1
|
Bogers L, Kuiper KL, Smolders J, Rip J, van Luijn MM. Epstein-Barr virus and genetic risk variants as determinants of T-bet + B cell-driven autoimmune diseases. Immunol Lett 2023; 261:66-74. [PMID: 37451321 DOI: 10.1016/j.imlet.2023.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 06/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
B cells expressing the transcription factor T-bet are found to have a protective role in viral infections, but are also considered major players in the onset of different types of autoimmune diseases. Currently, the exact mechanisms driving such 'atypical' memory B cells to contribute to protective immunity or autoimmunity are unclear. In addition to general autoimmune-related factors including sex and age, the ways T-bet+ B cells instigate autoimmune diseases may be determined by the close interplay between genetic risk variants and Epstein-Barr virus (EBV). The impact of EBV on T-bet+ B cells likely relies on the type of risk variants associated with each autoimmune disease, which may affect their differentiation, migratory routes and effector function. In this hypothesis-driven review, we discuss the lines of evidence pointing to such genetic and/or EBV-mediated influence on T-bet+ B cells in a range of autoimmune diseases, including systemic lupus erythematosus (SLE) and multiple sclerosis (MS). We provide examples of how genetic risk variants can be linked to certain signaling pathways and are differentially affected by EBV to shape T-bet+ B-cells. Finally, we propose options to improve current treatment of B cell-related autoimmune diseases by more selective targeting of pathways that are critical for pathogenic T-bet+ B-cell formation.
Collapse
Affiliation(s)
- Laurens Bogers
- MS Center ErasMS, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands
| | - Kirsten L Kuiper
- MS Center ErasMS, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands
| | - Joost Smolders
- MS Center ErasMS, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands; MS Center ErasMS, Department of Neurology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3015 CN, The Netherlands; Netherlands Institute for Neuroscience, Neuroimmunology research group, Amsterdam 1105 BA, The Netherlands
| | - Jasper Rip
- MS Center ErasMS, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands
| | - Marvin M van Luijn
- MS Center ErasMS, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands.
| |
Collapse
|
2
|
Saint Just Ribeiro M, Tripathi P, Namjou B, Harley JB, Chepelev I. Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1. Front Genet 2022; 13:1008582. [PMID: 36160011 PMCID: PMC9490475 DOI: 10.3389/fgene.2022.1008582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
A major goal of genetics research is to elucidate mechanisms explaining how genetic variation contributes to phenotypic variation. The genetic variants identified in genome-wide association studies (GWASs) generally explain only a small proportion of heritability of phenotypic traits, the so-called missing heritability problem. Recent evidence suggests that additional common variants beyond lead GWAS variants contribute to phenotypic variation; however, their mechanistic underpinnings generally remain unexplored. Herein, we undertake a study of haplotype-specific mechanisms of gene regulation at 8p23.1 in the human genome, a region associated with a number of complex diseases. The FAM167A-BLK locus in this region has been consistently found in the genome-wide association studies (GWASs) of systemic lupus erythematosus (SLE) in all major ancestries. Our haplotype-specific chromatin interaction (Hi-C) experiments, allele-specific enhancer activity measurements, genetic analyses, and epigenome editing experiments revealed that: 1) haplotype-specific long-range chromatin interactions are prevalent in 8p23.1; 2) BLK promoter and cis-regulatory elements cooperatively interact with haplotype-specificity; 3) genetic variants at distal regulatory elements are allele-specific modifiers of the promoter variants at FAM167A-BLK; 4) the BLK promoter interacts with and, as an enhancer-like promoter, regulates FAM167A expression and 5) local allele-specific enhancer activities are influenced by global haplotype structure due to chromatin looping. Although systemic lupus erythematosus causal variants at the FAM167A-BLK locus are thought to reside in the BLK promoter region, our results reveal that genetic variants at distal regulatory elements modulate promoter activity, changing BLK and FAM167A gene expression and disease risk. Our results suggest that global haplotype-specific 3-dimensional chromatin looping architecture has a strong influence on local allelic BLK and FAM167A gene expression, providing mechanistic details for how regional variants controlling the BLK promoter may influence disease risk.
Collapse
Affiliation(s)
- Mariana Saint Just Ribeiro
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Pulak Tripathi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - John B. Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
| | - Iouri Chepelev
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
| |
Collapse
|
3
|
Khatri B, Tessneer KL, Rasmussen A, Aghakhanian F, Reksten TR, Adler A, Alevizos I, Anaya JM, Aqrawi LA, Baecklund E, Brun JG, Bucher SM, Eloranta ML, Engelke F, Forsblad-d’Elia H, Glenn SB, Hammenfors D, Imgenberg-Kreuz J, Jensen JL, Johnsen SJA, Jonsson MV, Kvarnström M, Kelly JA, Li H, Mandl T, Martín J, Nocturne G, Norheim KB, Palm Ø, Skarstein K, Stolarczyk AM, Taylor KE, Teruel M, Theander E, Venuturupalli S, Wallace DJ, Grundahl KM, Hefner KS, Radfar L, Lewis DM, Stone DU, Kaufman CE, Brennan MT, Guthridge JM, James JA, Scofield RH, Gaffney PM, Criswell LA, Jonsson R, Eriksson P, Bowman SJ, Omdal R, Rönnblom L, Warner B, Rischmueller M, Witte T, Farris AD, Mariette X, Alarcon-Riquelme ME, Shiboski CH, Wahren-Herlenius M, Ng WF, Sivils KL, Adrianto I, Nordmark G, Lessard CJ. Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells. Nat Commun 2022; 13:4287. [PMID: 35896530 PMCID: PMC9329286 DOI: 10.1038/s41467-022-30773-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Sjögren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sjögren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.
Collapse
Affiliation(s)
- Bhuwan Khatri
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kandice L. Tessneer
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Astrid Rasmussen
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Farhang Aghakhanian
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Tove Ragna Reksten
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Adam Adler
- grid.274264.10000 0000 8527 6890NGS Core Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ilias Alevizos
- grid.419633.a0000 0001 2205 0568Salivary Disorder Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD USA
| | - Juan-Manuel Anaya
- grid.412191.e0000 0001 2205 5940Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Lara A. Aqrawi
- grid.5510.10000 0004 1936 8921Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, Oslo, Norway ,grid.457625.70000 0004 0383 3497Department of Health Sciences, Kristiania University College, Oslo, Norway
| | - Eva Baecklund
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan G. Brun
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Sara Magnusson Bucher
- grid.15895.300000 0001 0738 8966Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Maija-Leena Eloranta
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fiona Engelke
- grid.10423.340000 0000 9529 9877Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Helena Forsblad-d’Elia
- grid.8761.80000 0000 9919 9582Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Stuart B. Glenn
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Daniel Hammenfors
- grid.412008.f0000 0000 9753 1393Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Juliana Imgenberg-Kreuz
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Janicke Liaaen Jensen
- grid.5510.10000 0004 1936 8921Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Svein Joar Auglænd Johnsen
- grid.412835.90000 0004 0627 2891Department of Internal Medicine, Clinical Immunology Unit, Stavanger University Hospital, Stavanger, Norway
| | - Malin V. Jonsson
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Section for Oral and Maxillofacial Radiology, Department of Clinical Dentistry, Medical Faculty, University of Bergen, Bergen, Norway
| | - Marika Kvarnström
- grid.4714.60000 0004 1937 0626Rheumatology Unity, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden ,grid.425979.40000 0001 2326 2191Academic Specialist Center, Center for Rheumatology and Studieenheten, Stockholm Health Services, Region Stockholm, Sweden
| | - Jennifer A. Kelly
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - He Li
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.505430.7Translational Sciences, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA USA
| | - Thomas Mandl
- grid.4514.40000 0001 0930 2361Rheumatology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Javier Martín
- grid.4711.30000 0001 2183 4846Instituto de Biomedicina y Parasitología López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Gaétane Nocturne
- grid.413784.d0000 0001 2181 7253Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1184, Le Kremlin Bicêtre, France
| | - Katrine Brække Norheim
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412835.90000 0004 0627 2891Department of Rheumatology, Stavanger University Hospital, Stavanger, Norway
| | - Øyvind Palm
- grid.5510.10000 0004 1936 8921Department of Rheumatology, University of Oslo, Oslo, Norway
| | - Kathrine Skarstein
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Anna M. Stolarczyk
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kimberly E. Taylor
- grid.266102.10000 0001 2297 6811Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California USA
| | - Maria Teruel
- grid.4489.10000000121678994Genyo, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Elke Theander
- grid.411843.b0000 0004 0623 9987Department of Rheumatology, Skåne University Hospital, Malmö, Sweden ,Medical Affairs, Jannsen-Cilag EMEA (Europe/Middle East/Africa), Beerse, Belgium
| | - Swamy Venuturupalli
- grid.50956.3f0000 0001 2152 9905Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Daniel J. Wallace
- grid.50956.3f0000 0001 2152 9905Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Kiely M. Grundahl
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | | | - Lida Radfar
- grid.266900.b0000 0004 0447 0018Oral Diagnosis and Radiology Department, University of Oklahoma College of Dentistry, Oklahoma City, OK USA
| | - David M. Lewis
- grid.266900.b0000 0004 0447 0018Department of Oral and Maxillofacial Pathology, University of Oklahoma College of Dentistry, Oklahoma City, OK USA
| | - Donald U. Stone
- grid.266902.90000 0001 2179 3618Department of Ophthalmology, Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - C. Erick Kaufman
- grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Michael T. Brennan
- grid.239494.10000 0000 9553 6721Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC USA ,grid.241167.70000 0001 2185 3318Department of Otolaryngology/Head and Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC USA
| | - Joel M. Guthridge
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Judith A. James
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - R. Hal Scofield
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ,grid.413864.c0000 0004 0420 2582US Department of Veterans Affairs Medical Center, Oklahoma City, OK USA
| | - Patrick M. Gaffney
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Lindsey A. Criswell
- grid.266102.10000 0001 2297 6811Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California USA ,grid.266102.10000 0001 2297 6811Institute of Human Genetics (IHG), University of California San Francisco, San Francisco, CA USA ,grid.280128.10000 0001 2233 9230Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Roland Jonsson
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Per Eriksson
- grid.5640.70000 0001 2162 9922Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Simon J. Bowman
- grid.412563.70000 0004 0376 6589Rheumatology Department, University Hospital Birmingham NHS Foundation Trust, Birmingham, UK ,grid.6572.60000 0004 1936 7486Rheumatology Research Group, Institute of Inflammation & Ageing, University of Birmingham, Birmingham, UK ,grid.415667.7Rheumatology Department, Milton Keynes University Hospital, Milton Keynes, UK
| | - Roald Omdal
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.412835.90000 0004 0627 2891Department of Internal Medicine, Clinical Immunology Unit, Stavanger University Hospital, Stavanger, Norway
| | - Lars Rönnblom
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Blake Warner
- grid.419633.a0000 0001 2205 0568Salivary Disorder Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD USA
| | - Maureen Rischmueller
- grid.278859.90000 0004 0486 659XRheumatology Department, The Queen Elizabeth Hospital, Woodville, South Australia ,grid.1010.00000 0004 1936 7304University of Adelaide, Adelaide, South Australia
| | - Torsten Witte
- grid.10423.340000 0000 9529 9877Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - A. Darise Farris
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Xavier Mariette
- grid.413784.d0000 0001 2181 7253Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1184, Le Kremlin Bicêtre, France
| | - Marta E. Alarcon-Riquelme
- grid.4489.10000000121678994Genyo, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | | | - Caroline H. Shiboski
- grid.266102.10000 0001 2297 6811Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA USA
| | | | - Marie Wahren-Herlenius
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway ,grid.4714.60000 0004 1937 0626Rheumatology Unity, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Wan-Fai Ng
- grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK ,grid.420004.20000 0004 0444 2244NIHR Newcastle Biomedical Centre and NIHR Newcastle Clinical Research Facility, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Kathy L. Sivils
- grid.274264.10000 0000 8527 6890Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.505430.7Translational Sciences, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA USA
| | - Indra Adrianto
- grid.239864.20000 0000 8523 7701Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health System, Detroit, MI USA
| | - Gunnel Nordmark
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christopher J. Lessard
- grid.274264.10000 0000 8527 6890Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ,grid.266902.90000 0001 2179 3618Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| |
Collapse
|
4
|
Gazal S, Weissbrod O, Hormozdiari F, Dey KK, Nasser J, Jagadeesh KA, Weiner DJ, Shi H, Fulco CP, O'Connor LJ, Pasaniuc B, Engreitz JM, Price AL. Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nat Genet 2022; 54:827-836. [PMID: 35668300 PMCID: PMC9894581 DOI: 10.1038/s41588-022-01087-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/27/2022] [Indexed: 02/04/2023]
Abstract
Disease-associated single-nucleotide polymorphisms (SNPs) generally do not implicate target genes, as most disease SNPs are regulatory. Many SNP-to-gene (S2G) linking strategies have been developed to link regulatory SNPs to the genes that they regulate in cis. Here, we developed a heritability-based framework for evaluating and combining different S2G strategies to optimize their informativeness for common disease risk. Our optimal combined S2G strategy (cS2G) included seven constituent S2G strategies and achieved a precision of 0.75 and a recall of 0.33, more than doubling the recall of any individual strategy. We applied cS2G to fine-mapping results for 49 UK Biobank diseases/traits to predict 5,095 causal SNP-gene-disease triplets (with S2G-derived functional interpretation) with high confidence. We further applied cS2G to provide an empirical assessment of disease omnigenicity; we determined that the top 1% of genes explained roughly half of the SNP heritability linked to all genes and that gene-level architectures vary with variant allele frequency.
Collapse
Affiliation(s)
- Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kushal K Dey
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Huwenbo Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Bristol Myers Squibb, Cambridge, MA, USA
| | | | - Bogdan Pasaniuc
- Departments of Computational Medicine, Human Genetics, Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
5
|
Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
Collapse
Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| |
Collapse
|
6
|
Harley IT, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
Collapse
Affiliation(s)
- Isaac T.W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA,Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA,Rocky Mountain Regional Veteran’s Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA,Corresponding author at: Isaac TW Harley, MD, PhD, MS, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Barbara Davis Center, Mail Stop B115, 1775 Aurora Court, Aurora, CO 80045, USA, (I.T.W. Harley)
| | - Amr H. Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Corresponding author at: Amr H. Sawalha, MD, University of Pittsburgh, 7123 Rangos Research Center, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, (A.H. Sawalha)
| |
Collapse
|
7
|
Zhang Y, Day K, Absher DM. STAT3-mediated allelic imbalance of novel genetic variant Rs1047643 and B-cell-specific super-enhancer in association with systemic lupus erythematosus. eLife 2022; 11:72837. [PMID: 35188103 PMCID: PMC8884724 DOI: 10.7554/elife.72837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Mapping of allelic imbalance (AI) at heterozygous loci has the potential to establish links between genetic risk for disease and biological function. Leveraging multi-omics data for AI analysis and functional annotation, we discovered a novel functional risk variant rs1047643 at 8p23 in association with systemic lupus erythematosus (SLE). This variant displays dynamic AI of chromatin accessibility and allelic expression on FDFT1 gene in B cells with SLE. We further found a B-cell restricted super-enhancer (SE) that physically contacts with this SNP-residing locus, an interaction that also appears specifically in B cells. Quantitative analysis of chromatin accessibility and DNA methylation profiles further demonstrated that the SE exhibits aberrant activity in B cell development with SLE. Functional studies identified that STAT3, a master factor associated with autoimmune diseases, directly regulates both the AI of risk variant and the activity of SE in cultured B cells. Our study reveals that STAT3-mediated SE activity and cis-regulatory effects of SNP rs1047643 at 8p23 locus are associated with B cell deregulation in SLE.
Collapse
Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | | | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| |
Collapse
|
8
|
Sternhagen E, Bettendorf B, Lenert A, Lenert PS. The Role of Clinical Features and Serum Biomarkers in Identifying Patients with Incomplete Lupus Erythematosus at Higher Risk of Transitioning to Systemic Lupus Erythematosus: Current Perspectives. J Inflamm Res 2022; 15:1133-1145. [PMID: 35210816 PMCID: PMC8863324 DOI: 10.2147/jir.s275043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022] Open
Abstract
Discovery of antinuclear antibodies (ANA) enabled earlier diagnosis of systemic lupus erythematosus (SLE) and other ANA+ connective tissue diseases (CTD). Rheumatologists increasingly encounter high referral volume of ANA+ patients. It has been estimated that only a small percentage of these patients will eventually transition to either SLE or other specified CTD. Incomplete lupus erythematosus (ILE) has been defined as a subset of patients who have some SLE-specific clinical manifestations but do not meet currently accepted classification criteria for SLE. Several studies have been performed with the goal of identifying clinical features, serum and tissue biomarkers that can distinguish those patients with ILE at risk of transitioning to SLE from those who will not. Increased autoantibody diversity, presence of anti-double-stranded DNA (dsDNA) antibodies, high expression of type I and type II interferon (IFN)-gene products, increased serum levels of B-cell-activating factor of the TNF family (BAFF), and certain serum cytokines and complement products have been identified as markers with positive predictive value, particularly when combined together. Once this patient population is better characterized biochemically, clinical trials should be considered with the primary objective to completely halt or slow down the transition from ILE to SLE. Hydroxychloroquine (HCQ) appears to be a promising agent due to its good tolerability and low toxicity profile and open-label studies in ILE patients have already shown its ability to delay the onset of SLE. Other therapeutics, like those targeting abnormal type I and type II IFN-signatures, B-cell specific signaling pathways, complement activation pathways and high BAFF levels should also be evaluated, but the risk to benefit ratio must be carefully determined before they can be considered.
Collapse
Affiliation(s)
- Erin Sternhagen
- Division of Immunology, Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Brittany Bettendorf
- Division of Immunology, Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Aleksander Lenert
- Division of Immunology, Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Petar S Lenert
- Division of Immunology, Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
- Correspondence: Petar S Lenert, Clinical Professor of Medicine, C428-2GH, 200 Hawkins Drive, Iowa City, Iowa City, 52242, USA, Email
| |
Collapse
|
9
|
Functional Implications of Intergenic GWAS SNPs in Immune-Related LncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:147-160. [DOI: 10.1007/978-3-030-92034-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
10
|
Hou G, Harley ITW, Lu X, Zhou T, Xu N, Yao C, Qin Y, Ouyang Y, Ma J, Zhu X, Yu X, Xu H, Dai D, Ding H, Yin Z, Ye Z, Deng J, Zhou M, Tang Y, Namjou B, Guo Y, Weirauch MT, Kottyan LC, Harley JB, Shen N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nat Commun 2021; 12:135. [PMID: 33420081 PMCID: PMC7794586 DOI: 10.1038/s41467-020-20460-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.
Collapse
Affiliation(s)
- Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Isaac T W Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ning Xu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Chao Yao
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences(SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ye Ouyang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Hong Xu
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
- Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
| | - Dai Dai
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Jun Deng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Mi Zhou
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Leah C Kottyan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - John B Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, 45229, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China.
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China.
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA.
| |
Collapse
|
11
|
Src Family Protein Kinase Controls the Fate of B Cells in Autoimmune Diseases. Inflammation 2020; 44:423-433. [PMID: 33037966 DOI: 10.1007/s10753-020-01355-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/07/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
There are more than 80 kinds of autoimmune diseases known at present, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), inflammatory bowel disease (IBD), as well as other disorders. Autoimmune diseases have a characteristic of immune responses directly attacking own tissues, leading to systematic inflammation and subsequent tissue damage. B cells play a vital role in the development of autoimmune diseases and differentiate into plasma cells or memory B cells to secrete high-affinity antibody or provide long-lasting function. Drugs targeting B cells show good therapeutic effects for the treatment of autoimmune diseases, such as rituximab (anti-CD20 antibody). Src family protein kinases (SFKs) are believed to play important roles in a variety of cellular functions such as growth, proliferation, and differentiation of B cell via B cell antigen receptor (BCR). Lck/Yes-related novel protein tyrosine kinase (LYN), BLK (B lymphocyte kinase), and Fyn are three different kinds of SFKs mainly expressed in B cells. LYN has a dual role in the BCR signal. On the one hand, positive signals are beneficial to the development and maturation of B cells. On the other hand, LYN can also inhibit excessively activated B cells. BLK is involved in the proliferation, differentiation, and immune tolerance of B lymphocytes, and further affects the function of B cells, which may lead to autoreactive or regulatory cellular responses, increasing the risk of autoimmune diseases. Fyn may affect the development of autoimmune disorders via the differentiation of B cells in the early stage of B cell development. This article reviews the recent advances of SFKs in B lymphocytes in autoimmune diseases.
Collapse
|
12
|
Di D, Ye Q, Wu X, Zhang L, Wang X, Liu R, Huang Q, Ni J, Leng R. Polymorphisms of BLK are associated with renal disorder in patients with systemic lupus erythematosus. J Hum Genet 2020; 65:675-681. [PMID: 32313195 DOI: 10.1038/s10038-020-0756-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/28/2022]
Abstract
Previous studies are inconclusive on the relationships between BLK gene polymorphisms and clinical features of systemic lupus erythematosus (SLE). The present study aimed to estimate association between BLK loci and SLE clinical features in Chinese population. Associations between BLK single-nucleotide polymorphisms (SNPs) and susceptibility to SLE in this study were estimated using data of 1205 health controls previously reported in the same population. And a total of 814 SLE patients recruited from two different sources according with ACR criteria were analyzed for genotype-phenotype associations. A meta-analysis was conducted of the associations between BLK loci and renal disorder in SLE. The expression quantitative trait locus (eQTL) data were also extracted from the public databases for the selected SNPs. Significant associations were observed between these SNPs and susceptibility to SLE. In addition, the data showed that rs2618479 and rs7812879 were associated with renal disorder [OR = 1.51 (95% CI: 1.15, 1.99) and 1.61 (95% CI: 1.21, 2.14), Pcorr = 0.033 and 0.011, respectively] and proteinuria [OR = 1.47 (95% CI: 1.12, 1.95) and 1.52 (95% CI: 1.14, 2.03), Pcorr = 0.048 and 0.040, respectively]. The consistent associations were observed in two independent centers as well as new cases group. The result of meta-analysis for rs2618479 was also significant [OR = 1.35 (95% CI: 1.12, 1.62)]. In addition, bioinformatics analysis demonstrated that the two SNPs were significantly associated with the expression of BLK in whole blood and several immune cells. Our data support that variant loci of BLK are associated with presence of renal disorder in patients with SLE.
Collapse
Affiliation(s)
- Dongsheng Di
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Qianling Ye
- Department of Hematology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiaoxiao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Linlin Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Xufan Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Ruishan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Qian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Jing Ni
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ruixue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China. .,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China.
| |
Collapse
|
13
|
Ramírez-Bello J, Fragoso JM, Alemán-Ávila I, Jiménez-Morales S, Campos-Parra AD, Barbosa-Cobos RE, Moreno J. Association of BLK and BANK1 Polymorphisms and Interactions With Rheumatoid Arthritis in a Latin-American Population. Front Genet 2020; 11:58. [PMID: 32153635 PMCID: PMC7045059 DOI: 10.3389/fgene.2020.00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction BLK has been identified as a risk factor to rheumatoid arthritis (RA) primarily in Asian or European-derived populations. However, this finding has not been evaluated in other populations such as Latin-Americans, except for Colombians. On the other hand, BANK1 single nucleotide variants (SNVs) have been scarcely studied in RA patients. Objective The aim of this study was to determine whether the BLK rs2736340T/C, rs13277113A/G, and BANK1 rs10516487G/A (R61H) and rs3733197G/A (A383T) polymorphisms are risk factors to RA in a sample of patients from Central Mexico. Materials and Methods We studied 957 women; 487 controls and 470 patients with RA by means of a TaqMan® SNP genotyping assay with fluorescent probes for the BLK rs13277113A/G, rs2736340T/C and BANK1 10516487G/A (R61H) and rs3733197G/A (A383T) variants. Result The BLK rs2736340T/C and rs13277113A/G variants were associated with risk for RA: C vs T; OR 1.39, p = 0.001, and G vs A; OR 1.37, p = 0.004, respectively. In addition, there was also an association between BANK1 R61H and RA: A vs G; OR 1.49, p = 0.003, but no with BANK1 A383T. We also identified an interaction significant between genotypes of BLK rs2736340T/C-BANK1 rs10516487G/A and RA: OR 1.65, p = 0.0001. Conclusions Our data suggest that both BLK and BANK1 confer susceptibility to RA in Mexican patients. The individual association of BANK1 rs1054857G/A with RA had not been previously reported in a particular population (except for pooled patients from several countries), therefore, our study presents the first evidence of association between this BANK1 variant and RA.
Collapse
Affiliation(s)
| | - José M Fragoso
- Laboratorio de Biología Molecular, Instituto Nacional de Cardiología, Mexico City, Mexico
| | | | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alma D Campos-Parra
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | - José Moreno
- Dirección de Investigación, Hospital Juárez de México, Mexico City, Mexico
| |
Collapse
|
14
|
Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus. Sci Rep 2019; 9:15433. [PMID: 31659207 PMCID: PMC6817816 DOI: 10.1038/s41598-019-51864-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Personalized medicine approaches are increasingly sought for diseases with a heritable component. Systemic lupus erythematosus (SLE) is the prototypic autoimmune disease resulting from loss of immunologic tolerance, but the genetic basis of SLE remains incompletely understood. Genome wide association studies (GWAS) identify regions associated with disease, based on common single nucleotide polymorphisms (SNPs) within them, but these SNPs may simply be markers in linkage disequilibrium with other, causative mutations. Here we use an hierarchical screening approach for prediction and testing of true functional variants within regions identified in GWAS; this involved bioinformatic identification of putative regulatory elements within close proximity to SLE SNPs, screening those regions for potentially causative mutations by high resolution melt analysis, and functional validation using reporter assays. Using this approach, we screened 15 SLE associated loci in 143 SLE patients, identifying 7 new variants including 5 SNPs and 2 insertions. Reporter assays revealed that the 5 SNPs were functional, altering enhancer activity. One novel variant was linked to the relatively well characterized rs9888739 SNP at the ITGAM locus, and may explain some of the SLE heritability at this site. Our study demonstrates that non-coding regulatory elements can contain private sequence variants affecting gene expression, which may explain part of the heritability of SLE.
Collapse
|
15
|
Ramírez-Bello J, Jiménez-Morales S, Montufar-Robles I, Fragoso JM, Barbosa-Cobos RE, Saavedra MA, Sánchez-Muñoz F. BLK and BANK1 polymorphisms and interactions are associated in Mexican patients with systemic lupus erythematosus. Inflamm Res 2019; 68:705-713. [DOI: 10.1007/s00011-019-01253-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/30/2022] Open
|
16
|
Cheng CW, Yang SF, Wang YH, Fang WF, Lin YC, Tang KT, Lin JD. Associations of secreted phosphoprotein 1 and B lymphocyte kinase gene polymorphisms with autoimmune thyroid disease. Eur J Clin Invest 2019; 49:e13065. [PMID: 30589937 DOI: 10.1111/eci.13065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 12/23/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Dysregulation of the type 1 interferon (IFN)-related signalling pathway predisposes one to autoimmune diseases. Possible associations of single-nucleotide polymorphisms (SNPs) of secreted phosphoprotein 1 (SPP1) and B lymphocyte kinase (BLK) of the type 1 IFN-related signalling pathway with autoimmune thyroid disease (AITD) in an ethnic Chinese (ie Taiwanese) population were tested. METHODS Totally, 83 Hashimoto's thyroiditis (HT) patients, 319 Graves' disease (GD) patients and 369 controls were enrolled. Genotypes of the two SNPs (rs1126772 and rs1126616) of SPP1 and two SNPs (rs13277113 and rs2736340) of BLK were determined. RESULTS Our results showed reduced percentages of the G allele of rs13277113 of BLK in GD (P = 0.037, odds ratio [OR] = 0.78, 95% confidence interval [CI] = 0.62-0.99) and HT (P = 0.002, OR = 0.54, 95% CI = 0.36-0.81), compared to the controls. At the same time, lower frequencies of the C allele of rs2736340 of BLK in GD (P = 0.025, OR = 0.76, 95% CI = 0.60-0.97) and HT (P = 0.003, OR = 0.53, 95% CI = 0.35-0.81) than the controls were also observed. There were significantly higher AT haplotype frequencies of rs1327713 and rs2736340 in GD and HT patients than in the controls (P = 0.025, OR = 1.31, 95% CI = 1.03-1.67, and P = 0.003, OR = 1.89, 95% CI = 1.24-2.87, respectively). Moreover, the anti-microsomal antibody titre was associated with rs2736340. CONCLUSIONS Genetic variants of rs13277113 and rs2736340 of BLK were associated with susceptibility to GD, HT and AITD in an ethnic Chinese population. Our results suggest the BLK may participate in the pathogenesis of GD, HT and AITD.
Collapse
Affiliation(s)
- Chao-Wen Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Traditional Herb Medicine Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yuan-Hung Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Medical Research, Shuang-Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Wen-Fang Fang
- Department of Family Medicine, Shuang-Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Ying-Chin Lin
- Department of Family Medicine, Shuang-Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Kam-Tsun Tang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiunn-Diann Lin
- Division of Endocrinology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
17
|
Fike AJ, Elcheva I, Rahman ZSM. The Post-GWAS Era: How to Validate the Contribution of Gene Variants in Lupus. Curr Rheumatol Rep 2019; 21:3. [DOI: 10.1007/s11926-019-0801-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
18
|
High-resolution genetic mapping of putative causal interactions between regions of open chromatin. Nat Genet 2018; 51:128-137. [PMID: 30478436 PMCID: PMC6330062 DOI: 10.1038/s41588-018-0278-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 10/15/2018] [Indexed: 01/04/2023]
Abstract
Physical interaction of regulatory elements in three-dimensional space poses a challenge for studies of disease because non-coding risk variants may be great distances from the genes they regulate. Experimental methods to capture these interactions, such as chromosome conformation capture, usually cannot assign causal direction of effect between regulatory elements, an important component of fine-mapping studies. We developed a Bayesian hierarchical approach that uses two-stage least squares and applied it to an ATAC-seq (assay for transposase-accessible chromatin using sequencing) data set from 100 individuals, to identify over 15,000 high-confidence causal interactions. Most (60%) interactions occurred over <20 kb, where chromosome conformation capture-based methods perform poorly. For a fraction of loci, we identified a single variant that alters accessibility across multiple regions, and experimentally validated the BLK locus, which is associated with multiple autoimmune diseases, using CRISPR genome editing. Our study highlights how association genetics of chromatin state is a powerful approach for identifying interactions between regulatory elements.
Collapse
|
19
|
Joo YB, Lim J, Tsao BP, Nath SK, Kim K, Bae SC. Genetic variants in systemic lupus erythematosus susceptibility loci, XKR6 and GLT1D1 are associated with childhood-onset SLE in a Korean cohort. Sci Rep 2018; 8:9962. [PMID: 29967481 PMCID: PMC6028392 DOI: 10.1038/s41598-018-28128-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/15/2018] [Indexed: 12/21/2022] Open
Abstract
Impact of genetic variants on the age of systemic lupus erythematosus (SLE) onset was not fully understood. We investigated a cumulative effect of SLE-risk variants on the age of SLE onset and scanned genome-wide SNPs to search for new risk loci of childhood-onset SLE (cSLE). We analyzed 781 Korean single-center SLE subjects who previously genotyped by both Immunochip and genome-wide SNP arrays. Individual genetic risk scores (GRS) from well-validated SLE susceptibility loci were calculated and tested for their association with cSLE (<16 years at onset). Single-variant association tests were performed using a multivariable logistic regression adjusting for population stratification. GRS from SLE susceptibility loci was significantly higher in cSLE than aSLE (p = 1.23 × 10−3). Two SNPs, rs7460469 in XKR6 (p = 1.26 × 10−8, OR = 5.58) and rs7300146 in GLT1D1 p = 1.49 × 10−8, OR = 2.85), showed the most significant associations with cSLE. The model consisting of GRS of SLE and two newly identified loci showed an area under curve (AUC) of 0.71 in a receiver operating characteristics (ROC) curve for prediction of cSLE. In conclusion, cSLE is associated with a high cumulative SLE-risk effect and two novel SNPs rs7460469 and rs7300146, providing the first predictive model for cSLE in Koreans.
Collapse
Affiliation(s)
- Young Bin Joo
- Department of Rheumatology, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Republic of Korea
| | - Jiwoo Lim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Betty P Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea.
| |
Collapse
|
20
|
Gallagher MD, Chen-Plotkin AS. The Post-GWAS Era: From Association to Function. Am J Hum Genet 2018; 102:717-730. [PMID: 29727686 DOI: 10.1016/j.ajhg.2018.04.002] [Citation(s) in RCA: 464] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
During the past 12 years, genome-wide association studies (GWASs) have uncovered thousands of genetic variants that influence risk for complex human traits and diseases. Yet functional studies aimed at delineating the causal genetic variants and biological mechanisms underlying the observed statistical associations with disease risk have lagged. In this review, we highlight key advances in the field of functional genomics that may facilitate the derivation of biological meaning post-GWAS. We highlight the evidence suggesting that causal variants underlying disease risk often function through regulatory effects on the expression of target genes and that these expression effects might be modest and cell-type specific. We moreover discuss specific studies as proof-of-principle examples for current statistical, bioinformatic, and empirical bench-based approaches to downstream elucidation of GWAS-identified disease risk loci.
Collapse
|
21
|
Abstract
PURPOSE OF REVIEW Our understanding on genetic basis of SLE has been advanced through genome-wide association studies. We review recent progress in lupus genetics with a focus on SLE-associated loci that have been functionally characterized, and discuss the potential for clinical translation of genetics data. RECENT FINDINGS Over 100 loci have been confirmed to show robust association with SLE and many share with other immune-mediated diseases. Although causative variants captured at these established loci are limited, they guide biological studies of gene targets for functional characterization which highlight the importance of aberrant recognition of self-nucleic acid, type I interferon overproduction, and defective immune cell signaling underlying the pathogenesis of SLE. Increasing examples illustrate a predictive value of genetic findings in susceptibility/prognosis prediction, clinical classification, and pharmacological implication. Genetic findings provide a foundation for better understanding of disease pathogenic mechanisms and opportunities for target selection in lupus drug development.
Collapse
|
22
|
Odhams CA, Cunninghame Graham DS, Vyse TJ. Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease. PLoS Genet 2017; 13:e1007071. [PMID: 29059182 PMCID: PMC5695635 DOI: 10.1371/journal.pgen.1007071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/02/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines. After stringently testing for a shared causal variant using both the Joint Likelihood Mapping and Regulatory Trait Concordance frameworks, we found that gene-level quantification significantly underestimated the number of causal cis-eQTLs. Only 5.0-5.3% of loci were found to share a causal cis-eQTL at gene-level compared to 12.9-18.4% at exon-level and 9.6-10.5% at junction-level. More than a fifth of autoimmune loci shared an underlying causal variant in a single cell type by combining all five quantification types; a marked increase over current estimates of steady-state causal cis-eQTLs. Causal cis-eQTLs detected at different quantification types localised to discrete epigenetic annotations. We applied a linear mixed-effects model to distinguish cis-eQTLs modulating all expression elements of a gene from those where the signal is only evident in a subset of elements. Exon-level analysis detected disease-associated cis-eQTLs that subtly altered transcription globally across the target gene. We dissected in detail the genetic associations of systemic lupus erythematosus and functionally annotated the candidate genes. Many of the known and novel genes were concealed at gene-level (e.g. IKZF2, TYK2, LYST). Our findings are provided as a web resource.
Collapse
Affiliation(s)
- Christopher A. Odhams
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Deborah S. Cunninghame Graham
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
| | - Timothy J. Vyse
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
| |
Collapse
|
23
|
Teos LY, Alevizos I. Genetics of Sjögren's syndrome. Clin Immunol 2017; 182:41-47. [PMID: 28476436 PMCID: PMC5660941 DOI: 10.1016/j.clim.2017.04.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/30/2017] [Accepted: 04/30/2017] [Indexed: 12/14/2022]
Abstract
The pathogenesis of Sjögren's syndrome has not been elucidated. There has been evidence that genetics play an important role in the development of this disease from earlier studies. However, till now only a number of genes have been identified to be associated with SS, and these have only a weak or moderate effect. In this review we summarize the findings of the genetics studies and emphasize the need of large multicenter projects that will increase the sample sizes to provide more meaningful associations, as is the case in other common autoimmune diseases.
Collapse
Affiliation(s)
- Leyla Y Teos
- Sjögren's Syndrome and Salivary Gland Dysfunction Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Ilias Alevizos
- Sjögren's Syndrome and Salivary Gland Dysfunction Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
24
|
Zeng C, Fang C, Weng H, Xu X, Wu T, Li W. B-cell lymphocyte kinase polymorphisms rs13277113, rs2736340, and rs4840568 and risk of autoimmune diseases: A meta-analysis. Medicine (Baltimore) 2017; 96:e7855. [PMID: 28885337 PMCID: PMC6392982 DOI: 10.1097/md.0000000000007855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND B-cell lymphocyte kinase (BLK) is an inhibitor of B cells that has an important influence on several autoimmune diseases, but there is a lack of comprehensive analysis of its association with autoimmune diseases. Hence, it is meaningful to conduct a comprehensive analysis. METHODS A systematic literature search was performed on the PubMed, ScienceDirect, and Web of Science databases up to June 30, 2016. The data were extracted and quality-assessed before conducting the meta-analysis. The odds ratios (ORs) and 95% confidence intervals (95% CIs) were assessed with the STATA version 12.0 software. Subgroup and sensitivity analysis were conducted to explore potential sources of heterogeneity. RESULTS Altogether, 33 studies with 68,874 cases and 90,684 controls, 24 studies with 31,095 cases and 39,077 controls for rs13277113, 21 studies with 26,388 cases and 40,635 controls for rs2736340, and 4 studies with 11,391 cases and 10,972 controls for rs4840568 were included in this meta-analysis. The results revealed that the BLK rs13277113 and rs2736340 polymorphisms increased the risk of autoimmune diseases in the total analysis (A vs G: OR = 1.33, 95% CI = 1.27-1.39, P < .01; T vs C: OR = 1.34, 95% CI = 1.27-1.41, P < .01), and rs4840568 was positively associated with systemic lupus erythematosus (SLE) (A vs G: OR = 1.32, 95% CI = 1.22-1.43, P = .01). CONCLUSION This meta-analysis shows that the BLK (rs13277113, rs2736340, rs4840568) polymorphisms may be a risk factor for developing autoimmune diseases, especially for Asian populations and SLE.
Collapse
Affiliation(s)
- Chang Zeng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Cheng Fang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hong Weng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaoqing Xu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Tianyang Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Wenhua Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| |
Collapse
|
25
|
Odhams CA, Cortini A, Chen L, Roberts AL, Viñuela A, Buil A, Small KS, Dermitzakis ET, Morris DL, Vyse TJ, Cunninghame Graham DS. Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. Hum Mol Genet 2017; 26:1003-1017. [PMID: 28062664 PMCID: PMC5409091 DOI: 10.1093/hmg/ddw417] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered the greatest frequency of candidate-causal eQTLs using exon-level RNA-Seq, and identified novel SLE susceptibility genes (e.g. NADSYN1 and TCF7) that were concealed using microarrays, including four non-coding RNAs. Many of these eQTLs were found to influence the expression of several genes, supporting the notion that risk haplotypes may harbour multiple functional effects. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, and other candidate genes (e.g. WDFY4) through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. We conclude that to better understand the true functional consequence of regulatory variants, quantification by RNA-Seq should be performed at the exon-level as a minimum, and run in parallel with gene and splice-junction level quantification.
Collapse
Affiliation(s)
| | - Andrea Cortini
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Ana Viñuela
- Department of Twin Research, King's College London, London, UK
| | | | - Kerrin S Small
- Department of Twin Research, King's College London, London, UK
| | | | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | | |
Collapse
|
26
|
Demirci FY, Wang X, Morris DL, Feingold E, Bernatsky S, Pineau C, Clarke A, Ramsey-Goldman R, Manzi S, Vyse TJ, Kamboh MI. Multiple signals at the extended 8p23 locus are associated with susceptibility to systemic lupus erythematosus. J Med Genet 2017; 54:381-389. [PMID: 28289186 DOI: 10.1136/jmedgenet-2016-104247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/16/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND A major systemic lupus erythematosus (SLE) susceptibility locus lies within a common inversion polymorphism region (encompassing 3.8 - 4.5 Mb) located at 8p23. Initially implicated genes included FAM167A-BLK and XKR6, of which BLK received major attention due to its known role in B-cell biology. Recently, additional SLE risk carried in non-inverted background was also reported. OBJECTIVE AND METHODS In this case -control study, we further investigated the 'extended' 8p23 locus (~ 4 Mb) where we observed multiple SLE signals and assessed these signals for their relation to the inversion affecting this region. The study involved a North American discovery data set (~ 1200 subjects) and a replication data set (> 10 000 subjects) comprising European-descent individuals. RESULTS Meta-analysis of 8p23 SNPs, with p < 0.05 in both data sets, identified 51 genome-wide significant SNPs (p < 5.0 × 10-8). While most of these SNPs were related to previously implicated signals (XKR6-FAM167A-BLK subregion), our results also revealed two 'new' SLE signals, including SGK223-CLDN23-MFHAS1 (6.06 × 10-9 ≤ meta p ≤ 4.88 × 10-8) and CTSB (meta p = 4.87 × 10-8) subregions that are located > 2 Mb upstream and ~ 0.3 Mb downstream from previously reported signals. Functional assessment of relevant SNPs indicated putative cis-effects on the expression of various genes at 8p23. Additional analyses in discovery sample, where the inversion genotypes were inferred, replicated the association of non-inverted status with SLE risk and suggested that a number of SLE risk alleles are predominantly carried in non-inverted background. CONCLUSIONS Our results implicate multiple (known+novel) SLE signals/genes at the extended 8p23 locus, beyond previously reported signals/genes, and suggest that this broad locus contributes to SLE risk through the effects of multiple genes/pathways.
Collapse
Affiliation(s)
- F Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Xingbin Wang
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Sasha Bernatsky
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, Canada
| | - Christian Pineau
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, Canada
| | - Ann Clarke
- Division of Rheumatology, Department of Medicine, University of Calgary, Calgary, Canada
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Susan Manzi
- Department of Medicine, Lupus Center of Excellence, Allegheny Health Network, Pittsburgh, USA
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - M I Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| |
Collapse
|
27
|
Sung SSJ, Ge Y, Dai C, Wang H, Fu SM, Sharma R, Hahn YS, Yu J, Le TH, Okusa MD, Bolton WK, Lawler JR. Dependence of Glomerulonephritis Induction on Novel Intraglomerular Alternatively Activated Bone Marrow-Derived Macrophages and Mac-1 and PD-L1 in Lupus-Prone NZM2328 Mice. THE JOURNAL OF IMMUNOLOGY 2017; 198:2589-2601. [PMID: 28219886 DOI: 10.4049/jimmunol.1601565] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/26/2017] [Indexed: 01/01/2023]
Abstract
Glomerular damage mediated by glomerulus-infiltrating myeloid-derived cells is a key pathogenic event in lupus nephritis (LN), but the process is poorly understood. Confocal microscopy of kidney sections and flow cytometry analysis of glomerular cells from magnetic bead-purified glomeruli have identified glomerulus-infiltrating leukocyte populations in NZM2328 (NZM) lupus-prone mice with spontaneous chronic glomerulonephritis (GN) and anti-glomerular basement membrane-induced nephritis. The occurrence of a major glomerulus-infiltrating CD11b+F4/80-I-A- macrophage population exhibiting the markers programmed death ligand-1 (PD-L1), Mac-2, and macrophage mannose receptor (CD206) and producing Klf4, Il10, Retnla, Tnf, and Il6 mRNA, which are known to be expressed by alternatively activated (M2b) macrophages, correlated with proteinuria status. In NZM mice with spontaneous LN, glomerular macrophage infiltration is predominant. CD11b+F4/80-I-A- intraglomerular macrophages and polymorphonuclear neutrophils (PMN) are important in inducing GN, as anti-CD11b and -ICAM-1 mAb inhibited both proteinuria and macrophage and PMN infiltration. The predominant and high expression of PD-L1 by CD11b+F4/80-I-A- glomerular macrophages in kidneys of mice with GN and the inhibition of proteinuria by anti-PD-L1 mAb supported the pathogenic role of these macrophages but not the PD-L1- PMN in GN development and in inducing podocyte damage. In NZM mice with spontaneous chronic GN and severe proteinuria, few glomerulus-infiltrating PMN were found, leaving macrophages and, to a less extent, dendritic cells as the major infiltrating leukocytes. Taken together, these data support the important pathogenic effect of CD11b+F4/80-I-A- M2b-like glomerulus-infiltrating macrophages in LN and reinforce macrophages as a promising target for GN treatment.
Collapse
Affiliation(s)
- Sun-Sang J Sung
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908; .,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Yan Ge
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908; and
| | - Chao Dai
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Hongyang Wang
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Shu Man Fu
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908; and
| | - Rahul Sharma
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Young S Hahn
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908; and
| | - Jing Yu
- Department of Cell Biology, University of Virginia Health Sciences Center, Charlottesville, VA 22908
| | - Thu H Le
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Mark D Okusa
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Warren K Bolton
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Jessica R Lawler
- Department of Medicine, University of Virginia Health Sciences Center, Charlottesville, VA 22908.,Center for Immunity, Inflammation, and Regenerative Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| |
Collapse
|
28
|
Functional variant in the promoter region of IL-27 alters gene transcription and confers a risk for ulcerative colitis in northern Chinese Han. Hum Immunol 2017; 78:287-293. [PMID: 28069403 DOI: 10.1016/j.humimm.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/28/2016] [Accepted: 01/05/2017] [Indexed: 12/19/2022]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disorder of unknown etiology and a polygenic disease. IL-27 encodes p28, a subunit of IL-12 family cytokines, and has been implicated in the pathogenesis of UC. The aims of the present study were to evaluate the genetic association of a variant of the IL-27 gene with UC and to further characterize the functional variant in the IL-27 gene that influences the risk for UC. Our data demonstrated that the genetic variant rs153109 in the 5' upstream region of IL-27 is significantly associated with UC in Chinese Han individuals. Analysis of IL-27 transcripts demonstrated that individuals carrying the risk allele of rs153109 display reduced transcription of IL-27 in PBMCs. Luciferase activity assays demonstrated that the risk allele rs153109 results in decreased promoter activity compared to a non-risk allele in a tissue specific manner. Mechanistic characterization of histone modifications in the promoter region revealed that the risk haplotype tagged by the risk allele of rs153109 reduces the levels of H3K3me3 and H3K27ac.
Collapse
|
29
|
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay. Cell 2016; 165:1519-1529. [PMID: 27259153 DOI: 10.1016/j.cell.2016.04.027] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/25/2015] [Accepted: 04/12/2016] [Indexed: 01/20/2023]
Abstract
Although studies have identified hundreds of loci associated with human traits and diseases, pinpointing causal alleles remains difficult, particularly for non-coding variants. To address this challenge, we adapted the massively parallel reporter assay (MPRA) to identify variants that directly modulate gene expression. We applied it to 32,373 variants from 3,642 cis-expression quantitative trait loci and control regions. Detection by MPRA was strongly correlated with measures of regulatory function. We demonstrate MPRA's capabilities for pinpointing causal alleles, using it to identify 842 variants showing differential expression between alleles, including 53 well-annotated variants associated with diseases and traits. We investigated one in detail, a risk allele for ankylosing spondylitis, and provide direct evidence of a non-coding variant that alters expression of the prostaglandin EP4 receptor. These results create a resource of concrete leads and illustrate the promise of this approach for comprehensively interrogating how non-coding polymorphism shapes human biology.
Collapse
|
30
|
Abstract
Systemic lupus erythematosus is a heterogeneous autoimmune disease marked by the presence of pathogenic autoantibodies, immune dysregulation, and chronic inflammation that may lead to increased morbidity and early mortality from end-organ damage. More than half of all systemic lupus erythematosus patients will develop lupus nephritis. Genetic-association studies have identified more than 50 polymorphisms that contribute to lupus nephritis pathogenesis, including genetic variants associated with altered programmed cell death and defective immune clearance of programmed cell death debris. These variants may support the generation of autoantibody-containing immune complexes that contribute to lupus nephritis. Genetic variants associated with lupus nephritis also affect the initial phase of innate immunity and the amplifying, adaptive phase of the immune response. Finally, genetic variants associated with the kidney-specific effector response may influence end-organ damage and the progression to end-stage renal disease and death. This review discusses genetic insights of key pathogenic processes and pathways that may lead to lupus nephritis, as well as the clinical implications of these findings as they apply to recent advances in biologic therapies.
Collapse
|
31
|
Teruel M, Alarcón-Riquelme ME. The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned. J Autoimmun 2016; 74:161-175. [PMID: 27522116 DOI: 10.1016/j.jaut.2016.08.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Abstract
The genome-wide association study is a free-hypothesis approach based on screening of thousands or even millions of genetic variants distributed throughout the whole human genome in relation to a phenotype. The relevant role of the genome-wide association studies in the last decade is undisputed because it has permitted to elucidate multiple risk genetic factors associated with the susceptibility to several human complex diseases. Regarding systemic lupus erythematosus (SLE) this approach has allowed to identify more than 60 risk loci for SLE susceptibility across populations to date, increasing our understanding on the pathogenesis of this disease. We present the latest findings in the genetic of SLE across populations using genome-wide approaches. These studies revealed that most of the genetic risk is shared across borders and ethnicities. Finally, we focus on describing the most important risk loci for SLE attempting to cover the genetic findings in relation to functional polymorphisms, such as missense single nucleotide polymorphisms (SNPs) or regulatory variants involved in the development of the disease. The functional studies try to identify the causality of some GWAS-associated variants, many of which fall in non-coding regions of the genome, suggesting a regulatory role. Many loci show an environmental interaction, another aspect revealed by the studies of epigenetic modifications and those associated with genetic variants. Finally, new-generation sequencing technologies can open other paths in the research on SLE genetics, the role of rare variants and the detailed identification of causal regulatory variation. The clinical relevance of the genetic factors will be shown when we are able to use them or in combination with other molecular measurements to re-classify a heterogeneous disease such as SLE.
Collapse
Affiliation(s)
- Maria Teruel
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain.
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain; Institute of Environmental Medicine, Karolinska Institute, Stockholm, 171 67, Sweden.
| |
Collapse
|
32
|
Abstract
The genes associated with Sjögren syndrome (SS) can be assigned to the NF-kB pathway, the IFN signaling pathway, lymphocyte signaling, and antigen presentation. The frequencies of risk variants show they are common with modest genetic effects. The strongest genetic association outside the human leukocyte antigen region is in IRF5, a gene relevant in the IFN signaling pathway and for B cell differentiation. Although no association has been found with the NF-kB gene itself, associations in TNFAIP3 and TNIP1 (both genome-wide significant), VCAM1 and IRAK1BP (both suggestive), point to genetic explanations for dysregulation of the NF-kB pathway in SS.
Collapse
Affiliation(s)
- Tove Ragna Reksten
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, The Laboratory Building, Haukeland University Hospital, Jonas Lies vei 87, N-5021 Bergen, Norway
| | - Christopher J Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, MBSB 451, Oklahoma City, OK 73104, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, MBSB 451, Oklahoma City, OK 73104, USA.
| |
Collapse
|
33
|
Zhou Y, Li X, Wang G, Li X. Association of FAM167A-BLK rs2736340 Polymorphism with Susceptibility to Autoimmune Diseases: A Meta-Analysis. Immunol Invest 2016; 45:336-48. [PMID: 27105348 DOI: 10.3109/08820139.2016.1157812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The purpose of this study is to evaluate the correlation between family with sequence similarity 167A-B lymphoid tyrosine kinase (FAM167A-BLK) rs2736340 polymorphism and autoimmune diseases. METHODS Databases including PubMed, EMBASE, Chinese National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature database (CBM) and Chinese database, Wan Fang database were used in searching eligible studies from January 1, 1966 to October 2, 2015. The odds ratios (ORs) and their 95% confidence intervals (CIs) were pooled to estimate the strength of the association. RESULTS A total of 25 studies with 30,217 patients and 44,754 controls were included in the meta-analysis. The overall results showed FAM167A-BLK rs2736340 T allele was a risk allele for autoimmune diseases (OR 1.36, 95% CI 1.28-1.44, p < 0.001). In the subgroup by ethnicities, the results suggested T allele was an increased risk in North America, Europe, and Asia (OR 1.33, 95% CI 1.10-1.60, p = 0.004; OR 1.26, 95% CI 1.22-1.31, p < 0.001; and OR 1.46, 95% CI 1.40-1563, p < 0.001, respectively), but not in Africa. Subgroup analysis in different genetic models (recessive, dominant, and additive) revealed significant association between rs2736340 and autoimmune diseases in Asia and North America, but not the recessive model in Europe or Africa, or the additive model in Africa. Stratification analysis by diseases suggested FAM167A-BLK rs2736340 had a positive association with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc) and Kawasaki disease, primary Sjogren's syndrome (pSS), primary antiphosholipid syndrome (APS), and myositis. CONCLUSION The current meta-analysis suggested that FAM167A-BLK rs2736340 polymorphism is associated with several autoimmune diseases.
Collapse
Affiliation(s)
- Yingbo Zhou
- a Department of Rheumatology and Immunology , Anhui Provincial Hospital affiliated with Anhui Medical University , Hefei , Anhui , China
| | - Xiangpei Li
- a Department of Rheumatology and Immunology , Anhui Provincial Hospital affiliated with Anhui Medical University , Hefei , Anhui , China
| | - Guosheng Wang
- a Department of Rheumatology and Immunology , Anhui Provincial Hospital affiliated with Anhui Medical University , Hefei , Anhui , China
| | - Xiaomei Li
- a Department of Rheumatology and Immunology , Anhui Provincial Hospital affiliated with Anhui Medical University , Hefei , Anhui , China
| |
Collapse
|
34
|
Simpfendorfer KR, Armstead BE, Shih A, Li W, Curran M, Manjarrez-Orduño N, Lee AT, Diamond B, Gregersen PK. Autoimmune disease-associated haplotypes of BLK exhibit lowered thresholds for B cell activation and expansion of Ig class-switched B cells. Arthritis Rheumatol 2016; 67:2866-76. [PMID: 26246128 DOI: 10.1002/art.39301] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/21/2015] [Indexed: 12/26/2022]
Abstract
OBJECTIVE B lymphoid kinase (BLK) is associated with rheumatoid arthritis (RA) and several other B cell-associated autoimmune disorders. BLK risk variants are consistently associated with reduced BLK expression, but the mechanisms by which reduced expression alters human B cell function to confer autoimmune disease susceptibility are unknown. This study was undertaken to characterize the BLK risk haplotype and to determine associated B cell functional phenotypes involved in autoimmunity. METHODS The BLK risk haplotype association with RA (determined using whole-genome sequencing data) was confirmed in 2,526 RA cases and 2,134 controls. Peripheral blood mononuclear cells (PBMCs) from RA patients, healthy adults, and umbilical cord blood were used to study B cell functional phenotypes associated with the BLK risk genotype. Association of the BLK haplotype with B cell phenotypes was analyzed using cell culture and flow cytometry. RESULTS Two insertion/deletions were found on the RA risk haplotype in BLK, and the reduction in BLK expression associated with the risk haplotype was confirmed in primary B lymphocytes. Carriers of the RA-associated haplotype had evidence of lower basal B cell receptor (BCR) signaling activity, yet their B cells were hyperactivatable, with enhanced up-regulation of CD86 after BCR crosslinking and greater T cell stimulatory capacity. The number of isotype-switched memory B cells was also significantly increased in subjects carrying the risk haplotype. CONCLUSION A major mechanism underlying the BLK association with autoimmune disease involves lowered thresholds for BCR signaling, enhanced B cell-T cell interactions, and altered patterns of isotype switching.
Collapse
Affiliation(s)
| | | | - Andrew Shih
- Feinstein Institute for Medical Research, Manhasset, New York
| | - Wentian Li
- Feinstein Institute for Medical Research, Manhasset, New York
| | - Mark Curran
- Janssen Pharmaceuticals, Springhouse, Pennsylvania
| | | | - Annette T Lee
- Feinstein Institute for Medical Research, Manhasset, New York
| | - Betty Diamond
- Feinstein Institute for Medical Research, Manhasset, New York
| | | |
Collapse
|
35
|
The SLE variant Ala71Thr of BLK severely decreases protein abundance and binding to BANK1 through impairment of the SH3 domain function. Genes Immun 2016; 17:128-38. [PMID: 26821283 DOI: 10.1038/gene.2016.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 09/16/2015] [Accepted: 12/08/2015] [Indexed: 01/17/2023]
Abstract
The B-lymphocyte kinase (BLK) gene is associated genetically with several human autoimmune diseases including systemic lupus erythematosus. We recently described that the genetic risk is given by two haplotypes: one covering several strongly linked single-nucleotide polymorphisms within the promoter of the gene that correlated with low transcript levels, and a second haplotype that includes a rare nonsynonymous variant (Ala71Thr). Here we show that this variant, located within the BLK SH3 domain, is a major determinant of protein levels. In vitro analyses show that the 71Thr isoform is hyperphosphorylated and promotes kinase activation. As a consequence, BLK is ubiquitinated, its proteasomal degradation enhanced and the average life of the protein is reduced by half. Altogether, these findings suggest that an intrinsic autoregulatory mechanism previously unappreciated in BLK is disrupted by the 71Thr substitution. Because the SH3 domain is also involved in protein interactions, we sought for differences between the two isoforms in trafficking and binding to protein partners. We found that binding of the 71Thr variant to the adaptor protein BANK1 is severely reduced. Our study provides new insights on the intrinsic regulation of BLK activation and highlights the dominant role of its SH3 domain in BANK1 binding.
Collapse
|
36
|
High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet 2016; 48:323-30. [PMID: 26808113 PMCID: PMC4767573 DOI: 10.1038/ng.3496] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/23/2015] [Indexed: 01/04/2023]
Abstract
Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.
Collapse
|
37
|
Bentham J, Morris DL, Graham DSC, Pinder CL, Tombleson P, Behrens TW, Martín J, Fairfax BP, Knight JC, Chen L, Replogle J, Syvänen AC, Rönnblom L, Graham RR, Wither JE, Rioux JD, Alarcón-Riquelme ME, Vyse TJ. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat Genet 2015; 47:1457-1464. [PMID: 26502338 PMCID: PMC4668589 DOI: 10.1038/ng.3434] [Citation(s) in RCA: 575] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. Previous genome-wide association studies (GWAS) had modest sample sizes, reducing their scope and reliability. Our study comprised 7,219 cases and 15,991 controls of European ancestry, constituting a new GWAS, a meta-analysis with a published GWAS and a replication study. We have mapped 43 susceptibility loci, including ten new associations. Assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. Other likely causal genes were established by examining associated alleles for cis-acting eQTL effects in a range of ex vivo immune cells. We found an over-representation (n = 16) of transcription factors among SLE susceptibility genes. This finding supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing SLE.
Collapse
Affiliation(s)
- James Bentham
- Division of Genetics and Molecular Medicine, King's College London, UK
| | - David L Morris
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | | | - Philip Tombleson
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | - Javier Martín
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lingyan Chen
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | - Ann-Christine Syvänen
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Joan E Wither
- Toronto Western Research Institute (TWRI), University Health Network, Toronto, Ontario, Canada
| | - John D Rioux
- Université de Montréal, Montreal, Quebec, Canada
- Montreal Heart Institute, Montreal, Quebec, Canada
| | - Marta E Alarcón-Riquelme
- Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, UK
- Division of Immunology, Infection and Inflammatory Disease, King's College London, UK
| |
Collapse
|
38
|
Wiley GB, Kelly JA, Gaffney PM. Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease. Arthritis Res Ther 2015; 16:490. [PMID: 25789374 PMCID: PMC4396863 DOI: 10.1186/s13075-014-0490-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Next-generation DNA sequencing has revolutionized the field of genetics and genomics, providing researchers with the tools to efficiently identify novel rare and low frequency risk variants, which was not practical with previously available methodologies. These methods allow for the sequence capture of a specific locus or small genetic region all the way up to the entire six billion base pairs of the diploid human genome. Rheumatic diseases are a huge burden on the US population, affecting more than 46 million Americans. Those afflicted suffer from one or more of the more than 100 diseases characterized by inflammation and loss of function, mainly of the joints, tendons, ligaments, bones, and muscles. While genetics studies of many of these diseases (for example, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease) have had major successes in defining their genetic architecture, causal alleles and rare variants have still been elusive. This review describes the current high-throughput DNA sequencing methodologies commercially available and their application to rheumatic diseases in both case–control as well as family-based studies.
Collapse
|
39
|
Mohan C. The Long (and Sometimes Endless) Road to Murine Lupus Genes. THE JOURNAL OF IMMUNOLOGY 2015; 195:4043-6. [DOI: 10.4049/jimmunol.1501963] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
40
|
Ghodke-Puranik Y, Niewold TB. Immunogenetics of systemic lupus erythematosus: A comprehensive review. J Autoimmun 2015; 64:125-36. [PMID: 26324017 DOI: 10.1016/j.jaut.2015.08.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/24/2022]
Abstract
Our understanding of the genetic basis of systemic lupus erythematosus has progressed rapidly in recent years. While many genetic polymorphisms have been associated with disease susceptibility, the next major step involves integrating these genetic polymorphisms into the molecular mechanisms and cellular immunology of the human disease. In this review, we summarize some recent work in this area, including the genetics of the type I IFN response in SLE, including polygenic and monogenic factors, as well as epigenetic influences. Contributions of both HLA and non-HLA polymorphisms to the complex genetics of SLE are reviewed. We also review recent reports of specific gene deficits leading to monogenic SLE-like syndromes. The molecular functions of common SLE-risk variants are reviewed in depth, including regulatory variations in promoter and enhancer elements and coding-change polymorphisms, and studies which are beginning to define the molecular and cellular functions of these polymorphisms in the immune system. We discuss epigenetic influences on lupus, with an emphasis on micro-RNA expression and binding, as well as epigenetic modifications that regulate the expression levels of various genes involved in SLE pathogenesis and the ways epigenetic marks modify SLE susceptibility genes. The work summarized in this review provides a fascinating window into the biology and molecular mechanisms of human SLE. Understanding the functional mechanisms of causal genetic variants underlying the human disease greatly facilitates our ability to translate genetic associations toward personalized care, and may identify new therapeutic targets relevant to human SLE disease mechanisms.
Collapse
Affiliation(s)
| | - Timothy B Niewold
- Division of Rheumatology, Department of Immunology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
41
|
Konsta OD, Le Dantec C, Charras A, Brooks WH, Arleevskaya MI, Bordron A, Renaudineau Y. An in silico Approach Reveals Associations between Genetic and Epigenetic Factors within Regulatory Elements in B Cells from Primary Sjögren's Syndrome Patients. Front Immunol 2015; 6:437. [PMID: 26379672 PMCID: PMC4549647 DOI: 10.3389/fimmu.2015.00437] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/11/2015] [Indexed: 12/13/2022] Open
Abstract
Recent advances in genetics have highlighted several regions and candidate genes associated with primary Sjögren’s syndrome (SS), a systemic autoimmune epithelitis that combines exocrine gland dysfunctions, and focal lymphocytic infiltrations. In addition to genetic factors, it is now clear that epigenetic deregulations are present during SS and restricted to specific cell type subsets, such as lymphocytes and salivary gland epithelial cells. In this study, 72 single nucleotide polymorphisms (SNPs) associated with 43 SS gene risk factors were selected from publicly available and peer reviewed literature for further in silico analysis. SS risk variant location was tested revealing a broad distribution in coding sequences (5.6%), intronic sequences (55.6%), upstream/downstream genic regions (30.5%), and intergenic regions (8.3%). Moreover, a significant enrichment of regulatory motifs (promoter, enhancer, insulator, DNAse peak, and expression quantitative trait loci) characterizes SS risk variants (94.4%). Next, screening SNPs in high linkage disequilibrium (r2 ≥ 0.8 in Caucasians) revealed 645 new variants including 5 SNPs with missense mutations, and indicated an enrichment of transcriptionally active motifs according to the cell type (B cells > monocytes > T cells ≫ A549). Finally, we looked at SS risk variants for histone markers in B cells (GM12878), monocytes (CD14+) and epithelial cells (A548). Active histone markers were associated with SS risk variants at both promoters and enhancers in B cells, and within enhancers in monocytes. In conclusion and based on the obtained in silico results that need further confirmation, associations were observed between SS genetic risk factors and epigenetic factors and these associations predominate in B cells, such as those observed at the FAM167A–BLK locus.
Collapse
Affiliation(s)
- Orsia D Konsta
- INSERM ESPRI, ERI29/EA2216, SFR ScInBioS, LabEx IGO "Immunotherapy Graft Oncology", Innovative Medicines Initiative PRECISESADS, Réseau épigénétique et réseau canaux ioniques du Cancéropole Grand Ouest, European University of Brittany , Brest , France
| | - Christelle Le Dantec
- INSERM ESPRI, ERI29/EA2216, SFR ScInBioS, LabEx IGO "Immunotherapy Graft Oncology", Innovative Medicines Initiative PRECISESADS, Réseau épigénétique et réseau canaux ioniques du Cancéropole Grand Ouest, European University of Brittany , Brest , France
| | - Amandine Charras
- INSERM ESPRI, ERI29/EA2216, SFR ScInBioS, LabEx IGO "Immunotherapy Graft Oncology", Innovative Medicines Initiative PRECISESADS, Réseau épigénétique et réseau canaux ioniques du Cancéropole Grand Ouest, European University of Brittany , Brest , France
| | - Wesley H Brooks
- Department of Chemistry, University of South Florida , Tampa, FL , USA
| | | | - Anne Bordron
- INSERM ESPRI, ERI29/EA2216, SFR ScInBioS, LabEx IGO "Immunotherapy Graft Oncology", Innovative Medicines Initiative PRECISESADS, Réseau épigénétique et réseau canaux ioniques du Cancéropole Grand Ouest, European University of Brittany , Brest , France
| | - Yves Renaudineau
- INSERM ESPRI, ERI29/EA2216, SFR ScInBioS, LabEx IGO "Immunotherapy Graft Oncology", Innovative Medicines Initiative PRECISESADS, Réseau épigénétique et réseau canaux ioniques du Cancéropole Grand Ouest, European University of Brittany , Brest , France ; Laboratory of Immunology and Immunotherapy, CHU Morvan , Brest , France
| |
Collapse
|
42
|
IRF5, PTPN22, CD28, IL2RA, KIF5A, BLK and TNFAIP3 genes polymorphisms and lupus susceptibility in a cohort from the Egypt Delta; relation to other ethnic groups. Hum Immunol 2015; 76:525-31. [DOI: 10.1016/j.humimm.2015.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 01/28/2015] [Accepted: 06/02/2015] [Indexed: 01/28/2023]
|
43
|
Wu YY, Georg I, Díaz-Barreiro A, Varela N, Lauwerys B, Kumar R, Bagavant H, Castillo-Martín M, El Salem F, Marañón C, Alarcón-Riquelme ME. Concordance of increased B1 cell subset and lupus phenotypes in mice and humans is dependent on BLK expression levels. THE JOURNAL OF IMMUNOLOGY 2015; 194:5692-702. [PMID: 25972485 DOI: 10.4049/jimmunol.1402736] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/13/2015] [Indexed: 01/20/2023]
Abstract
Polymorphisms in the B lymphoid tyrosine kinase (BLK) gene have been associated with autoimmune diseases, including systemic lupus erythematosus, with risk correlating with reduced expression of BLK. How reduced expression of BLK causes autoimmunity is unknown. Using Blk(+/+) , Blk(+/-) , and Blk(-/-) mice, we show that aged female Blk(+/-) and Blk(-/-) mice produced higher anti-dsDNA IgG Abs and developed immune complex-mediated glomerulonephritis, compared with Blk(+/+) mice. Starting at young age, Blk(+/-) and Blk(-/-) mice accumulated increased numbers of splenic B1a cells, which differentiated into class-switched CD138(+) IgG-secreting B1a cells. Increased infiltration of B1a-like cells into the kidneys was also observed in aged Blk(+/-) and Blk(-/-) mice. In humans, we found that healthy individuals had BLK genotype-dependent levels of anti-dsDNA IgG Abs as well as increased numbers of a B1-like cell population, CD19(+)CD3(-)CD20(+)CD43(+)CD27(+), in peripheral blood. Furthermore, we describe the presence of B1-like cells in the tubulointerstitial space of human lupus kidney biopsies. Taken together, our study reveals a previously unappreciated role of reduced BLK expression on extraperitoneal accumulation of B1a cells in mice, as well as the presence of IgG autoantibodies and B1-like cells in humans.
Collapse
Affiliation(s)
- Ying-Yu Wu
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104;
| | - Ina Georg
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain
| | - Alejandro Díaz-Barreiro
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain
| | - Nieves Varela
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain
| | - Bernard Lauwerys
- Pôle de Pathologies Rhumatismales, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium; and
| | - Ramesh Kumar
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Harini Bagavant
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | | | - Fadi El Salem
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Concepción Marañón
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain
| | - Marta E Alarcón-Riquelme
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain;
| |
Collapse
|
44
|
Abstract
PURPOSE OF REVIEW Genome-wide association studies have identified more than 50 robust loci associated with systemic lupus erythematosus (SLE) susceptibility, and follow-up studies help reveal candidate causative genetic variants and their biological relevance contributing to the development of SLE. Epigenetic modulation is emerging as an important mechanism for understanding how the implicated genes interact with environmental factors. We review recent progress toward identifying causative variants of SLE-associated loci and epigenetic impact on lupus, especially genetic-epigenetic interactions that modulate expression levels of SLE susceptibility genes. RECENT FINDINGS A few SLE-risk loci have been refined to localize likely causative variants responsible for the observed genome-wide association study signals. Few of such variants disrupt coding sequences resulting in gain or loss of function for the encoded protein, whereas most fall in noncoding regions with potential to regulate gene expression through alterations in transcriptional activity, splicing, mRNA stability and epigenetic modifications. Multiple key pathways related to the SLE pathogenesis have been indicated by the identified genetic risk factors, including type I interferon signaling pathway that can also be regulated by epigenetic changes occurred in SLE. SUMMARY These findings provide novel insights into the disease pathogenesis and promise better diagnostic accuracy and new therapeutic targets for patient management.
Collapse
Affiliation(s)
- Yun Deng
- Division of Rheumatology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | | |
Collapse
|
45
|
Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJH, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JBA, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One 2015; 10:e0122271. [PMID: 25849893 PMCID: PMC4388675 DOI: 10.1371/journal.pone.0122271] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.
Collapse
Affiliation(s)
- Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine P. Liao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert R. Graham
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeffrey D. Greenberg
- New York University Hospital for Joint Diseases, New York, New York, United States of America
| | - Steve Eyre
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Jing Cui
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Lee
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Dimitrios A. Pappas
- Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
| | - Joel M. Kremer
- The Albany Medical College and The Center for Rheumatology, Albany, New York, United States of America
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Marieke J. H. Coenen
- Radboud university medical center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Barbara Franke
- Radboud University Medical Center, Donders Centre for Neurosciences, Department of Psychiatry and Human Genetics, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Xavier Mariette
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Corrine Richard-Miceli
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Helena Canhão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - João E. Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Niek de Vries
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P. Tak
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - J. Bart A. Crusius
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Michael T. Nurmohamed
- Amsterdam Rheumatology and Immunology Center, Department of Rheumatology, Reade, Amsterdam, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ted R. Mikuls
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yukinori Okada
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eli A. Stahl
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - David E. Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tracie L. Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda L. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Roman Kosoy
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Michael Ransom
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Tushar R. Bhangale
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Ward Ortmann
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Andrew Cagan
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Vivian Gainer
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Elizabeth W. Karlson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac Kohane
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Shawn N. Murphy
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, 18100, Spain
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
- Genetics Department, University Medical Center and Groningen University, Groningen, The Netherlands
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael F. Seldin
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Timothy Behrens
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| |
Collapse
|
46
|
Abstract
Systemic lupus erythematosus (SLE) is a multisystem autoimmune disorder that has a broad spectrum of effects on the majority of organs, including the kidneys. Approximately 40-70% of patients with SLE will develop lupus nephritis. Renal assault during SLE is initiated by genes that breach immune tolerance and promote autoantibody production. These genes might act in concert with other genetic factors that augment innate immune signalling and IFN-I production, which in turn can generate an influx of effector leucocytes, inflammatory mediators and autoantibodies into end organs, such as the kidneys. The presence of cognate antigens in the glomerular matrix, together with intrinsic molecular abnormalities in resident renal cells, might further accentuate disease progression. This Review discusses the genetic insights and molecular mechanisms for key pathogenic contributors in SLE and lupus nephritis. We have categorized the genes identified in human studies of SLE into one of four pathogenic events that lead to lupus nephritis. We selected these categories on the basis of the cell types in which these genes are expressed, and the emerging paradigms of SLE pathogenesis arising from murine models. Deciphering the molecular basis of SLE and/or lupus nephritis in each patient will help physicians to tailor specific therapies.
Collapse
|
47
|
The effect of inversion at 8p23 on BLK association with lupus in Caucasian population. PLoS One 2014; 9:e115614. [PMID: 25545785 PMCID: PMC4278715 DOI: 10.1371/journal.pone.0115614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/06/2014] [Indexed: 11/19/2022] Open
Abstract
To explore the potential influence of the polymorphic 8p23.1 inversion on known autoimmune susceptibility risk at or near BLK locus, we validated a new bioinformatics method that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion in a Caucasian population. Methods: Principal components analysis (PCA) was performed using markers inside the inversion territory followed by k-means cluster analyses on 7416 European derived and 267 HapMaP CEU and TSI samples. A logistic regression conditional analysis was performed. Results: Three subgroups have been identified; inversion homozygous, heterozygous and non-inversion homozygous. The status of inversion was further validated using HapMap samples that had previously undergone Fluorescence in situ hybridization (FISH) assays with a concordance rate of above 98%. Conditional analyses based on the status of inversion were performed. We found that overall association signals in the BLK region remain significant after controlling for inversion status. The proportion of lupus cases and controls (cases/controls) in each subgroup was determined to be 0.97 for the inverted homozygous group (1067 cases and 1095 controls), 1.12 for the inverted heterozygous group (1935 cases 1717 controls) and 1.36 for non-inverted subgroups (924 cases and 678 controls). After calculating the linkage disequilibrium between inversion status and lupus risk haplotype we found that the lupus risk haplotype tends to reside on non-inversion background. As a result, a new association effect between non-inversion status and lupus phenotype has been identified ((p = 8.18×10−7, OR = 1.18, 95%CI = 1.10–1.26). Conclusion: Our results demonstrate that both known lupus risk haplotype and inversion status act additively in the pathogenesis of lupus. Since inversion regulates expression of many genes in its territory, altered expression of other genes might also be involved in the development of lupus.
Collapse
|
48
|
Dai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM. Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Curr Opin Immunol 2014; 31:87-96. [PMID: 25458999 DOI: 10.1016/j.coi.2014.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/10/2014] [Accepted: 10/10/2014] [Indexed: 01/13/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic systemic autoimmune disorder. Considerable progress has been made to delineate the genetic control of this complex disorder. In this review, selected aspects of human and mouse genetics related to SLE are reviewed with emphasis on genes that contribute to both innate and adaptive immunity and to genes that contribute directly to susceptibility to end organ damage. It is concluded that the interactions among these two major pathways will provide further insight into the pathogenesis of SLE. An interactive model of the two major pathways is proposed without emphasis on the importance of breaking tolerance to autoantigens.
Collapse
Affiliation(s)
- Chao Dai
- Division of Rheumatology, Center of Inflammation, Immunity and Regenerative Medicine, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, United States
| | - Yun Deng
- Division of Rheumatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Aaron Quinlan
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, United States
| | - Felicia Gaskin
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, United States
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, United States.
| | - Shu Man Fu
- Division of Rheumatology, Center of Inflammation, Immunity and Regenerative Medicine, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, United States.
| |
Collapse
|
49
|
Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J. Illumina human exome genotyping array clustering and quality control. Nat Protoc 2014; 9:2643-62. [PMID: 25321409 DOI: 10.1038/nprot.2014.174] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the rise of high-throughput sequencing technology, traditional genotyping arrays are gradually being replaced by sequencing technology. Against this trend, Illumina has introduced an exome genotyping array that provides an alternative approach to sequencing, especially suited to large-scale genome-wide association studies (GWASs). The exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted common SNPs. Researchers have struggled to generate a reliable protocol for processing exome genotyping array data. The Vanderbilt Epidemiology Center, in cooperation with Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), has developed a thorough exome chip-processing protocol. The protocol was developed during the processing of several large exome genotyping array-based studies, which included over 60,000 participants combined. The protocol described herein contains detailed clustering techniques and robust quality control procedures, and it can benefit future exome genotyping array-based GWASs.
Collapse
Affiliation(s)
- Yan Guo
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jing He
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Shilin Zhao
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Hui Wu
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Xue Zhong
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - David C Samuels
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jirong Long
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|