023; 29:1024-1037. [PMID: 36662167 PMCID: PMC10320374 DOI: 10.1093/ibd/izac281] [Citation(s) in RCA: 3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation. METHODS We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients. RESULTS We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location. CONCLUSIONS Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.
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Affiliation(s)
- Romain Ferru-Clément
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Laboratoire Histocompatibilité et Immunogénétique, Établissement français du sang–Nouvelle-Aquitaine, site de Poitiers, Poitiers, France
| | | | - Anik Forest
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Alain Bitton
- Division of Gastroenterology, McGill University Health Centre, Montreal, QC, Canada
| | - Sylvie Lesage
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, IL, USA
| | - Mark Lazarev
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steve Brant
- 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
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pennsylvania, PA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Silverberg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Judy H Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ashwin Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médicine, Université de Montréal, Montreal, QC, Canada
| | - Christine Des Rosiers
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Nutrition, Université de Montréal, Montreal, QC, Canada
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5
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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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6
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Wang X, Xu Z, Hu H, Zhou X, Zhang Y, Lafyatis R, Chen K, Huang H, Ding Y, Duerr RH, Chen W. SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics. PNAS Nexus 2022; 1:pgac165. [PMID: 36157595 PMCID: PMC9491696 DOI: 10.1093/pnasnexus/pgac165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023]
Abstract
The recent advance of single cell sequencing (scRNA-seq) technology such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) allows researchers to quantify cell surface protein abundance and RNA expression simultaneously at single cell resolution. Although CITE-seq and other similar technologies have gained enormous popularity, novel methods for analyzing this type of single cell multi-omics data are in urgent need. A limited number of available tools utilize data-driven approach, which may undermine the biological importance of surface protein data. In this study, we developed SECANT, a biology-guided SEmi-supervised method for Clustering, classification, and ANnoTation of single-cell multi-omics. SECANT is used to analyze CITE-seq data, or jointly analyze CITE-seq and scRNA-seq data. The novelties of SECANT include (1) using confident cell type label identified from surface protein data as guidance for cell clustering, (2) providing general annotation of confident cell types for each cell cluster, (3) utilizing cells with uncertain or missing cell type label to increase performance, and (4) accurate prediction of confident cell types for scRNA-seq data. Besides, as a model-based approach, SECANT can quantify the uncertainty of the results through easily interpretable posterior probability, and our framework can be potentially extended to handle other types of multi-omics data. We successfully demonstrated the validity and advantages of SECANT via simulation studies and analysis of public and in-house datasets from multiple tissues. We believe this new method will be complementary to existing tools for characterizing novel cell types and make new biological discoveries using single-cell multi-omics data.
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Affiliation(s)
- Xinjun Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhongli Xu
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haoran Hu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xueping Zhou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yanfu Zhang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert Lafyatis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Heng Huang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
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7
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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: 50] [Impact Index Per Article: 25.0] [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: 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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8
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Xu Z, Heidrich-O'Hare E, Chen W, Duerr RH. Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics. Genome Biol 2022; 23:135. [PMID: 35739535 PMCID: PMC9219143 DOI: 10.1186/s13059-022-02698-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/10/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The recently developed method TEA-seq and similar DOGMA-seq single cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent evaluation is lacking. We explore the utility of DOGMA-seq compared to the bimodal CITE-seq assay in activated and stimulated human peripheral blood T cells. We find that single cell trimodal omics measurements after digitonin (DIG) permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we find that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, although its mRNA and cell surface protein libraries have slightly inferior quality, compared to CITE-seq.
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Affiliation(s)
- Zhongli Xu
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - Elisa Heidrich-O'Hare
- Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA, 15261, USA
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA. .,Department of Biostatistics, University of Pittsburgh School of Public Health, 130 De Soto Street, Pittsburgh, PA, 15261, USA.
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA, 15261, USA. .,Department of Human Genetics, University of Pittsburgh School of Public Health, 130 De Soto Street, Pittsburgh, PA, 15261, USA.
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9
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Walshe M, Nayeri S, Ji J, Hernandez-Rocha C, Sabic K, Hu L, Giri M, Nayar S, Brant S, McGovern DPB, Rioux JD, Duerr RH, Cho JH, Schumm PL, Lazarev M, Silverberg MS. A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence. J Crohns Colitis 2021; 16:900-910. [PMID: 34698823 PMCID: PMC9282882 DOI: 10.1093/ecco-jcc/jjab186] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] recurrence following ileocolic resection [ICR] is common. We sought to identify blood-based biomarkers associated with CD recurrence. METHODS CD patients undergoing ICR were recruited across six centres. Serum samples were obtained at post-operative colonoscopy. A multiplex immunoassay was used to analyse 92 inflammation-related proteins [Olink Proteomics]. Bayesian analysis was used to identify proteins associated with increasing Rutgeerts score. Identified proteins were used in receiver operating characteristic [ROC] analysis to examine the ability to identify CD recurrence [Rutgeerts score ≥i2]. Existing single cell data were interrogated to further elucidate the role of the identified proteins. RESULTS Data from 276 colonoscopies in 213 patients were available. Median time from surgery to first and second colonoscopy was 7 (interquartile range [IQR] 6-9) and 19 [IQR 16-23] months, respectively. Disease recurrence was evident at 60 [30%] first and 36 [49%] second colonoscopies. Of 14 proteins significantly associated with Rutgeerts score, the strongest signal was seen for CXCL9 and MMP1. Among patients on anti-tumour necrosis factor drugs, CXCL9 and CXCL11 were most strongly associated with Rutgeerts score. Both are CXCR3 ligands. Incorporation of identified proteins into ROC analysis improved the ability to identify disease recurrence as compared to C-reactive protein alone: area under the curve [AUC] 0.75 (95% confidence interval [CI]: 0.66-0.82] vs 0.64 [95% CI 0.56-0.72], p = 0.012. Single cell transcriptomic data provide evidence that innate immune cells are the primary source of the identified proteins. CONCLUSIONS CXCR3 ligands are associated with CD recurrence following ICR. Incorporation of novel blood-based candidate biomarkers may aid in identification of CD recurrence.
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Affiliation(s)
- Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Shadi Nayeri
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cristian Hernandez-Rocha
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Ksenija Sabic
- 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
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- 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
| | - Shikha Nayar
- 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
| | - Steven Brant
- Crohn’s and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada,Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA,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
| | - Phil L Schumm
- Department of Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Mark S Silverberg
- Corresponding author: Dr Mark Silverberg, MD, PhD, FRCPC, University of Toronto, Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, 441–600 University Avenue, Toronto, Ontario, M5G1X5, Canada. Tel: +1-416-586-4800 ext 8236; Fax: +1-416-619-5524;
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10
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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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11
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Gettler K, Levantovsky R, Moscati A, Giri M, Wu Y, Hsu NY, Chuang LS, Sazonovs A, Venkateswaran S, Korie U, Chasteau C, Duerr RH, Silverberg MS, Snapper SB, Daly MJ, McGovern DP, Brant SR, Rioux JD, Kugathasan S, Anderson CA, Itan Y, Cho JH. Common and Rare Variant Prediction and Penetrance of IBD in a Large, Multi-ethnic, Health System-based Biobank Cohort. Gastroenterology 2021; 160:1546-1557. [PMID: 33359885 PMCID: PMC8237248 DOI: 10.1053/j.gastro.2020.12.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Polygenic risk scores (PRS) may soon be used to predict inflammatory bowel disease (IBD) risk in prevention efforts. We leveraged exome-sequence and single nucleotide polymorphism (SNP) array data from 29,358 individuals in the multiethnic, randomly ascertained health system-based BioMe biobank to define effects of common and rare IBD variants on disease prediction and pathophysiology. METHODS PRS were calculated from European, African American, and Ashkenazi Jewish (AJ) reference case-control studies, and a meta-GWAS run using all three association datasets. PRS were then combined using regression to assess which combination of scores best predicted IBD status in European, AJ, Hispanic, and African American cohorts in BioMe. Additionally, rare variants were assessed in genes associated with very early-onset IBD (VEO-IBD), by estimating genetic penetrance in each BioMe population. RESULTS Combining risk scores based on association data from distinct ancestral populations improved IBD prediction for every population in BioMe and significantly improved prediction among European ancestry UK Biobank individuals. Lower predictive power for non-Europeans was observed, reflecting in part substantially lower African IBD case-control reference sizes. We replicated associations for two VEO-IBD genes, ADAM17 and LRBA, with high dominant model penetrance in BioMe. Autosomal recessive LRBA risk alleles are associated with severe, early-onset autoimmunity; we show that heterozygous carriage of an African-predominant LRBA protein-altering allele is associated with significantly decreased LRBA and CTLA-4 expression with T-cell activation. CONCLUSIONS Greater genetic diversity in African populations improves prediction across populations, and generalizes some VEO-IBD genes. Increasing African American IBD case-collections should be prioritized to reduce health disparities and enhance pathophysiological insight.
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Affiliation(s)
- Kyle Gettler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rachel Levantovsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aleksejs Sazonovs
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, Georgia
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Colleen Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, Toronto, Ontario, Canada
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology & Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Mark J Daly
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Dermot P McGovern
- Medicine and Biomedical Sciences, Cedars-Sinai, Los Angeles, California
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, 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, New Jersey; Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John D Rioux
- Montreal Heart Institute, University of Montreal, Montreal, Canada
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Carl A Anderson
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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12
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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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13
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Wang X, Sun Z, Zhang Y, Xu Z, Xin H, Huang H, Duerr RH, Chen K, Ding Y, Chen W. BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data. Nucleic Acids Res 2020; 48:5814-5824. [PMID: 32379315 PMCID: PMC7293045 DOI: 10.1093/nar/gkaa314] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 01/07/2020] [Revised: 03/17/2020] [Accepted: 04/20/2020] [Indexed: 12/25/2022] Open
Abstract
Droplet-based single cell transcriptome sequencing (scRNA-seq) technology, largely represented by the 10× Genomics Chromium system, is able to measure the gene expression from tens of thousands of single cells simultaneously. More recently, coupled with the cutting-edge Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), the droplet-based system has allowed for immunophenotyping of single cells based on cell surface expression of specific proteins together with simultaneous transcriptome profiling in the same cell. Despite the rapid advances in technologies, novel statistical methods and computational tools for analyzing multi-modal CITE-Seq data are lacking. In this study, we developed BREM-SC, a novel Bayesian Random Effects Mixture model that jointly clusters paired single cell transcriptomic and proteomic data. Through simulation studies and analysis of public and in-house real data sets, we successfully demonstrated the validity and advantages of this method in fully utilizing both types of data to accurately identify cell clusters. In addition, as a probabilistic model-based approach, BREM-SC is able to quantify the clustering uncertainty for each single cell. This new method will greatly facilitate researchers to jointly study transcriptome and surface proteins at the single cell level to make new biological discoveries, particularly in the area of immunology.
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Affiliation(s)
- Xinjun Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sun
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yanfu Zhang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - Hongyi Xin
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Huang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
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14
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Xin H, Lian Q, Jiang Y, Luo J, Wang X, Erb C, Xu Z, Zhang X, Heidrich-O’Hare E, Yan Q, Duerr RH, Chen K, Chen W. GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biol 2020; 21:188. [PMID: 32731885 PMCID: PMC7393741 DOI: 10.1186/s13059-020-02084-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 12/18/2019] [Accepted: 06/24/2020] [Indexed: 11/10/2022] Open
Abstract
Identifying and removing multiplets are essential to improving the scalability and the reliability of single cell RNA sequencing (scRNA-seq). Multiplets create artificial cell types in the dataset. We propose a Gaussian mixture model-based multiplet identification method, GMM-Demux. GMM-Demux accurately identifies and removes multiplets through sample barcoding, including cell hashing and MULTI-seq. GMM-Demux uses a droplet formation model to authenticate putative cell types discovered from a scRNA-seq dataset. We generate two in-house cell-hashing datasets and compared GMM-Demux against three state-of-the-art sample barcoding classifiers. We show that GMM-Demux is stable and highly accurate and recognizes 9 multiplet-induced fake cell types in a PBMC dataset.
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Affiliation(s)
- Hongyi Xin
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai, 200240 China
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Qiuyu Lian
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
- Department of Automation, Tsinghua University, Beijing, 100086 China
| | - Yale Jiang
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
- School of Medicine, Tsinghua University, Beijing, 100086 China
| | - Jiadi Luo
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Xinjun Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Carla Erb
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Zhongli Xu
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
- School of Medicine, Tsinghua University, Beijing, 100086 China
| | - Xiaoyi Zhang
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Elisa Heidrich-O’Hare
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Qi Yan
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Richard H. Duerr
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Kong Chen
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
| | - Wei Chen
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15260 USA
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15
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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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16
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Denson LA, Curran M, McGovern DPB, Koltun WA, Duerr RH, Kim SC, Sartor RB, Sylvester FA, Abraham C, de Zoeten EF, Siegel CA, Burns RM, Dobes AM, Shtraizent N, Honig G, Heller CA, Hurtado-Lorenzo A, Cho JH. Challenges in IBD Research: Precision Medicine. Inflamm Bowel Dis 2019; 25:S31-S39. [PMID: 31095701 DOI: 10.1093/ibd/izz078] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 03/29/2019] [Indexed: 12/12/2022]
Abstract
Precision medicine is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. The Challenges in IBD Research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the precision medicine section is focused on highlighting the main gap areas that must be addressed to get closer to treatments tailored to the biological and clinical characteristics of each patient, which is the aim of precision medicine. The main gaps were identified in: 1) understanding and predicting the natural history of IBD: disease susceptibility, activity, and behavior; 2) predicting disease course and treatment response; and 3) optimizing current and developing new molecular technologies. Suggested approaches to bridge these gaps include prospective longitudinal cohort studies to identify and validate precision biomarkers for prognostication of disease course, and prediction and monitoring of treatment response. To achieve this, harmonization across studies is key as well as development of standardized methods and infrastructure. The implementation of state-of-the-art molecular technologies, systems biology and machine learning approaches for multi-omics and clinical data integration and analysis will be also fundamental. Finally, randomized biomarker-stratified trials will be critical to evaluate the clinical utility of validated signatures and biomarkers in improving patient outcomes and cost-effective care.
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Affiliation(s)
- Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mark Curran
- Janssen Research and Development, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Walter A Koltun
- Department of Surgery, Division of Colon and Rectal Surgery, Pennsylvania State University, Hershey, PA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra C Kim
- Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - R Balfour Sartor
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Francisco A Sylvester
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hil, Chapel Hill, NC, USA
| | | | - Edwin F de Zoeten
- University of Colorado School of Medicine, Childrens Hospital Colorado, Aurora, CO, USA
| | - Corey A Siegel
- Dartmouth Hitchcock Medical Center, Section of Gastroenterology and Hepatology, Lebanon NH, USA
| | - Richéal M Burns
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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17
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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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18
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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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19
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Parian A, Limketkai B, Koh J, Brant SR, Bitton A, Cho JH, Duerr RH, McGovern DP, Proctor DD, Regueiro MD, Rioux JD, Schumm P, Taylor KD, Silverberg MS, Steinhart AH, Hernaez R, Lazarev M. Appendectomy does not decrease the risk of future colectomy in UC: results from a large cohort and meta-analysis. Gut 2017; 66:1390-1397. [PMID: 27196594 PMCID: PMC5065377 DOI: 10.1136/gutjnl-2016-311550] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 01/31/2016] [Revised: 03/15/2016] [Accepted: 03/21/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Early appendectomy is inversely associated with the development of UC. However, the impact of appendectomy on the clinical course of UC is controversial, generally favouring a milder disease course. We aim to describe the effect appendectomy has on the disease course of UC with focus on the timing of appendectomy in relation to UC diagnosis. DESIGN Using the National Institute of Diabetes and Digestive and Kidney Diseases Inflammatory Bowel Disease Genetics Consortium database of patients with UC, the risk of colectomy was compared between patients who did and did not undergo appendectomy. In addition, we performed a meta-analysis of studies that examined the association between appendectomy and colectomy. RESULTS 2980 patients with UC were initially included. 111 (4.4%) patients with UC had an appendectomy; of which 63 were performed prior to UC diagnosis and 48 after diagnosis. In multivariable analysis, appendectomy performed at any time was an independent risk factor for colectomy (OR 1.9, 95% CI 1.1 to 3.1), with appendectomy performed after UC diagnosis most strongly associated with colectomy (OR 2.2, 95% CI 1.1 to 4.5). An updated meta-analysis showed appendectomy performed either prior to or after UC diagnosis had no effect on colectomy rates. CONCLUSIONS Appendectomy performed at any time in relation to UC diagnosis was not associated with a decrease in severity of disease. In fact, appendectomy after UC diagnosis may be associated with a higher risk of colectomy. These findings question the proposed use of appendectomy as treatment for UC.
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Affiliation(s)
- Alyssa Parian
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Berkeley Limketkai
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA, Division of Gastroenterology & Hepatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joyce Koh
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven R. Brant
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alain Bitton
- Division of Gastroenterology, McGill University, Montreal, Québec, Canada
| | - Judy H. Cho
- Division of Gastroenterology, Mount Sinai Hospital, New York, NY, USA
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dermot P. McGovern
- Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Deborah D. Proctor
- Division of Digestive Disease, Yale School of Medicine, New Haven, CT, USA
| | - Miguel D. Regueiro
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - John D. Rioux
- Division of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Phil Schumm
- Department of Health Studies, University of Chicago, Chicago, IL, USA
| | - Kent D. Taylor
- Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Ruben Hernaez
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mark Lazarev
- Division of Gastroenterology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
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20
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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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21
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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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22
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Ombrello MJ, Arthur VL, Remmers EF, Hinks A, Tachmazidou I, Grom AA, Foell D, Martini A, Gattorno M, Özen S, Prahalad S, Zeft AS, Bohnsack JF, Ilowite NT, Mellins ED, Russo R, Len C, Hilario MOE, Oliveira S, Yeung RSM, Rosenberg AM, Wedderburn LR, Anton J, Haas JP, Rosen-Wolff A, Minden K, Tenbrock K, Demirkaya E, Cobb J, Baskin E, Signa S, Shuldiner E, Duerr RH, Achkar JP, Kamboh MI, Kaufman KM, Kottyan LC, Pinto D, Scherer SW, Alarcón-Riquelme ME, Docampo E, Estivill X, Gül A, Langefeld CD, Thompson S, Zeggini E, Kastner DL, Woo P, Thomson W. Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications. Ann Rheum Dis 2017; 76:906-913. [PMID: 27927641 PMCID: PMC5530341 DOI: 10.1136/annrheumdis-2016-210324] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [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: 08/05/2016] [Revised: 10/27/2016] [Accepted: 11/12/2016] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Juvenile idiopathic arthritis (JIA) is a heterogeneous group of conditions unified by the presence of chronic childhood arthritis without an identifiable cause. Systemic JIA (sJIA) is a rare form of JIA characterised by systemic inflammation. sJIA is distinguished from other forms of JIA by unique clinical features and treatment responses that are similar to autoinflammatory diseases. However, approximately half of children with sJIA develop destructive, long-standing arthritis that appears similar to other forms of JIA. Using genomic approaches, we sought to gain novel insights into the pathophysiology of sJIA and its relationship with other forms of JIA. METHODS We performed a genome-wide association study of 770 children with sJIA collected in nine countries by the International Childhood Arthritis Genetics Consortium. Single nucleotide polymorphisms were tested for association with sJIA. Weighted genetic risk scores were used to compare the genetic architecture of sJIA with other JIA subtypes. RESULTS The major histocompatibility complex locus and a locus on chromosome 1 each showed association with sJIA exceeding the threshold for genome-wide significance, while 23 other novel loci were suggestive of association with sJIA. Using a combination of genetic and statistical approaches, we found no evidence of shared genetic architecture between sJIA and other common JIA subtypes. CONCLUSIONS The lack of shared genetic risk factors between sJIA and other JIA subtypes supports the hypothesis that sJIA is a unique disease process and argues for a different classification framework. Research to improve sJIA therapy should target its unique genetics and specific pathophysiological pathways.
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Affiliation(s)
- Michael J Ombrello
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health,US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Victoria L Arthur
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health,US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Elaine F Remmers
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Anne Hinks
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Alexei A Grom
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Dirk Foell
- Department of Pediatric Rheumatology and Immunology, University Hospital Münster, Münster, Germany
| | - Alberto Martini
- Department of Pediatrics, University of Genova, Genoa, Italy
- Pediatrics II Unit, Giannina Gaslini Institute, Genoa, Italy
| | - Marco Gattorno
- Pediatrics II Unit, Giannina Gaslini Institute, Genoa, Italy
| | - Seza Özen
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Sampath Prahalad
- Departments of Pediatrics and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
- Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Andrew S Zeft
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
| | - John F Bohnsack
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Norman T Ilowite
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, New York, USA
| | | | - Ricardo Russo
- Service of Immunology and Rheumatology, Hospital de Pediatria Garrahan, Buenos Aires, Argentina
| | - Claudio Len
- Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Sheila Oliveira
- Universidade Federal de Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rae S M Yeung
- Department of Pediatrics, University of Toronto, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Alan M Rosenberg
- Department of Pediatrics, University of Saskatchewan, Saskatoon, Canada
| | - Lucy R Wedderburn
- Institute of Child Health, University College London, London, UK
- Center of Paediatric and Adolescent Rheumatology, University College London, London, UK
| | - Jordi Anton
- Pediatric Rheumatology Unit, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Johannes-Peter Haas
- German Center for Pediatric and Adolescent Rheumatology, Garmisch-Partenkirchen, Germany
| | | | - Kirsten Minden
- Department of Rheumatology and Clinical Immunology, Charité -University Medicine, Berlin, Germany
- Epidemiology Unit, German Rheumatism Research Centre, Berlin, Germany
| | - Klaus Tenbrock
- Department of Pediatrics, RWTH Aachen University, Aachen, Germany
| | - Erkan Demirkaya
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Joanna Cobb
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, Manchester, UK
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Elizabeth Baskin
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health,US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Sara Signa
- Department of Pediatrics, University of Genova, Genoa, Italy
| | - Emily Shuldiner
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health,US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jean-Paul Achkar
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathobiology, Cleveland Clinic, Cleveland, Ohio, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kenneth M Kaufman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Leah C Kottyan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Government, Granada, Spain
- Unit of Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Elisa Docampo
- Interdisciplinary Cluster for Applied Genoproteomics-Université de Liège, Liège, Belgium
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, and Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Sidra Medical and Research Centre, Doha, Qatar
| | - Ahmet Gül
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Susan Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Patricia Woo
- Center of Paediatric and Adolescent Rheumatology, University College London, London, UK
| | - Wendy Thomson
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, Manchester, UK
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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23
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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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24
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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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25
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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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26
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Kopylov U, Boucher G, Waterman M, Rivers CR, Patel M, Cho JH, Colombel JF, Duerr RH, Binion D, McGovern DP, Schumm PP, Brant SR, Silverberg MS, Rioux JD, Bitton A. Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Inflamm Bowel Dis 2016; 22:2311-6. [PMID: 27575496 PMCID: PMC5098421 DOI: 10.1097/mib.0000000000000913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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] [Indexed: 12/31/2022]
Abstract
BACKGROUND A subset of patients with ulcerative colitis (UC) have a benign course and an overall favorable prognosis. Early identification of these low-risk patients may allow for a less aggressive therapeutic approach and possible reduction of therapy-associated risks. The aim of this project was to identify the genetic predictors of benign UC phenotype. METHODS UC patients were selected from the National Institute of Diabetes and Digestive and Kidney Diseases Inflammatory Bowel Disease Genetics Consortium. Benign phenotype was defined as no need for immunomodulatory or biological therapy, hospitalizations, or colectomy. The association between benign UC phenotype and known loci linked to the risk of inflammatory bowel disease (IBD) was evaluated. The results for 156 index single-nucleotide polymorphisms (SNPs) from the known IBD loci were extracted for the main analysis. The association of the benign phenotype to a genetic burden score was also evaluated. RESULTS None of the index SNPs from the IBD loci reached the predefined threshold of 1 × 10. In the exploratory analysis of the remaining Immunochip SNPs and imputed major histocompatibility complex data, 5 distinct suggestive association signals are identified (rs1697950, rs2523639, rs17836409, rs11742854, and rs75001121). CONCLUSIONS No SNPs from IBD susceptibility loci were found to be associated (at our predefined threshold of 1 × 10) with a benign UC disease course. The rs11742570 variant on chromosome 5 was the one with the greatest association to benign disease although the association did not reach the predefined significant threshold. Given the modest power of our study, the findings suggested on the exploratory analysis merit extension to larger discovery cohorts.
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Affiliation(s)
- Uri Kopylov
- McGill University Health Centre, Division of Gastroenterology, Montreal, Quebec, Canada
| | - Gabrielle Boucher
- Montreal Heart Institute, Montreal, Quebec, Canada,Université de Montréal, Montreal, Quebec, Canada
| | - Matti Waterman
- Mount Sinai Hospital, Division of Gastroenterology, Toronto, Ontario, Canada
| | - Claudia Ramos Rivers
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - Mohini Patel
- Yale University, Section of Digestive Diseases, New Haven, CT, USA
| | - Judy H. Cho
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York,Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean Frederic Colombel
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Richard H. Duerr
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - David Binion
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - Dermot P.B McGovern
- Translational Genomics Group, F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Diseases Center, Division of Gastroenterology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Mark S. Silverberg
- Mount Sinai Hospital, Division of Gastroenterology, Toronto, Ontario, Canada
| | - John D. Rioux
- Montreal Heart Institute, Montreal, Quebec, Canada,Université de Montréal, Montreal, Quebec, Canada
| | - Alain Bitton
- McGill University Health Centre, Division of Gastroenterology, Montreal, Quebec, Canada
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27
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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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28
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Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, Andersen V, Andrews JM, Annese V, Brand S, Brant SR, Cho JH, Daly MJ, Dubinsky M, Duerr RH, Ferguson LR, Franke A, Gearry RB, Goyette P, Hakonarson H, Halfvarson J, Hov JR, Huang H, Kennedy NA, Kupcinskas L, Lawrance IC, Lee JC, Satsangi J, Schreiber S, Théâtre E, van der Meulen-de Jong AE, Weersma RK, Wilson DC, Parkes M, Vermeire S, Rioux JD, Mansfield J, Silverberg MS, Radford-Smith G, McGovern DPB, Barrett JC, Lees CW. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Lancet 2016; 387:156-67. [PMID: 26490195 PMCID: PMC4714968 DOI: 10.1016/s0140-6736(15)00465-1] [Citation(s) in RCA: 493] [Impact Index Per Article: 61.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Crohn's disease and ulcerative colitis are the two major forms of inflammatory bowel disease; treatment strategies have historically been determined by this binary categorisation. Genetic studies have identified 163 susceptibility loci for inflammatory bowel disease, mostly shared between Crohn's disease and ulcerative colitis. We undertook the largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases. METHODS This study included patients from 49 centres in 16 countries in Europe, North America, and Australasia. We applied the Montreal classification system of inflammatory bowel disease subphenotypes to 34,819 patients (19,713 with Crohn's disease, 14,683 with ulcerative colitis) genotyped on the Immunochip array. We tested for genotype-phenotype associations across 156,154 genetic variants. We generated genetic risk scores by combining information from all known inflammatory bowel disease associations to summarise the total load of genetic risk for a particular phenotype. We used these risk scores to test the hypothesis that colonic Crohn's disease, ileal Crohn's disease, and ulcerative colitis are all genetically distinct from each other, and to attempt to identify patients with a mismatch between clinical diagnosis and genetic risk profile. FINDINGS After quality control, the primary analysis included 29,838 patients (16,902 with Crohn's disease, 12,597 with ulcerative colitis). Three loci (NOD2, MHC, and MST1 3p21) were associated with subphenotypes of inflammatory bowel disease, mainly disease location (essentially fixed over time; median follow-up of 10·5 years). Little or no genetic association with disease behaviour (which changed dramatically over time) remained after conditioning on disease location and age at onset. The genetic risk score representing all known risk alleles for inflammatory bowel disease showed strong association with disease subphenotype (p=1·65 × 10(-78)), even after exclusion of NOD2, MHC, and 3p21 (p=9·23 × 10(-18)). Predictive models based on the genetic risk score strongly distinguished colonic from ileal Crohn's disease. Our genetic risk score could also identify a small number of patients with discrepant genetic risk profiles who were significantly more likely to have a revised diagnosis after follow-up (p=6·8 × 10(-4)). INTERPRETATION Our data support a continuum of disorders within inflammatory bowel disease, much better explained by three groups (ileal Crohn's disease, colonic Crohn's disease, and ulcerative colitis) than by Crohn's disease and ulcerative colitis as currently defined. Disease location is an intrinsic aspect of a patient's disease, in part genetically determined, and the major driver to changes in disease behaviour over time. FUNDING International Inflammatory Bowel Disease Genetics Consortium members funding sources (see Acknowledgments for full list).
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Affiliation(s)
- Isabelle Cleynen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium
| | - Gabrielle Boucher
- Université de Montréal and the Montreal Heart Institute, Research Center, Montréal, Québec, Canada
| | - Luke Jostins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Christ Church, University of Oxford, St Aldates, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Sebastian Zeissig
- Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter, UK
| | - Vibeke Andersen
- Medical Department, Viborg Regional Hospital, Viborg, Denmark; Hospital of Southern Jutland Aabenraa, Aabenraa, Denmark
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, Adelaide, Australia; School of Medicine, University of Adelaide, Adelaide, Australia
| | - Vito Annese
- Unit of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, San Giovanni Rotondo, Italy; Azienda Ospedaliero Universitaria (AOU) Careggi, Unit of Gastroenterology SOD2, Florence, Italy
| | - Stephan Brand
- Department of Medicine II, University Hospital Munich-Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marla Dubinsky
- Department of Pediatrics, 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
| | - Lynnette R Ferguson
- School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand; Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand
| | - Philippe Goyette
- Université de Montréal and the Montreal Heart Institute, Research Center, Montréal, Québec, Canada
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Sweden; School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Johannes R Hov
- Norwegian PSC Research Center, Research Insitute of Internal Medicine and Department of Transplantation Medicine, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hailang Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas A Kennedy
- Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Limas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco WA and School of Medicine and Pharmacology, University of Western Australia, Harry Perkins Institute for Medical Research, Murdoch, WA, Australia
| | - James C Lee
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stephan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany; Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Emilie Théâtre
- Unit of Animal Genomics, Groupe Interdisciplinaire de Genoproteomique Appliquee (GIGA-R) and Faculty of Veterinary Medicine, University of Liege, Liege, Belgium; Division of Gastroenterology, Centre Hospitalier Universitaire, Universite de Liege, Liege, Belgium
| | | | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - David C Wilson
- Child Life and Health, University of Edinburgh, Edinburgh, UK; Royal Hospital for Sick Children, Paediatric Gastroenterology and Nutrition, Glasgow, UK
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium; Division of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - John D Rioux
- Université de Montréal and the Montreal Heart Institute, Research Center, Montréal, Québec, Canada
| | - John Mansfield
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, UK
| | - Mark S Silverberg
- Mount Sinai Hospital Inflammatory Bowel Disease Centre, University of Toronto, Toronto, ON, Canada
| | - Graham Radford-Smith
- Inflammatory Bowel Diseases, Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane, Australia; Department of Gastroenterology, Royal Brisbane and Women's Hospital, and School of Medicine, University of Queensland, Brisbane, Australia
| | - Dermot P B McGovern
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Charlie W Lees
- Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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29
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Stittrich AB, Ashworth J, Shi M, Robinson M, Mauldin D, Brunkow ME, Biswas S, Kim JM, Kwon KS, Jung JU, Galas D, Serikawa K, Duerr RH, Guthery SL, Peschon J, Hood L, Roach JC, Glusman G. Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals. Hum Genome Var 2016; 3:15060. [PMID: 27081563 PMCID: PMC4785573 DOI: 10.1038/hgv.2015.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023] Open
Abstract
Currently, the best clinical predictor for inflammatory bowel disease (IBD) is family history. Over 163 sequence variants have been associated with IBD in genome-wide association studies, but they have weak effects and explain only a fraction of the observed heritability. It is expected that additional variants contribute to the genomic architecture of IBD, possibly including rare variants with effect sizes larger than the identified common variants. Here we applied a family study design and sequenced 38 individuals from five families, under the hypothesis that families with multiple IBD-affected individuals harbor one or more risk variants that (i) are shared among affected family members, (ii) are rare and (iii) have substantial effect on disease development. Our analysis revealed not only novel candidate risk variants but also high polygenic risk scores for common known risk variants in four out of the five families. Functional analysis of our top novel variant in the remaining family, a rare missense mutation in the ubiquitin ligase TRIM11, suggests that it leads to increased nuclear factor of kappa light chain enhancer in B-cells (NF-κB) signaling. We conclude that an accumulation of common weak-effect variants accounts for the high incidence of IBD in most, but not all families we analyzed and that a family study design can identify novel rare variants conferring risk for IBD with potentially large effect size, such as the TRIM11 p.H414Y mutation.
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Affiliation(s)
| | | | - Mude Shi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Korea
| | - Ki-Sun Kwon
- Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen L Guthery
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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30
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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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31
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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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Goyette P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, Ripke S, Gusareva ES, Annese V, Hauser SL, Oksenberg JR, Thomsen I, Leslie S, Daly MJ, Van Steen K, Duerr RH, Barrett JC, McGovern DPB, Schumm LP, Traherne JA, Carrington MN, Kosmoliaptsis V, Karlsen TH, Franke A, Rioux JD. High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Nat Genet 2015; 47:172-9. [PMID: 25559196 PMCID: PMC4310771 DOI: 10.1038/ng.3176] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/04/2014] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn’s disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC). This region encodes a large number of immunological candidates, including the antigen-presenting classical HLA molecules1. Studies in IBD have indicated that multiple independent associations exist at HLA and non-HLA genes, but lacked the statistical power to define the architecture of association and causal alleles2,3. To address this, we performed high-density SNP typing of the MHC in >32,000 patients with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn’s disease and ulcerative colitis. Significant differences were observed between these diseases, including a predominant role of class II HLA variants and heterozygous advantage observed in ulcerative colitis, suggesting an important role of the adaptive immune response to the colonic environment in the pathogenesis of IBD.
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Affiliation(s)
- Philippe Goyette
- Research Center, Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - Dermot Mallon
- 1] Department of Surgery, University of Cambridge, Cambridge, UK. [2] National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
| | - Luke Jostins
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK. [2] Christ Church, University of Oxford, St Aldates, UK
| | - Hailiang Huang
- 1] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephan Ripke
- 1] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Elena S Gusareva
- 1] Systems and Modeling Unit, Montefiore Institute, University of Liege, Liege, Belgium. [2] Bioinformatics and Modeling, GIGA-R (Groupe Interdisciplinaire de Génoprotéomique Appliquée) Research Center, University of Liege, Liege, Belgium
| | - Vito Annese
- 1] Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy. [2] Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy
| | - Stephen L Hauser
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Ingo Thomsen
- Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
| | - Stephen Leslie
- 1] Murdoch Children's Research Institute, Parkville, Victoria, Australia. [2] Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | | | | | | | | | | | | | - Mark J Daly
- 1] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristel Van Steen
- 1] Systems and Modeling Unit, Montefiore Institute, University of Liege, Liege, Belgium. [2] Bioinformatics and Modeling, GIGA-R (Groupe Interdisciplinaire de Génoprotéomique Appliquée) Research Center, University of Liege, Liege, Belgium
| | - Richard H Duerr
- 1] Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA. [2] Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA
| | - James A Traherne
- 1] Cambridge Institute for Medical Research, Cambridge, UK. [2] Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mary N Carrington
- 1] Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. [2] Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vasilis Kosmoliaptsis
- 1] Department of Surgery, University of Cambridge, Cambridge, UK. [2] National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Tom H Karlsen
- 1] Research Institute of Internal Medicine, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway. [2] Norwegian Primary Sclerosing Cholangitis Research Center, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway. [3] K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
| | - John D Rioux
- 1] Research Center, Montreal Heart Institute, Montreal, Quebec, Canada. [2] Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada
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33
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Wang MH, Fiocchi C, Zhu X, Ripke S, Kamboh MI, Rebert N, Duerr RH, Achkar JP. Gene-gene and gene-environment interactions in ulcerative colitis. Hum Genet 2013; 133:547-58. [PMID: 24241240 DOI: 10.1007/s00439-013-1395-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 06/21/2013] [Accepted: 11/07/2013] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene-gene and gene-environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust Case-Control Consortium (WTCCC) IBD GWAS was used as a replication cohort. We applied logic regression (LR), a novel adaptive regression methodology, to search for high-order interactions. Exploratory genotype correlations with UC sub-phenotypes [extent of disease, need of surgery, age of onset, extra-intestinal manifestations and primary sclerosing cholangitis (PSC)] were conducted. The combination of 133 UC loci yielded good UC risk predictability [area under the curve (AUC) of 0.86]. A higher cumulative allele score predicted higher UC risk. Through LR, several lines of evidence for genetic interactions were identified and successfully replicated in the WTCCC cohort. The genetic interactions combined with the gene-smoking interaction significantly improved predictability in the model (AUC, from 0.86 to 0.89, P = 3.26E-05). Explained UC variance increased from 37 to 42 % after adding the interaction terms. A within case analysis found suggested genetic association with PSC. Our study demonstrates that the LR methodology allows the identification and replication of high-order genetic interactions in UC GWAS datasets. UC risk can be predicted by a 133 loci and improved by adding gene-gene and gene-environment interactions.
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Affiliation(s)
- Ming-Hsi Wang
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, 9500 Euclid Avenue, Desk A31, Cleveland, OH, 44195, USA,
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34
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Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Törkvist L, Goel G, Lagacé C, Annese V, Bitton A, Begun J, Brant SR, Bresso F, Cho JH, Duerr RH, Halfvarson J, McGovern DPB, Radford-Smith G, Schreiber S, Schumm PL, Sharma Y, Silverberg MS, Weersma RK, D'Amato M, Vermeire S, Franke A, Lettre G, Xavier RJ, Daly MJ, Rioux JD. Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis. PLoS Genet 2013; 9:e1003723. [PMID: 24068945 PMCID: PMC3772057 DOI: 10.1371/journal.pgen.1003723] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/01/2013] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (~14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.
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Affiliation(s)
- Mélissa Beaudoin
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - Philippe Goyette
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | | | - Ken Sin Lo
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - Manuel A. Rivas
- Center for the Study of IBD (CSIBD) Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Christine Stevens
- Center for the Study of IBD (CSIBD) Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Martin Ladouceur
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Leif Törkvist
- Department of Clinical Science Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Gautam Goel
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, United States of America
| | - Caroline Lagacé
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - Vito Annese
- Unit of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, San Giovanni Rotondo, Italy
- Azienda Ospedaliero Universitaria (AOU) Careggi, Unit of Gastroenterology SOD2, Florence, Italy
| | - Alain Bitton
- Division of Gastroenterology, McGill University Health Centre, Royal Victoria Hospital, Montréal, Québec, Canada
| | - Jakob Begun
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, United States of America
| | - Steve R. Brant
- Meyerhoff Inflammatory Bowel Diseases Center, Department of Medicine, Johns Hopkins University School of Medicine, and Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Francesca Bresso
- Department of Medicine of the Karolinska University Hospital, Solna, Sweden
| | - Judy H. Cho
- Departments of Medicine and Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, and Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Jonas Halfvarson
- Department of Internal Medicine, Division of Gastroenterology, Örebro University Hospital and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Dermot P. B. McGovern
- Cedars-Sinai F.Widjaja Inflammatory Bowel and Immunobiology Research Institute, and Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Graham Radford-Smith
- Inflammatory Bowel Diseases, Genetic and Computational Biology, Queensland Institute of Medical Research, and Department of Gastroenterology, Royal Brisbane and Womens Hospital, and School of Medicine, University of Queensland, Brisbane, Australia
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
- Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Philip L. Schumm
- Department of Health Studies, University of Chicago, Chicago, Illinois, United States of America
| | - Yashoda Sharma
- Departments of Medicine and Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Mark S. Silverberg
- Mount Sinai Hospital Inflammatory Bowel Disease Centre, University of Toronto, Toronto, Ontario, Canada
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Severine Vermeire
- Division of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Andre Franke
- Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Guillaume Lettre
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Université de Montréal, Faculté de Médecine, Montréal, Québec, Canada
| | - Ramnik J. Xavier
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - John D. Rioux
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Université de Montréal, Faculté de Médecine, Montréal, Québec, Canada
- * E-mail:
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35
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Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA, Skieceviciene J, Doncheva NT, Liu X, Liu Q, Jiang F, Forster M, Mayr G, Albrecht M, Häsler R, Boehm BO, Goodall J, Berzuini CR, Lee J, Andersen V, Vogel U, Kupcinskas L, Kayser M, Krawczak M, Nikolaus S, Weersma RK, Ponsioen CY, Sans M, Wijmenga C, Strachan DP, McArdle WL, Vermeire S, Rutgeerts P, Sanderson JD, Mathew CG, Vatn MH, Wang J, Nöthen MM, Duerr RH, Büning C, Brand S, Glas J, Winkelmann J, Illig T, Latiano A, Annese V, Halfvarson J, D’Amato M, Daly MJ, Nothnagel M, Karlsen TH, Subramani S, Rosenstiel P, Schreiber S, Parkes M, Franke A. Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology 2013; 145:339-47. [PMID: 23624108 PMCID: PMC3753067 DOI: 10.1053/j.gastro.2013.04.040] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [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: 12/07/2012] [Revised: 03/26/2013] [Accepted: 04/17/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies (GWAS) have identified 140 Crohn's disease (CD) susceptibility loci. For most loci, the variants that cause disease are not known and the genes affected by these variants have not been identified. We aimed to identify variants that cause CD through detailed sequencing, genetic association, expression, and functional studies. METHODS We sequenced whole exomes of 42 unrelated subjects with CD and 5 healthy subjects (controls) and then filtered single nucleotide variants by incorporating association results from meta-analyses of CD GWAS and in silico mutation effect prediction algorithms. We then genotyped 9348 subjects with CD, 2868 subjects with ulcerative colitis, and 14,567 control subjects and associated variants analyzed in functional studies using materials from subjects and controls and in vitro model systems. RESULTS We identified rare missense mutations in PR domain-containing 1 (PRDM1) and associated these with CD. These mutations increased proliferation of T cells and secretion of cytokines on activation and increased expression of the adhesion molecule L-selectin. A common CD risk allele, identified in GWAS, correlated with reduced expression of PRDM1 in ileal biopsy specimens and peripheral blood mononuclear cells (combined P = 1.6 × 10(-8)). We identified an association between CD and a common missense variant, Val248Ala, in nuclear domain 10 protein 52 (NDP52) (P = 4.83 × 10(-9)). We found that this variant impairs the regulatory functions of NDP52 to inhibit nuclear factor κB activation of genes that regulate inflammation and affect the stability of proteins in Toll-like receptor pathways. CONCLUSIONS We have extended the results of GWAS and provide evidence that variants in PRDM1 and NDP52 determine susceptibility to CD. PRDM1 maps adjacent to a CD interval identified in GWAS and encodes a transcription factor expressed by T and B cells. NDP52 is an adaptor protein that functions in selective autophagy of intracellular bacteria and signaling molecules, supporting the role of autophagy in the pathogenesis of CD.
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Affiliation(s)
- David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hu Zhang
- Addenbrooke’s Hospital, University of Cambridge, Gastroenterology Research Unit, Cambridge, UK,Department of Gastroenterology & State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Sebastian Zeissig
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simone Lipinski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andreas Till
- Section of Molecular Biology, University of California San Diego & San Diego Center for Systems Biology (SDCSB), La Jolla, California, USA
| | | | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New York, USA
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andreas Keller
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Manuel A Rivas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Department of Gastroenterology, Kaunas University of Medicine, Kaunas, Lithuania
| | | | | | | | | | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Gabriele Mayr
- Max-Planck Institute for Informatics, Saarbrücken, Germany
| | - Mario Albrecht
- Max-Planck Institute for Informatics, Saarbrücken, Germany,Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernhard O Boehm
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Medical Center Ulm and Center of Excellence “Metabolic Disorders” Baden-Württemberg, Ulm, Germany
| | - Jane Goodall
- Department of Medicine, University of Cambridge, UK
| | - Carlo R Berzuini
- Statistical Laboratory, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - James Lee
- Addenbrooke’s Hospital, University of Cambridge, Gastroenterology Research Unit, Cambridge, UK
| | - Vibeke Andersen
- Viborg Regional Hospital, Medical Department, Viborg, Denmark,Aabenraa SHS, Medical Department, Aabenraa, Denmark
| | - Ulla Vogel
- National Research Centre for Working Environment, Copenhagen, Denmark
| | - Limas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Department of Gastroenterology, Kaunas University of Medicine, Kaunas, Lithuania
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany,PopGen Biobank, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rinse K Weersma
- University Medical Center Groningen, Department of Gastroenterology, Groningen, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Miquel Sans
- Service of Digestive Diseases, Centro Médico Teknon, Barcelona, Spain
| | - Cisca Wijmenga
- University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - David P Strachan
- Division of Population Health Sciences and Education, St George’s, University of London, London, UK
| | - Wendy L McArdle
- Avon Longitudinal Study of Parents and Children (ALSPAC) Laboratory, Department of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Séverine Vermeire
- University Hospital Gasthuisberg, Division of Gastroenterology, Leuven, Belgium
| | - Paul Rutgeerts
- University Hospital Gasthuisberg, Division of Gastroenterology, Leuven, Belgium
| | - Jeremy D Sanderson
- Department of Gastroenterology, Guy’s & St. Thomas’ National Health Service Foundation Trust, London, UK
| | | | - Morten H Vatn
- Rikshospitalet University Hospital, Medical Department, Oslo, Norway
| | | | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Richard H Duerr
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Pittsburgh, Pennsylvania, USA,University of Pittsburgh Graduate School of Public Health, Department of Human Genetics, Pittsburgh, Pennsylvania, USA
| | - Carsten Büning
- Department of Gastroenterology, Hepatology and Endocrinology, Charité, Campus Mitte, Berlin, Germany
| | - Stephan Brand
- Department of Medicine II - Grosshadern, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Jürgen Glas
- Department of Medicine II - Grosshadern, Ludwig-Maximilians-University (LMU), Munich, Germany,Department of Preventive Dentistry and Periodontology, LMU, Munich, Germany,Department of Human Genetics, Rheinisch-Westfälische Technische Hochschule (RWTH), Aachen, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany,Institute of Human Genetics, MRI, Technische Universität München, Munich, Germany,Departement of Neurology, MRI, Technische Universität München, Munich, Germany
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany,Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Anna Latiano
- Division of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, San Giovanni Rotondo, Italy
| | - Vito Annese
- Division of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, San Giovanni Rotondo, Italy,Azienda Ospedaliero Universitaria (AOU) Careggi, Unit of Gastroenterology SOD2, Florence, Italy
| | - Jonas Halfvarson
- Division of Gastroenterology, Örebro University Hospital and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Mauro D’Amato
- Karolinska Institute, Department of Biosciences and Nutrition, Stockholm, Sweden
| | - Mark J Daly
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Michael Nothnagel
- Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Tom H Karlsen
- Norwegian PSC Research Center, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Medicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Suresh Subramani
- Section of Molecular Biology, University of California San Diego & San Diego Center for Systems Biology (SDCSB), La Jolla, California, USA
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Miles Parkes
- Addenbrooke’s Hospital, University of Cambridge, Gastroenterology Research Unit, Cambridge, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,To whom correspondence should be addressed: Prof. Dr. rer. nat. Andre Franke (@mucosa.de), Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstr. 12, D-24105 Kiel, Germany, Tel.: +49-431-597-4138, Fax.: +49-431-597-2196
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Liu JZ, Hov JR, Folseraas T, Ellinghaus E, Rushbrook SM, Doncheva NT, Andreassen OA, Weersma RK, Weismüller TJ, Eksteen B, Invernizzi P, Hirschfield GM, Gotthardt DN, Pares A, Ellinghaus D, Shah T, Juran BD, Milkiewicz P, Rust C, Schramm C, Müller T, Srivastava B, Dalekos G, Nöthen MM, Herms S, Winkelmann J, Mitrovic M, Braun F, Ponsioen CY, Croucher PJP, Sterneck M, Teufel A, Mason AL, Saarela J, Leppa V, Dorfman R, Alvaro D, Floreani A, Onengut-Gumuscu S, Rich SS, Thompson WK, Schork AJ, Næss S, Thomsen I, Mayr G, König IR, Hveem K, Cleynen I, Gutierrez-Achury J, Ricaño-Ponce I, van Heel D, Björnsson E, Sandford RN, Durie PR, Melum E, Vatn MH, Silverberg MS, Duerr RH, Padyukov L, Brand S, Sans M, Annese V, Achkar JP, Boberg KM, Marschall HU, Chazouillères O, Bowlus CL, Wijmenga C, Schrumpf E, Vermeire S, Albrecht M, Rioux JD, Alexander G, Bergquist A, Cho J, Schreiber S, Manns MP, Färkkilä M, Dale AM, Chapman RW, Lazaridis KN, Franke A, Anderson CA, Karlsen TH. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet 2013; 45:670-5. [PMID: 23603763 PMCID: PMC3667736 DOI: 10.1038/ng.2616] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [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: 10/09/2012] [Accepted: 03/29/2013] [Indexed: 12/14/2022]
Abstract
Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.
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Affiliation(s)
- Jimmy Z. Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Johannes Roksund Hov
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Trine Folseraas
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Simon M. Rushbrook
- Department of Gastroenterology and Hepatology, Norfolk and Norwich, University Hospitals NHS Trust, Norwich, UK
| | | | - Ole A. Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Ulleval, Oslo, Norway
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, the Netherlands
| | - Tobias J. Weismüller
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
- Current affiliation: Department of Internal Medicine 1, University Hospital of Bonn, Bonn, Germany
| | - Bertus Eksteen
- Snyder Institute of Chronic Diseases, Department of Medicine, University of Calgary, Calgary, Canada
| | - Pietro Invernizzi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano (MI), Italy
| | - Gideon M. Hirschfield
- Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, Canada
- Centre for Liver Research, NIHR Biomedical Research Unit, Birmingham, UK
| | | | - Albert Pares
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tejas Shah
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Brian D. Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | - Piotr Milkiewicz
- Liver Unit and Liver Research Laboratories, Pomeranian Medical University, Szczecin, Poland
| | - Christian Rust
- Department of Medicine 2, Grosshadern, University of Munich, Munich, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Müller
- Department of Internal Medicine, Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Brijesh Srivastava
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Georgios Dalekos
- Department of Medicine, Medical School, University of Thessaly, Larissa, Greece
- Research Laboratory of Internal Medicine, Medical School, University of Thessaly, Larissa, Greece
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mitja Mitrovic
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Felix Braun
- Department of General, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Medical Centre Schleswig-Holstein, Campus Kiel, Germany
| | - Cyriel Y. Ponsioen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands
| | - Peter J. P. Croucher
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, United States of America
| | - Martina Sterneck
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Teufel
- 1st Department of Medicine, University of Mainz, Mainz, Germany
| | - Andrew L. Mason
- Division of Gastroenterology and Hepatology, University of Alberta, Edmonton, Alberta, Canada
| | - Janna Saarela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Virpi Leppa
- Public Health Genomics Unit, Institute for Molecular Medicine Finland FIMM, University of Helsinki and National Institute for Health and Welfare, Helsinki, Finland
| | - Ruslan Dorfman
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada
| | - Domenico Alvaro
- Department of Clinical Medicine, Division of Gastroenterology, Sapienza University of Rome, Rome, Italy
| | - Annarosa Floreani
- Dept. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, Division of Endocrinology & Metabolism, University of Virginia, Charlottesville, USA
- Department of Internal Medicine, Division of Endocrinology & Metabolism, University of Virginia, Charlottesville, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, USA
| | - Wesley K. Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Andrew J. Schork
- Graduate Program in Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Sigrid Næss
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingo Thomsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Gabriele Mayr
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Inke R. König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Isabelle Cleynen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Clinical and Experimental Medicine, KU Leuven, Leuven, Belgium
| | - Javier Gutierrez-Achury
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - David van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Einar Björnsson
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Peter R. Durie
- Physiology and Experimental Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Espen Melum
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- EpiGen, Campus AHUS, Akershus University Hospital, Nordbyhagen, Norway
| | - Mark S. Silverberg
- Inflammatory Bowel Disease (IBD) Group, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Toronto, Ontario, Canada
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Stephan Brand
- Department of Medicine II, University Hospital Munich-Grosshadern, Ludwig-Maximilians-University Munich, Germany
| | - Miquel Sans
- Department of Digestive Diseases, Centro Médico Teknon, Barcelona, Spain
| | - Vito Annese
- Division of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievodella Sofferenza Hospital, San Giovanni Rotondo, Italy
- Unit of Gastroenterology SOD2, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - Jean-Paul Achkar
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kirsten Muri Boberg
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Hanns-Ulrich Marschall
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy and University Hospital, Gothenburg, Sweden
| | - Olivier Chazouillères
- AP-HP, Hôpital Saint Antoine, Department of Hepatology, UPMC Univ Paris 06, Paris, France
| | - Christopher L. Bowlus
- Division of Gastroenterology and Hepatology, University of California Davis, Davis, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Erik Schrumpf
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, KU Leuven, Leuven, Belgium
- Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
| | - Mario Albrecht
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - John D. Rioux
- Université de Montréal, Research Center, Montreal, Quebec, Canada
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | - Graeme Alexander
- Department of Medicine, Division of Hepatology, University of Cambridge, Cambridge, UK
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Judy Cho
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, USA
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
- Popgen Biobank, University Hospital Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Michael P. Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
| | - Martti Färkkilä
- Division of Gastroenterology, Department of Medicine, Helsinki University Hospital, Finland
| | - Anders M. Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Roger W. Chapman
- Department of Hepatology, John Radcliffe University Hospitals NHS Trust, Oxford, UK
| | - Konstantinos N. Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Tom H. Karlsen
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gastroenterology, Institute of Medicine, University of Bergen, Bergen, Norway
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Lazarev M, Huang C, Bitton A, Cho JH, Duerr RH, McGovern DP, Proctor DD, Regueiro M, Rioux JD, Schumm PP, Taylor KD, Silverberg MS, Steinhart AH, Hutfless S, Brant SR. Relationship between proximal Crohn's disease location and disease behavior and surgery: a cross-sectional study of the IBD Genetics Consortium. Am J Gastroenterol 2013; 108:106-12. [PMID: 23229423 PMCID: PMC4059598 DOI: 10.1038/ajg.2012.389] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [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: 02/07/2023]
Abstract
OBJECTIVES In classifying Crohn's disease (CD) location, proximal (L4) disease includes esophagogastroduodenal (EGD) and jejunal disease. Our aim was to determine the influence of proximal disease on outcomes of behavior and need for surgery and to determine if there was significant clinical heterogeneity between EGD and jejunal disease. METHODS We performed a cross-sectional query of the NIDDK (National Institute of Diabetes and Digestive and Kidney Disease) Inflammatory Bowel Disease Genetics Consortium (IBDGC) database of patients with a confirmed diagnosis of CD and phenotyped per the IBDGC manual. Presence of any L4, L4-EGD, L4-jejunal, and non-L4 disease (L1-ileal, L2-colonic, and L3-ileocolonic) was compared with demographic features including age, race, ethnicity, smoking and inflammatory bowel disease (IBD) family history, diagnosis age, disease duration, clinical outcomes of inflammatory, stricturing or penetrating behavior, and CD abdominal surgeries. Univariate and multivariable analyses were performed with R. RESULTS Among 2,105 patients with complete disease location data, 346 had L4 disease (175 L4-EGD, 115 L4-jejunal, and 56 EGD and jejunal) with 321 having concurrent L1-L3 disease. In all, 1,759 had only L1-L3 disease. L4 vs. non-L4 patients were more likely (P<0.001) to be younger at diagnosis, non-smokers, have coexisting ileal involvement, and have stricturing disease. L4-jejunal vs. L4-EGD patients were at least twice as likely (P<0.001) to have had ileal disease, stricturing behavior, and any or multiple abdominal surgeries. Remarkably, L4-jejunal patients had more (P<0.001) stricturing behavior and multiple abdominal surgeries than non-L4 ileal disease patients. Logistic regression showed stricturing risks were ileal (without proximal) site (odds ratio (OR) 3.18; 95% confidence interval 2.23-4.64), longer disease duration (OR 1.33/decade; 1.19-1.49), jejunal site (OR 2.90; 1.89-4.45), and older age at diagnosis (OR 1.21/decade; 1.10-1.34). Multiple surgery risks were disease duration (OR 3.74/decade; 3.05-4.64), penetrating disease (OR 2.60; 1.64-4.21), and jejunal site (OR 2.39; 1.36-4.20), with short duration from diagnosis to first surgery protective (OR 0.87/decade to first surgery; 0.84-0.90). CONCLUSIONS Jejunal disease is a significantly greater risk factor for stricturing disease and multiple abdominal surgeries than either EGD or ileal (without proximal) disease. The Montreal site classification should be revised to include separate designations for jejunal and EGD disease.
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Affiliation(s)
- Mark Lazarev
- Division of Gastroenterology, Meyerhoff Inflammatory Bowel Diseases Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
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Glas J, Seiderer J, Czamara D, Pasciuto G, Diegelmann J, Wetzke M, Olszak T, Wolf C, Müller-Myhsok B, Balschun T, Achkar JP, Kamboh MI, Franke A, Duerr RH, Brand S. PTGER4 expression-modulating polymorphisms in the 5p13.1 region predispose to Crohn's disease and affect NF-κB and XBP1 binding sites. PLoS One 2012; 7:e52873. [PMID: 23300802 PMCID: PMC3531335 DOI: 10.1371/journal.pone.0052873] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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: 05/04/2012] [Accepted: 11/22/2012] [Indexed: 01/08/2023] Open
Abstract
Background Genome-wide association studies identified a PTGER4 expression-modulating region on chromosome 5p13.1 as Crohn's disease (CD) susceptibility region. The study aim was to test this association in a large cohort of patients with inflammatory bowel disease (IBD) and to elucidate genotypic and phenotypic interactions with other IBD genes. Methodology/Principal Findings A total of 7073 patients and controls were genotyped: 844 CD and 471 patients with ulcerative colitis and 1488 controls were analyzed for the single nucleotide polymorphisms (SNPs) rs4495224 and rs7720838 on chromosome 5p13.1. The study included two replication cohorts of North American (CD: n = 684; controls: n = 1440) and of German origin (CD: n = 1098; controls: n = 1048). Genotype-phenotype, epistasis and transcription factor binding analyses were performed. In the discovery cohort, an association of rs4495224 (p = 4.10×10−5; 0.76 [0.67–0.87]) and of rs7720838 (p = 6.91×10−4; 0.81 [0.71–0.91]) with susceptibility to CD was demonstrated. These associations were confirmed in both replication cohorts. In silico analysis predicted rs4495224 and rs7720838 as essential parts of binding sites for the transcription factors NF-κB and XBP1 with higher binding scores for carriers of the CD risk alleles, providing an explanation of how these SNPs might contribute to increased PTGER4 expression. There was no association of the PTGER4 SNPs with IBD phenotypes. Epistasis detected between 5p13.1 and ATG16L1 for CD susceptibility in the discovery cohort (p = 5.99×10−7 for rs7720838 and rs2241880) could not be replicated in both replication cohorts arguing against a major role of this gene-gene interaction in the susceptibility to CD. Conclusions/Significance We confirmed 5p13.1 as a major CD susceptibility locus and demonstrate by in silico analysis rs4495224 and rs7720838 as part of binding sites for NF-κB and XBP1. Further functional studies are necessary to confirm the results of our in silico analysis and to analyze if changes in PTGER4 expression modulate CD susceptibility.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Binding Sites
- Child
- Chromosomes, Human, Pair 5/genetics
- Crohn Disease/genetics
- DNA-Binding Proteins/metabolism
- Epistasis, Genetic
- Female
- Gene Expression
- Gene Frequency
- Genetic Predisposition to Disease
- Humans
- Male
- Middle Aged
- NF-kappa B/metabolism
- Polymorphism, Single Nucleotide
- Receptors, Prostaglandin E, EP4 Subtype/genetics
- Receptors, Prostaglandin E, EP4 Subtype/metabolism
- Regulatory Factor X Transcription Factors
- Sequence Analysis, DNA
- Transcription Factors/metabolism
- X-Box Binding Protein 1
- Young Adult
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Affiliation(s)
- Jürgen Glas
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
- Department of Preventive Dentistry and Periodontology, University of Munich, Munich, Germany
- Department of Human Genetics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen, Germany
| | - Julia Seiderer
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
| | | | - Giulia Pasciuto
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
| | - Julia Diegelmann
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
- Department of Preventive Dentistry and Periodontology, University of Munich, Munich, Germany
| | - Martin Wetzke
- Center for Pediatrics, Hannover Medical School, Hannover, Germany
| | - Torsten Olszak
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
- Division of Gastroenterology, Brigham & Women's Hospital, Harvard Medical School, Boston, United States of America
| | | | | | - Tobias Balschun
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Jean-Paul Achkar
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - M. Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Richard H. Duerr
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Gastroenterology, Hepatology and Nutrition, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephan Brand
- Department of Medicine II - Grosshadern, University of Munich, Munich, Germany
- * E-mail:
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Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491:119-24. [PMID: 23128233 PMCID: PMC3491803 DOI: 10.1038/nature11582] [Citation(s) in RCA: 3320] [Impact Index Per Article: 276.7] [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: 05/17/2012] [Accepted: 09/12/2012] [Indexed: 02/06/2023]
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
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Affiliation(s)
- Luke Jostins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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Wang MH, Okazaki T, Kugathasan S, Cho JH, Isaacs KL, Lewis JD, Smoot DT, Valentine JF, Kader HA, Ford JG, Harris ML, Oliva-Hemker M, Cuffari C, Torbenson MS, Duerr RH, Silverberg MS, Rioux JD, Taylor KD, Nguyen GC, Wu Y, Datta LW, Hooker S, Dassopoulos T, Kittles RA, Kao LW, Brant SR. Contribution of higher risk genes and European admixture to Crohn's disease in African Americans. Inflamm Bowel Dis 2012; 18:2277-87. [PMID: 22411504 PMCID: PMC3810419 DOI: 10.1002/ibd.22931] [Citation(s) in RCA: 22] [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: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 12/13/2022]
Abstract
BACKGROUND African Americans (AAs) are an admixed population of West African (WA) and European ancestry (EA). Crohn's disease (CD) susceptibility genes have not been established. We therefore evaluated the contribution of European admixture and major established risk genes to AA CD. METHODS Ninety-seven admixture informative markers were genotyped for ancestry estimates using STRUCTURE. Overall, 354 AA CD cases and 354 ethnicity-matched controls were genotyped for total 21 single nucleotide polymorphisms (SNPs) in ATG16L1, NOD2, IBD5, IL23R and IRGM by TaqMan or direct sequencing. Association was evaluated by logistic regression, adjusted for ancestry. RESULTS Mean EA was similar among the CD cases and controls (20.9% and 20.4%, respectively, P = 0.58). No significant admixture differences were observed among 211 to 227 cases stratified by phenotypic subclassifications including onset, surgery, site, and behavior. CD was associated with NOD2 carrier (6.93% CD, 2.15% Controls, P = 0.007), ATG16L1 Thr300Ala (36.1% CD, 29.3% Controls, P = 0.003), SLC22A4 and SLC22A5 (IBD5 locus) functional SNPs (Leu503Phe [10.5% CD, 7.6% Controls, P = 0.05] and g-207c [41.3% CD, 35.7% Controls, P = 0.03], respectively), and IL23R rs2201841 (18.2% CD, 13.8% Controls, P = 0.03), but not IRGM variants, nor three African ancestral NOD2 nonsynonymous variants. IBD5 risk was recessive. An all-minor allele IBD5 haplotype from EA was associated (P = 0.05), whereas a more common haplotype isolating g-207c was not. CONCLUSIONS Specific functional gene variations contribute significantly to AA CD risk. Established NOD2, SLC22A4-A5, and ATG16L1 variants show increased CD risk, with IBD5 recessive. Although CD is more common in whites, European admixture is similar among AA cases and controls.
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Affiliation(s)
- Ming-Hsi Wang
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD,Department of Medicine, St Agnes Hospital Center, Baltimore, MD
| | - Toshihiko Okazaki
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Judy H. Cho
- Department of Medicine and Genetics, Yale University, New Haven, CT
| | - Kim L. Isaacs
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James D. Lewis
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA
| | - Duane T. Smoot
- Department of Medicine, Howard University College of Medicine, Washington, DC
| | - John F. Valentine
- Division of Gastroenterology, Hepatology & Nutrition, University of Florida, Gainesville, FL
| | - Howard A. Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD
| | - Jean G. Ford
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Mary L. Harris
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD,The Institute for Digestive Health & Liver Disease at Mercy Hospital, Baltimore, Maryland
| | - Maria Oliva-Hemker
- Division of Pediatric Gastroenterology and Nutrition, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Carmen Cuffari
- Division of Pediatric Gastroenterology and Nutrition, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael S. Torbenson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - 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
| | - 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, Canada; The Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - John D. Rioux
- Université de Montréal and the Montreal Heart Institute, Research Center, 5000 rue Belanger, Montreal, Quebec H1T 1C8, Canada.; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kent D. Taylor
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Geoffrey C. Nguyen
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD,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, Canada; The Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Yuqiong Wu
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lisa W. Datta
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stanley Hooker
- Section of Genetic Medicine, Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Themistocles Dassopoulos
- The Institute for Digestive Health & Liver Disease at Mercy Hospital, Baltimore, Maryland,Gastroenterology Division, Washington University School of Medicine, St. Louis, MO
| | - Rick A. Kittles
- Section of Genetic Medicine, Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL,Department of Medicine and Division of Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, Illinois
| | - Linda W.H. Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Steven R. Brant
- Lyn P. and Harvey M. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD,Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
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Muise AM, Xu W, Guo CH, Walters TD, Wolters VM, Fattouh R, Lam GY, Hu P, Murchie R, Sherlock M, Gana JC, Russell RK, Glogauer M, Duerr RH, Cho JH, Lees CW, Satsangi J, Wilson DC, Paterson AD, Griffiths AM, Silverberg MS, Brumell JH. NADPH oxidase complex and IBD candidate gene studies: identification of a rare variant in NCF2 that results in reduced binding to RAC2. Gut 2012; 61:1028-35. [PMID: 21900546 PMCID: PMC3806486 DOI: 10.1136/gutjnl-2011-300078] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The NOX2 NADPH oxidase complex produces reactive oxygen species and plays a critical role in the killing of microbes by phagocytes. Genetic mutations in genes encoding components of the complex result in both X-linked and autosomal recessive forms of chronic granulomatous disease (CGD). Patients with CGD often develop intestinal inflammation that is histologically similar to Crohn's colitis, suggesting a common aetiology for both diseases. The aim of this study is to determine if polymorphisms in NOX2 NADPH oxidase complex genes that do not cause CGD are associated with the development of inflammatory bowel disease (IBD). METHODS Direct sequencing and candidate gene approaches were used to identify susceptibility loci in NADPH oxidase complex genes. Functional studies were carried out on identified variants. Novel findings were replicated in independent cohorts. RESULTS Sequence analysis identified a novel missense variant in the neutrophil cytosolic factor 2 (NCF2) gene that is associated with very early onset IBD (VEO-IBD) and subsequently found in 4% of patients with VEO-IBD compared with 0.2% of controls (p=1.3×10(-5), OR 23.8 (95% CI 3.9 to 142.5); Fisher exact test). This variant reduced binding of the NCF2 gene product p67(phox) to RAC2. This study found a novel genetic association of RAC2 with Crohn's disease (CD) and replicated the previously reported association of NCF4 with ileal CD. CONCLUSION These studies suggest that the rare novel p67(phox) variant results in partial inhibition of oxidase function and are associated with CD in a subgroup of patients with VEO-IBD; and suggest that components of the NADPH oxidase complex are associated with CD.
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Affiliation(s)
- Aleixo M Muise
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada.
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Achkar JP, Klei L, de Bakker PI, Bellone G, Rebert N, Scott R, Lu Y, Regueiro M, Brzezinski A, Kamboh MI, Fiocchi C, Devlin B, Trucco M, Ringquist S, Roeder K, Duerr RH. Amino acid position 11 of HLA-DRβ1 is a major determinant of chromosome 6p association with ulcerative colitis. Genes Immun 2012; 13:245-52. [PMID: 22170232 PMCID: PMC3341846 DOI: 10.1038/gene.2011.79] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 08/22/2011] [Revised: 10/12/2011] [Accepted: 10/31/2011] [Indexed: 01/25/2023]
Abstract
The major histocompatibility complex (MHC) on chromosome 6p is an established risk locus for ulcerative colitis (UC) and Crohn's disease (CD). We aimed to better define MHC association signals in UC and CD by combining data from dense single-nucleotide polymorphism (SNP) genotyping and from imputation of classical human leukocyte antigen (HLA) types, their constituent SNPs and corresponding amino acids in 562 UC, 611 CD and 1428 control subjects. Univariate and multivariate association analyses were performed, controlling for ancestry. In univariate analyses, absence of the rs9269955 C allele was strongly associated with risk for UC (P = 2.67 × 10(-13)). rs9269955 is a SNP in the codon for amino acid position 11 of HLA-DRβ1, located in the P6 pocket of the HLA-DR antigen binding cleft. This amino acid position was also the most significantly UC-associated amino acid in omnibus tests (P = 2.68 × 10(-13)). Multivariate modeling identified rs9269955-C and 13 other variants in best predicting UC vs control status. In contrast, there was only suggestive association evidence between the MHC and CD. Taken together, these data demonstrate that variation at HLA-DRβ1, amino acid 11 in the P6 pocket of the HLA-DR complex antigen binding cleft is a major determinant of chromosome 6p association with UC.
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Affiliation(s)
- Jean-Paul Achkar
- Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Paul I.W. de Bakker
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Julius Center for Health Sciences and Primary Care, and Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gaia Bellone
- Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Nancy Rebert
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Regan Scott
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ying Lu
- Division of Immunogenetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Miguel Regueiro
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Aaron Brzezinski
- Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio
| | - M. Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Claudio Fiocchi
- Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Massimo Trucco
- Division of Immunogenetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Steven Ringquist
- Division of Immunogenetics, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
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Kenny EE, Pe'er I, Karban A, Ozelius L, Mitchell AA, Ng SM, Erazo M, Ostrer H, Abraham C, Abreu MT, Atzmon G, Barzilai N, Brant SR, Bressman S, Burns ER, Chowers Y, Clark LN, Darvasi A, Doheny D, Duerr RH, Eliakim R, Giladi N, Gregersen PK, Hakonarson H, Jones MR, Marder K, McGovern DPB, Mulle J, Orr-Urtreger A, Proctor DD, Pulver A, Rotter JI, Silverberg MS, Ullman T, Warren ST, Waterman M, Zhang W, Bergman A, Mayer L, Katz S, Desnick RJ, Cho JH, Peter I. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. PLoS Genet 2012; 8:e1002559. [PMID: 22412388 PMCID: PMC3297573 DOI: 10.1371/journal.pgen.1002559] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [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: 04/29/2011] [Accepted: 01/12/2012] [Indexed: 12/19/2022] Open
Abstract
Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD-susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2-4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (p<5×10⁻⁶). Novel signals detected among AJs were mapped to chromosomes 5q21.1 (rs7705924, combined p = 2×10⁻⁸; combined odds ratio OR = 1.48), 2p15 (rs6545946, p = 7×10⁻⁹; OR = 1.16), 8q21.11 (rs12677663, p = 2×10⁻⁸; OR = 1.15), 10q26.3 (rs10734105, p = 3×10⁻⁸; OR = 1.27), and 11q12.1 (rs11229030, p = 8×10⁻⁹; OR = 1.15), implicating biologically plausible candidate genes, including RPL7, CPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim.
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Affiliation(s)
- Eimear E. Kenny
- Department of Computer Sciences, Columbia University, New York, New York, United States of America
| | - Itsik Pe'er
- Department of Computer Sciences, Columbia University, New York, New York, United States of America
| | - Amir Karban
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Adele A. Mitchell
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Sok Meng Ng
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Monica Erazo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Clara Abraham
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Maria T. Abreu
- Division of Gastroenterology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Gil Atzmon
- Genetic Core for Longevity, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nir Barzilai
- Genetic Core for Longevity, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Susan Bressman
- Mirken Department of Neurology, Beth Israel Medical Center, New York, New York, United States of America
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Edward R. Burns
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yehuda Chowers
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lorraine N. Clark
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Ariel Darvasi
- The Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Doheny
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Rami Eliakim
- Department of Gastroenterology and Hepatology, Sheba Medical Center, Raman Gan, Israel
| | - Nir Giladi
- Department of Neurology, Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michelle R. Jones
- Division of Endocrinology, Diabetes, and Metabolism, Graduate Program in Biomedical Sciences and Translational Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Karen Marder
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Dermot P. B. McGovern
- Department of Translational Medicine, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jennifer Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Avi Orr-Urtreger
- Genetic Institute, Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Deborah D. Proctor
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Ann Pulver
- Epidemiology-Genetics Program in Schizophrenia, Bipolar Disorders, and Related Disorders, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Thomas Ullman
- Division of Gastroenterology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Matti Waterman
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wei Zhang
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Lloyd Mayer
- Division of Gastroenterology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Seymour Katz
- Albert Einstein College of Medicine, North Shore University Hospital-Long Island Jewish Hospital Systems, St. Francis Hospital, Great Neck, New York, United States of America
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Judy H. Cho
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (JH Cho) (JC); (I Peter) (IP)
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (JH Cho) (JC); (I Peter) (IP)
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Zucchelli M, Camilleri M, Andreasson AN, Bresso F, Dlugosz A, Halfvarson J, Törkvist L, Schmidt PT, Karling P, Ohlsson B, Duerr RH, Simren M, Lindberg G, Agreus L, Carlson P, Zinsmeister AR, D'Amato M. Association of TNFSF15 polymorphism with irritable bowel syndrome. Gut 2011; 60:1671-1677. [PMID: 21636646 PMCID: PMC3922294 DOI: 10.1136/gut.2011.241877] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [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: 12/13/2022]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is the most common gastrointestinal disorder, affecting more than 10% of the general population worldwide. Although a genetic component is suspected, unambiguous susceptibility genes have so far not been identified. This study tested the hypothesis that genes contributing to epithelial barrier integrity, control of mucosal immune responses and interactions with bacteria in the gut are associated with IBS. METHODS Single nucleotide polymorphisms (SNPs) corresponding to top signals of association with Crohn's disease at 30 known susceptibility loci were tested for their effect on IBS risk in 1992 individuals from two independent case-control cohorts from Sweden and the USA. Association tests included a conservative Bonferroni correction for multiple comparisons, and were also performed on specific subgroups of patients characterised by constipation (IBS-C), diarrhoea (IBS-D) or alternating constipation and diarrhoea (IBS-A). RESULTS The Crohn's disease risk allele rs4263839 G in the TNFSF15 gene was significantly associated with an increased risk of both IBS (p=2.2×10(-5); OR 1.37) and more pronouncedly, IBS-C (p=8.7×10(-7); OR 1.79) in the entire sample. Similar associations and risk effects of the same magnitude were observed in the two cohorts analysed separately. A correlation between rs4263839 genotype and TNFSF15 mRNA expression was detected both in peripheral blood and in rectal mucosal biopsies from healthy individuals (combined p=0.0033). CONCLUSIONS TNFSF15 is a susceptibility gene for IBS and IBS constipation. As TL1A, the protein encoded by TNFSF15, contributes to the modulation of inflammatory responses, the results support a role of immune activation in IBS.
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Affiliation(s)
- Marco Zucchelli
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Anna Nixon Andreasson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden,Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Francesca Bresso
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aldona Dlugosz
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Internal Medicine,Örebro University Hospital,Örebro, Sweden
| | - Leif Törkvist
- Department of Clinical Science Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Peter T Schmidt
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Bodil Ohlsson
- Department of Clinical Sciences, Skånes University Hospital, Malmoe, Sweden
| | - Richard H Duerr
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Magnus Simren
- Department of Internal Medicine, Gothenburg University, Gothenburg, Sweden
| | - Greger Lindberg
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Paula Carlson
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Alan R Zinsmeister
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G, de la Concha EG, de Almeida RC, Dias KRM, van Diemen CC, Dubois PCA, Duerr RH, Edkins S, Franke L, Fransen K, Gutierrez J, Heap GAR, Hrdlickova B, Hunt S, Plaza Izurieta L, Izzo V, Joosten LAB, Langford C, Mazzilli MC, Mein CA, Midah V, Mitrovic M, Mora B, Morelli M, Nutland S, Núñez C, Onengut-Gumuscu S, Pearce K, Platteel M, Polanco I, Potter S, Ribes-Koninckx C, Ricaño-Ponce I, Rich SS, Rybak A, Santiago JL, Senapati S, Sood A, Szajewska H, Troncone R, Varadé J, Wallace C, Wolters VM, Zhernakova A, Thelma BK, Cukrowska B, Urcelay E, Bilbao JR, Mearin ML, Barisani D, Barrett JC, Plagnol V, Deloukas P, Wijmenga C, van Heel DA. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011; 43:1193-201. [PMID: 22057235 PMCID: PMC3242065 DOI: 10.1038/ng.998] [Citation(s) in RCA: 554] [Impact Index Per Article: 42.6] [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: 04/15/2011] [Accepted: 10/05/2011] [Indexed: 12/13/2022]
Abstract
Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.
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Affiliation(s)
- Gosia Trynka
- Genetics Department, University Medical Center and University of Groningen, The Netherlands
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46
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Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, Dubinsky M, Brant SR, Silverberg M, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D’Amato M, McGovern DP, Cho JH, Rioux JD, Xavier RJ, Daly MJ. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 2011; 43:1066-73. [PMID: 21983784 PMCID: PMC3378381 DOI: 10.1038/ng.952] [Citation(s) in RCA: 568] [Impact Index Per Article: 43.7] [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: 01/05/2011] [Accepted: 08/31/2011] [Indexed: 02/08/2023]
Abstract
More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10(-16), odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.
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Affiliation(s)
- Manuel A. Rivas
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Melissa Beaudoin
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Agnes Gardet
- Gastrointenstinal Unit, Center for the Study of the Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Yashoda Sharma
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - Clarence K. Zhang
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - Gabrielle Boucher
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Stephan Ripke
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Schittenhelmstr. 12, D-24105 Kiel, Germany
| | - Noel Burtt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tim Fennell
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrew Kirby
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anna Latiano
- Unit of Gastroenterology, IRCCS - Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Philippe Goyette
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Todd Green
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jonas Halfvarson
- Örebro University Hospital, Department of Medicine and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Talin Haritunians
- The Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - Finny Kuruvilla
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Clarus Ventures, Cambridge, MA, USA
| | - Caroline Lagacé
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Benjamin Neale
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ken Sin Lo
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Phil Schumm
- Department of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Leif Törkvist
- Karolinska Institutet, Department of Clinical Science Intervention and Technology, Stockholm, Sweden
| | | | | | - Marla Dubinsky
- The Pedriatic IBD Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Steven R. Brant
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark Silverberg
- Mount Sinai Hospital Inflammatory Bowel Disease Centre, University of Toronto, Toronto, Ontario, Canada
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David Altshuler
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Guillaume Lettre
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Andre Franke
- Institute of Clinical Molecular Biology, Schittenhelmstr. 12, D-24105 Kiel, Germany
| | - Mauro D’Amato
- Karolinska Institutet, Department of Biosciences and Nutrition, Stockholm, Sweden
| | - Dermot P.B. McGovern
- The Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Judy H. Cho
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - John D. Rioux
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Ramnik J. Xavier
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gastrointenstinal Unit, Center for the Study of the Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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47
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Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RSN, Floyd JAB, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD. Erratum: Corrigendum: Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011. [DOI: 10.1038/ng0911-919b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Muise AM, Walters T, Xu W, Shen-Tu G, Guo CH, Fattouh R, Lam GY, Wolters VM, Bennitz J, Van Limbergen J, Renbaum P, Kasirer Y, Ngan BY, Turner D, Denson LA, Sherman PM, Duerr RH, Cho J, Lees CW, Satsangi J, Wilson DC, Paterson AD, Griffiths AM, Glogauer M, Silverberg MS, Brumell JH. Single nucleotide polymorphisms that increase expression of the guanosine triphosphatase RAC1 are associated with ulcerative colitis. Gastroenterology 2011; 141:633-41. [PMID: 21684284 PMCID: PMC3152589 DOI: 10.1053/j.gastro.2011.04.057] [Citation(s) in RCA: 59] [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: 07/27/2010] [Revised: 04/16/2011] [Accepted: 04/26/2011] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS RAC1 is a guanosine triphosphatase that has an evolutionarily conserved role in coordinating immune defenses, from plants to mammals. Chronic inflammatory bowel diseases are associated with dysregulation of immune defenses. We studied the role of RAC1 in inflammatory bowel diseases using human genetic and functional studies and animal models of colitis. METHODS We used a candidate gene approach to HapMap-Tag single nucleotide polymorphisms in a discovery cohort; findings were confirmed in 2 additional cohorts. RAC1 messenger RNA expression was examined from peripheral blood cells of patients. Colitis was induced in mice with conditional disruption of Rac1 in phagocytes by administration of dextran sulfate sodium. RESULTS We observed a genetic association between RAC1 with ulcerative colitis in a discovery cohort, 2 independent replication cohorts, and in combined analysis for the single nucleotide polymorphisms rs10951982 (P(combined UC) = 3.3 × 10(-8), odds ratio = 1.43 [95% confidence interval: 1.26-1.63]) and rs4720672 (P(combined UC) = 4.7 × 10(-6), odds ratio = 1.36 [95% confidence interval: 1.19-1.58]). Patients with inflammatory bowel disease who had the rs10951982 risk allele had increased expression of RAC1 compared to those without this allele. Conditional disruption of Rac1 in macrophage and neutrophils of mice protected against dextran sulfate sodium-induced colitis. CONCLUSIONS Human studies and knockout mice demonstrated a role for the guanosine triphosphatase RAC1 in the development of ulcerative colitis; increased expression of RAC1 was associated with susceptibility to colitis.
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Affiliation(s)
- Aleixo M Muise
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.
| | - Thomas Walters
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Wei Xu
- Public Health Sciences, University of Toronto, 5-507, Princess Margaret Hospital 610 University Ave, Toronto, Ontario, M5G 2M9
| | - Grace Shen-Tu
- Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Cong-Hui Guo
- Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Ramzi Fattouh
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8,Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Grace Y Lam
- Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8,Institute of Medical Science, University of Toronto
| | - Victorien M Wolters
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Joshua Bennitz
- Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Johan Van Limbergen
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Paul Renbaum
- Genetic Institute, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel, P.O.B 3235, Jerusalem 91031
| | - Yair Kasirer
- Pediatric Gastroenterology Unit, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel, P.O.B 3235, Jerusalem 91031
| | - Bo-Yee Ngan
- Department of Pathology, the Hospital for Sick Children and University of Toronto
| | - Dan Turner
- Pediatric Gastroenterology Unit, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel, P.O.B 3235, Jerusalem 91031
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition Fellowship Cincinnati Children's Hospital Medical Center MLC 2010 3333 Burnet Avenue Cincinnati, OH 45229-3039
| | - Philip M Sherman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8,Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, UPMC Presbyterian, Mezzanine Level, C-Wing, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Judy Cho
- Diseases, Departments of Medicine and Genetics, Yale University
| | - Charlie W Lees
- Department of Gastroenterology, Western General Hospital, University of Edinburgh, Edinburgh
| | - Jack Satsangi
- Department of Gastroenterology, Western General Hospital, University of Edinburgh, Edinburgh
| | - David C Wilson
- Child Life and Health, Department of Pediatrics, University of Edinburgh, Edinburgh
| | | | - Anne M Griffiths
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, 555 University Ave, Toronto, Ontario M5G 1X8
| | | | - Mark S Silverberg
- Mount Sinai Hospital Inflammatory Bowel Disease Disease Group, University of Toronto Group, Dr. Zane Cohen Digestive Diseases Clinical Research Centre, 600 University Ave, Toronto, Ontario M5G 1X5
| | - John H Brumell
- Program in Cell Biology, the Hospital for Sick Children and University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8,Institute of Medical Science, University of Toronto,Department of Molecular Genetics, University of Toronto
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Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RSN, Floyd JAB, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011. [PMID: 21297633 DOI: 10.1038/ng.764ng.764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 × 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.
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Affiliation(s)
- Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RSN, Floyd JAB, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011; 43:246-52. [PMID: 21297633 PMCID: PMC3084597 DOI: 10.1038/ng.764] [Citation(s) in RCA: 1003] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/14/2011] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) and candidate gene studies in ulcerative colitis (UC) have identified 18 susceptibility loci. We conducted a meta-analysis of 6 UC GWAS, comprising 6,687 cases and 19,718 controls, and followed-up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P<5×10-8), increasing the number of UC associated loci to 47. After annotating associated regions using GRAIL, eQTL data and correlations with non-synonymous SNPs, we identified many candidate genes providing potentially important insights into disease pathogenesis, including IL1R2, IL8RA/B, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease (IBD) risk loci is now 99, including a minimum of 28 shared association signals between Crohn’s disease (CD) and UC.
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Affiliation(s)
- Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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