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Abstract
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization provide evidence that HLA variants mediate risk for MS via changes in the HLA-DRB1 DMR that modify HLA-DRB1 expression. Meta-analysis of 14,259 cases and 171,347 controls confirms that these variants confer risk from DRB1*15:01 and also identifies a protective variant (rs9267649, p < 3.32 × 10−8, odds ratio = 0.86) after conditioning for all MS-associated variants in the region. rs9267649 is associated with increased DNA methylation at the HLA-DRB1 DMR and reduced expression of HLA-DRB1, suggesting a modulation of the DRB1*15:01 effect. Our integrative approach provides insights into the molecular mechanisms of MS susceptibility and suggests putative therapeutic strategies targeting a methylation-mediated regulation of the major risk gene.
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1 Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
2 Center for Epigenetics, and Departments of Medicine, Biomedical Engineering and Mental Health, Johns Hopkins University, Baltimore, MD, USA; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education; Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
3 Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
4 Max Planck Institute of Psychiatry, Munich, Germany; Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany; German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
5 Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany; German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
6 German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
7 German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; Department of Neurology, University Medicine Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
8 German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
9 German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; Neuroimmunology Center, Marburg University, Marburg, Germany
10 Max Planck Institute of Psychiatry, Munich, Germany; German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
11 Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany; German Competence Network Multiple Sclerosis (KKNMS), Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
12 Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany and Institute of Medical Informatics, Biometry, and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
13 Institute of Human Genetics, University Hospital Bonn and Division of Genomics, Life & Brain Research Centre, University of Bonn School of Medicine, Bonn, Germany
14 Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
15 Department of Neurology, University Medicine Greifswald, Greifswald, Germany
16 Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
17 Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University and University Medicine Greifswald, Greifswald, Germany
18 Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
19 Department I of Internal Medicine, Kiel University, Kiel, Germany
20 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Institute of Medical Microbiology and Hospital Hygiene Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
21 Department of Neurology, Oslo University Hospital, Oslo, Norway; Institute of Health and Society, Faculty of Medicine, University of Oslo, Olso, Norway
22 Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
23 Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
24 Department of Neurology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
25 deCODE genetics/Amgen Inc, Reykjavik, Iceland
26 deCODE genetics/Amgen Inc, Reykjavik, Iceland; School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
27 Department of Neurology, Landspitali, The National University of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
28 deCODE genetics/Amgen Inc, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Department of Immunology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
29 deCODE genetics/Amgen Inc, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
30 Center for Epigenetics, and Departments of Medicine, Biomedical Engineering and Mental Health, Johns Hopkins University, Baltimore, MD, USA