503
|
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.
Collapse
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
| |
Collapse
|