1
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Zhang H, Patrick MT, Tejasvi T, Sarkar MK, Wasikowski R, Stuart PE, Li Q, Xing X, Voorhees JJ, Ward NL, He K, Zhou X, Gudjonsson JE, Nair RP, Elder JT, Tsoi LC. Retrospective pharmacogenetic study of psoriasis highlights the role of KLK7 in tumour necrosis factor signalling. Br J Dermatol 2023; 190:70-79. [PMID: 37672660 PMCID: PMC10733628 DOI: 10.1093/bjd/ljad332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Multiple treatment options are available for the management of psoriasis, but clinical response varies among individual patients and no biomarkers are available to facilitate treatment selection for improved patient outcomes. OBJECTIVES To utilize retrospective data to conduct a pharmacogenetic study to explore the potential genetic pathways associated with drug response in the treatment of psoriasis. METHODS We conducted a retrospective pharmacogenetic study using self-evaluated treatment response from 1942 genotyped patients with psoriasis. We examined 6 502 658 genetic markers to model their associations with response to six treatment options using linear regression, adjusting for cohort variables and demographic features. We further utilized an integrative approach incorporating epigenomics, transcriptomics and a longitudinal clinical cohort to provide biological implications for the topmost signals associated with drug response. RESULTS Two novel markers were revealed to be associated with treatment response: rs1991820 (P = 1.30 × 10-6) for anti-tumour necrosis factor (TNF) biologics; and rs62264137 (P = 2.94 × 10-6) for methotrexate, which was also associated with cutaneous mRNA expression levels of two known psoriasis-related genes KLK7 (P = 1.0 × 10-12) and CD200 (P = 5.4 × 10-6). We demonstrated that KLK7 expression was increased in the psoriatic epidermis, as shown by immunohistochemistry, as well as single-cell RNA sequencing, and its responsiveness to anti-TNF treatment was highlighted. By inhibiting the expression of KLK7, we further illustrated that keratinocytes have decreased proinflammatory responses to TNF. CONCLUSIONS Our study implicates the genetic regulation of cytokine responses in predicting clinical drug response and supports the association between pharmacogenetic loci and anti-TNF response, as shown here for KLK7.
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Affiliation(s)
| | | | - Trilokraj Tejasvi
- Department of Dermatology
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Nicole L Ward
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Johann E Gudjonsson
- Department of Dermatology
- Taubman Medical Research Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Departments of Biostatistics
- Department of Dermatology
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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2
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Dand N, Stuart PE, Bowes J, Ellinghaus D, Nititham J, Saklatvala JR, Teder-Laving M, Thomas LF, Traks T, Uebe S, Assmann G, Baudry D, Behrens F, Billi AC, Brown MA, Burkhardt H, Capon F, Chung R, Curtis CJ, Duckworth M, Ellinghaus E, FitzGerald O, Gerdes S, Griffiths CEM, Gulliver S, Helliwell P, Ho P, Hoffmann P, Holmen OL, Huang ZM, Hveem K, Jadon D, Köhm M, Kraus C, Lamacchia C, Lee SH, Ma F, Mahil SK, McHugh N, McManus R, Modalsli EH, Nissen MJ, Nöthen M, Oji V, Oksenberg JR, Patrick MT, Perez-White BE, Ramming A, Rech J, Rosen C, Sarkar MK, Schett G, Schmidt B, Tejasvi T, Traupe H, Voorhees JJ, Wacker EM, Warren RB, Wasikowski R, Weidinger S, Wen X, Zhang Z, Barton A, Chandran V, Esko T, Foerster J, Franke A, Gladman DD, Gudjonsson JE, Gulliver W, Hüffmeier U, Kingo K, Kõks S, Liao W, Løset M, Mägi R, Nair RP, Rahman P, Reis A, Smith CH, Di Meglio P, Barker JN, Tsoi LC, Simpson MA, Elder JT. GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets. medRxiv 2023:2023.10.04.23296543. [PMID: 37873414 PMCID: PMC10593001 DOI: 10.1101/2023.10.04.23296543] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To move towards a saturation map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 45 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.
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Affiliation(s)
- Nick Dand
- Department of Medical & Molecular Genetics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- Health Data Research UK, London, UK
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, The University of Manchester, Manchester, UK
- National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre, The University of Manchester, Manchester, UK
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Joanne Nititham
- Deparment of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jake R Saklatvala
- Department of Medical & Molecular Genetics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Laurent F Thomas
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St.Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Tanel Traks
- Department of Dermatology and Venereology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Gunter Assmann
- RUB University Hospital JWK Minden, Department of Rheumatology, Minden, Germany
- Jose-Carreras Centrum for Immuno- and Gene Therapy, University of Saarland Medical School, Homburg, Germany
| | - David Baudry
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Frank Behrens
- Division of Translational Rheumatology, Immunology - Inflammation Medicine, University Hospital, Goethe University, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-mediated Diseases CIMD, Frankfurt am Main, Germany
- Division of Rheumatology, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Allison C Billi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matthew A Brown
- Department of Medical & Molecular Genetics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- Genomics England, Canary Wharf, London, UK
| | - Harald Burkhardt
- Division of Rheumatology, University Hospital, Goethe University, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-mediated Diseases CIMD, Frankfurt am Main, Germany
| | - Francesca Capon
- Department of Medical & Molecular Genetics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Raymond Chung
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Denmark Hill, Camberwell, London, UK
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley Hospital, London, UK
| | - Charles J Curtis
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Denmark Hill, Camberwell, London, UK
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley Hospital, London, UK
| | - Michael Duckworth
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Oliver FitzGerald
- UCD School of Medicine and Medical Sciences and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland
| | - Sascha Gerdes
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Christopher E M Griffiths
- Centre for Dermatology Research, University of Manchester, NIHR Manchester Biomedical Research Centre, Manchester, UK
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- Department of Dermatology, King's College Hospital NHS Foundation Trust, London, UK
| | | | - Philip Helliwell
- National Institute for Health and Care Research (NIHR) Leeds Biomedical Research Centre, Leeds Teaching Hospitals Trust, UK
- Leeds Institute of Rheumatic and Musculoskeletal Disease, University of Leeds, UK
| | - Pauline Ho
- Centre for Genetics and Genomics Versus Arthritis, The University of Manchester, Manchester, UK
- National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre, The University of Manchester, Manchester, UK
- The Kellgren Centre for Rheumatology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oddgeir L Holmen
- HUNT Research Centre, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Zhi-Ming Huang
- Deparment of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Deepak Jadon
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Michaela Köhm
- Division of Translational Rheumatology, Immunology - Inflammation Medicine, University Hospital, Goethe University, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence Immune-mediated Diseases CIMD, Frankfurt am Main, Germany
- Division of Rheumatology, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Céline Lamacchia
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Sang Hyuck Lee
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Denmark Hill, Camberwell, London, UK
- National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley Hospital, London, UK
| | - Feiyang Ma
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- St John's Institute of Dermatology, Guy's and St Thomas' National Health Service (NHS) Foundation Trust, London, UK
| | - Neil McHugh
- Royal National Hospital for Rheumatic Diseases and Dept Pharmacy and Pharmacology, University of Bath, UK
| | - Ross McManus
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Ellen H Modalsli
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Dermatology, Clinic of Orthopedy, Rheumatology and Dermatology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Michael J Nissen
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Vinzenz Oji
- Department of Dermatology, University of Münster, Münster, Germany
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Andreas Ramming
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jürgen Rech
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Cheryl Rosen
- Division of Dermatology, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Georg Schett
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Börge Schmidt
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Heiko Traupe
- Department of Dermatology, University of Münster, Münster, Germany
| | - John J Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eike Matthias Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Richard B Warren
- Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, UK
- Centre for Dermatology Research, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M6 8HD, UK
| | - Rachael Wasikowski
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Xiaoquan Wen
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Zhaolin Zhang
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, The University of Manchester, Manchester, UK
- National Institute for Health and Care Research (NIHR) Manchester Biomedical Research Centre, The University of Manchester, Manchester, UK
- The Kellgren Centre for Rheumatology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Vinod Chandran
- Schroeder Arthritis Institute, Krembil Research Institute, and Toronto Western Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John Foerster
- College of Medicine, Dentistry, and Nursing, University of Dundee, Dundee, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Dafna D Gladman
- Schroeder Arthritis Institute, Krembil Research Institute, and Toronto Western Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wayne Gulliver
- Newlab Clinical Research Inc, St. John's, NL, Canada
- Department of Dermatology, Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Külli Kingo
- Department of Dermatology and Venereology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Wilson Liao
- Deparment of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Mari Løset
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Dermatology, Clinic of Orthopedy, Rheumatology and Dermatology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Catherine H Smith
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- St John's Institute of Dermatology, Guy's and St Thomas' National Health Service (NHS) Foundation Trust, London, UK
| | - Paola Di Meglio
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- St John's Institute of Dermatology, Guy's and St Thomas' National Health Service (NHS) Foundation Trust, London, UK
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Simpson
- Department of Medical & Molecular Genetics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
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Ogawa K, Tsoi LC, Tanaka H, Kanai M, Stuart PE, Nair RP, Tanaka Y, Mochizuki H, Elder JT, Okada Y. A Cross-Trait Genetic Correlation Study Identified Eight Diseases and Traits Associated with Psoriasis. J Invest Dermatol 2023; 143:1813-1816.e2. [PMID: 36906125 DOI: 10.1016/j.jid.2023.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 03/13/2023]
Affiliation(s)
- Kotaro Ogawa
- Department of Statistical Genetics, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan; Department of Neurology, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hiroaki Tanaka
- Department of Statistical Genetics, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan; The First Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Masahiro Kanai
- Department of Statistical Genetics, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan; Analytic and Translational Genetics Unit, Massachusetts General Hospital & Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan; Department of Genome Informatics, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan; Laboratory of Statistical Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
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Patrick MT, Nair RP, He K, Stuart PE, Billi AC, Zhou X, Gudjonsson JE, Oksenberg JR, Elder JT, Tsoi LC. Shared Genetic Risk Factors for Multiple Sclerosis/Psoriasis Suggest Involvement of Interleukin-17 and Janus Kinase-Signal Transducers and Activators of Transcription Signaling. Ann Neurol 2023; 94:384-397. [PMID: 37127916 PMCID: PMC10524664 DOI: 10.1002/ana.26672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/03/2023]
Abstract
OBJECTIVE Psoriasis and multiple sclerosis (MS) are complex immune diseases that are mediated by T cells and share multiple comorbidities. Previous studies have suggested psoriatic patients are at higher risk of MS; however, causal relationships between the two conditions remain unclear. Through epidemiology and genetics, we provide a comprehensive understanding of the relationship, and share molecular factors between psoriasis and MS. METHODS We used logistic regression, trans-disease meta-analysis and Mendelian randomization. Medical claims data were included from 30 million patients, including 141,544 with MS and 742,919 with psoriasis. We used genome-wide association study summary statistics from 11,024 psoriatic, 14,802 MS cases, and 43,039 controls for trans-disease meta-analysis, with additional summary statistics from 5 million individuals for Mendelian randomization. RESULTS Psoriatic patients have a significantly higher risk of MS (4,637 patients with both diseases; odds ratio [OR] 1.07, p = 1.2 × 10-5 ) after controlling for potential confounders. Using inverse variance and equally weighted trans-disease meta-analysis, we revealed >20 shared and opposing (direction of effect) genetic loci outside the major histocompatibility complex that showed significant genetic colocalization (in COLOC and COLOC-SuSiE v5.1.0). Co-expression analysis of genes from these loci further identified distinct clusters that were enriched among pathways for interleukin-17/tumor necrosis factor-α (OR >39, p < 1.6 × 10-3 ) and Janus kinase-signal transducers and activators of transcription (OR 35, p = 1.1 × 10-5 ), including genes, such as TNFAIP3, TYK2, and TNFRSF1A. Mendelian randomization found psoriasis as an exposure has a significant causal effect on MS (OR 1.04, p = 5.8 × 10-3 ), independent of type 1 diabetes (OR 1.05, p = 4.3 × 10-7 ), type 2 diabetes (OR 1.08, p = 2.3 × 10-3 ), inflammatory bowel disease (OR 1.11, p = 1.6 × 10-11 ), and vitamin D level (OR 0.75, p = 9.4 × 10-3 ). INTERPRETATION By investigating the shared genetics of psoriasis and MS, along with their modifiable risk factors, our findings will advance innovations in treatment for patients suffering from comorbidities. ANN NEUROL 2023;94:384-397.
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Affiliation(s)
- Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kevin He
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Allison C. Billi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Xiang Zhou
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, California, United States of America
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
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5
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Martin S, Tyrrell J, Thomas EL, Bown MJ, Wood AR, Beaumont RN, Tsoi LC, Stuart PE, Elder JT, Law P, Houlston R, Kabrhel C, Papadimitriou N, Gunter M, Bull C, Bell JA, Vincent EE, Sattar N, Dunlop MG, Tomlinson IPM, Lindström S, Bell JD, Frayling T, Yaghootkar H. Correction: Disease consequences of higher adiposity uncoupled from its adverse metabolic effects using Mendelian randomisation. eLife 2022; 11:e80233. [PMID: 35583923 PMCID: PMC9116939 DOI: 10.7554/elife.80233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
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6
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Martin S, Tyrrell J, Thomas EL, Bown MJ, Wood AR, Beaumont RN, Tsoi LC, Stuart PE, Elder JT, Law P, Houlston R, Kabrhel C, Papadimitriou N, Gunter MJ, Bull CJ, Bell JA, Vincent EE, Sattar N, Dunlop MG, Tomlinson IPM, Lindström S, Bell JD, Frayling TM, Yaghootkar H. Disease consequences of higher adiposity uncoupled from its adverse metabolic effects using Mendelian randomisation. eLife 2022; 11:e72452. [PMID: 35074047 PMCID: PMC8789289 DOI: 10.7554/elife.72452] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Background Some individuals living with obesity may be relatively metabolically healthy, whilst others suffer from multiple conditions that may be linked to adverse metabolic effects or other factors. The extent to which the adverse metabolic component of obesity contributes to disease compared to the non-metabolic components is often uncertain. We aimed to use Mendelian randomisation (MR) and specific genetic variants to separately test the causal roles of higher adiposity with and without its adverse metabolic effects on diseases. Methods We selected 37 chronic diseases associated with obesity and genetic variants associated with different aspects of excess weight. These genetic variants included those associated with metabolically 'favourable adiposity' (FA) and 'unfavourable adiposity' (UFA) that are both associated with higher adiposity but with opposite effects on metabolic risk. We used these variants and two sample MR to test the effects on the chronic diseases. Results MR identified two sets of diseases. First, 11 conditions where the metabolic effect of higher adiposity is the likely primary cause of the disease. Here, MR with the FA and UFA genetics showed opposing effects on risk of disease: coronary artery disease, peripheral artery disease, hypertension, stroke, type 2 diabetes, polycystic ovary syndrome, heart failure, atrial fibrillation, chronic kidney disease, renal cancer, and gout. Second, 9 conditions where the non-metabolic effects of excess weight (e.g. mechanical effect) are likely a cause. Here, MR with the FA genetics, despite leading to lower metabolic risk, and MR with the UFA genetics, both indicated higher disease risk: osteoarthritis, rheumatoid arthritis, osteoporosis, gastro-oesophageal reflux disease, gallstones, adult-onset asthma, psoriasis, deep vein thrombosis, and venous thromboembolism. Conclusions Our results assist in understanding the consequences of higher adiposity uncoupled from its adverse metabolic effects, including the risks to individuals with high body mass index who may be relatively metabolically healthy. Funding Diabetes UK, UK Medical Research Council, World Cancer Research Fund, National Cancer Institute.
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Affiliation(s)
- Susan Martin
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
| | - E Louise Thomas
- Research Centre for Optimal Health, School of Life Sciences, University of WestminsterLondonUnited Kingdom
| | - Matthew J Bown
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research CentreLeicesterUnited Kingdom
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
| | - Lam C Tsoi
- Department of Dermatology, University of MichiganAnn ArborUnited States
| | - Philip E Stuart
- Department of Dermatology, University of MichiganAnn ArborUnited States
| | - James T Elder
- Department of Dermatology, University of MichiganAnn ArborUnited States
- Ann Arbor Veterans Affairs HospitalAnn ArborUnited States
| | - Philip Law
- The Institute of Cancer ResearchLondonUnited Kingdom
| | | | - Christopher Kabrhel
- Department of Emergency Medicine, Massachusetts General HospitalBostonUnited States
- Department of Emergency Medicine, Harvard Medical SchoolBostonUnited States
| | - Nikos Papadimitriou
- Nutrition and Metabolism Branch, International Agency for Research on CancerLyonFrance
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on CancerLyonFrance
| | - Caroline J Bull
- MRC Integrative Epidemiology Unit at the University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical School, University of BristolBristolUnited Kingdom
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Joshua A Bell
- MRC Integrative Epidemiology Unit at the University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical School, University of BristolBristolUnited Kingdom
| | - Emma E Vincent
- MRC Integrative Epidemiology Unit at the University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical School, University of BristolBristolUnited Kingdom
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Malcolm G Dunlop
- University of EdinburghEdinburghUnited Kingdom
- Western General HospitalEdinburghUnited Kingdom
| | - Ian PM Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of EdinburghEdinburghUnited Kingdom
| | - Sara Lindström
- Department of Epidemiology, University of WashingtonSeattleUnited States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | | | - Jimmy D Bell
- Research Centre for Optimal Health, School of Life Sciences, University of WestminsterLondonUnited Kingdom
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter HospitalExeterUnited Kingdom
- Research Centre for Optimal Health, School of Life Sciences, University of WestminsterLondonUnited Kingdom
- Centre for Inflammation Research and Translational Medicine (CIRTM), Department of Life Sciences, Brunel University LondonUxbridgeUnited Kingdom
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7
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Stuart PE, Tsoi LC, Nair RP, Ghosh M, Kabra M, Shaiq PA, Raja GK, Qamar R, Thelma B, Patrick MT, Parihar A, Singh S, Khandpur S, Kumar U, Wittig M, Degenhardt F, Tejasvi T, Voorhees JJ, Weidinger S, Franke A, Abecasis GR, Sharma VK, Elder JT. Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide. HGG Adv 2022; 3:100069. [PMID: 34927100 PMCID: PMC8682265 DOI: 10.1016/j.xhgg.2021.100069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/24/2021] [Indexed: 02/06/2023] Open
Abstract
Because transethnic analysis may facilitate prioritization of causal genetic variants, we performed a genomewide association study (GWAS) of psoriasis in South Asians (SAS), consisting of 2,590 cases and 1,720 controls. Comparison with our existing European-origin (EUR) GWAS showed that effect sizes of known psoriasis signals were highly correlated in SAS and EUR (Spearman ρ = 0.78; p < 2 × 10-14). Transethnic meta-analysis identified two non-MHC psoriasis loci (1p36.22 and 1q24.2) not previously identified in EUR, which may have regulatory roles. For these two loci, the transethnic GWAS provided higher genetic resolution and reduced the number of potential causal variants compared to using the EUR sample alone. We then explored multiple strategies to develop reference panels for accurately imputing MHC genotypes in both SAS and EUR populations and conducted a fine-mapping of MHC psoriasis associations in SAS and the largest such effort for EUR. HLA-C*06 was the top-ranking MHC locus in both populations but was even more prominent in SAS based on odds ratio, disease liability, model fit and predictive power. Transethnic modeling also substantially boosted the probability that the HLA-C*06 protein variant is causal. Secondary MHC signals included coding variants of HLA-C and HLA-B, but also potential regulatory variants of these two genes as well as HLA-A and several HLA class II genes, with effects on both chromatin accessibility and gene expression. This study highlights the shared genetic basis of psoriasis in SAS and EUR populations and the value of transethnic meta-analysis for discovery and fine-mapping of susceptibility loci.
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Affiliation(s)
- Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI, USA
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Manju Ghosh
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Pakeeza A. Shaiq
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Ghazala K. Raja
- Department of Biochemistry, PMASAA University, Rawalpindi, Pakistan
| | - Raheel Qamar
- COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - B.K. Thelma
- Department of Genetics, University of Delhi South Campus, 110021 New Delhi, India
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita Parihar
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sonam Singh
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Sujay Khandpur
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Michael Wittig
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - John J. Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephan Weidinger
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Goncalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vinod K. Sharma
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, India
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
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8
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Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schönherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YDI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B, McLaren PJ, Raychaudhuri S. Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 2021; 53:1722. [PMID: 34728834 PMCID: PMC8978071 DOI: 10.1038/s41588-021-00979-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Masahiro Kanai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Xinyi Li
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research,North Short LIJ Health System, Manhasset, NY, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - David W Haas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Adolfo Correa
- Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Paul J McLaren
- J.C. Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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9
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Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schönherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YDI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B, McLaren PJ, Raychaudhuri S. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 2021; 53:1504-1516. [PMID: 34611364 PMCID: PMC8959399 DOI: 10.1038/s41588-021-00935-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [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: 07/14/2020] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.
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Affiliation(s)
- Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Masahiro Kanai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Xinyi Li
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research,North Short LIJ Health System, Manhasset, NY, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - David W Haas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Adolfo Correa
- Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Paul J McLaren
- J.C. Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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10
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Patrick MT, Stuart PE, Zhang H, Zhao Q, Yin X, He K, Zhou XJ, Mehta NN, Voorhees JJ, Boehnke M, Gudjonsson JE, Nair RP, Handelman SK, Elder JT, Liu DJ, Tsoi LC. Causal Relationship and Shared Genetic Loci between Psoriasis and Type 2 Diabetes through Trans-Disease Meta-Analysis. J Invest Dermatol 2020; 141:1493-1502. [PMID: 33385400 DOI: 10.1016/j.jid.2020.11.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023]
Abstract
Psoriasis and type 2 diabetes (T2D) are complex conditions with significant impacts on health. Patients with psoriasis have a higher risk of T2D (∼1.5 OR) and vice versa, controlling for body mass index; yet, there has been a limited study comparing their genetic architecture. We hypothesized that there are shared genetic components between psoriasis and T2D. Trans-disease meta-analysis was applied to 8,016,731 well-imputed genetic markers from large-scale meta-analyses of psoriasis (11,024 cases and 16,336 controls) and T2D (74,124 cases and 824,006 controls), adjusted for body mass index. We confirmed our findings in a hospital-based study (42,112 patients) and tested for causal relationships with multivariable Mendelian randomization. Mendelian randomization identified a causal relationship between psoriasis and T2D (P = 1.6 × 10‒4, OR = 1.01) and highlighted the impact of body mass index. Trans-disease meta-analysis further revealed four genome-wide significant loci (P < 5 × 10‒8) with evidence of colocalization and shared directions of effect between psoriasis and T2D not present in body mass index. The proteins coded by genes in these loci (ACTR2, ERLIN1, TRMT112, and BECN1) are connected through NF-κB signaling. Our results provide insight into the immunological components that connect immune-mediated skin conditions and metabolic diseases, independent of confounding factors.
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Affiliation(s)
- Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Haihan Zhang
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Qingyuan Zhao
- Statistical Laboratory, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Xianyong Yin
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kevin He
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Beijing, China
| | - Nehal N Mehta
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Samuel K Handelman
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Pennsylvania, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor Michigan, USA.
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11
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Xia J, Xie SY, Liu KQ, Xu L, Zhao PP, Gai SR, Guan PL, Zhao JQ, Zhu YP, Tsoi LC, Stuart PE, Nair RP, Yang HQ, Liao YT, Mao K, Qiu MC, Ying ZM, Hu B, Yang ZH, Bai WY, Zhu XW, Cong PK, Elder JT, Ye ZM, Wang B, Zheng HF. Systemic evaluation of the relationship between psoriasis, psoriatic arthritis and osteoporosis: observational and Mendelian randomisation study. Ann Rheum Dis 2020; 79:1460-1467. [PMID: 32737104 PMCID: PMC7970448 DOI: 10.1136/annrheumdis-2020-217892] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVES AND METHODS With 432 513 samples from UK Biobank dataset, multivariable linear/logistic regression were used to estimate the relationship between psoriasis/psoriatic arthritis (PsA) and estimated bone mineral density (eBMD)/osteoporosis, controlling for potential confounders. Here, confounders were set in three ways: model0 (including age, height, weight, smoking and drinking), model1 (model0 +regular physical activity) and model2 (model1 +medication treatments). The eBMD was derived from heel ultrasound measurement. And 4904 patients with psoriasis and 847 patients with PsA were included in final analysis. Mendelian randomisation (MR) approach was used to evaluate the causal effect between them. RESULTS Lower eBMD were observed in patients with PsA than in controls in both model0 (β-coefficient=-0.014, p=0.0006) and model1 (β-coefficient=-0.013, p=0.002); however, the association disappeared when conditioning on treatment with methotrexate or ciclosporin (model2) (β-coefficient=-0.005, p=0.28), mediation analysis showed that 63% of the intermediary effect on eBMD was mediated by medication treatment (p<2E-16). Patients with psoriasis without arthritis showed no difference of eBMD compared with controls. Similarly, the significance of higher risk of osteopenia in patients with PsA (OR=1.27, p=0.002 in model0) could be eliminated by conditioning on medication treatment (p=0.244 in model2). Psoriasis without arthritis was not related to osteopenia and osteoporosis. The weighted Genetic Risk Score analysis found that genetically determined psoriasis/PsA were not associated with eBMD (p=0.24 and p=0.88). Finally, MR analysis showed that psoriasis/PsA had no causal effect on eBMD, osteoporosis and fracture. CONCLUSIONS The effect of PsA on osteoporosis was secondary (eg, medication) but not causal. Under this hypothesis, psoriasis without arthritis was not a risk factor for osteoporosis.
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Affiliation(s)
- Jiangwei Xia
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Shu-Yang Xie
- Binzhou Medical University, Yantai, Shandong, 264003, China
| | - Ke-Qi Liu
- Jiangxi Medical College, Shangrao, Jiangxi, China
| | - Lin Xu
- Binzhou Medical University, Yantai, Shandong, 264003, China
| | - Pian-Pian Zhao
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Si-Rui Gai
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Peng-Lin Guan
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Jin-Qiu Zhao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan-Ping Zhu
- Binzhou Medical University, Yantai, Shandong, 264003, China
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States
| | - Philip E. Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States
| | - Han-Qi Yang
- School of Public Health, Boston University, Boston, Massachusetts, 02118, United States
| | - Yu-Ting Liao
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kaijing Mao
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mo-Chang Qiu
- Jiangxi Medical College, Shangrao, Jiangxi, China
| | - Zhi-Min Ying
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Bin Hu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Zhi-Hua Yang
- Department of Orthopedic Surgery, Zhejiang Xiaoshan hospital, Hangzhou, Zhejiang, China
| | - Wei-Yang Bai
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Xiao-Wei Zhu
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Pei-Kuan Cong
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, United States
| | - Zhao-Ming Ye
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Bin Wang
- Binzhou Medical University, Yantai, Shandong, 264003, China
| | - Hou-Feng Zheng
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China,Instituteof Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
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12
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Patrick MT, Stuart PE, Raja K, Chi S, He Z, Voorhees JJ, Tejasvi T, Gudjonsson JE, Kahlenberg JM, Chandran V, Rahman P, Gladman DD, Nair RP, Elder JT, Tsoi LC. Integrative Approach to Reveal Cell Type Specificity and Gene Candidates for Psoriatic Arthritis Outside the MHC. Front Genet 2019; 10:304. [PMID: 31031798 PMCID: PMC6470186 DOI: 10.3389/fgene.2019.00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
We recently conducted a large association analysis to compare the genetic profiles between patients with psoriatic arthritis (PsA) and cutaneous-only psoriasis (PsC). Despite including over 7,000 genotyped patients, only the MHC achieved genome-wide significance. In this study, we hypothesized that appropriate epigenomic elements (H3K27ac marks for active enhancers) can guide us to reveal valuable information about the loci with suggestive evidence of association. Our aim is to investigate these loci and explore how they may lead to the development of PsA. We evaluated this potential by investigating the genes connected with these loci from the perspective of pharmacogenomics and gene expression. We illustrated that markers with suggestive evidence of association outside the MHC region are enriched in H3K27ac marks for osteoblast and chondrogenic differentiated cells; using pharmacogenomics resources, we showed that genes near these markers are targeted by existing drugs used to treat psoriatic arthritis. Significantly, six of the ten suggestive significant loci overlapping the regulatory elements encompass genes differentially expressed (FDR < 5%) in differentiated osteoblasts, including genes participating in the Wnt signaling such as RUNX1, FUT8, and CTNNAL1. Our approach shows that epigenomic information can be used as cost-effective approach to enhance the inferences for GWAS results, especially in situations when few genome-wide significant loci are available. Our results also point the way to more directed investigations comparing the genetics of PsA and PsC.
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Affiliation(s)
- Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kalpana Raja
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Morgridge Institute for Research, Madison, WI, United States
| | - Sunyi Chi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Zhi He
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
| | - John J. Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, United States
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - J. Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Vinod Chandran
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Proton Rahman
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Dafna D. Gladman
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Centre for Prognosis Studies in the Rheumatic Diseases, Krembil Research Institute, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
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13
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Ogawa K, Stuart PE, Tsoi LC, Suzuki K, Nair RP, Mochizuki H, Elder JT, Okada Y. A Transethnic Mendelian Randomization Study Identifies Causality of Obesity on Risk of Psoriasis. J Invest Dermatol 2018; 139:1397-1400. [PMID: 30528826 DOI: 10.1016/j.jid.2018.11.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
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14
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Lambert S, Hambro CA, Johnston A, Stuart PE, Tsoi LC, Nair RP, Elder JT. Neutrophil Extracellular Traps Induce Human Th17 Cells: Effect of Psoriasis-Associated TRAF3IP2 Genotype. J Invest Dermatol 2018; 139:1245-1253. [PMID: 30528823 DOI: 10.1016/j.jid.2018.11.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/08/2018] [Accepted: 11/23/2018] [Indexed: 01/14/2023]
Abstract
Psoriasis lesions are rich in IL-17-producing T cells as well as neutrophils, which release webs of DNA-protein complexes known as neutrophil extracellular traps (NETs). Because we and others have observed increased NETosis in psoriatic lesions, we hypothesized that NETs contribute to increased T helper type 17 (Th17) cells in psoriasis. After stimulating peripheral blood mononuclear cells with anti-CD3/CD28 beads for 7 days, we found significantly higher percentages of CD3+CD4+IL-17+ (Th17) cells in the presence versus absence of NETs, as assessed by flow cytometry, IL-17 ELISA, and IL17A/F and RORC mRNAs. Memory, but not naïve, T cells were competent and monocytes were required for CD3/CD28-mediated Th17 induction, with or without NETs. Th17 induction was enhanced by the T allele of rs33980500 (T/C), a psoriasis risk-associated variant in the TRAF3IP2 gene encoding the D10N variant of Act1, a key mediator of IL-17 signal transduction. Global transcriptome analysis of CD3/CD28-stimulated peripheral blood mononuclear cells by RNA sequencing confirmed the stimulatory effects of NETs, demonstrated NET-induced enhancement of cytokine gene expression, and verified that the effect of Act1 D10N was greater in the presence of NETs. Collectively, these results implicate NETs and the Act1 D10N variant in human Th17 induction from peripheral blood mononuclear cells, with ramifications for immunogenetic studies of psoriasis and other autoimmune diseases.
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Affiliation(s)
- Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Caely A Hambro
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA.
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15
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Enerbäck C, Sandin C, Lambert S, Zawistowski M, Stuart PE, Verma D, Tsoi LC, Nair RP, Johnston A, Elder JT. The psoriasis-protective TYK2 I684S variant impairs IL-12 stimulated pSTAT4 response in skin-homing CD4+ and CD8+ memory T-cells. Sci Rep 2018; 8:7043. [PMID: 29728633 PMCID: PMC5935702 DOI: 10.1038/s41598-018-25282-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 10/24/2017] [Accepted: 04/16/2018] [Indexed: 01/11/2023] Open
Abstract
Tyrosine kinase 2 (TYK2) belongs to the Janus kinase (JAK) family of tyrosine kinases, which transmit signals from activated cytokine receptors. GWAS have consistently implicated TYK2 in psoriasis susceptibility. We performed an in-depth association analysis of TYK2 using GWAS and resequencing data. Strong genetic association of three nonsynonymous variants in the exonic regions of the TYK2 gene (rs34536443, rs12720356, and rs2304256) were found. rs12720356 encoding I684S is predicted to be deleterious based on its location in the pseudokinase domain. We analyzed PBMCs from 29 individuals representing the haplotypes containing each of the significantly associated signals. STAT4 phosphorylation was evaluated by phospho-flow cytometry after CD3/CD28 activation of cells followed by IL-12 stimulation. Individuals carrying the protective I684S variant manifested significantly reduced p-STAT4 levels in CD4 + CD25 + CD45RO+ (mean Stimulation Index (S.I.) 48.08, n = 10) and CD8 + CD25 + CD45RO + cells (S.I. 55.71, n = 10), compared to controls homozygous for the ancestral haplotype (S.I. 68.19, n = 10 (p = 0.002) and 76.76 n = 10 (p = 0.0008) respectively). Reduced p-STAT4 levels were also observed in skin-homing, cutaneous lymphocyte associated antigen (CLA)-positive CD4 and CD8 cells from I684S carriers. No significant changes in p-STAT4 for the psoriasis-associated variant rs34536443 was found. These data establish the functional significance of the TYK2 I684S variant in psoriasis susceptibility.
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Affiliation(s)
- C Enerbäck
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA. .,Ingrid Asp Psoriasis Research Center, Department of Dermatology, Linköping University, Linköping, Sweden.
| | - C Sandin
- Ingrid Asp Psoriasis Research Center, Department of Dermatology, Linköping University, Linköping, Sweden
| | - S Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - M Zawistowski
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - P E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - D Verma
- Ingrid Asp Psoriasis Research Center, Department of Dermatology, Linköping University, Linköping, Sweden
| | - L C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - R P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - A Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - J T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA.,Ann Arbor Veterans Affairs Health System, Ann Arbor, MI, USA
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16
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Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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17
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Mehta NN, Teague HL, Swindell WR, Baumer Y, Ward NL, Xing X, Baugous B, Johnston A, Joshi AA, Silverman J, Barnes DH, Wolterink L, Nair RP, Stuart PE, Playford M, Voorhees JJ, Sarkar MK, Elder JT, Gallagher K, Ganesh SK, Gudjonsson JE. IFN-γ and TNF-α synergism may provide a link between psoriasis and inflammatory atherogenesis. Sci Rep 2017; 7:13831. [PMID: 29062018 PMCID: PMC5653789 DOI: 10.1038/s41598-017-14365-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [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: 05/30/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Chronic inflammation is a critical component of atherogenesis, however, reliable human translational models aimed at characterizing these mechanisms are lacking. Psoriasis, a chronic inflammatory skin disease associated with increased susceptibility to atherosclerosis, provides a clinical human model that can be utilized to investigate the links between chronic inflammation and atherosclerosis development. We sought to investigate key biological processes in psoriasis skin and human vascular tissue to identify biological components that may promote atherosclerosis in chronic inflammatory conditions. Using a bioinformatics approach of human skin and vascular tissue, we determined IFN-γ and TNF-α are the dominant pro-inflammatory signals linking atherosclerosis and psoriasis. We then stimulated primary aortic endothelial cells and ex-vivo atherosclerotic tissue with IFN-γ and TNF-α and found they synergistically increased monocyte and T-cell chemoattractants, expression of adhesion molecules on the endothelial cell surface, and decreased endothelial barrier integrity in vitro, therefore increasing permeability. Our data provide strong evidence of synergism between IFN-γ and TNF- α in inflammatory atherogenesis and provide rationale for dual cytokine antagonism in future studies.
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Affiliation(s)
- Nehal N Mehta
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Heather L Teague
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yvonne Baumer
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Xianying Xing
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Brooke Baugous
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Andrew Johnston
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Aditya A Joshi
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joanna Silverman
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Drew H Barnes
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Liza Wolterink
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Rajan P Nair
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Philip E Stuart
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Martin Playford
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John J Voorhees
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Mrinal K Sarkar
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Katherine Gallagher
- Department of Surgery, Division of Vascular Surgery, Univ. of Michigan, Ann Arbor, MI, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, and Department of Human Genetics, Univ. of Michigan, Ann Arbor, MI, USA
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18
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Niehues H, Tsoi LC, van der Krieken DA, Jansen PAM, Oortveld MAW, Rodijk-Olthuis D, van Vlijmen IMJJ, Hendriks WJAJ, Helder RW, Bouwstra JA, van den Bogaard EH, Stuart PE, Nair RP, Elder JT, Zeeuwen PLJM, Schalkwijk J. Psoriasis-Associated Late Cornified Envelope (LCE) Proteins Have Antibacterial Activity. J Invest Dermatol 2017. [PMID: 28634035 DOI: 10.1016/j.jid.2017.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terminally differentiating epidermal keratinocytes express a large number of structural and antimicrobial proteins that are involved in the physical barrier function of the stratum corneum and provide innate cutaneous host defense. Late cornified envelope (LCE) genes, located in the epidermal differentiation complex on chromosome 1, encode a family of 18 proteins of unknown function, whose expression is largely restricted to epidermis. Deletion of two members, LCE3B and LCE3C (LCE3B/C-del), is a widely-replicated psoriasis risk factor that interacts with the major psoriasis-psoriasis risk gene HLA-C*06. Here we performed quantitative trait locus analysis, utilizing RNA-seq data from human skin and found that LCE3B/C-del was associated with a markedly increased expression of LCE3A, a gene directly adjacent to LCE3B/C-del. We confirmed these findings in a 3-dimensional skin model using primary keratinocytes from LCE3B/C-del genotyped donors. Functional analysis revealed that LCE3 proteins, and LCE3A in particular, have defensin-like antimicrobial activity against a variety of bacterial taxa at low micromolar concentrations. No genotype-dependent effect was observed for the inside-out or outside-in physical skin barrier function. Our findings identify an unknown biological function for LCE3 proteins and suggest a role in epidermal host defense and LCE3B/C-del-mediated psoriasis risk.
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Affiliation(s)
- Hanna Niehues
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Danique A van der Krieken
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Patrick A M Jansen
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Merel A W Oortveld
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Diana Rodijk-Olthuis
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Ivonne M J J van Vlijmen
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Wiljan J A J Hendriks
- Department of Cell Biology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Richard W Helder
- Leiden Academic Center for Drug Research, Department of Drug Delivery Technology, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
| | - Joke A Bouwstra
- Leiden Academic Center for Drug Research, Department of Drug Delivery Technology, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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19
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Tsoi LC, Stuart PE, Tian C, Gudjonsson JE, Das S, Zawistowski M, Ellinghaus E, Barker JN, Chandran V, Dand N, Duffin KC, Enerbäck C, Esko T, Franke A, Gladman DD, Hoffmann P, Kingo K, Kõks S, Krueger GG, Lim HW, Metspalu A, Mrowietz U, Mucha S, Rahman P, Reis A, Tejasvi T, Trembath R, Voorhees JJ, Weidinger S, Weichenthal M, Wen X, Eriksson N, Kang HM, Hinds DA, Nair RP, Abecasis GR, Elder JT. Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants. Nat Commun 2017; 8:15382. [PMID: 28537254 PMCID: PMC5458077 DOI: 10.1038/ncomms15382] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Psoriasis is a complex disease of skin with a prevalence of about 2%. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for psoriasis to date, including data from eight different Caucasian cohorts, with a combined effective sample size >39,000 individuals. We identified 16 additional psoriasis susceptibility loci achieving genome-wide significance, increasing the number of identified loci to 63 for European-origin individuals. Functional analysis highlighted the roles of interferon signalling and the NFκB cascade, and we showed that the psoriasis signals are enriched in regulatory elements from different T cells (CD8+ T-cells and CD4+ T-cells including TH0, TH1 and TH17). The identified loci explain ∼28% of the genetic heritability and generate a discriminatory genetic risk score (AUC=0.76 in our sample) that is significantly correlated with age at onset (p=2 × 10-89). This study provides a comprehensive layout for the genetic architecture of common variants for psoriasis.
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Affiliation(s)
- Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Computational Medicine &Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Chao Tian
- 23andMe, Inc., Mountain View, California 94041, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Sayantan Das
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Jonathan N Barker
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, UK
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Centre for Prognosis Studies in the Rheumatic Diseases, Toronto Western Research Institute, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Nick Dand
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, UK
| | | | - Charlotta Enerbäck
- Department of Dermatology, Linköping University, Linköping SE-581 83, Sweden
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Centre for Prognosis Studies in the Rheumatic Diseases, Toronto Western Research Institute, University of Toronto, Toronto, Ontario, Canada M5T 2S8
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn 53127, Germany.,Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel 4031, Switzerland
| | - Külli Kingo
- Dermatology Clinic, Tartu University Hospital, Department of Dermatology and Venereology, University of Tartu, Tartu 50417, Estonia
| | - Sulev Kõks
- Department of Pathophysiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, Tartu 50411, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, Utah 84132, USA
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Ulrich Mrowietz
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Proton Rahman
- Memorial University, St. John's, Newfoundland, Newfoundland and Labrador, Canada A1B 3X9
| | - Andre Reis
- Institute of Human Genetics, FAU Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA
| | - Richard Trembath
- Department of Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK
| | - John J Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Stephan Weidinger
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Xiaoquan Wen
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA
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20
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Budu-Aggrey A, Bowes J, Stuart PE, Zawistowski M, Tsoi LC, Nair R, Jadon DR, McHugh N, Korendowych E, Elder JT, Barton A, Raychaudhuri S. A rare coding allele in IFIH1 is protective for psoriatic arthritis. Ann Rheum Dis 2017; 76:1321-1324. [PMID: 28501801 PMCID: PMC5530346 DOI: 10.1136/annrheumdis-2016-210592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/01/2017] [Accepted: 03/12/2017] [Indexed: 12/18/2022]
Abstract
Objectives Psoriatic arthritis (PsA) is an inflammatory arthritis associated with psoriasis. While many common risk alleles have been reported for association with PsA as well as psoriasis, few rare coding alleles have yet been identified. Methods To identify rare coding variation associated with PsA risk or protection, we genotyped 41 267 variants with the exome chip and investigated association within an initial cohort of 1980 PsA cases and 5913 controls. Genotype data for an independent cohort of 2234 PsA cases and 5708 controls was also made available, allowing for a meta-analysis to be performed with the discovery dataset. Results We identified an association with the rare variant rs35667974 (p=2.39x10−6, OR=0.47), encoding an Ile923Val amino acid change in the IFIH1 gene protein product. The association was reproduced in our independent cohort, which reached a high level of significance on meta-analysis with the discovery and replication datasets (p=4.67x10−10). We identified a strong association with IFIH1 when performing multiple-variant analysis (p=6.77x10−6), and found evidence of independent effects between the rare allele and the common PsA variant at the same locus. Conclusion For the first time, we report a rare coding allele in IFIH1 to be protective for PsA. This rare allele has also been identified to have the same direction of effect on type I diabetes and psoriasis. While this association further supports existing evidence for IFIH1 as a causal gene for PsA, mechanistic studies will need to be pursued to confirm that IFIH1 is indeed causal.
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Affiliation(s)
- Ashley Budu-Aggrey
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester Foundation Trust and University of Manchester, Manchester Academy of Health Sciences, Manchester, UK
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Deepak Rohit Jadon
- Royal National Hospital for Rheumatic Diseases, University of Bath, Bath, UK.,Department of Rheumatology, Cambridge University Hospitals NHSFT, Cambridge, UK
| | - Neil McHugh
- Royal National Hospital for Rheumatic Diseases, University of Bath, Bath, UK.,Department of Pharmacy and Parmacology, University of Bath, Bath, UK
| | - Eleanor Korendowych
- Royal National Hospital for Rheumatic Diseases, University of Bath, Bath, UK
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester Foundation Trust and University of Manchester, Manchester Academy of Health Sciences, Manchester, UK
| | - Soumya Raychaudhuri
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester Foundation Trust and University of Manchester, Manchester Academy of Health Sciences, Manchester, UK.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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21
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Liang Y, Tsoi LC, Xing X, Beamer MA, Swindell WR, Sarkar MK, Berthier CC, Stuart PE, Harms PW, Nair RP, Elder JT, Voorhees JJ, Kahlenberg JM, Gudjonsson JE. A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases. Nat Immunol 2016; 18:152-160. [PMID: 27992404 PMCID: PMC5289297 DOI: 10.1038/ni.3643] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [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: 08/02/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022]
Abstract
Autoimmune diseases affect 7.5% of the US population, and they are among the leading causes of death and disability. A notable feature of many autoimmune diseases is their greater prevalence in females than in males, but the underlying mechanisms of this have remained unclear. Through the use of high-resolution global transcriptome analyses, we demonstrated a female-biased molecular signature associated with susceptibility to autoimmune disease and linked this to extensive sex-dependent co-expression networks. This signature was independent of biological age and sex-hormone regulation and was regulated by the transcription factor VGLL3, which also had a strong female-biased expression. On a genome-wide level, VGLL3-regulated genes had a strong association with multiple autoimmune diseases, including lupus, scleroderma and Sjögren's syndrome, and had a prominent transcriptomic overlap with inflammatory processes in cutaneous lupus. These results identified a VGLL3-regulated network as a previously unknown inflammatory pathway that promotes female-biased autoimmunity. They demonstrate the importance of studying immunological processes in females and males separately and suggest new avenues for therapeutic development.
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Affiliation(s)
- Yun Liang
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria A Beamer
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Celine C Berthier
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Michigan, USA
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22
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Stoll SW, Stuart PE, Lambert S, Gandarillas A, Rittié L, Johnston A, Elder JT. Membrane-Tethered Intracellular Domain of Amphiregulin Promotes Keratinocyte Proliferation. J Invest Dermatol 2016; 136:444-452. [PMID: 26802239 DOI: 10.1016/j.jid.2015.10.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 09/16/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022]
Abstract
The epidermal growth factor receptor (EGFR) and its ligands are essential regulators of epithelial biology, which are often amplified in cancer cells. We have previously shown that shRNA-mediated silencing of one of these ligands, amphiregulin (AREG), results in keratinocyte growth arrest that cannot be rescued by soluble extracellular EGFR ligands. To further explore the functional importance of specific AREG domains, we stably transduced keratinocytes expressing tetracycline-inducible AREG-targeted shRNA with lentiviruses expressing silencing-proof, membrane-tethered AREG cytoplasmic and extracellular domains (AREG-CTD and AREG-ECD), as well as full-length AREG precursor (proAREG). Here we show that growth arrest of AREG-silenced keratinocytes occurs in G2/M and is significantly restored by proAREG and AREG-CTD but not by AREG-ECD. Moreover, the AREG-CTD was sufficient to normalize cell cycle distribution profiles and expression of mitosis-related genes. Our findings uncover an important role of the AREG-CTD in regulating cell division, which may be relevant to tumor resistance to EGFR-directed therapies.
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Affiliation(s)
- Stefan W Stoll
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alberto Gandarillas
- Cell Cycle, Stem Cells and Cancer Lab, Instituto de Investigación Marques de Valdecilla (IDIVAL), Santander, Spain
| | - Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Health System, Ann Arbor, Michigan, USA
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23
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Prins BP, Abbasi A, Wong A, Vaez A, Nolte I, Franceschini N, Stuart PE, Guterriez Achury J, Mistry V, Bradfield JP, Valdes AM, Bras J, Shatunov A, Lu C, Han B, Raychaudhuri S, Bevan S, Mayes MD, Tsoi LC, Evangelou E, Nair RP, Grant SFA, Polychronakos C, Radstake TRD, van Heel DA, Dunstan ML, Wood NW, Al-Chalabi A, Dehghan A, Hakonarson H, Markus HS, Elder JT, Knight J, Arking DE, Spector TD, Koeleman BPC, van Duijn CM, Martin J, Morris AP, Weersma RK, Wijmenga C, Munroe PB, Perry JRB, Pouget JG, Jamshidi Y, Snieder H, Alizadeh BZ. Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study. PLoS Med 2016; 13:e1001976. [PMID: 27327646 PMCID: PMC4915710 DOI: 10.1371/journal.pmed.1001976] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [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] [Received: 06/21/2015] [Accepted: 02/03/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND C-reactive protein (CRP) is associated with immune, cardiometabolic, and psychiatric traits and diseases. Yet it is inconclusive whether these associations are causal. METHODS AND FINDINGS We performed Mendelian randomization (MR) analyses using two genetic risk scores (GRSs) as instrumental variables (IVs). The first GRS consisted of four single nucleotide polymorphisms (SNPs) in the CRP gene (GRSCRP), and the second consisted of 18 SNPs that were significantly associated with CRP levels in the largest genome-wide association study (GWAS) to date (GRSGWAS). To optimize power, we used summary statistics from GWAS consortia and tested the association of these two GRSs with 32 complex somatic and psychiatric outcomes, with up to 123,865 participants per outcome from populations of European ancestry. We performed heterogeneity tests to disentangle the pleiotropic effect of IVs. A Bonferroni-corrected significance level of less than 0.0016 was considered statistically significant. An observed p-value equal to or less than 0.05 was considered nominally significant evidence for a potential causal association, yet to be confirmed. The strengths (F-statistics) of the IVs were 31.92-3,761.29 and 82.32-9,403.21 for GRSCRP and GRSGWAS, respectively. CRP GRSGWAS showed a statistically significant protective relationship of a 10% genetically elevated CRP level with the risk of schizophrenia (odds ratio [OR] 0.86 [95% CI 0.79-0.94]; p < 0.001). We validated this finding with individual-level genotype data from the schizophrenia GWAS (OR 0.96 [95% CI 0.94-0.98]; p < 1.72 × 10-6). Further, we found that a standardized CRP polygenic risk score (CRPPRS) at p-value thresholds of 1 × 10-4, 0.001, 0.01, 0.05, and 0.1 using individual-level data also showed a protective effect (OR < 1.00) against schizophrenia; the first CRPPRS (built of SNPs with p < 1 × 10-4) showed a statistically significant (p < 2.45 × 10-4) protective effect with an OR of 0.97 (95% CI 0.95-0.99). The CRP GRSGWAS showed that a 10% increase in genetically determined CRP level was significantly associated with coronary artery disease (OR 0.88 [95% CI 0.84-0.94]; p < 2.4 × 10-5) and was nominally associated with the risk of inflammatory bowel disease (OR 0.85 [95% CI 0.74-0.98]; p < 0.03), Crohn disease (OR 0.81 [95% CI 0.70-0.94]; p < 0.005), psoriatic arthritis (OR 1.36 [95% CI 1.00-1.84]; p < 0.049), knee osteoarthritis (OR 1.17 [95% CI 1.01-1.36]; p < 0.04), and bipolar disorder (OR 1.21 [95% CI 1.05-1.40]; p < 0.007) and with an increase of 0.72 (95% CI 0.11-1.34; p < 0.02) mm Hg in systolic blood pressure, 0.45 (95% CI 0.06-0.84; p < 0.02) mm Hg in diastolic blood pressure, 0.01 ml/min/1.73 m2 (95% CI 0.003-0.02; p < 0.005) in estimated glomerular filtration rate from serum creatinine, 0.01 g/dl (95% CI 0.0004-0.02; p < 0.04) in serum albumin level, and 0.03 g/dl (95% CI 0.008-0.05; p < 0.009) in serum protein level. However, after adjustment for heterogeneity, neither GRS showed a significant effect of CRP level (at p < 0.0016) on any of these outcomes, including coronary artery disease, nor on the other 20 complex outcomes studied. Our study has two potential limitations: the limited variance explained by our genetic instruments modeling CRP levels in blood and the unobserved bias introduced by the use of summary statistics in our MR analyses. CONCLUSIONS Genetically elevated CRP levels showed a significant potentially protective causal relationship with risk of schizophrenia. We observed nominal evidence at an observed p < 0.05 using either GRSCRP or GRSGWAS-with persistence after correction for heterogeneity-for a causal relationship of elevated CRP levels with psoriatic osteoarthritis, rheumatoid arthritis, knee osteoarthritis, systolic blood pressure, diastolic blood pressure, serum albumin, and bipolar disorder. These associations remain yet to be confirmed. We cannot verify any causal effect of CRP level on any of the other common somatic and neuropsychiatric outcomes investigated in the present study. This implies that interventions that lower CRP level are unlikely to result in decreased risk for the majority of common complex outcomes.
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Affiliation(s)
- Bram. P. Prins
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail: (BPP); (BZA)
| | - Ali Abbasi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anson Wong
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ilja Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Philip E. Stuart
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Javier Guterriez Achury
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Vanisha Mistry
- Metabolic Research Laboratories, Wellcome Trust–MRC Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge, Cambridge, United Kingdom
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, United States of America
| | - Ana M. Valdes
- Department of Academic Rheumatology, University of Nottingham, Nottingham, United Kingdom
| | - Jose Bras
- Department of Molecular Neuroscience, Institute of Neurology, London, United Kingdom
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - PAGE Consortium
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Systemic Sclerosis consortium
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Treat OA consortium
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - DIAGRAM Consortium
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - ALS consortium
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | | | | | - CKDGen consortium
- NHLBI’s Framingham Heart Study, Center for Population Studies and Harvard Medical School, Framingham, Massachusetts, United States of America
| | - GERAD1 Consortium
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | | | | | - Chen Lu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Buhm Han
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Rheumatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - Steve Bevan
- Neurology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Maureen D. Mayes
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Lam C. Tsoi
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Rajan P. Nair
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Struan F. A. Grant
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Constantin Polychronakos
- Endocrine Genetics Research Institute, McGill University Health Center, Montreal, Quebec, Canada
| | - Timothy R. D. Radstake
- Department of Rheumatology & Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - David A. van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Melanie L. Dunstan
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicholas W. Wood
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Complex Disease Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Rotterdam, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Hugh S. Markus
- Neurology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - James T. Elder
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jo Knight
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine and Department of Medicine, Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Bobby P. C. Koeleman
- Complex Genetic Section, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Rotterdam, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Patricia B. Munroe
- NIHR Barts Cardiovascular Biomedical Research Unit, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - John R. B. Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Jennie G. Pouget
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Yalda Jamshidi
- Cardiogenetics Lab, Cardiovascular and Cell Sciences Institute, St George’s Hospital Medical School, London, United Kingdom
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- * E-mail: (BPP); (BZA)
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24
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Stoll SW, Stuart PE, Swindell WR, Tsoi LC, Li B, Gandarillas A, Lambert S, Johnston A, Nair RP, Elder JT. The EGF receptor ligand amphiregulin controls cell division via FoxM1. Oncogene 2016; 35:2075-86. [PMID: 26234682 PMCID: PMC4788585 DOI: 10.1038/onc.2015.269] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 06/04/2015] [Accepted: 06/13/2015] [Indexed: 12/26/2022]
Abstract
Epidermal growth factor receptor (EGFR) is central to epithelial cell physiology, and deregulated EGFR signaling has an important role in a variety of human carcinomas. Here we show that silencing of the EGF-related factor amphiregulin (AREG) markedly inhibits the expansion of human keratinocytes through mitotic failure and accumulation of cells with ⩾ 4n DNA content. RNA-sequencing-based transcriptome analysis revealed that tetracycline-mediated AREG silencing significantly altered the expression of 2331 genes, 623 of which were not normalized by treatment with EGF. Interestingly, genes irreversibly upregulated by suppression of AREG overlapped with genes involved in keratinocyte differentiation. Moreover, a significant proportion of the irreversibly downregulated genes featured upstream binding sites recognized by forkhead box protein M1 (FoxM1), a key transcription factor in the control of mitosis that is widely dysregulated in cancer. The downregulation of FoxM1 and its target genes preceded mitotic arrest. Constitutive expression of FoxM1 in AREG knockdown cells normalized cell proliferation, reduced the number of cells with ⩾ 4n DNA content and rescued expression of FoxM1 target genes. These results demonstrate that AREG controls G2/M progression and cytokinesis in keratinocytes via activation of a FoxM1-dependent transcriptional program, suggesting new avenues for treatment of epithelial cancer.
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Affiliation(s)
- Stefan W. Stoll
- Department of Dermatology, University of Michigan, Ann Arbor, MI
| | - Philip E. Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI
| | | | - Lam C. Tsoi
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Bingshan Li
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Alberto Gandarillas
- Cell Cycle, Stem Cells and Cancer Lab, Instituto de Investigación Marques de Valdecilla-IDIVAL), Santander, Spain
| | - Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, MI
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, MI
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI
- Ann Arbor Veterans Affairs Health System, Ann Arbor, MI
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25
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Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Huizinga TWJ, Abecasis G, Becker J, Boeckxstaens GE, Chen WM, Franke A, Gladman DD, Gockel I, Gutierrez-Achury J, Martin J, Nair RP, Nöthen MM, Onengut-Gumuscu S, Rahman P, Rantapää-Dahlqvist S, Stuart PE, Tsoi LC, van Heel DA, Worthington J, Wouters MM, Klareskog L, Elder JT, Gregersen PK, Schumacher J, Rich SS, Wijmenga C, Sunyaev SR, de Bakker PIW, Raychaudhuri S. Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases. Nat Genet 2015; 47:1085-90. [PMID: 26258845 PMCID: PMC4552599 DOI: 10.1038/ng.3379] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [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: 02/12/2015] [Accepted: 07/16/2015] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen (HLA) genes confer strong risk for autoimmune diseases on a log-additive scale. Here we speculated that differences in autoantigen binding repertoires between a heterozygote’s two expressed HLA variants may result in additional non-additive risk effects. We tested non-additive disease contributions of classical HLA alleles in patients and matched controls for five common autoimmune diseases: rheumatoid arthritis (RA, Ncases=5,337), type 1 diabetes (T1D, Ncases=5,567), psoriasis vulgaris (Ncases=3,089), idiopathic achalasia (Ncases=727), and celiac disease (Ncases=11,115). In four out of five diseases, we observed highly significant non-additive dominance effects (RA: P=2.5×1012; T1D: P=2.4×10−10; psoriasis: P=5.9×10−6; celiac disease: P=1.2×10−87). In three of these diseases, the dominance effects were explained by interactions between specific classical HLA alleles (RA: P=1.8×10−3; T1D: P=8.6×1027; celiac disease: P=6.0×10−100). These interactions generally increased disease risk and explained moderate but significant fractions of phenotypic variance (RA: 1.4%, T1D: 4.0%, and celiac disease: 4.1%, beyond a simple additive model).
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Affiliation(s)
- Tobias L Lenz
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Aaron J Deutsch
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, USA
| | - Buhm Han
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Xinli Hu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, USA
| | - Yukinori Okada
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Stephen Eyre
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK.,National Institute for Health Research (NIHR) Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Alexandra Zhernakova
- Genetics Department, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.,Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Guy E Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Dafna D Gladman
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Centre for Prognosis Studies in the Rheumatic Diseases, Toronto Western Research Institute, University of Toronto, Toronto, Ontario, Canada.,Toronto Western Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Javier Gutierrez-Achury
- Genetics Department, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Proton Rahman
- Department of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Solbritt Rantapää-Dahlqvist
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden.,Department of Rheumatology, Umeå University, Umeå, Sweden
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.,Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK.,National Institute for Health Research (NIHR) Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Mira M Wouters
- Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, USA
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Cisca Wijmenga
- Genetics Department, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Shamil R Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Paul I W de Bakker
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Soumya Raychaudhuri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.,Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK.,Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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26
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Tsoi LC, Spain SL, Ellinghaus E, Stuart PE, Capon F, Knight J, Tejasvi T, Kang HM, Allen MH, Lambert S, Stoll SW, Weidinger S, Gudjonsson JE, Koks S, Kingo K, Esko T, Das S, Metspalu A, Weichenthal M, Enerback C, Krueger GG, Voorhees JJ, Chandran V, Rosen CF, Rahman P, Gladman DD, Reis A, Nair RP, Franke A, Barker JNWN, Abecasis GR, Trembath RC, Elder JT. Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci. Nat Commun 2015; 6:7001. [PMID: 25939698 PMCID: PMC4422106 DOI: 10.1038/ncomms8001] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/24/2015] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a chronic autoimmune disease with complex genetic architecture. Previous genome-wide association studies (GWAS) and a recent meta-analysis using Immunochip data have uncovered 36 susceptibility loci. Here, we extend our previous meta-analysis of European ancestry by refined genotype calling and imputation and by the addition of 5,033 cases and 5,707 controls. The combined analysis, consisting of over 15,000 cases and 27,000 controls, identifies five new psoriasis susceptibility loci at genome-wide significance (P<5 × 10(-8)). The newly identified signals include two that reside in intergenic regions (1q31.1 and 5p13.1) and three residing near PLCL2 (3p24.3), NFKBIZ (3q12.3) and CAMK2G (10q22.2). We further demonstrate that NFKBIZ is a TRAF3IP2-dependent target of IL-17 signalling in human skin keratinocytes, thereby functionally linking two strong candidate genes. These results further integrate the genetics and immunology of psoriasis, suggesting new avenues for functional analysis and improved therapies.
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Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, Ontario, Canada M5T 1R8.,National Institute for Health Research (NIHR), Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stefan W Stoll
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sulev Koks
- Department of Pathophysiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venereology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Sayantan Das
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Charlotta Enerback
- Department of Dermatology, Linköping University, SE-581 83 Linköping, Sweden
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, Utah 84132, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St John's, Newfoundland, Canada A1C 5B8
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen 91054, Germany
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Jonathan N W N Barker
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard C Trembath
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA
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27
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Swindell WR, Sarkar MK, Stuart PE, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. Clin Transl Med 2015; 4:13. [PMID: 25883770 PMCID: PMC4392043 DOI: 10.1186/s40169-015-0054-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
Background Psoriasis is a cytokine-mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy. Methods Meta-analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically-determined binding affinities of TFs and unconventional DNA-binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs. Results PREs are recognized by IRF1, ISGF3, NF-kappaB and multiple TFs with helix-turn-helix (homeo) or other all-alpha-helical (high-mobility group) DNA-binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine-encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis-activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF-kappaB). Finally, we screened psoriasis-associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele-specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles. Conclusions We identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility. Electronic supplementary material The online version of this article (doi:10.1186/s40169-015-0054-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
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28
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Tsoi LC, Iyer MK, Stuart PE, Swindell WR, Gudjonsson JE, Tejasvi T, Sarkar MK, Li B, Ding J, Voorhees JJ, Kang HM, Nair RP, Chinnaiyan AM, Abecasis GR, Elder JT. Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. Genome Biol 2015; 16:24. [PMID: 25723451 PMCID: PMC4311508 DOI: 10.1186/s13059-014-0570-4] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [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: 09/09/2014] [Accepted: 12/11/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Although analysis pipelines have been developed to use RNA-seq to identify long non-coding RNAs (lncRNAs), inference of their biological and pathological relevance remains a challenge. As a result, most transcriptome studies of autoimmune disease have only assessed protein-coding transcripts. RESULTS We used RNA-seq data from 99 lesional psoriatic, 27 uninvolved psoriatic, and 90 normal skin biopsies, and applied computational approaches to identify and characterize expressed lncRNAs. We detect 2,942 previously annotated and 1,080 novel lncRNAs which are expected to be skin specific. Notably, over 40% of the novel lncRNAs are differentially expressed and the proportions of differentially expressed transcripts among protein-coding mRNAs and previously-annotated lncRNAs are lower in psoriasis lesions versus uninvolved or normal skin. We find that many lncRNAs, in particular those that are differentially expressed, are co-expressed with genes involved in immune related functions, and that novel lncRNAs are enriched for localization in the epidermal differentiation complex. We also identify distinct tissue-specific expression patterns and epigenetic profiles for novel lncRNAs, some of which are shown to be regulated by cytokine treatment in cultured human keratinocytes. CONCLUSIONS Together, our results implicate many lncRNAs in the immunopathogenesis of psoriasis, and our results provide a resource for lncRNA studies in other autoimmune diseases.
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Affiliation(s)
- Lam C Tsoi
- />Department of Biostatistics, Center for Statistical Genetics, School of Public Health, M4614 SPH I, University of Michigan, Box 2029, Ann Arbor, MI 48109-2029 USA
| | - Matthew K Iyer
- />Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Philip E Stuart
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
| | | | | | - Trilokraj Tejasvi
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
- />Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, MI USA
| | - Mrinal K Sarkar
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
| | - Bingshan Li
- />Department of Biostatistics, Center for Statistical Genetics, School of Public Health, M4614 SPH I, University of Michigan, Box 2029, Ann Arbor, MI 48109-2029 USA
- />Department of Molecular Physiology and Biophysics, Center for Quantitative Sciences, Vanderbilt University, Nashville, TN USA
| | - Jun Ding
- />Department of Biostatistics, Center for Statistical Genetics, School of Public Health, M4614 SPH I, University of Michigan, Box 2029, Ann Arbor, MI 48109-2029 USA
- />Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD USA
| | - John J Voorhees
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
| | - Hyun M Kang
- />Department of Biostatistics, Center for Statistical Genetics, School of Public Health, M4614 SPH I, University of Michigan, Box 2029, Ann Arbor, MI 48109-2029 USA
| | - Rajan P Nair
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
| | - Arul M Chinnaiyan
- />Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI USA
- />Department of Pathology, University of Michigan Medical School, Ann Arbor, MI USA
- />Department of Urology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Goncalo R Abecasis
- />Department of Biostatistics, Center for Statistical Genetics, School of Public Health, M4614 SPH I, University of Michigan, Box 2029, Ann Arbor, MI 48109-2029 USA
| | - James T Elder
- />Department of Dermatology, University of Michigan, Ann Arbor, MI USA
- />Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, MI USA
- />University of Michigan Medical School, 7412 Medical Sciences Building 1, 1301 E. Catherine, Ann Arbor, MI 48109-5675 USA
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29
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Swindell WR, Stuart PE, Sarkar MK, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era. BMC Med Genomics 2014; 7:27. [PMID: 24885462 PMCID: PMC4060870 DOI: 10.1186/1755-8794-7-27] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [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: 11/03/2013] [Accepted: 05/16/2014] [Indexed: 12/20/2022] Open
Abstract
Background Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings. Methods We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding. Results Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4. Conclusions These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA.
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30
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Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT. Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. J Invest Dermatol 2014; 134:1828-1838. [PMID: 24441097 PMCID: PMC4057954 DOI: 10.1038/jid.2014.28] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [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: 07/19/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 02/08/2023]
Abstract
To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived cDNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ~38 million single-end 80-bp reads per sample. Comparison of 42 samples examined by both RNA-seq and microarray revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes. Weighted gene co-expression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long non-coding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally-expressed genes were significantly down-regulated in psoriatic biopsies, most likely due to expansion of the epidermal compartment. These results demonstrate the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and co-expression analysis.
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Affiliation(s)
- Bingshan Li
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jun Ding
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA; Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James J Kochkodan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Hyun M Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA.
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31
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Shaiq PA, Stuart PE, Latif A, Schmotzer C, Kazmi AH, Khan MS, Azam M, Tejasvi T, Voorhees JJ, Raja GK, Elder JT, Qamar R, Nair RP. Genetic associations of psoriasis in a Pakistani population. Br J Dermatol 2013; 169:406-11. [PMID: 23495851 PMCID: PMC3731395 DOI: 10.1111/bjd.12313] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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] [Accepted: 03/12/2013] [Indexed: 02/06/2023]
Abstract
BACKGROUND Genetic predisposition to psoriasis, an inflammatory skin disease affecting 0·2-4% of the world population, is well established. Thus far, 41 psoriasis susceptibility loci reach genome-wide significance (P ≤ 5 × 10(-8) ). Identification of genetic susceptibility loci in diverse populations will help understand the underlying biology of psoriasis susceptibility. OBJECTIVES The primary objective of this study was to examine psoriasis susceptibility associations previously reported in Chinese and caucasian populations in a Pakistani cohort. METHODS Blood samples and phenotype data were collected from psoriasis cases and controls in Islamabad, Pakistan. DNA was isolated and genotypes of selected susceptibility markers were determined. The data were analysed using χ(2) tests or logistic regression for psoriasis association. RESULTS HLA-Cw6 showed the strongest association [odds ratio (OR) 2·43, P = 2·3 × 10(-12) ]. HLA-Cw1 showed marginally significant association (OR 1·66, P = 0·049), suggesting that the HLA-Cw1-B46 risk haplotype may be present in the Pakistani population. Three other loci (IL4/IL13, NOS2, TRAF3IP2) showed nominally significant association (P < 0·05). CONCLUSIONS HLA-Cw6 is strongly associated with psoriasis susceptibility in the Pakistani population, as has been found in every other population studied. In addition, HLA-Cw1 showed marginal association, reflecting the relative geographical proximity and thus likely genetic relatedness to other populations in which the HLA-Cw1-B46 haplotype is known to be associated. A larger cohort and a denser marker set will be required for further analysis of psoriasis associations in the South Asian population.
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Affiliation(s)
- P A Shaiq
- PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
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32
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Johnston A, Xing X, Swindell WR, Kochkodan J, Riblett M, Nair RP, Stuart PE, Ding J, Voorhees JJ, Elder JT, Gudjonsson JE. Susceptibility-associated genetic variation at IL12B enhances Th1 polarization in psoriasis. Hum Mol Genet 2013; 22:1807-15. [PMID: 23376980 DOI: 10.1093/hmg/ddt034] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The IL12B gene encodes the common p40 subunit of IL-12 and IL-23, cytokines with key roles in Th1 and Th17 biology, respectively, and genetic variation in this region significantly influences risk of psoriasis. Here, we demonstrate that a psoriasis-associated risk haplotype at the IL12B locus leads to increased expression of IL12B by monocytes and correlated with increased serum levels of IL-12, IFN-γ and the IFN-γ induced chemokine, CXCL10. In contrast, serum IL-23 levels were decreased in risk carriers when compared with non-carriers. We further demonstrate that IL-12 is increased in psoriatic skin and that risk carriers manifest a skewing of the inflammatory network toward stronger IFN-γ responses. Taken together, our data demonstrate that the risk variant in IL12B associates with its increased expression and predisposes to stronger Th1 polarization through deviation of the local inflammatory environment toward increased IL-12/IFN-γ at the expense of IL-23/IL-17 responses.
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Affiliation(s)
- Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
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33
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Tsoi LC, Spain SL, Knight J, Ellinghaus E, Stuart PE, Capon F, Ding J, Li Y, Tejasvi T, Gudjonsson JE, Kang HM, Allen MH, McManus R, Novelli G, Samuelsson L, Schalkwijk J, Ståhle M, Burden AD, Smith CH, Cork MJ, Estivill X, Bowcock AM, Krueger GG, Weger W, Worthington J, Tazi-Ahnini R, Nestle FO, Hayday A, Hoffmann P, Winkelmann J, Wijmenga C, Langford C, Edkins S, Andrews R, Blackburn H, Strange A, Band G, Pearson RD, Vukcevic D, Spencer CCA, Deloukas P, Mrowietz U, Schreiber S, Weidinger S, Koks S, Kingo K, Esko T, Metspalu A, Lim HW, Voorhees JJ, Weichenthal M, Wichmann HE, Chandran V, Rosen CF, Rahman P, Gladman DD, Griffiths CEM, Reis A, Kere J, Nair RP, Franke A, Barker JNWN, Abecasis GR, Elder JT, Trembath RC. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet 2012; 44:1341-8. [PMID: 23143594 PMCID: PMC3510312 DOI: 10.1038/ng.2467] [Citation(s) in RCA: 706] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/17/2012] [Indexed: 02/08/2023]
Abstract
To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.
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Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
- National Institute for Health Research (NIHR), Biomedical Research Centre, Guy’s and St. Thomas’ NHS Foundation Trust
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jun Ding
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Yanming Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Ross McManus
- Department of Clinical Medicine Trinity College Dublin, Ireland
- Institute of Molecular Medicine, Trinity College Dublin, Ireland
| | - Giuseppe Novelli
- National Agency for Evaluation of Universities and Research Institutes (ANVUR)
- Research Center San Pietro Hospital, Rome, Italy
| | - Lena Samuelsson
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Mona Ståhle
- Dermatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Catherine H Smith
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Michael J Cork
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Xavier Estivill
- Genes and Disease Programme, Centre for Genomic Regulation (CRG) and UPF, Hospital del Mar Research Institute (CRG) and Public Health and Epidemiology Network Biomedical Research Centre (CIBERESP), Barcelona, Spain
| | - Anne M Bowcock
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | | | - Wolfgang Weger
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachid Tazi-Ahnini
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Frank O Nestle
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Adrian Hayday
- Division of Immunology, Infection and Inflammatory Disease; King’s College London, London, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 54127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 54127 Bonn, Germany
| | - Juliane Winkelmann
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany
| | - Cisca Wijmenga
- Genetics Department, University Medical Center and University of Groningen, Groningen, The Netherlands
| | | | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Amy Strange
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Damjan Vukcevic
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Chris CA Spencer
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | | | - Ulrich Mrowietz
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- PopGen biobank, University Hospital S.-H., Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Sulev Koks
- Department of Physiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venerology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - H. Erich Wichmann
- Institute of Epidemiology I, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St. John’s, Newfoundland A1C 5B8, Canada
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Christopher EM Griffiths
- Dermatological Sciences, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Finland
| | | | | | | | | | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Jonathan NWN Barker
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, UK
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Jordan CT, Cao L, Roberson EDO, Duan S, Helms CA, Nair RP, Duffin KC, Stuart PE, Goldgar D, Hayashi G, Olfson EH, Feng BJ, Pullinger CR, Kane JP, Wise CA, Goldbach-Mansky R, Lowes MA, Peddle L, Chandran V, Liao W, Rahman P, Krueger GG, Gladman D, Elder JT, Menter A, Bowcock AM. Rare and common variants in CARD14, encoding an epidermal regulator of NF-kappaB, in psoriasis. Am J Hum Genet 2012; 90:796-808. [PMID: 22521419 PMCID: PMC3376540 DOI: 10.1016/j.ajhg.2012.03.013] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/29/2012] [Accepted: 03/13/2012] [Indexed: 11/26/2022] Open
Abstract
Psoriasis is a common inflammatory disorder of the skin and other organs. We have determined that mutations in CARD14, encoding a nuclear factor of kappa light chain enhancer in B cells (NF-kB) activator within skin epidermis, account for PSORS2. Here, we describe fifteen additional rare missense variants in CARD14, their distribution in seven psoriasis cohorts (>6,000 cases and >4,000 controls), and their effects on NF-kB activation and the transcriptome of keratinocytes. There were more CARD14 rare variants in cases than in controls (burden test p value = 0.0015). Some variants were only seen in a single case, and these included putative pathogenic mutations (c.424G>A [p.Glu142Lys] and c.425A>G [p.Glu142Gly]) and the generalized-pustular-psoriasis mutation, c.413A>C (p.Glu138Ala); these three mutations lie within the coiled-coil domain of CARD14. The c.349G>A (p.Gly117Ser) familial-psoriasis mutation was present at a frequency of 0.0005 in cases of European ancestry. CARD14 variants led to a range of NF-kB activities; in particular, putative pathogenic variants led to levels >2.5× higher than did wild-type CARD14. Two variants (c.511C>A [p.His171Asn] and c.536G>A [p.Arg179His]) required stimulation with tumor necrosis factor alpha (TNF-α) to achieve significant increases in NF-kB levels. Transcriptome profiling of wild-type and variant CARD14 transfectants in keratinocytes differentiated probably pathogenic mutations from neutral variants such as polymorphisms. Over 20 CARD14 polymorphisms were also genotyped, and meta-analysis revealed an association between psoriasis and rs11652075 (c.2458C>T [p.Arg820Trp]; p value = 2.1 × 10(-6)). In the two largest psoriasis cohorts, evidence for association increased when rs11652075 was conditioned on HLA-Cw*0602 (PSORS1). These studies contribute to our understanding of the genetic basis of psoriasis and illustrate the challenges faced in identifying pathogenic variants in common disease.
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Affiliation(s)
- Catherine T Jordan
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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35
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Ellinghaus D, Ellinghaus E, Nair RP, Stuart PE, Esko T, Metspalu A, Debrus S, Raelson JV, Tejasvi T, Belouchi M, West SL, Barker JN, Kõks S, Kingo K, Balschun T, Palmieri O, Annese V, Gieger C, Wichmann HE, Kabesch M, Trembath RC, Mathew CG, Abecasis GR, Weidinger S, Nikolaus S, Schreiber S, Elder JT, Weichenthal M, Nothnagel M, Franke A. Combined analysis of genome-wide association studies for Crohn disease and psoriasis identifies seven shared susceptibility loci. Am J Hum Genet 2012; 90:636-47. [PMID: 22482804 DOI: 10.1016/j.ajhg.2012.02.020] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/30/2012] [Accepted: 02/16/2012] [Indexed: 12/15/2022] Open
Abstract
Psoriasis (PS) and Crohn disease (CD) have been shown to be epidemiologically, pathologically, and therapeutically connected, but little is known about their shared genetic causes. We performed meta-analyses of five published genome-wide association studies on PS (2,529 cases and 4,955 controls) and CD (2,142 cases and 5,505 controls), followed up 20 loci that showed strongest evidence for shared disease association and, furthermore, tested cross-disease associations for previously reported PS and CD risk alleles in additional 6,115 PS cases, 4,073 CD cases, and 10,100 controls. We identified seven susceptibility loci outside the human leukocyte antigen region (9p24 near JAK2, 10q22 at ZMIZ1, 11q13 near PRDX5, 16p13 near SOCS1, 17q21 at STAT3, 19p13 near FUT2, and 22q11 at YDJC) shared between PS and CD with genome-wide significance (p < 5 × 10(-8)) and confirmed four already established PS and CD risk loci (IL23R, IL12B, REL, and TYK2). Three of the shared loci are also genome-wide significantly associated with PS alone (10q22 at ZMIZ1, p(rs1250544) = 3.53 × 10(-8), 11q13 near PRDX5, p(rs694739) = 3.71 × 10(-09), 22q11 at YDJC, p(rs181359) = 8.02 × 10(-10)). In addition, we identified one susceptibility locus for CD (16p13 near SOCS1, p(rs4780355) = 4.99 × 10(-8)). Refinement of association signals identified shared genome-wide significant associations for exonic SNPs at 10q22 (ZMIZ1) and in silico expression quantitative trait locus analyses revealed that the associations at ZMIZ1 and near SOCS1 have a potential functional effect on gene expression. Our results show the usefulness of joint analyses of clinically distinct immune-mediated diseases and enlarge the map of shared genetic risk loci.
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Affiliation(s)
- David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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36
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Swindell WR, Xing X, Stuart PE, Chen CS, Aphale A, Nair RP, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Heterogeneity of inflammatory and cytokine networks in chronic plaque psoriasis. PLoS One 2012; 7:e34594. [PMID: 22479649 PMCID: PMC3315545 DOI: 10.1371/journal.pone.0034594] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [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: 12/13/2011] [Accepted: 03/02/2012] [Indexed: 11/19/2022] Open
Abstract
The clinical features of psoriasis, characterized by sharply demarcated scaly erythematous plaques, are typically so distinctive that a diagnosis can easily be made on these grounds alone. However, there is great variability in treatment response between individual patients, and this may reflect heterogeneity of inflammatory networks driving the disease. In this study, whole-genome transcriptional profiling was used to characterize inflammatory and cytokine networks in 62 lesional skin samples obtained from patients with stable chronic plaque psoriasis. We were able to stratify lesions according to their inflammatory gene expression signatures, identifying those associated with strong (37% of patients), moderate (39%) and weak inflammatory infiltrates (24%). Additionally, we identified differences in cytokine signatures with heightened cytokine-response patterns in one sub-group of lesions (IL-13-strong; 50%) and attenuation of these patterns in a second sub-group (IL-13-weak; 50%). These sub-groups correlated with the composition of the inflammatory infiltrate, but were only weakly associated with increased risk allele frequency at some psoriasis susceptibility loci (e.g., REL, TRAF3IP2 and NOS2). Our findings highlight variable points in the inflammatory and cytokine networks known to drive chronic plaque psoriasis. Such heterogeneous aspects may shape clinical course and treatment responses, and can provide avenues for development of personalized treatments.
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Affiliation(s)
- William R. Swindell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Philip E. Stuart
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Cynthia S. Chen
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Abhishek Aphale
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - John J. Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - James T. Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- * E-mail:
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37
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Ellinghaus E, Stuart PE, Ellinghaus D, Nair RP, Debrus S, Raelson JV, Belouchi M, Tejasvi T, Li Y, Tsoi LC, Onken AT, Esko T, Metspalu A, Rahman P, Gladman DD, Bowcock AM, Helms C, Krueger GG, Koks S, Kingo K, Gieger C, Wichmann HE, Mrowietz U, Weidinger S, Schreiber S, Abecasis GR, Elder JT, Weichenthal M, Franke A. Genome-wide meta-analysis of psoriatic arthritis identifies susceptibility locus at REL. J Invest Dermatol 2011; 132:1133-40. [PMID: 22170493 PMCID: PMC3305829 DOI: 10.1038/jid.2011.415] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [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] [Indexed: 11/24/2022]
Abstract
Psoriatic arthritis (PsA) is a chronic inflammatory musculoskeletal disease affecting up to 30% of psoriasis vulgaris (PsV) cases and approximately 0.25% to 1% of the general population. To identify common susceptibility loci, we performed a meta-analysis of three imputed genome-wide association studies (GWAS) on psoriasis, stratified for PsA. A total of 1,160,703 SNPs were analyzed in the discovery set consisting of 535 PsA cases and 3,432 controls from Germany, the United States and Canada. We followed up two SNPs in 1,931 PsA cases and 6,785 controls comprising six independent replication panels from Germany, Estonia, the United States and Canada. In the combined analysis, a genome-wide significant association was detected at 2p16 near the REL locus encoding c-Rel (rs13017599, P=1.18×10−8, OR=1.27, 95% CI=1.18–1.35). The rs13017599 polymorphism is known to associate with rheumatoid arthritis (RA), and another SNP near REL (rs702873) was recently implicated in PsV susceptibility. However, conditional analysis indicated that rs13017599, rather than rs702873, accounts for the PsA association at REL. We hypothesize that c-Rel, as a member of the Rel/NF-κB family, is associated with PsA in the context of disease pathways that involve other identified PsA and PsV susceptibility genes including TNIP1, TNFAIP3 and NFκBIA.
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Affiliation(s)
- Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany.
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38
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Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, Chen W, Weichenthal M, Ellinghaus E, Franke A, Cookson W, Nair RP, Elder JT, Abecasis GR. Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet 2010; 87:779-89. [PMID: 21129726 DOI: 10.1016/j.ajhg.2010.10.024] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/13/2010] [Accepted: 10/22/2010] [Indexed: 11/27/2022] Open
Abstract
Psoriasis, an immune-mediated, inflammatory disease of the skin and joints, provides an ideal system for expression quantitative trait locus (eQTL) analysis, because it has a strong genetic basis and disease-relevant tissue (skin) is readily accessible. To better understand the role of genetic variants regulating cutaneous gene expression, we identified 841 cis-acting eQTLs using RNA extracted from skin biopsies of 53 psoriatic individuals and 57 healthy controls. We found substantial overlap between cis-eQTLs of normal control, uninvolved psoriatic, and lesional psoriatic skin. Consistent with recent studies and with the idea that control of gene expression can mediate relationships between genetic variants and disease risk, we found that eQTL SNPs are more likely to be associated with psoriasis than are randomly selected SNPs. To explore the tissue specificity of these eQTLs and hence to quantify the benefits of studying eQTLs in different tissues, we developed a refined statistical method for estimating eQTL overlap and used it to compare skin eQTLs to a published panel of lymphoblastoid cell line (LCL) eQTLs. Our method accounts for the fact that most eQTL studies are likely to miss some true eQTLs as a result of power limitations and shows that ∼70% of cis-eQTLs in LCLs are shared with skin, as compared with the naive estimate of < 50% sharing. Our results provide a useful method for estimating the overlap between various eQTL studies and provide a catalog of cis-eQTLs in skin that can facilitate efforts to understand the functional impact of identified susceptibility variants on psoriasis and other skin traits.
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39
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Stuart PE, Nair RP, Ellinghaus E, Ding J, Tejasvi T, Gudjonsson JE, Li Y, Weidinger S, Eberlein B, Gieger C, Wichmann HE, Kunz M, Ike R, Krueger GG, Bowcock AM, Mroweitz U, Lim HW, Voorhees JJ, Abecasis GR, Weichenthal M, Franke A, Rahman P, Gladman DD, Elder JT. Genome-wide association analysis identifies three psoriasis susceptibility loci. Nat Genet 2010; 42:1000-4. [PMID: 20953189 PMCID: PMC2965799 DOI: 10.1038/ng.693] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [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: 03/09/2010] [Accepted: 07/09/2010] [Indexed: 12/13/2022]
Abstract
We carried out a meta-analysis of two recent psoriasis genome-wide association studies with a combined discovery sample of 1,831 affected individuals (cases) and 2,546 controls. One hundred and two loci selected based on P value rankings were followed up in a three-stage replication study including 4,064 cases and 4,685 controls from Michigan, Toronto, Newfoundland and Germany. In the combined meta-analysis, we identified three new susceptibility loci, including one at NOS2 (rs4795067, combined P = 4 × 10⁻¹¹), one at FBXL19 (rs10782001, combined P = 9 × 10⁻¹⁰) and one near PSMA6-NFKBIA (rs12586317, combined P = 2 × 10⁻⁸). All three loci were also associated with psoriatic arthritis (rs4795067, combined P = 1 × 10⁻⁵; rs10782001, combined P = 4 × 10⁻⁸; and rs12586317, combined P = 6 × 1⁻⁵) and purely cutaneous psoriasis (rs4795067, combined P = 1 × 10⁻⁸; rs10782001, combined P = 2 × 10⁻⁶; and rs12586317, combined P = 1 × 10⁻⁶). We also replicated a recently identified association signal near RNF114 (rs495337, combined P = 2 × 10⁻⁷).
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Affiliation(s)
- Philip E. Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rajan P. Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eva Ellinghaus
- Institute for Clinical Molecular Biology, University of Kiel, Kiel D-24105, Germany
| | - Jun Ding
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109 USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yun Li
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109 USA
| | - Stephan Weidinger
- Departments of Dermatology and Allergy, Technical University Munich, 80333 Munich, Germany
| | - Bernadette Eberlein
- Departments of Dermatology and Allergy, Technical University Munich, 80333 Munich, Germany
| | - Christian Gieger
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - H. Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Manfred Kunz
- Comprehensive Center for Inflammation Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Robert Ike
- Department of Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Anne M. Bowcock
- Division of Human Genetics, Department of Genetics, Washington University at St. Louis, St. Louis, MO
| | - Ulrich Mroweitz
- Department of Dermatology, University of Kiel, Kiel D-24105, Germany
| | - Henry W. Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI 48202 USA
| | - John J. Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Goncalo R. Abecasis
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Andre Franke
- Institute for Clinical Molecular Biology, University of Kiel, Kiel D-24105, Germany
| | - Proton Rahman
- Department of Medicine, Memorial University, St. John's, Newfoundland A1C 5B8, Canada
| | - Dafna D. Gladman
- Department of Rheumatology, University of Toronto, Toronto, Ontario M5T 2S8, Canada
| | - James T. Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Ann Arbor Veteran Affairs Medical Center, Ann Arbor, MI
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Ellinghaus E, Ellinghaus D, Stuart PE, Nair RP, Debrus S, Raelson JV, Belouchi M, Fournier H, Reinhard C, Ding J, Li Y, Tejasvi T, Gudjonsson J, Stoll SW, Voorhees JJ, Lambert S, Weidinger S, Eberlein B, Kunz M, Rahman P, Gladman DD, Gieger C, Wichmann HE, Karlsen TH, Mayr G, Albrecht M, Kabelitz D, Mrowietz U, Abecasis GR, Elder JT, Schreiber S, Weichenthal M, Franke A. Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2. Nat Genet 2010; 42:991-5. [PMID: 20953188 DOI: 10.1038/ng.689] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 07/26/2010] [Indexed: 12/22/2022]
Abstract
Psoriasis is a multifactorial skin disease characterized by epidermal hyperproliferation and chronic inflammation, the most common form of which is psoriasis vulgaris (PsV). We present a genome-wide association analysis of 2,339,118 SNPs in 472 PsV cases and 1,146 controls from Germany, with follow-up of the 147 most significant SNPs in 2,746 PsV cases and 4,140 controls from three independent replication panels. We identified an association at TRAF3IP2 on 6q21 and genotyped two SNPs at this locus in two additional replication panels (the combined discovery and replication panels consisted of 6,487 cases and 8,037 controls; combined P = 2.36 × 10⁻¹⁰ for rs13210247 and combined P = 1.24 × 10⁻¹⁶ for rs33980500). About 15% of psoriasis cases develop psoriatic arthritis (PsA). A stratified analysis of our datasets including only PsA cases (1,922 cases compared to 8,037 controls, P = 4.57 × 10⁻¹² for rs33980500) suggested that TRAF3IP2 represents a shared susceptibility for PsV and PsA. TRAF3IP2 encodes a protein involved in IL-17 signaling and which interacts with members of the Rel/NF-κB transcription factor family.
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Affiliation(s)
- Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
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Sun LD, Cheng H, Wang ZX, Zhang AP, Wang PG, Xu JH, Zhu QX, Zhou HS, Ellinghaus E, Zhang FR, Pu XM, Yang XQ, Zhang JZ, Xu AE, Wu RN, Xu LM, Peng L, Helms CA, Ren YQ, Zhang C, Zhang SM, Nair RP, Wang HY, Lin GS, Stuart PE, Fan X, Chen G, Tejasvi T, Li P, Zhu J, Li ZM, Ge HM, Weichenthal M, Ye WZ, Zhang C, Shen SK, Yang BQ, Sun YY, Li SS, Lin Y, Jiang JH, Li CT, Chen RX, Cheng J, Jiang X, Zhang P, Song WM, Tang J, Zhang HQ, Sun L, Cui J, Zhang LJ, Tang B, Huang F, Qin Q, Pei XP, Zhou AM, Shao LM, Liu JL, Zhang FY, Du WD, Franke A, Bowcock AM, Elder JT, Liu JJ, Yang S, Zhang XJ. Association analyses identify six new psoriasis susceptibility loci in the Chinese population. Nat Genet 2010; 42:1005-9. [PMID: 20953187 DOI: 10.1038/ng.690] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 07/20/2010] [Indexed: 02/08/2023]
Abstract
We extended our previous genome-wide association study for psoriasis with a multistage replication study including 8,312 individuals with psoriasis (cases) and 12,919 controls from China as well as 3,293 cases and 4,188 controls from Germany and the United States and 254 nuclear families from the United States. We identified six new susceptibility loci associated with psoriasis in the Chinese study containing the candidate genes ERAP1, PTTG1, CSMD1, GJB2, SERPINB8 and ZNF816A (combined P < 5 × 10⁻⁸) and replicated one locus, 5q33.1 (TNIP1-ANXA6), previously reported (combined P = 3.8 × 10⁻²¹) in the European studies. Two of these loci showed evidence for association in the German study at ZNF816A and GJB2 with P = 3.6 × 10⁻³ and P = 7.9 × 10⁻³, respectively. ERAP1 and ZNF816A were associated with type 1 (early onset) psoriasis in the Chinese Han population (test for heterogeneity P = 6.5 × 10⁻³ and P = 1.5 × 10⁻³, respectively). Comparisons with the results of previous GWAS of psoriasis highlight the heterogeneity of disease susceptibility between the Chinese and European populations. Our study identifies new genetic susceptibility factors and suggests new biological pathways in psoriasis.
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Affiliation(s)
- Liang-Dan Sun
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Hefei, Anhui, China
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Stuart PE, Nair RP, Hiremagalore R, Kullavanijaya P, Kullavanijaya P, Tejasvi T, Lim HW, Voorhees JJ, Elder JT. Comparison of MHC class I risk haplotypes in Thai and Caucasian psoriatics shows locus heterogeneity at PSORS1. ACTA ACUST UNITED AC 2010; 76:387-97. [PMID: 20604894 DOI: 10.1111/j.1399-0039.2010.01526.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Earlier studies have shown that psoriasis in Japan and Thailand is associated with two different major histocompatibility complex (MHC) haplotypes - those bearing HLA-Cw6 and those bearing HLA-Cw1 and HLA-B46. In an independent case-control sample from Thailand, we confirmed the association of psoriasis with both haplotypes. No association was seen in Thai HLA-Cw1 haplotypes lacking HLA-B46, nor was HLA-Cw1 associated with psoriasis in a large Caucasian sample. To assess whether these risk haplotypes share a common origin, we sequenced genomic DNA from a Thai HLA-Cw1-B46 homozygote across the ∼300 kb MHC risk interval, and compared it with sequence of a HLA-Cw6-B57 risk haplotype. Three small regions of homology were found, but these regions share equivalent sequence similarity with one or more clearly non-risk haplotypes, and they contain no polymorphism alleles unique to all risk haplotypes. Differences in psoriasis phenotype were also observed, including lower risk of disease, greater nail involvement, and later age at onset in HLA-Cw1-B46 carriers compared with HLA-Cw6 carriers. These findings suggest locus heterogeneity at PSORS1 (psoriasis susceptibility 1), the major psoriasis susceptibility locus in the MHC, with HLA-Cw6 imparting risk in both Caucasians and Asians, and an allele other than HLA-Cw1 on the HLA-Cw1-B46 haplotype acting as an additional risk variant in East Asians.
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Affiliation(s)
- P E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109-5675, USA
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Elder JT, Bruce AT, Gudjonsson JE, Johnston A, Stuart PE, Tejasvi T, Voorhees JJ, Abecasis GR, Nair RP. Molecular dissection of psoriasis: integrating genetics and biology. J Invest Dermatol 2009; 130:1213-26. [PMID: 19812592 DOI: 10.1038/jid.2009.319] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Psoriasis is a common and debilitating disease of the skin, nails, and joints, with an acknowledged but complex genetic basis. Early genome-wide linkage studies of psoriasis focused on segregation of microsatellite markers in families; however, the only locus consistently identified resided in the major histocompatibility complex. Subsequently, several groups mapped this locus to the vicinity of HLA-C, and two groups have reported HLA-Cw6 itself to be the major susceptibility allele. More recently, the development of millions of single-nucleotide polymorphisms, coupled with the development of high-throughput genotyping platforms and a comprehensive map of human haplotypes, has made possible a genome-wide association approach using cases and controls rather than families. Taking advantage of these developments, we participated in a collaborative genome-wide association study of psoriasis involving thousands of cases and controls. Initial analysis of these data revealed and/or confirmed association between psoriasis and seven genetic loci-HLA-C, IL12B, IL23R, IL23A, IL4/IL13, TNFAIP3, and TNIP1-and ongoing studies are revealing additional loci. Here, we review the epidemiology, immunopathology, and genetics of psoriasis, and present a disease model integrating its genetics and immunology.
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Affiliation(s)
- James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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Nair RP, Stuart PE, Kullavanijaya P, Kullavanijaya P, Tejasvi T, Voorhees JJ, Elder JT. Genetic evidence for involvement of the IL23 pathway in Thai psoriatics. Arch Dermatol Res 2009; 302:139-43. [PMID: 19705136 DOI: 10.1007/s00403-009-0986-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [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: 06/12/2009] [Revised: 07/21/2009] [Accepted: 08/04/2009] [Indexed: 01/13/2023]
Abstract
A recent genome-wide association analysis of psoriasis identified IL12B and IL23R as significantly associated with psoriasis. Here we report association test results of a Thai cohort consisting of 206 psoriasis cases and 114 controls. The IL23R SNPs rs7530511 and rs11209026, and IL12B SNPs rs3212227 and rs6887695 were genotyped using Taqman assays. Data were analyzed using a logistic regression model for linear trend of association. One of the IL23R markers, rs7530511, was marginally significant (P = 0.017). The other IL23R marker, rs11209026, was not polymorphic. One of the IL12B markers, rs3212227, showed significant association with psoriasis (OR = 1.64, P = 0.0058) while the other, rs6887695, did not (OR = 1.29, P = 0.12). Haplotype analysis of the two IL12B SNPs yielded highly significant association (P = 0.00081, OR = 1.73). These results showed that IL12B is an important genetic factor in psoriasis pathogenesis in the Thai population, with an association strong enough to yield significant confirmatory evidence using a modest sample size. Together with previously reported evidence for IL12B association in Caucasian, Japanese, and Chinese psoriatics, our results support the hypothesis that genes encoding components of the IL23-mediated inflammatory pathway are important determinants of psoriasis pathogenesis across multiple racial groups.
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Affiliation(s)
- Rajan P Nair
- Department of Dermatology, University of Michigan, 3430 CCGC, Box 5932, 1500 East Medical Center Dr., Ann Arbor, MI 48109-5932, USA.
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Nair RP, Ruether A, Stuart PE, Jenisch S, Tejasvi T, Hiremagalore R, Schreiber S, Kabelitz D, Lim HW, Voorhees JJ, Christophers E, Elder JT, Weichenthal M. Polymorphisms of the IL12B and IL23R genes are associated with psoriasis. J Invest Dermatol 2008; 128:1653-61. [PMID: 18219280 DOI: 10.1038/sj.jid.5701255] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Psoriasis is a common inflammatory and hyperproliferative skin disease with a multifactorial genetic basis. A recent study reported that psoriasis was associated with the IL12B haplotype rs3212227 (3'-untranslated region)-rs6887695 (60 kb, 5') and the IL23R haplotype rs7530511 (L310P)-rs11209026 (Q381R). We examined these four single-nucleotide polymorphisms (SNPs) for association with psoriasis in two groups of North American and German Caucasians: (1) 1,810 cases and 2,522 controls; and (2) 509 pedigrees. Both IL12B markers showed highly significant association with psoriasis in the case-control (rs3212227, odds ratio (OR)=1.62, P=1.7 x 10(-15); rs6887695, OR=1.49, P=2.7 x 10(-15)) and in the family-based analysis (rs3212227, P=2.2 x 10(-3); rs6887695, P=1.7 x 10(-3)). The IL23R SNPs also showed significant association in the cases and controls (rs7530511, OR=1.22, P=3.9 x 10(-3); rs11209026, OR=1.40, P=3.8 x 10(-4)). For both genes, common risk haplotypes were identified whose statistical significance approached (IL23R) or exceeded (IL12B) genome-wide criteria. We found no statistical evidence for interactions of these haplotypes with HLA-Cw6. Our results confirm associations between IL12B and IL23R and psoriasis in Caucasians, and provide a genetic basis for the clinical association between psoriasis and Crohn's disease.
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Affiliation(s)
- Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0932, USA
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Nair RP, Stuart PE, Nistor I, Hiremagalore R, Chia NVC, Jenisch S, Weichenthal M, Abecasis GR, Lim HW, Christophers E, Voorhees JJ, Elder JT. Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene. Am J Hum Genet 2006; 78:827-851. [PMID: 16642438 PMCID: PMC1474031 DOI: 10.1086/503821] [Citation(s) in RCA: 426] [Impact Index Per Article: 23.7] [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: 11/28/2005] [Accepted: 03/02/2006] [Indexed: 01/15/2023] Open
Abstract
Previous studies have narrowed the interval containing PSORS1, the psoriasis-susceptibility locus in the major histocompatibility complex (MHC), to an approximately 300-kb region containing HLA-C and at least 10 other genes. In an effort to identify the PSORS1 gene, we cloned and completely sequenced this region from both chromosomes of five individuals. Two of the sequenced haplotypes were associated with psoriasis (risk), and the other eight were clearly unassociated (nonrisk). Comparison of sequence of the two risk haplotypes identified a 298-kb region of homology, extending from just telomeric of HLA-B to the HCG22 gene, which was flanked by clearly nonhomologous regions. Similar haplotypes cloned from unrelated individuals had nearly identical sequence. Combinatorial analysis of exonic variations in the known genes of the candidate interval revealed that HCG27, PSORS1C3, OTF3, TCF19, HCR, STG, and HCG22 bore no alleles unique to risk haplotypes among the 10 sequenced haplotypes. SPR1 and SEEK1 both had messenger RNA alleles specific to risk haplotypes, but only HLA-C and CDSN yielded protein alleles unique to risk. The risk alleles of HLA-C and CDSN (HLA-Cw6 and CDSN*TTC) were genotyped in 678 families with early-onset psoriasis; 620 of these families were also typed for 34 microsatellite markers spanning the PSORS1 interval. Recombinant haplotypes retaining HLA-Cw6 but lacking CDSN*TTC were significantly associated with psoriasis, whereas recombinants retaining CDSN*TTC but lacking HLA-Cw6 were not associated, despite good statistical power. By grouping recombinants with similar breakpoints, the most telomeric quarter of the 298-kb candidate interval could be excluded with high confidence. These results strongly suggest that HLA-Cw6 is the PSORS1 risk allele that confers susceptibility to early-onset psoriasis.
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Affiliation(s)
- Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - Ioana Nistor
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - Ravi Hiremagalore
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - Nicholas V C Chia
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - Stefan Jenisch
- Department of Immunology, University of Kiel, Kiel, Germany
| | | | - Gonçalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit
| | | | - John J Voorhees
- Department of Dermatology, University of Michigan Medical School, Ann Arbor
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor; Department of Radiation Oncology (Cancer Biology), University of Michigan Medical School, Ann Arbor; Department of Dermatology, Ann Arbor Veterans Affairs Hospital, Ann Arbor.
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Graham RR, Ortmann WA, Langefeld CD, Jawaheer D, Selby SA, Rodine PR, Baechler EC, Rohlf KE, Shark KB, Espe KJ, Green LE, Nair RP, Stuart PE, Elder JT, King RA, Moser KL, Gaffney PM, Bugawan TL, Erlich HA, Rich SS, Gregersen PK, Behrens TW. Visualizing human leukocyte antigen class II risk haplotypes in human systemic lupus erythematosus. Am J Hum Genet 2002; 71:543-53. [PMID: 12145745 PMCID: PMC379191 DOI: 10.1086/342290] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2002] [Accepted: 06/11/2002] [Indexed: 11/03/2022] Open
Abstract
Human leukocyte antigen (HLA) class I and class II alleles are implicated as genetic risk factors for many autoimmune diseases. However, the role of the HLA loci in human systemic lupus erythematosus (SLE) remains unclear. Using a dense map of polymorphic microsatellites across the HLA region in a large collection of families with SLE, we identified three distinct haplotypes that encompassed the class II region and exhibited transmission distortion. DRB1 and DQB1 typing of founders showed that the three haplotypes contained DRB1*1501/ DQB1*0602, DRB1*0801/ DQB1*0402, and DRB1*0301/DQB1*0201 alleles, respectively. By visualizing ancestral recombinants, we narrowed the disease-associated haplotypes containing DRB1*1501 and DRB1*0801 to an approximately 500-kb region. We conclude that HLA class II haplotypes containing DRB1 and DQB1 alleles are strong risk factors for human SLE.
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Affiliation(s)
- Robert R. Graham
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Ward A. Ortmann
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Carl D. Langefeld
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Damini Jawaheer
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Scott A. Selby
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Peter R. Rodine
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Emily C. Baechler
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Kristine E. Rohlf
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Katherine B. Shark
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Karl J. Espe
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Linda E. Green
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Rajan P. Nair
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Philip E. Stuart
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - James T. Elder
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Richard A. King
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Kathy L. Moser
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Patrick M. Gaffney
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Teodorica L. Bugawan
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Henry A. Erlich
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Stephen S. Rich
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Peter K. Gregersen
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
| | - Timothy W. Behrens
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis; Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC; Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY; Department of Dermatology, University of Michigan Medical School, Ann Arbor; and Human Genetics Department, Roche Molecular Systems, Alameda, CA
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Graham RR, Langefeld CD, Gaffney PM, Ortmann WA, Selby SA, Baechler EC, Shark KB, Ockenden TC, Rohlf KE, Moser KL, Brown WM, Gabriel SE, Messner RP, King RA, Horak P, Elder JT, Stuart PE, Rich SS, Behrens TW. Genetic linkage and transmission disequilibrium of marker haplotypes at chromosome 1q41 in human systemic lupus erythematosus. Arthritis Res 2001; 3:299-305. [PMID: 11549371 PMCID: PMC64842 DOI: 10.1186/ar319] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2001] [Revised: 05/30/2001] [Accepted: 06/19/2001] [Indexed: 01/17/2023]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of autoantibodies to a wide range of self-antigens. Recent genome screens have implicated numerous chromosomal regions as potential SLE susceptibility loci. Among these, the 1q41 locus is of particular interest, because evidence for linkage has been found in several independent SLE family collections. Additionally, the 1q41 locus appears to be syntenic with a susceptibility interval identified in the NZM2410 mouse model for SLE. Here, we report the results of genotyping of 11 microsatellite markers within the 1q41 region in 210 SLE sibpair and 122 SLE trio families. These data confirm the modest evidence for linkage at 1q41 in our family collection (LOD = 1.21 at marker D1S2616). Evidence for significant linkage disequilibrium in this interval was also found. Multiple markers in the region exhibit transmission disequilibrium, with the peak single marker multiallelic linkage disequilibrium noted at D1S490 (pedigree disequilibrium test [PDT] global P value = 0.0091). Two- and three-marker haplotypes from the 1q41 region similarly showed strong transmission distortion in the collection of 332 SLE families. The finding of linkage together with significant transmission disequilibrium provides strong evidence for a susceptibility locus at 1q41 in human SLE.
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Affiliation(s)
- Robert R Graham
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Carl D Langefeld
- Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patrick M Gaffney
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ward A Ortmann
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Scott A Selby
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Emily C Baechler
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Katherine B Shark
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Theresa C Ockenden
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Kristine E Rohlf
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Kathleen L Moser
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - William M Brown
- Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Sherine E Gabriel
- Department of Health Sciences Research and Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ronald P Messner
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Richard A King
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | | | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Steven S Rich
- Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Timothy W Behrens
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
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