1
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Vazzana KM, Musolf AM, Bailey-Wilson JE, Hiraki LT, Silverman ED, Scott C, Dalgard CL, Hasni S, Deng Z, Kaplan MJ, Lewandowski LB. Transmission disequilibrium analysis of whole genome data in childhood-onset systemic lupus erythematosus. Genes Immun 2023; 24:200-206. [PMID: 37488248 PMCID: PMC10529982 DOI: 10.1038/s41435-023-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Childhood-onset systemic lupus erythematosus (cSLE) patients are unique, with hallmarks of Mendelian disorders (early-onset and severe disease) and thus are an ideal population for genetic investigation of SLE. In this study, we use the transmission disequilibrium test (TDT), a family-based genetic association analysis that employs robust methodology, to analyze whole genome sequencing data. We aim to identify novel genetic associations in an ancestrally diverse, international cSLE cohort. Forty-two cSLE patients and 84 unaffected parents from 3 countries underwent whole genome sequencing. First, we performed TDT with single nucleotide variant (SNV)-based (common variants) using PLINK 1.9, and gene-based (rare variants) analyses using Efficient and Parallelizable Association Container Toolbox (EPACTS) and rare variant TDT (rvTDT), which applies multiple gene-based burden tests adapted for TDT, including the burden of rare variants test. Applying the GWAS standard threshold (5.0 × 10-8) to common variants, our SNV-based analysis did not return any genome-wide significant SNVs. The rare variant gene-based TDT analysis identified many novel genes significantly enriched in cSLE patients, including HNRNPUL2, a DNA repair protein, and DNAH11, a ciliary movement protein, among others. Our approach identifies several novel SLE susceptibility genes in an ancestrally diverse childhood-onset lupus cohort.
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Affiliation(s)
- Kathleen M Vazzana
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Linda T Hiraki
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Earl D Silverman
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Christiaan Scott
- Paediatric Rheumatology, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa
| | - Clifton L Dalgard
- The American Genome Center, Department of Anatomy, Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Sarfaraz Hasni
- Clinical Program, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zuoming Deng
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura B Lewandowski
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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2
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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.
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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
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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Carmona‐Pérez L, Rojas M, Muñoz‐Vahos C, Vanegas‐García A, Vásquez G. Plasma microparticles from patients with systemic lupus erythematosus modulate the content of miRNAs in U937 cells. Immunology 2021; 164:253-265. [PMID: 34003488 PMCID: PMC8442235 DOI: 10.1111/imm.13366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022] Open
Abstract
In systemic lupus erythematosus (SLE), the clearance of apoptotic cells and microparticles (MPs) is reduced. Some MPs contain molecules that can modulate immune responses. This study aimed to evaluate the presence of miR-126 and miR-146a in plasma MPs of patients with SLE (SLE MPs) and analyse the ability of MPs to modulate some events in the promonocytic U937 cell line. Circulating MPs were isolated from plasma samples of healthy controls (HCs), patients with SLE and other autoimmune diseases (OAD). MPs were analysed for size and cell origin by flow cytometry and content of miR-126 and miR-146a by RT-qPCR. MPs were then added to U937 cell cultures to evaluate changes in cell phenotype, cytokine expression, content of miR-126 and miR-146a, and levels of IRF5. Patients with active SLE (aSLE) showed an increase in concentration of plasma MPs that positively correlated with the SLEDAI (SLE Disease Activity Index) score. CD14+ MPs were significantly more abundant in patients with SLE than HCs. SLE MPs contained decreased levels of miR-146a, but the miR-126 content in aSLE MPs was increased. The miR-126 content in SLE MPs correlated positively with the SLEDAI score. The treatment of U937 cells with MPs from HCs and patients induced reduced expression of HLA-DR, CD18 and CD119, increased frequency of IL-6+ and TNF-α+ cells, accumulation of IL-8 in culture supernatants, increased miR-126 levels and decreased miR-146a content, but no change in the expression of IRF5. These findings suggest that plasma MPs, especially SLE MPs, could modulate some biological events in U937 cells.
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Affiliation(s)
- Liseth Carmona‐Pérez
- Grupo de Inmunología Celular e Inmunogenética (GICIG)Facultad de MedicinaInstituto de Investigaciones MédicasUniversidad de Antioquia (UDEA)MedellínColombia
| | - Mauricio Rojas
- Grupo de Inmunología Celular e Inmunogenética (GICIG)Facultad de MedicinaInstituto de Investigaciones MédicasUniversidad de Antioquia (UDEA)MedellínColombia
- Unidad de Citometría de FlujoSede de Investigación UniversitariaUniversidad de Antioquia (UDEA)MedellínColombia
| | - Carlos Muñoz‐Vahos
- Sección de ReumatologíaHospital San Vicente FundaciónMedellínColombia
- Grupo de Reumatología de la Universidad de Antioquia (GRUA)MedellínColombia
| | - Adiana Vanegas‐García
- Sección de ReumatologíaHospital San Vicente FundaciónMedellínColombia
- Grupo de Reumatología de la Universidad de Antioquia (GRUA)MedellínColombia
| | - Gloria Vásquez
- Grupo de Inmunología Celular e Inmunogenética (GICIG)Facultad de MedicinaInstituto de Investigaciones MédicasUniversidad de Antioquia (UDEA)MedellínColombia
- Grupo de Reumatología de la Universidad de Antioquia (GRUA)MedellínColombia
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Gómez Hernández G, Morell M, Alarcón-Riquelme ME. The Role of BANK1 in B Cell Signaling and Disease. Cells 2021; 10:cells10051184. [PMID: 34066164 PMCID: PMC8151866 DOI: 10.3390/cells10051184] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 01/03/2023] Open
Abstract
The B cell scaffold protein with ankyrin repeats (BANK1) is expressed primarily in B cells and with multiple but discrete roles in B cell signaling, including B cell receptor signaling, CD40-related signaling, and Toll-like receptor (TLR) signaling. The gene for BANK1, located in chromosome 4, has been found to contain genetic variants that are associated with several autoimmune diseases and also other complex phenotypes, in particular, with systemic lupus erythematosus. Common genetic variants are associated with changes in BANK1 expression in B cells, while rare variants modify their capacity to bind efferent effectors during signaling. A BANK1-deficient model has shown the importance of BANK1 during TLR7 and TLR9 signaling and has confirmed its role in the disease. Still, much needs to be done to fully understand the function of BANK1, but the main conclusion is that it may be the link between different signaling functions within the B cells and they may act to synergize the various pathways within a cell. With this review, we hope to enhance the interest in this molecule.
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Affiliation(s)
- Gonzalo Gómez Hernández
- GENYO, Center for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain; (G.G.H.); (M.M.)
| | - María Morell
- GENYO, Center for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain; (G.G.H.); (M.M.)
| | - Marta E. Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain; (G.G.H.); (M.M.)
- Department of Environmental Medicine, Karolinska Institutet, 17167 Solna, Sweden
- Correspondence:
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Brant EJ, Rietman EA, Klement GL, Cavaglia M, Tuszynski JA. Personalized therapy design for systemic lupus erythematosus based on the analysis of protein-protein interaction networks. PLoS One 2020; 15:e0226883. [PMID: 32191711 PMCID: PMC7081981 DOI: 10.1371/journal.pone.0226883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 12/08/2019] [Indexed: 12/26/2022] Open
Abstract
We analyzed protein expression data for Lupus patients, which have been obtained from publicly available databases. A combination of systems biology and statistical thermodynamics approaches was used to extract topological properties of the associated protein-protein interaction networks for each of the 291 patients whose samples were used to provide the molecular data. We have concluded that among the many proteins that appear to play critical roles in this pathology, most of them are either ribosomal proteins, ubiquitination pathway proteins or heat shock proteins. We propose some of the proteins identified in this study to be considered for drug targeting.
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Affiliation(s)
- Elizabeth J. Brant
- Nephrology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, United States of America
| | - Edward A. Rietman
- BINDS lab, College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Mechanical and Industrial Engineering, University of Mass, Amherst, Massachusetts, United States of America
| | | | | | - Jack A. Tuszynski
- DIMEAS, Politecnico di Torino, Torino, Italy
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Li KG, Yin RX, Huang F, Chen WX, Wu JZ, Cao XL. XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke. Clin Appl Thromb Hemost 2020; 26:1076029620902844. [PMID: 32024373 PMCID: PMC7288804 DOI: 10.1177/1076029620902844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The X Kell blood group complex subunit-related family member 6
(XKR6) gene single-nucleotide polymorphisms (SNPs) have
been associated with serum lipid profiles and the risk of coronary heart disease
(CHD) and ischemic stroke (IS) in several previous studies, but the association
between the XKR6 rs7014968 SNP and serum lipid levels and the
risk of CHD and IS has not been detected previously. This study aims to explore
the association between the XKR6 rs7014968 SNP and serum lipid
traits and the susceptibility to CHD and IS in the Guangxi Han Chinese
population. Snapshot technology was used to determine the genotypes of the
XKR6 rs7014968 SNP in 624 controls, 588 patients with CHD,
and 544 patients with IS. The XKR6 rs7014968C allele carriers
in the control group had higher serum total cholesterol (TC) levels than the C
allele noncarriers (P = .025). The XKR6
rs7014968C allele carriers also had an increased risk of CHD and IS
(P < .05-.01). Stratified analysis showed that the
patients with the rs7014968C allele in the female, age >60 years, body mass
index (BMI) >24 kg/m2, and hypertension subgroups had a higher
risk of CHD than those in the subgroup counterparts. The patients with the
rs7014968C allele in the male, BMI > 24 kg/m2, smoker, and
hypertension subgroups also had a higher risk of IS than those in the subgroup
counterparts. These results suggest that the XKR6 rs7014968 SNP
is likely to increase the risk of CHD and IS by increasing serum TC levels in
our study populations.
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Affiliation(s)
- Kai-Guang Li
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China
| | - Wu-Xian Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiao-Li Cao
- Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China.,Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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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
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9
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Genetics of serum concentration of IL-6 and TNFα in systemic lupus erythematosus and rheumatoid arthritis: a candidate gene analysis. Clin Rheumatol 2015; 34:1375-82. [PMID: 25652333 DOI: 10.1007/s10067-015-2881-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/05/2015] [Accepted: 01/19/2015] [Indexed: 12/19/2022]
Abstract
Elevated concentrations of inflammatory mediators are characteristic of autoimmune disease accompanied by chronic or recurrent inflammation. We examined the hypothesis that mediators of inflammation known to be elevated in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are associated with genetic polymorphism previously identified in studies of inflammatory disease. Serum interleukin 6 (IL-6) and tumor necrosis factor alpha (TNFα) concentrations in patients with SLE (n = 117) or RA (n = 164) and in inflammatory disease-free control subjects (n = 172) were measured by multiplex ELISA. Candidate genes were chosen from studies of autoimmune and inflammatory disease. Genotypes were determined for 345 SNP markers in 75 genes. Association between serum analytes and single alleles was tested by linear regression. Polymorphisms in several genes were associated with IL-6 levels (including IL10, TYK2, and CD40L in SLE and DRB1, NOD2, and CSF1 in RA) or with TNFα levels (including TNFSF4 and CSF2 in SLE and PTPN2, DRB1, and NOD2 in RA). Some associations were shared between disease and control groups or between IL-6 and TNFα within a group. In conclusion, variation in genes implicated in disease pathology is associated with serum IL-6 or TNFα concentration. Some genetic associations are more apparent in healthy controls than in SLE or RA, suggesting dysregulation of the principal mediators of chronic inflammation in disease. Susceptibility genes may affect inflammatory response with variable effect on disease etiology.
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10
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Yu RY, Brazaitis J, Gallagher G. The human IL-23 receptor rs11209026 A allele promotes the expression of a soluble IL-23R-encoding mRNA species. THE JOURNAL OF IMMUNOLOGY 2014; 194:1062-8. [PMID: 25552541 DOI: 10.4049/jimmunol.1401850] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The human IL23R gene single nucleotide polymorphism rs11209026 A allele confers protection against inflammatory diseases. However, although this difference has been associated with reductions in IL-23-induced IL-17A production and STAT3 phosphorylation, the molecular mechanism underlying these changes remains undefined. Th17 cell maturation depends on IL-23 signaling. Multiple splice forms of the human IL23R transcript exist, and one, Δ9, encodes a soluble form of the receptor. In this study, we asked whether this protective allele was associated with mRNA splicing. Using mini-gene constructs and competitive oligonucleotide binding, we showed that the A allele alters IL-23R α-chain mRNA splicing and favors exon 9 skipping by reducing the binding of the splicing enhancer SF2. This enhances expression of the Δ9 mRNA and consequently diminishes IL-23 signaling. Thus, the presence of the A allele increases expression of the soluble form of IL23R mRNA (which then functions as a decoy receptor) and lowers the ability to develop a Th17 phenotype upon IL-23 stimulation. We further showed that antisense oligonucleotides targeting the SF2 binding site could efficiently induce exon 9 skipping in the presence of the G allele, and thereby replicate the effect of the A allele. Antisense oligonucleotide treatment caused dose-responsive induction of the IL23RΔ9 mRNA and interfered with in vitro differentiation of human Th17 cells, reducing their expression of the signature Th17 cytokines IL-17A and IL-17F. This may represent a novel approach to therapy of Th17-mediated diseases by elevating soluble IL-23R while simultaneously reducing the remaining cell surface receptor density.
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Affiliation(s)
- Raymond Y Yu
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
| | - Jonathan Brazaitis
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
| | - Grant Gallagher
- Genetic Immunology Laboratory, HUMIGEN, The Institute for Genetic Immunology, Genesis Biotechnology Group, Hamilton, NJ 08690
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11
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Chatzikyriakidou A, Voulgari PV, Drosos AA. Evidence of ERBB3 gene association with rheumatoid arthritis predisposition. Int J Rheum Dis 2014; 19:146-9. [PMID: 25530448 DOI: 10.1111/1756-185x.12514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 3) gene was reported to be related with susceptibility to several autoimmune diseases. Taking this into account, we searched, for the first time, the ERBB3 gene association with rheumatoid arthritis liability. METHODS One hundred and eighty-six RA patients and 147 controls were enrolled in the study. Polymerase chain reaction - restriction fragment length polymorphism assay was conducted in rs2271189 and rs2292239 genotyping. RESULTS A statistically significant difference was observed in rs2271189 allele distribution between RA patients and controls (P = 0.029, odds ratio: 1.460, 95% confidence interval: 1.040-2.050). CONCLUSION As far as we know, this is the first study which correlates ERBB3 gene with RA susceptibility, adding to a previous report of chromosome 12q13 association with RA liability. Furthermore, we confirmed that polymorphism rs2271189 can predict better ERBB3 gene association with disorders than the previously reported ERBB3 variants. More studies in other ethnic groups of patients are needed so as to reveal the extent of the herein observed genetic association.
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Affiliation(s)
- Anthoula Chatzikyriakidou
- Laboratory of General Biology and Genetics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Paraskevi V Voulgari
- Rheumatology Clinic, Department of Internal Medicine, Medical School, University of Ioannina, Ioannina, Greece
| | - Alexandros A Drosos
- Rheumatology Clinic, Department of Internal Medicine, Medical School, University of Ioannina, Ioannina, Greece
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12
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Dey-Rao R, Smith J, Chow S, Sinha A. Differential gene expression analysis in CCLE lesions provides new insights regarding the genetics basis of skin vs. systemic disease. Genomics 2014; 104:144-55. [DOI: 10.1016/j.ygeno.2014.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/15/2014] [Indexed: 01/06/2023]
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13
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Compromised central tolerance of ICA69 induces multiple organ autoimmunity. J Autoimmun 2014; 53:10-25. [PMID: 25088457 DOI: 10.1016/j.jaut.2014.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/01/2014] [Accepted: 07/09/2014] [Indexed: 12/23/2022]
Abstract
For reasons not fully understood, patients with an organ-specific autoimmune disease have increased risks of developing autoimmune responses against other organs/tissues. We identified ICA69, a known β-cell autoantigen in Type 1 diabetes, as a potential common target in multi-organ autoimmunity. NOD mice immunized with ICA69 polypeptides exhibited exacerbated inflammation not only in the islets, but also in the salivary glands. To further investigate ICA69 autoimmunity, two genetically modified mouse lines were generated to modulate thymic ICA69 expression: the heterozygous ICA69(del/wt) line and the thymic medullary epithelial cell-specific deletion Aire-ΔICA69 line. Suboptimal central negative selection of ICA69-reactive T-cells was observed in both lines. Aire-ΔICA69 mice spontaneously developed coincident autoimmune responses to the pancreas, the salivary glands, the thyroid, and the stomach. Our findings establish a direct link between compromised thymic ICA69 expression and autoimmunity against multiple ICA69-expressing organs, and identify a potential novel mechanism for the development of multi-organ autoimmune diseases.
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Mirkazemi S, Akbarian M, Jamshidi AR, Mansouri R, Ghoroghi S, Salimi Y, Tahmasebi Z, Mahmoudi M. Association of STAT4 rs7574865 with susceptibility to systemic lupus erythematosus in Iranian population. Inflammation 2014; 36:1548-52. [PMID: 23912645 DOI: 10.1007/s10753-013-9698-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease with complex genetic inheritance that affecting different organs and systems. STAT4 has been newly identified as a susceptible gene in the development of SLE. According to recent studies, STAT4 has been associated with SLE in various populations. We investigated whether STAT4 single nucleotide polymorphisms (SNPs) were associated with susceptibility and clinical features of SLE in Iranian patients. The study group comprised 280 patients with SLE and 281 sex-, age-, and ethnicity-matched healthy controls of Iranian ancestry. Two SNPs (rs7574865 and rs7601754) were genotyped using the TaqMan MGB Allelic Discrimination method. Our results showed a significant association between rs7574865 T allele (odds ratio (OR) = 1.50, 95 % CI = 1.18-1.92, P = 0.002) and susceptibility to SLE. The rs7574865TT genotype (P = 0.02, OR = 1.94, 95 % CI = 1.74-3.19) and GT genotype (P = 0.008, OR = 1.71, 95 % CI = 1.19-2.45) showed a significant association with the risk of SLE in the Iranian population. We concluded that STAT4 rs7574865 is associated with SLE susceptibility in the Iranian population and this SNP might be a factor in the pathogenesis of SLE. However, further studies are required to investigate the mechanism by which polymorphisms in this gene lead to SLE.
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Affiliation(s)
- Sedigheh Mirkazemi
- Immunology Department, Shahid Sadoughi University of Medical Sciences (International Campus), Yazd, Iran
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15
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Abstract
PTPN22 encodes a tyrosine phosphatase that is expressed by haematopoietic cells and functions as a key regulator of immune homeostasis by inhibiting T-cell receptor signalling and by selectively promoting type I interferon responses after activation of myeloid-cell pattern-recognition receptors. A single nucleotide polymorphism of PTPN22, 1858C>T (rs2476601), disrupts an interaction motif in the protein, and is the most important non-HLA genetic risk factor for rheumatoid arthritis and the second most important for juvenile idiopathic arthritis. PTPN22 exemplifies a shared autoimmunity gene, affecting the pathogenesis of systemic lupus erythematosus, vasculitis and other autoimmune diseases. In this Review, we explore the role of PTPN22 in autoimmune connective tissue disease, with particular emphasis on candidate-gene and genome-wide association studies and clinical variability of disease. We also propose a number of PTPN22-dependent functional models of the pathogenesis of autoimmune diseases.
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16
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James JA. Clinical perspectives on lupus genetics: advances and opportunities. Rheum Dis Clin North Am 2014; 40:413-32, vii. [PMID: 25034154 DOI: 10.1016/j.rdc.2014.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In recent years, genome-wide association studies have led to an expansion in the identification of regions containing confirmed genetic risk variants within complex human diseases, such as systemic lupus erythematosus (SLE). Many of the strongest SLE genetic associations can be divided into groups based on their potential roles in different processes implicated in lupus pathogenesis, including ubiquitination, DNA degradation, innate immunity, cellular immunity, lymphocyte development, and antigen presentation. Recent advances have also shown several genetic associations with SLE subphenotypes and subcriteria. Many areas for further exploration remain to move lupus genetic studies toward clinically informative end points.
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Affiliation(s)
- Judith A James
- Oklahoma Clinical & Translational Science Institute, University of Oklahoma Health Sciences Center, 920 Stanton L Young Boulevard, Oklahoma City, OK 73104, USA; Departments of Medicine, Pathology, Microbiology & Immunology, University of Oklahoma Health Sciences Center, 920 Stanton L Young Boulevard, Oklahoma City, OK 73104, USA.
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17
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Chong Y, Mia-Jan K, Ryu H, Abdul-Ghafar J, Munkhdelger J, Lkhagvadorj S, Jung SY, Lee M, Ji SY, Choi E, Cho MY. DNA methylation status of a distinctively different subset of genes is associated with each histologic Lauren classification subtype in early gastric carcinogenesis. Oncol Rep 2014; 31:2535-44. [PMID: 24737029 DOI: 10.3892/or.2014.3133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 02/26/2014] [Indexed: 11/06/2022] Open
Abstract
DNA methylation change is known to play a crucial role in early gastric carcinogenesis. The present study aimed to identify and validate the correlation between differentially methylated regions (DMRs) and the subtypes of early gastric cancers (EGCs). Illumina Infinium methylation assay (IIMA; 450K BeadChip kit) was performed on fresh tumor and non‑tumor tissues of 12 EGCs to screen the methylation status of 450,000 CpG sites. To evaluate the significance of DNA methylation in each histologic subtype, pyrosequencing assay (PA) was performed on 38 EGCs (18 intestinal-, 12 mixed- and 8 diffuse-type) using 12 genes selected from the screening. Between tumors of the intestinal-type (n=6), and diffuse- (n=4) plus mixed-types (n=2), 169 regions showed significant differences (intensity>3,000, Δβ>0.2) in IIMA. Hierarchical clustering using the 169 DMRs revealed distinct separation between the two groups. In PA using 12 selected genes from the IIMA results, the aberrant methylation statuses of DVL2 (p=0.0186) and ETS1 (p=0.0222) were significantly related to diffuse- and mixed-types rather than the intestinal-type, while C19orf35 (p=0.019) and CNRIP1 (p=0.0473) were related to the diffuse‑type rather than intestinal‑type, and GAL3ST2 (p=0.0158) and ITGA3 (p=0.0273) were related to the mixed-type rather than the other two types. The methylation of other genes, CLIP4, XKR6, CCDC57, MAML3 and SDC2, was related with age, tumor location, or Helicobacter infection rather than the histologic subtype. Aberrant DNA methylation of certain genes may be independently involved in each histologic subtype of EGC. Furthermore, mixed-type EGCs may be a distinctive histologic subtype based on the different subset of DMRs compared to those of other subtypes.
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Affiliation(s)
- Yosep Chong
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Khalilullah Mia-Jan
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Hoon Ryu
- Department of Surgery, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Jamshid Abdul-Ghafar
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Jijgee Munkhdelger
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Sayamaa Lkhagvadorj
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - So Young Jung
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Mira Lee
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Sun-Young Ji
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Eunhee Choi
- Division of Statistics, Institute of Life Style Medicine, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
| | - Mee-Yon Cho
- Department of Pathology, Yonsei University, Wonju College of Medicine, Wonju, Gangwon-do, Republic of Korea
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Gommerman JL, Browning JL, Ware CF. The Lymphotoxin Network: orchestrating a type I interferon response to optimize adaptive immunity. Cytokine Growth Factor Rev 2014; 25:139-45. [PMID: 24698108 DOI: 10.1016/j.cytogfr.2014.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/24/2014] [Indexed: 12/13/2022]
Abstract
The Lymphotoxin (LT) pathway is best known for its role in orchestrating the development and homeostasis of lymph nodes and Peyer's patches through the regulation of homeostatic chemokines. More recently an appreciation of the LTβR pathway in the production of Type I interferons (IFN-I) during homeostasis and infection has emerged. LTβR signaling is essential in differentiating stromal cells and macrophages in lymphoid organs to rapidly produce IFN-I in response to virus infections independently of the conventional TLR signaling systems. In addition, LTβR signaling is required to produce homeostatic levels of IFN-I from dendritic cells in order to effectively cross-prime a CD8+ T cell response to protein antigen. Importantly, pharmacological inhibition of LTβR signaling in mice has a profound positive impact on a number of autoimmune disease models, although it remains unclear if this efficacy is linked to IFN-I production during chronic inflammation. In this review, we will provide a brief overview of how the "Lymphotoxin Network" is linked to the IFN-I response and its impact on the immune system.
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Affiliation(s)
| | - Jeffrey L Browning
- Department of Microbiology and Section of Rheumatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Carl F Ware
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
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19
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Hussain N, Jaffery G. Distribution of human leukocyte antigen alleles in systemic lupus erythematosus patients with angiotensin converting enzyme insertion/deletion polymorphism. Bosn J Basic Med Sci 2013; 13:57-62. [PMID: 23448612 DOI: 10.17305/bjbms.2013.2420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Systemic Lupus Erythematosus is one of the classic examples of autoimmune diseases among human beings and is a rare disease in Pakistani population. Clinically it is a quite diverse and complicated autoimmune disease in a sense that it involves multiple organs of the body and mimics with other diseases as well. This study focused on the distribution of HLA alleles in SLE patients with ACE I/D Polymorphism. A total of 122 individuals were enrolled in this study, 61 were the SLE patients who fulfilled revised ACR criteria and 61 were the healthy controls. Mean age of SLE patients at diagnosis was 30.35 ± 1.687 years (Range: 12-68 years). ACE gene I/D polymorphism was performed by nested PCR and DNA based HLA typing technique was used. ACE gene I/D polymorphism of Intron16 was studied and found to be involved in the activity of SLE. There is high frequency of HLA-A*01, HLA-B*40, HLA-DRB1*01 alleles in SLE patients with ACE DD genotype. The distribution of HLA-A, -B, -DRB1 alleles was analyzed in SLE patients with various disease phenotypes. HLA-A*01 and HLA-B*40 was the most common allele found in SLE patients with the involvement of skin. HLA-A*01, -A*03, HLA-B*13 and -B*46 were common in SLE patients with arthritis while HLA-A*26 and -A*69 were commonly found in Lupus nephritis cases. SLE patients involving both skin and kidney had an allele HLA-DRB1*01 common in them.
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Affiliation(s)
- Nageen Hussain
- Department of Microbiology and Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, 818-R Model Town, Lahore, Pakistan.
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20
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Zhai JX, Zou LW, Zhang ZX, Fan WJ, Wang HY, Liu T, Ren Z, Dai RX, Ye D. CTLA-4 polymorphisms and systemic lupus erythematosus (SLE): a meta-analysis. Mol Biol Rep 2013; 40:5213-23. [PMID: 23922195 DOI: 10.1007/s11033-012-2125-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/03/2012] [Indexed: 11/25/2022]
Abstract
The aim of this study was to summarize results on the association of cytotoxic T-lymphocyte antigen-4 (CTLA-4) promoter exon-1 +49 and 1722T/C polymorphism with systemic lupus erythematosus (SLE) susceptibility by using the meta-analysis. We searched all the publications about the association between CTLA-4) promoter exon-1 +49 and 1722T/C polymorphism and SLE from PubMed, Elsevier Science Direct, Chinese Biomedical Literature Database (CBM), Chinese National Knowledge Infrastructure (CNKI), and Wanfang (Chinese). Previous CTLA-4 association studies with SLE, however, have produced inconsistent results. We have performed a meta-analysis to better assess the purported associations. A total of 17 independent studies (to June 2012) testing association between one or more CTLA-4 polymorphisms and SLE were used in this analysis. We have compared allele and genotype frequencies at two polymorphic sites found in exon-1 (at +49) and the promoter region (at -1722). The data demonstrate that the exon-1 +49 polymorphism is associated with SLE susceptibility in Asian population. The overall risk, measured by odds ratio (OR), stratification by ethnicity indicates the exon-1 +49 GG+GA genotype is associated with SLE, at least in Asians (OR = 0.85, 95 % CI = 0.73-0.99, P = 0.04 for GG+GA vs. AA; OR = 0.85, 95 % CI = 0.72-1.00, P = 0.05 for AG vs. AA). Similar trends are found in allele-specific risk estimates and disease association. Overall, there was significant association between the 1722T/C polymorphism and overall SLE risks (OR = 0.78, 95 % CI = 0.63-0.97, P = 0.04 for GG+GA vs. AA, OR = 0.87, 95 % CI = 0.76-0.99, P = 0.04 for G vs. A) in Asian population.In summary, this meta-analysis demonstrates that the CTLA-4 promoter +49A/G and promoter -1722C/T polymorphism may confer susceptibility to SLE, especially in Asian-derived population.
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Affiliation(s)
- Jin-Xia Zhai
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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21
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Reksten TR, Johnsen SJA, Jonsson MV, Omdal R, Brun JG, Theander E, Eriksson P, Wahren-Herlenius M, Jonsson R, Nordmark G. Genetic associations to germinal centre formation in primary Sjögren's syndrome. Ann Rheum Dis 2013; 73:1253-8. [DOI: 10.1136/annrheumdis-2012-202500] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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AlFadhli S. Overexpression and secretion of the soluble CTLA-4 splice variant in various autoimmune diseases and in cases with overlapping autoimmunity. Genet Test Mol Biomarkers 2013; 17:336-41. [PMID: 23448385 DOI: 10.1089/gtmb.2012.0391] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM To explore the potential genetic association of CTLA-4 Exon1 +49A/G and 3'UTR (AT)(n) to susceptibility to systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and overlapping (OP) autoimmunity; affected with more than one autoimmune disease. Expression of two major CTLA-4 isoforms; full length (mCTLA-4) and soluble (sCTLA-4) were explored in all subjects. A total of 680-age/gender/ethnically matched Kuwaitis were recruited and polymerase chain reaction (PCR)-fragment analysis was employed for genotyping both markers. mCTLA-4 and sCTLA-4 mRNA expression were analyzed using quantitative real time-PCR. The enzyme-linked immunosorbent assay (ELISA) was used to screen sCTLA-4 in all subjects' sera. RESULTS Only two CTLA-4 3'UTR (AT)(n) allelotypes; (AT)(15) and (AT)(6) were detected. The heterozygous (AT)(15/6) genotype confers protectivity rather than susceptibility to SLE (p=0.01, odds ratio=0.43, and confidence interval=0.21-0.86). No significant association was observed between Exon 1 +49A/G and any of the tested diseases. A consistently high serum sCTLA-4 level was observed in RA (6.8 ng/mL, p=0.005), SLE (6.34 ng/mL, p=0.007), and OP (8.75 ng/mL, p=0.012) compared to healthy control. A significant increase in the expression of sCTLA-4 mRNA was observed in OP (p=0.05) and SLE (p=0.047), while a significant increase in the expression of mCTLA-4 (p=0.01) was observed only in OP. CONCLUSION The present study is the first to report a statistically significant association between OP and serum sCTLA-4. The novelty of our study is the significance of CTLA-4 in the pathogenesis of OP besides SLE and RA.
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Affiliation(s)
- Suad AlFadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait, Kuwait.
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Rubicz R, Yolken R, Drigalenko E, Carless MA, Dyer TD, Bauman L, Melton PE, Kent JW, Harley JB, Curran JE, Johnson MP, Cole SA, Almasy L, Moses EK, Dhurandhar NV, Kraig E, Blangero J, Leach CT, Göring HHH. A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1). PLoS Genet 2013; 9:e1003147. [PMID: 23326239 PMCID: PMC3542101 DOI: 10.1371/journal.pgen.1003147] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/23/2012] [Indexed: 12/20/2022] Open
Abstract
Infection with Epstein-Barr virus (EBV) is highly prevalent worldwide, and it has been associated with infectious mononucleosis and severe diseases including Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal lymphoma, and lymphoproliferative disorders. Although EBV has been the focus of extensive research, much still remains unknown concerning what makes some individuals more sensitive to infection and to adverse outcomes as a result of infection. Here we use an integrative genomics approach in order to localize genetic factors influencing levels of Epstein Barr virus (EBV) nuclear antigen-1 (EBNA-1) IgG antibodies, as a measure of history of infection with this pathogen, in large Mexican American families. Genome-wide evidence of both significant linkage and association was obtained on chromosome 6 in the human leukocyte antigen (HLA) region and replicated in an independent Mexican American sample of large families (minimum p-value in combined analysis of both datasets is 1.4×10(-15) for SNPs rs477515 and rs2516049). Conditional association analyses indicate the presence of at least two separate loci within MHC class II, and along with lymphocyte expression data suggest genes HLA-DRB1 and HLA-DQB1 as the best candidates. The association signals are specific to EBV and are not found with IgG antibodies to 12 other pathogens examined, and therefore do not simply reveal a general HLA effect. We investigated whether SNPs significantly associated with diseases in which EBV is known or suspected to play a role (namely nasopharyngeal lymphoma, Hodgkin lymphoma, systemic lupus erythematosus, and multiple sclerosis) also show evidence of associated with EBNA-1 antibody levels, finding an overlap only for the HLA locus, but none elsewhere in the genome. The significance of this work is that a major locus related to EBV infection has been identified, which may ultimately reveal the underlying mechanisms by which the immune system regulates infection with this pathogen.
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Affiliation(s)
- Rohina Rubicz
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America.
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Yougbaré I, Boire G, Roy M, Lugnier C, Rouseau E. NCS 613 exhibits anti-inflammatory effects on PBMCs from lupus patients by inhibiting p38 MAPK and NF-κB signalling pathways while reducing proinflammatory cytokine production. Can J Physiol Pharmacol 2013; 91:353-61. [PMID: 23656347 DOI: 10.1139/cjpp-2012-0233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Systemic lupus erythematosus (SLE) is a polymorphic and multigenic autoimmune disease that evolves into progressive and chronic inflammation of multiple joints and organs. Phosphorylation and activation of p38 MAPK, along with the resulting overproduction of interleukin (IL)-1β, IL-6, and tumour necrosis factor (TNF)-α is a hallmark of inflammatory disorders. Here, we investigated the anti-inflammatory pathway modulated by NCS 613, a specific PDE4 inhibitor, on human peripheral blood mononuclear cells (PBMCs) from 5 healthy donors and 12 SLE patients. PDE4 subtypes, p38 MAPK, and IκBα protein levels were analyzed by Western blot, while NF-κB and PDE4B immunostaining was assessed in control and lipopolysaccharide (LPS) -pretreated PBMCs. Proinflammatory cytokines were quantified by ELISA, while IL-1β mRNA was resolved by RT-qPCR. NCS 613 treatment decreased PDE4B and upregulated PDE4C in human PBMCs from healthy donors and SLE patients. LPS stimulation increased p38 MAPK phosphorylation and NF-κB translocation to the nucleus, which was abolished by NCS 613 treatment. Concomitantly, NCS 613 restored IκBα detection levels in human PBMCs from both healthy donors and SLE patients. This compound also abolished LPS-induced inflammation in PBMCs by reducing IL-6, IL-8, and TNF-α cytokines. NCS 613 is a small molecule displaying anti-inflammatory properties that may provide an alternative or complementary strategy for SLE management.
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Affiliation(s)
- Issaka Yougbaré
- Le Bilarium, Department of Physiology and Biophysics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Canada
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Rullo OJ, Tsao BP. Recent insights into the genetic basis of systemic lupus erythematosus. Ann Rheum Dis 2012; 72 Suppl 2:ii56-61. [PMID: 23253915 DOI: 10.1136/annrheumdis-2012-202351] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Many identified genetic risk factors for systemic lupus erythematosus (SLE) contribute to the function of the immune system, which has expanded our understanding of disease pathogenesis. We outline the genetic variants in recently identified SLE-associated loci, the immunological pathways affected by these gene products and the disease manifestations linked to these loci. Pathways potentially influenced by SLE risk variants include: apoptosis, DNA degradation and clearance of cellular debris; antigen presentation; type I interferon, Toll-like receptor and nuclear factor kappa κB activation; defective clearance of immune complexes containing nuclear antigens; B and T-cell function and signalling; and monocyte and neutrophil function and signalling. These identified SLE susceptibility loci are predominantly common variants that have been confirmed among multiple ancestries, suggesting shared mechanisms in disease aetiology. Ongoing genetic studies continue the investigation of specific functional variants, and their potential consequences on immune dysregulation, enhancing our understanding of links between genotypes and specific disease manifestations. The next generation of sequencing explores the identification of causal rare variants that may contribute robust genetic effects to developing SLE. Novel insights coming from genetic studies of SLE provide the opportunity to elucidate pathogenic mechanisms as well as contribute to the development of innovative therapeutic targets for this complex disease.
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Topete-Reyes JF, Soto-Vargas J, Morán-Moguel MC, Dávalos-Rodríguez IP, Chávez-González EL, García-de la Torre I, Parra-Michel R, Medina-Pérez M, Jalomo-Martínez B, Salazar-Páramo M. Insertion/deletion polymorphism of the angiotensin-converting enzyme gene in lupus nephritis among Mexicans. Immunopharmacol Immunotoxicol 2012; 35:174-80. [DOI: 10.3109/08923973.2012.739175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Alonso-Perez E, Suarez-Gestal M, Calaza M, Ordi-Ros J, Balada E, Bijl M, Papasteriades C, Carreira P, Skopouli FN, Witte T, Endreffy E, Marchini M, Migliaresi S, Sebastiani GD, Santos MJ, Suarez A, Blanco FJ, Barizzone N, Pullmann R, Ruzickova S, Lauwerys BR, Gomez-Reino JJ, Gonzalez A. Further evidence of subphenotype association with systemic lupus erythematosus susceptibility loci: a European cases only study. PLoS One 2012; 7:e45356. [PMID: 23049788 PMCID: PMC3458859 DOI: 10.1371/journal.pone.0045356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
Introduction Systemic Lupus Erythematosus (SLE) shows a spectrum of clinical manifestations that complicate its diagnosis, treatment and research. This variability is likely related with environmental exposures and genetic factors among which known SLE susceptibility loci are prime candidates. The first published analyses seem to indicate that this is the case for some of them, but results are still inconclusive and we aimed to further explore this question. Methods European SLE patients, 1444, recruited at 17 centres from 10 countries were analyzed. Genotypes for 26 SLE associated SNPs were compared between patients with and without each of 11 clinical features: ten of the American College of Rheumatology (ACR) classification criteria (except ANAs) and age of disease onset. These analyses were adjusted for centre of recruitment, top ancestry informative markers, gender and time of follow-up. Overlap of samples with previous studies was excluded for assessing replication. Results There were three new associations: the SNPs in XKR6 and in FAM167A-BLK were associated with lupus nephritis (OR = 0.76 and 1.30, Pcorr = 0.007 and 0.03, respectively) and the SNP of MECP2, which is in chromosome X, with earlier age of disease onset in men. The previously reported association of STAT4 with early age of disease onset was replicated. Some other results were suggestive of the presence of additional associations. Together, the association signals provided support to some previous findings and to the characterization of lupus nephritis, autoantibodies and age of disease onset as the clinical features more associated with SLE loci. Conclusion Some of the SLE loci shape the disease phenotype in addition to increase susceptibility to SLE. This influence is more prominent for some clinical features than for others. However, results are only partially consistent between studies and subphenotype specific GWAS are needed to unravel their genetic component.
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Affiliation(s)
- Elisa Alonso-Perez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Marian Suarez-Gestal
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Manuel Calaza
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Josep Ordi-Ros
- Internal Medicine, Research Laboratory in Autoimmune Diseases, Hospital Vall d’Hebron, Barcelona, Spain
| | - Eva Balada
- Internal Medicine, Research Laboratory in Autoimmune Diseases, Hospital Vall d’Hebron, Barcelona, Spain
| | - Marc Bijl
- Department of Internal Medicine and Rheumatology, Martini Hospital, Groningen, The Netherlands
| | - Chryssa Papasteriades
- Department of Histocompatibility and Immunology, Evangelismos Hospital, Athens, Greece
| | | | - Fotini N. Skopouli
- Pathophysiology Department, Athens University Medical School, Athens, Greece
| | - Torsten Witte
- Division of Clinical Immunology, Department of Internal Medicine of the Hannover Medical School, Hannover, Germany
| | - Emöke Endreffy
- Paediatrics Department, Albert Szent-Györgyi Medical Centre, University of Szeged, Szeged, Hungary
| | - Maurizio Marchini
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico and University of Milan, Milan, Italy
| | | | | | - Maria Jose Santos
- Rheumatology Department, Hospital Garcia de Orta and Rheumatology Research Unit, Instituto Medicina Molecular, Lisboa, Portugal
| | - Ana Suarez
- Department of Functional Biology, Hospital Universitario Central de Asturias, Universidad de Oviedo, Oviedo, Spain
| | | | - Nadia Barizzone
- Department of Medical Sciences and IRCAD, Eastern Piedmont University, Novara, Italy
| | - Rudolf Pullmann
- Institute of Clinical Biochemistry, Martin Faculty Hospital, Jessenius Medical Faculty, Martin, Slovakia
| | - Sarka Ruzickova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bernard R. Lauwerys
- Cliniques Universitaires Saint-Luc and Université Catholique de Louvain, Brussels, Belgium
| | - Juan J. Gomez-Reino
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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Maiti AK, Nath SK. Gene network analysis of small molecules with autoimmune disease associated genes predicts a novel strategy for drug efficacy. Autoimmun Rev 2012; 12:510-22. [PMID: 23000205 DOI: 10.1016/j.autrev.2012.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/10/2012] [Indexed: 02/09/2023]
Abstract
Numerous genes/SNPs in autoimmune diseases (ADs) are identified through genome-wide association studies (GWAS) and likely to contribute in developing autoimmune phenotypes. Constructions of biologically meaningful pathways are necessary to determine how these genes interact with each other and with other small molecules to develop various complex AD phenotypes prior to beginning time-consuming rigorous experimentation. We have constructed biological pathways with genetically identified genes leading to shared AD phenotypes. Various environmental and endogenous factors interact with these AD associated genes suggesting their critical role in developing diseases and further association studies could be designed for assessing the role of these factors with risk allele in a specific gene. Additionally, existing drugs that have been used long before the identification of these genetically associated genes also interact with these newly associated genes. Thus advanced therapeutic strategies could be designed by grouping patients with risk allele(s) in particular genes that directly or closely interact with the specified drugs. This drug-susceptible gene network will not only increase our understanding about the additional molecular basis for effectiveness against these diseases but also indicate which drug could be more effective for those patients carrying risk allele(s) in that gene. Additionally, we have also identified several interlinking genes in the pathways that could be used for designing future association studies.
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Affiliation(s)
- Amit K Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104, United States.
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Vaughn SE, Kottyan LC, Munroe ME, Harley JB. Genetic susceptibility to lupus: the biological basis of genetic risk found in B cell signaling pathways. J Leukoc Biol 2012; 92:577-91. [PMID: 22753952 DOI: 10.1189/jlb.0212095] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Over 50 genetic variants have been statistically associated with the development of SLE (or lupus). Each genetic association is a key component of a pathway to lupus pathogenesis, the majority of which requires further mechanistic studies to understand the functional changes to cellular physiology. Whereas their use in clinical practice has yet to be established, these genes guide efforts to develop more specific therapeutic approaches. The BCR signaling pathways are rich in lupus susceptibility genes and may well provide novel opportunities for the understanding and clinical treatment of this complex disease.
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Affiliation(s)
- Samuel E Vaughn
- Cincinnati Children’s Hosptial Medical Center, Cincinnati, OH 45229-3039, USA
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Role of MHC-linked susceptibility genes in the pathogenesis of human and murine lupus. Clin Dev Immunol 2012; 2012:584374. [PMID: 22761632 PMCID: PMC3385965 DOI: 10.1155/2012/584374] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/07/2012] [Indexed: 02/08/2023]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of autoantibodies against nuclear antigens and a systemic inflammation that can damage a broad spectrum of organs. SLE patients suffer from a wide variety of symptoms, which can affect virtually almost any tissue. As lupus is difficult to diagnose, the worldwide prevalence of SLE can only be roughly estimated to range from 10 and 200 cases per 100,000 individuals with dramatic differences depending on gender, ethnicity, and location. Although the treatment of this disease has been significantly ameliorated by new therapies, improved conventional drug therapy options, and a trained expert eye, the underlying pathogenesis of lupus still remain widely unknown. The complex etiology reflects the complex genetic background of the disease, which is also not well understood yet. However, in the past few years advances in lupus genetics have been made, notably with the publication of genome-wide association studies (GWAS) in humans and the identification of susceptibility genes and loci in mice. This paper reviews the role of MHC-linked susceptibility genes in the pathogenesis of systemic lupus erythematosus.
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Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP, Beems M, Giannoukakis N, Trucco G, Palumbo MO, Solimena M, Pugliese A, Polychronakos C, Trucco M, Pietropaolo M. Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression. J Biol Chem 2012; 287:17882-17893. [PMID: 22447927 PMCID: PMC3366781 DOI: 10.1074/jbc.m111.319020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 03/15/2012] [Indexed: 12/22/2022] Open
Abstract
ICA69 (islet cell autoantigen 69 kDa) is a protein implicated in type 1 diabetes mellitus in both the non-obese diabetic (NOD) mouse model and humans. ICA69 is encoded by the Ica1 gene on mouse chromosome 6 A1-A2. We previously reported reduced ICA69 expression in the thymus of NOD mice compared with thymus of several non-diabetic mouse strains. We propose that reduced thymic ICA69 expression could result from variations in transcriptional regulation of the gene and that polymorphisms within the Ica1 core promoter may partially determine this transcriptional variability. We characterized the functional promoter of Ica1 in NOD mice and compared it with the corresponding portions of Ica1 in non-diabetic C57BL/6 mice. Luciferase reporter constructs demonstrated that the NOD Ica1 promoter region exhibited markedly reduced luciferase expression in transiently transfected medullary thymus epithelial (mTEC(+)) and B-cell (M12)-derived cell lines. However, in a non-diabetic strain, C57BL/6, the Ica1 promoter region was transcriptionally active when transiently transfected into the same cell lines. We concomitantly identified five single nucleotide polymorphisms within the NOD Ica1 promoter. One of these single nucleotide polymorphisms increases the binding affinity for the transcription factor AIRE (autoimmune regulator), which is highly expressed in thymic epithelial cells, where it is known to play a key role regulating self-antigen expression. We conclude that polymorphisms within the NOD Ica1 core promoter may determine AIRE-mediated down-regulation of ICA69 expression in medullary thymic epithelial cells, thus providing a novel mechanistic explanation for the loss of immunologic tolerance to this self-antigen in autoimmunity.
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Affiliation(s)
- Samantha M Bonner
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Susan L Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Yong Fan
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Yigang Chang
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Michael P Morran
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Megan Beems
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Nick Giannoukakis
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224; Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Giuliana Trucco
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Michael O Palumbo
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Michele Solimena
- Department of Molecular Diabetology, Paul Langerhans Institute Dresden, Carl Gustav Carus School of Medicine, Dresden University of Technology, 01307 Dresden, Germany
| | - Alberto Pugliese
- Immunogenetics Program, Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Massimo Trucco
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Massimo Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105.
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Alonso-Perez E, Suarez-Gestal M, Calaza M, Sebastiani GD, Pullmann R, Papasteriades C, Kovacs A, Skopouli FN, Bijl M, Suarez A, Marchini M, Migliaresi S, Carreira P, Ordi-Ros J, Witte T, Ruzickova S, Santos MJ, Barizzone N, Blanco FJ, Lauwerys BR, Gomez-Reino JJ, Gonzalez A. Bias in effect size of systemic lupus erythematosus susceptibility loci across Europe: a case-control study. Arthritis Res Ther 2012; 14:R94. [PMID: 22541939 PMCID: PMC3446468 DOI: 10.1186/ar3818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/27/2012] [Accepted: 04/27/2012] [Indexed: 01/11/2023] Open
Abstract
Introduction We aimed to investigate whether the effect size of the systemic lupus erythematosus (SLE) risk alleles varies across European subpopulations. Methods European SLE patients (n = 1,742) and ethnically matched healthy controls (n = 2,101) were recruited at 17 centres from 10 different countries. Only individuals with self-reported ancestry from the country of origin were included. In addition, participants were genotyped for top ancestry informative markers and for 25 SLE associated SNPs. The results were used to compare effect sizes between the Central Eureopan and Southern European subgroups. Results Twenty of the 25 SNPs showed independent association with SLE, These SNPs showed a significant bias to larger effect sizes in the Southern subgroup, with 15/20 showing this trend (P = 0.019) and a larger mean odds ratio of the 20 SNPs (1.46 vs. 1.34, P = 0.02) as well as a larger difference in the number of risk alleles (2.06 vs. 1.63, P = 0.027) between SLE patients and controls than for Central Europeans. This bias was reflected in a very significant difference in the cumulative genetic risk score (4.31 vs. 3.48, P = 1.8 × 10-32). Effect size bias was accompanied by a lower number of SLE risk alleles in the Southern subjects, both patients and controls, the difference being more marked between the controls (P = 1.1 × 10-8) than between the Southern and Central European patients (P = 0.016). Seven of these SNPs showed significant allele frequency clines. Conclusion Our findings showed a bias to larger effect sizes of SLE loci in the Southern Europeans relative to the Central Europeans together with clines of SLE risk allele frequencies. These results indicate the need to study risk allele clines and the implications of the polygenic model of inheritance in SLE.
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Affiliation(s)
- Elisa Alonso-Perez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clinico Universitario de Santiago, Choupana s/n, Santiago de Compostela 15706, Spain
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Lupus nephritis: an overview of recent findings. Autoimmune Dis 2012; 2012:849684. [PMID: 22536486 PMCID: PMC3318208 DOI: 10.1155/2012/849684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 11/30/2011] [Indexed: 11/18/2022] Open
Abstract
Lupus nephritis (LN) is one of the most serious complications of systemic lupus erythematosus (SLE) since it is the major predictor of poor prognosis. In susceptible individuals suffering of SLE, in situ formation and deposit of immune complexes (ICs) from apoptotic bodies occur in the kidneys as a result of an amplified epitope immunological response. IC glomerular deposits generate release of proinflammatory cytokines and cell adhesion molecules causing inflammation. This leads to monocytes and polymorphonuclear cells chemotaxis. Subsequent release of proteases generates endothelial injury and mesangial proliferation. Presence of ICs promotes adaptive immune response and causes dendritic cells to release type I interferon. This induces maturation and activation of infiltrating T cells, and amplification of Th2, Th1 and Th17 lymphocytes. Each of them, amplify B cells and activates macrophages to release more proinflammatory molecules, generating effector cells that cannot be modulated promoting kidney epithelial proliferation and fibrosis. Herein immunopathological findings of LN are reviewed.
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Coustet B, Bouaziz M, Dieudé P, Guedj M, Bossini-Castillo L, Agarwal S, Radstake T, Martin J, Gourh P, Elhai M, Koumakis E, Avouac J, Ruiz B, Mayes M, Arnett F, Hachulla E, Diot E, Cracowski JL, Tiev K, Sibilia J, Mouthon L, Frances C, Amoura Z, Carpentier P, Cosnes A, Meyer O, Kahan A, Boileau C, Chiocchia G, Allanore Y. Independent replication and meta analysis of association studies establish TNFSF4 as a susceptibility gene preferentially associated with the subset of anticentromere-positive patients with systemic sclerosis. J Rheumatol 2012; 39:997-1003. [PMID: 22422496 DOI: 10.3899/jrheum.111270] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Independent replication with large cohorts and metaanalysis of genetic associations are necessary to validate genetic susceptibility factors. The known tumor necrosis factor (ligand) superfamily, member 4 gene (TNFSF4) systemic lupus erythematosus (SLE) risk locus has been found to be associated with systemic sclerosis (SSc) in 2 studies, but with discrepancies between them for genotype-phenotype correlation. Our objective was to validate TNFSF4 association with SSc and determine the subset with the higher risk. METHODS Known SLE and SSc TNFSF4 susceptibility variants (rs2205960, rs1234317, rs12039904, rs10912580, and rs844648) were genotyped in 1031 patients with SSc and 1014 controls of French white ancestry. Genotype-phenotype association analysis and meta analysis of available data were performed, providing a population study of 4989 patients with SSc and 4661 controls, all of European white ancestry. RESULTS Allelic and genotypic associations were observed for the 5 single-nucleotide polymorphisms (SNP) with the subset of patients with SSc who are positive for anticentromere antibodies (ACA) and only a trend for association with SSc and limited cutaneous SSc. Rs2205960 exhibited the strongest allelic association in ACA+ patients with SSc [p = 0.0015; OR 1.37 (1.12-1.66)], with significant intra-cohort association when compared to patients with SSc positive for ACA. Metaanalysis confirmed overall association with SSc but also raised preferential association with the ACA+ subset and strongest effect with rs2205960 [T allele p = 0.00013; OR 1.33 (1.15-1.54) and TT genotype p = 0.00046; OR 2.02 (1.36-2.98)]. CONCLUSION We confirm TNFSF4 as an SSc susceptibility gene and rs2205960 as a putative causal variant with preferential association in the ACA+ SSc subphenotype.
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Affiliation(s)
- Baptiste Coustet
- Université Paris Descartes, Rhumatologie A, INSERM U1016, Hôpital Cochin, APHP, Paris, France
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Agik S, Franek BS, Kumar AA, Kumabe M, Utset TO, Mikolaitis RA, Jolly M, Niewold TB. The autoimmune disease risk allele of UBE2L3 in African American patients with systemic lupus erythematosus: a recessive effect upon subphenotypes. J Rheumatol 2012; 39:73-8. [PMID: 22045845 PMCID: PMC3304461 DOI: 10.3899/jrheum.110590] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE UBE2L3 is associated with susceptibility to systemic lupus erythematosus (SLE) and rheumatoid arthritis in European ancestry populations, and this locus has not been investigated fully in non-European populations. We studied the UBE2L3 risk allele for association with SLE, interferon-α (IFN-α), and autoantibodies in a predominantly African American SLE cohort. METHODS We studied 395 patients with SLE and 344 controls. The UBE2L3 rs5754217 polymorphism was genotyped using Taqman primer-probe sets, and IFN-α was measured using a reporter cell assay. RESULTS The UBE2L3 rs5754217 T allele was strongly enriched in African American patients with anti-La antibodies as compared to controls, and a recessive model was the best fit for this association (OR 2.55, p = 0.0061). Serum IFN-α also demonstrated a recessive association with the rs5754217 genotype in African American patients, and the TT/anti-La-positive patients formed a significantly high IFN-α subgroup (p = 0.0040). Similar nonstatistically significant patterns of association were observed in the European American patients with SLE. Case-control analysis did not show large allele frequency differences, supporting the idea that this allele is most strongly associated with anti-La-positive patients. CONCLUSION This pattern of recessive influence within a subgroup of patients may explain why this allele does not produce a strong signal in standard case-control studies, and subphenotypes should be included in future studies of UBE2L3. The interaction we observed between UBE2L3 genotype and autoantibodies upon serum IFN-α suggests a biological role for this locus in patients with SLE in vivo.
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Affiliation(s)
- Sandra Agik
- University of Chicago, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, 924 East 57th Street, R420, Chicago, IL 60637, USA
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CTLA-4 gene polymorphism and the risk of systemic lupus erythematosus in the Chinese population. J Biomed Biotechnol 2011; 2011:167395. [PMID: 21915163 PMCID: PMC3170903 DOI: 10.1155/2011/167395] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 05/25/2011] [Accepted: 06/09/2011] [Indexed: 11/28/2022] Open
Abstract
Several variants of CTLA-4 have been reported to be associated with susceptibility systemic lupus erythematosus (SLE); however, findings have been inconsistent across different populations. Using a case-control study design, we have investigated the role of CTLA-4 polymorphism at positions −1661 and −1722 on SLE susceptibility in our Chinese SLE population in central China's Hubei province. Samples were collected from 148 SLE patients and 170 healthy controls. Polymerase chain reaction restriction fragments length polymorphism (PCR-RFLP) was used to analyze the genotypes of the two sites. Statistically significant difference was observed in genotypes for −1722, but not for −1661. The frequency of the T allele on the −1722 SNP was significantly increased in SLE patients: 57.8% versus 40.6% in controls (P < 0.001, OR = 2.002). While the detected C allele frequency in the controls was significantly elevated in comparison to that in the SLE patients (59.4% versus 42.2%). On the contrary, no association was found between SLE and CTLA-4 polymorphism at position −1661.
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