1
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Mohammed S, Zalzala M, Gorial F. Association of tumor necrosis factor-alpha promoter region gene polymorphism at positions -308G/A, -857C/T, and -863C/A with etanercept response in Iraqi rheumatoid arthritis patients. Arch Rheumatol 2022; 37:613-625. [PMID: 36879565 PMCID: PMC9985381 DOI: 10.46497/archrheumatol.2022.9272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 11/03/2022] Open
Abstract
Objectives This study aims to evaluate the association between polymorphisms in the promoter region of the tumor necrosis factor-alpha (TNF-α) gene at locations -308G/A, -857C/T, and -863C/A with the tendency of being non-responder to etanercept. Patients and methods Between October 2020 and August 2021, a total of 80 patients (10 males, 70 females; mean age: 50 years; range, 30 to 72 years) with rheumatoid arthritis (RA) receiving etanercept for at least six months were included. The patients were divided into two groups responders and non-responders, based on their response after six months of continuous treatment. Following polymerase chain reaction amplification of the extracted deoxyribonucleic acid, sequencing by Sanger method was performed to identify the polymorphism at the TNF-α promoter region. Results In the responder group, the GG genotype of (-308G/A) and the AA genotype of (-863C/A) were both significantly present. The CC genotype of (-863C/A) was significantly present in the non-responders group. The CC of (-863C/A) SNP was the only genotype that appeared to increase the likelihood of being resistant to etanercept. The GG genotype of (-308G/A) was negatively correlated with the likelihood of being a non-responder. The (-857CC) and (-863CC) genotypes were significantly more prevalent in the non-responders group. Conclusion The presence of the (-863CC) genotype, alone or in combination with (-857CC), is linked to an increased likelihood of becoming a non-responder to etanercept. The GG genotype of -308G/A and the AA genotype of -863C/A significantly increase the likelihood of becoming responder to etanercept.
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Affiliation(s)
- Samer Mohammed
- Department of Clinical Pharmacy, University of Baghdad-College of Pharmacy, Baghdad, Iraq
| | - Munaf Zalzala
- Department of Pharmacology and Toxicology, University of Baghdad-College of Pharmacy, Baghdad, Iraq
| | - Faiq Gorial
- Department of Rheumatology, University of Baghdad-College of Medicine, Baghdad, Iraq
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2
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Kachuri L, Francis SS, Morrison ML, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. Genome Med 2020; 12:93. [PMID: 33109261 PMCID: PMC7590248 DOI: 10.1186/s13073-020-00790-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/07/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr virus (EBV), Varicella zoster virus (VZV), human herpesvirus 7, (HHV7), and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P < 5.0 × 10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, and CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P = 5.0 × 10-15 (MCV), NTN5: P = 1.1 × 10-9 (BKV), and P2RY13: P = 1.1 × 10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases, from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA, USA
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, CA, USA
- Department of Mathematics, The University of Texas, Austin, TX, USA
| | - George A Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Université Laval, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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3
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Kachuri L, Francis SS, Morrison M, Wendt GA, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in immune response to common viral infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.05.01.20088054. [PMID: 32511533 PMCID: PMC7273301 DOI: 10.1101/2020.05.01.20088054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities. METHODS We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort. RESULTS Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRβ1 at positions 11, 13, 71, and 74 for Epstein-Barr Virus (EBV), Varicella Zoster Virus (VZV), Human Herpes virus 7, (HHV7) and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P<5.×10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, as well as CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0×10-15 (MCV), NTN5: P=1.1×10-9 (BKV), and P2RY13: P=1.1×10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases; from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions. CONCLUSIONS Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
| | - Stephen S. Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | - Maike Morrison
- Summer Research Training Program, Graduate Division, University of California San Francisco, San Francisco, USA
- Department of Mathematics, The University of Texas at Austin, Austin, USA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Université Laval, Quebec City, Canada
| | - Taylor B. Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, USA
| | - Sara R. Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Department of Medicine, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California San Francisco, San Francisco, USA
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4
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Rajaei E, Jalali MT, Shahrabi S, Asnafi AA, Pezeshki SMS. HLAs in Autoimmune Diseases: Dependable Diagnostic Biomarkers? Curr Rheumatol Rev 2020; 15:269-276. [PMID: 30644346 DOI: 10.2174/1573397115666190115143226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/08/2018] [Accepted: 04/05/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND The process of antigen presentation to immune cells is an undeniable contributor to the pathogenesis of autoimmune diseases. Different studies have indicated several factors that are related to autoimmunity. Human Leukocyte Antigens (HLAs) are among such factors, which have a key role in autoimmunity because of their involvement in antigen presentation process. METHODS Relevant English language literature was searched and retrieved from Google Scholar search engine and PubMed database (1996-2018). The following keywords were used: "Human leukocyte antigen", "Behcet's syndrome", "Rheumatoid arthritis", "Systemic lupus erythematosus", "Type 1 diabetes", "Celiac Disease" and "Autoimmunity". RESULTS There is a strong association between HLA alleles and autoimmune diseases. For instance, HLA-B alleles and Behcet's syndrome are strongly correlated, and systemic lupus erythematosus and Type 1 diabetes are related to HLA-DQA1 and HLA-DQB1, respectively. CONCLUSION Association between numerous HLA alleles and autoimmune diseases may justify and rationalize their use as biomarkers as well as possible diagnostic laboratory parameters.
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Affiliation(s)
- Elham Rajaei
- Golestan Hospital Clinical Research Development Unit, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Taha Jalali
- Hyperlipidemia Research Center, Diabetes Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeid Shahrabi
- Department of Biochemistry and Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Amin Asnafi
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Mohammad Sadegh Pezeshki
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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5
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Wu EK, Ambrosini RD, Kottmann RM, Ritchlin CT, Schwarz EM, Rahimi H. Reinterpreting Evidence of Rheumatoid Arthritis-Associated Interstitial Lung Disease to Understand Etiology. Curr Rheumatol Rev 2020; 15:277-289. [PMID: 30652645 DOI: 10.2174/1573397115666190116102451] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/19/2018] [Accepted: 01/05/2019] [Indexed: 02/07/2023]
Abstract
Interstitial Lung Disease (ILD) is a well-known complication of rheumatoid arthritis (RA) which often results in significant morbidity and mortality. It is often diagnosed late in the disease process via descriptive criteria. Multiple subtypes of RA-ILD exist as defined by chest CT and histopathology. In the absence of formal natural history studies and definitive diagnostics, a conventional dogma has emerged that there are two major subtypes of RA-ILD (nonspecific interstitial pneumonia (NSIP) and Usual Interstitial Pneumonia (UIP)). These subtypes are based on clinical experience and correlation studies. However, recent animal model data are incongruous with established paradigms of RA-ILD and beg reassessment of the clinical evidence in order to better understand etiology, pathogenesis, prognosis, and response to therapy. To this end, here we: 1) review the literature on epidemiology, radiology, histopathology and clinical outcomes of the various RAILD subtypes, existing animal models, and current theories on RA-ILD pathogenesis; 2) highlight the major gaps in our knowledge; and 3) propose future research to test an emerging theory of RAILD that posits initial rheumatic lung inflammation in the form of NSIP-like pathology transforms mesenchymal cells to derive chimeric disease, and subsequently develops into frank UIP-like fibrosis in some RA patients. Elucidation of the pathogenesis of RA-ILD is critical for the development of effective interventions for RA-ILD.
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Affiliation(s)
- Emily K Wu
- Center for Musculoskeletal Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States.,Department of Microbiology & Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - Robert D Ambrosini
- Department of Imaging Sciences, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - R Matthew Kottmann
- Division of Pulmonary Diseases and Critical Care, Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - Christopher T Ritchlin
- Center for Musculoskeletal Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States.,Division of Allergy, Immunology, Rheumatology, Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - Edward M Schwarz
- Center for Musculoskeletal Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States.,Department of Microbiology & Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States.,Department of Orthopaedics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - Homaira Rahimi
- Center for Musculoskeletal Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States.,Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
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6
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Amariuta T, Luo Y, Knevel R, Okada Y, Raychaudhuri S. Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis. Immunol Rev 2019; 294:188-204. [PMID: 31782165 DOI: 10.1111/imr.12827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis (RA) risk has a large genetic component (~60%) that is still not fully understood. This has hampered the design of effective treatments that could promise lifelong remission. RA is a polygenic disease with 106 known genome-wide significant associated loci and thousands of small effect causal variants. Our current understanding of RA risk has suggested cell-type-specific contexts for causal variants, implicating CD4 + effector memory T cells, as well as monocytes, B cells and stromal fibroblasts. While these cellular states and categories are still mechanistically broad, future studies may identify causal cell subpopulations. These efforts are propelled by advances in single cell profiling. Identification of causal cell subpopulations may accelerate therapeutic intervention to achieve lifelong remission.
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Affiliation(s)
- Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Graduate School of Arts and Sciences, Harvard University, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Rachel Knevel
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yukinori Okada
- Division of Medicine, Osaka University, Osaka, Japan.,Osaka University Graduate School of Medicine, Osaka, Japan
| | - Soumya Raychaudhuri
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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7
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Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
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Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
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8
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Sadaf T, John P, Bhatti A, Malik JM. Lack of association of -863C/A (rs1800630) polymorphism of tumor necrosis factor-a gene with rheumatoid arthritis. Arch Med Sci 2019; 15:531-536. [PMID: 30899307 PMCID: PMC6425217 DOI: 10.5114/aoms.2018.76946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/02/2017] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Multifunctional pro-inflammatory cytokine tumor necrosis factor-α (TNF-α) has been implicated in a variety of inflammatory diseases including rheumatoid arthritis (RA). TNF-α polymorphisms are mostly located in its promoter region and play a significant role in disease susceptibility and severity. We therefore sought to investigate TNFA -863C/A (rs1800630) polymorphism association with RA activity in our Pakistani study group. MATERIAL AND METHODS A total of 268 human subjects were enrolled. Among them, 134 were RA patients and 134 were controls. In this study the physical parameters of RA patients were collected, and the disease activity was measured by DAS28. The genotypes were determined following the allele-specific PCR along with the pre-requisite internal amplification controls. Subsequently, data were analyzed statistically for any significant association including χ2/Fisher's exact test using GraphPad prism 6 software. RESULTS We found that the TNF-α -863 C/A (rs1800630) variant was not differentially segregated between cases and controls in either genotype frequency, with χ2 of 2.771 and a p-value of 0.2502, or allele frequency, with χ2 of 2.741 and a p-value of 0.0978, with an odds ratio (95% CI) of 0.7490 (0.5317-1.055). CONCLUSIONS The lack of positive association of TNF-α -863(rs1800630) polymorphism in our study group implies that TNF-α -863 polymorphism is not a susceptible marker to RA and cannot serve as a genetic factor for screening RA patients in Pakistan. There might be other factors that may influence disease susceptibility. However, further investigations on additional larger and multi-regional population samples are required to determine the consequences of genetic variations for disease prognosis.
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Affiliation(s)
- Tayyaba Sadaf
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Peter John
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Attya Bhatti
- Department of Health Care Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Javaid M. Malik
- Arthritis Research Center, Rahmat Noor Clinic, Rawalpindi, Pakistan
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9
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Stromberg SJ, Thomasy SM, Marangakis AD, Kim S, Cooper AE, Brown EA, Maggs DJ, Bannasch DL. Evaluation of the major histocompatibility complex (MHC) class II as a candidate for sudden acquired retinal degeneration syndrome (SARDS) in Dachshunds. Vet Ophthalmol 2019; 22:751-759. [PMID: 30791205 PMCID: PMC6703976 DOI: 10.1111/vop.12646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/23/2018] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
Objective Sudden acquired retinal degeneration syndrome (SARDS) is one of the leading causes of acute blindness in dogs, with an unknown etiology and no effective treatment. Certain breeds such as Dachshunds are overrepresented among SARDS patients, and therefore, the syndrome is suspected to have a genetic component. The objective of this study was to determine if a genetic locus associated with SARDS in Dachshunds could be identified using a genome‐wide association study (GWAS). Procedures Genome‐wide association mapping was performed in 15 SARDS‐affected and 16 unaffected Dachshunds. Genotyping of three classical DLA class II genes (DLA‐DRB1, DLA‐DQA1, and DLA‐DQB1) was performed in 34 SARDS‐affected and 66 unaffected Dachshunds to evaluate for an association in this region. Results Although no single nucleotide polymorphisms (SNPs) were of genome‐wide statistical significance (PBonferroni < 0.05), 5 of the top 9 SNPs were in the major histocompatibility complex (MHC). Using DLA typing, the allele DLA‐DRB1*09401 was identified as a risk factor for the development of SARDS (P = 0.0032, OR = 4.0). The alleles DLA‐DQB1*00101 (P = 0.0050, OR = 0.31), DLA‐DQA1*00901 (P = 0.0087, OR = 0.33), and a previously identified DLA‐DRB1allele described as “DRB1‐T” (P = 0.0284, OR = 0.37) were identified as protective factors. Conclusions Although far from definitive, association of SARDS with alleles of immunologic importance further supports the hypothesis that autoimmunity may play a role in the pathogenesis of SARDS.
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Affiliation(s)
- Stephanie J Stromberg
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California.,Department of Ophthalmology & Vision Science, School of Medicine, UC Davis Medical Center, Sacramento, California
| | - Ariana D Marangakis
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California
| | - Soohyun Kim
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California
| | - Ann E Cooper
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California
| | - Emily A Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California
| | - David J Maggs
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, California
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California
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10
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Clinical and immunological aspects of anti-peptidylarginine deiminase type 4 (anti-PAD4) autoantibodies in rheumatoid arthritis. Autoimmun Rev 2018; 17:94-102. [DOI: 10.1016/j.autrev.2017.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/31/2022]
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11
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Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling. Gene 2017; 634:62-67. [PMID: 28882568 DOI: 10.1016/j.gene.2017.08.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/23/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023]
Abstract
The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA.
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12
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Cruz GI, Shao X, Quach H, Ho KA, Sterba K, Noble JA, Patsopoulos NA, Busch MP, Triulzi DJ, Wong WS, Solomon BD, Niederhuber JE, Criswell LA, Barcellos LF. Increased risk of rheumatoid arthritis among mothers with children who carry DRB1 risk-associated alleles. Ann Rheum Dis 2017; 76:1405-1410. [PMID: 28391248 DOI: 10.1136/annrheumdis-2016-210662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 03/13/2017] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate whether a child's genotype affects a mother's risk of rheumatoid arthritis (RA) beyond the risk associated with her genotype and to test whether exposure to fetal alleles inherited from the father increases risk of RA among mothers without risk alleles. METHODS A case-control study was conducted among 1165 mothers (170 cases/995 controls) and their respective 1482 children. We tested the association between having any child with alleles encoding amino acids (AAs) associated with RA including the 'shared epitope' (SE) and DERAA AA sequences at positions 70-74; AA valine, lysine and alanine at positions 11, 71 and 74 of HLA-DRB1; aspartic acid at position 9 of HLA-B and phenylalanine at position 9 of DPB1. We used logistic regression models to estimate OR and 95% CI for each group of alleles, adjusting for maternal genotype and number of live births. RESULTS We found increased risk of RA among mothers who had any child with SE (OR 3.0; 95% CI 2.0 to 4.6); DERAA (OR 1.7; 95% CI 1.1 to 2.6); or valine (OR 2.3; 95% CI 1.6 to 3.5), lysine (OR 2.3; 95% CI 1.5 to 3.4) and alanine (OR 2.8; 95% CI 1.2 to 6.4) at DRB1 positions 11, 71 and 74, respectively. Among non-carrier mothers, increased risk of RA was associated with having children who carried DERAA (OR 1.7; 95% CI 1.0 to 2.7) and alleles encoding lysine at DRB1 position 71 (OR 2.3; 95% CI 1.5 to 4.8). CONCLUSION Findings support the hypothesis that a child's genotype can contribute independently to risk of RA among mothers.
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Affiliation(s)
- Giovanna Ibeth Cruz
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Xiaorong Shao
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Hong Quach
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Kimberly A Ho
- Department of Medicine, University of San Francisco, Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, San Francisco, California, USA
| | - Kirsten Sterba
- Department of Medicine, University of San Francisco, Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, San Francisco, California, USA
| | - Janelle A Noble
- Childrens Hospital Oakland Research Institute, Oakland, California, USA
| | | | - Michael P Busch
- Laboratory of Medicine, Blood Systems Research Institute, San Francisco, California, USA
| | - Darrell J Triulzi
- Department of Pathology, University of Pittsburgh, Institute for Transfusion Medicine, Pittsburgh, Pennsylvania, USA
| | - Wendy Sw Wong
- Division of Medical Genomics, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Benjamin D Solomon
- Division of Medical Genomics, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - John E Niederhuber
- Division of Medical Genomics, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Lindsey A Criswell
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, California, USA
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Bijanzadeh M. The recurrence risk of genetic complex diseases. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2017; 22:32. [PMID: 28461818 PMCID: PMC5390543 DOI: 10.4103/1735-1995.202143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/30/2016] [Accepted: 12/18/2016] [Indexed: 12/19/2022]
Abstract
Complex inherited diseases affected by an interaction between collective effects of the genotype at one or multiple loci either to increase or to lower susceptibility to disease, combined with a variety of environmental exposures that may trigger, accelerate, exacerbate, or protect against the disease process. The new aspects of genetic techniques have been opened for diagnosis and analysis of inherited disorders. While appropriate Mendelian laws is applied to estimate the recurrence risk of single gene diseases, using empirical recurrence risks are the most important and available method to evaluate pedigree of complex (multifactorial), chromosomal, and unknown etiology disorders. Although, generally, empirical recurrent risks are not accurate, either because of the difference of gene frequencies and environmental factors among populations or heterogeneity of disease; using results of plenty family population studies, computerized estimating programs, genotyping technologies, and Genome-wide association studies (GWASs) of single nucleotide polymorphisms (SNPs), can make it possible nowadays to estimate these risks. The specific family situation and importance recurrence risks of some common complex genetic diseases will be presented in this review and some important multifactorial disorders’ recurrence risks will be summarized to help genetic counselors for supporting families and representing better view of genetic disorders.
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Affiliation(s)
- Mahdi Bijanzadeh
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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14
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Sapir-Koren R, Livshits G. Rheumatoid arthritis onset in postmenopausal women: Does the ACPA seropositive subset result from genetic effects, estrogen deficiency, skewed profile of CD4(+) T-cells, and their interactions? Mol Cell Endocrinol 2016; 431:145-63. [PMID: 27178986 DOI: 10.1016/j.mce.2016.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/28/2022]
Abstract
Rheumatoid arthritis (RA) incidence displays a differentiated age-dependent female-to-male ratio in which women outnumber men. Evidence that the peak incidence of RA in women coincides with menopause age, suggests a potential estrogenic role to disease etiology. Estrogens exert physiologically both stimulatory and inhibitory effects on the immune system. Epidemiologic and animal model studies with estrogen deprivation or supplementation suggested estrogens as to play, mainly, a protective role in RA immunopathology. In this review, we propose that some yet unidentified disturbances associated with estrogen circulating levels, differentiated by the menopausal status, play a major role in women's RA susceptibility. We focus on the interaction between estrogen deprivation and genetic risk alleles for anti-citrullinated protein antibodies (ACPA) seropositive RA, as a major driving force for increased immune reactivity and RA susceptibility, in postmenopausal women. This opens up new fields for research concerning the association among different irregular estrogenic conditions, the cytokine milieu, and age/menopausal status bias in RA.
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Affiliation(s)
- Rony Sapir-Koren
- Human Population Biology Research Group, Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gregory Livshits
- Human Population Biology Research Group, Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Lilian and Marcel Pollak Chair of Biological Anthropology, Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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Terao C, Raychaudhuri S, Gregersen PK. Recent Advances in Defining the Genetic Basis of Rheumatoid Arthritis. Annu Rev Genomics Hum Genet 2016; 17:273-301. [PMID: 27216775 DOI: 10.1146/annurev-genom-090314-045919] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthritis and exhibits genetic overlap with other autoimmune and inflammatory disorders. Although predominant associations with the HLA-DRB1 locus have been known for decades, recent data have revealed additional insight into the likely causative variants within HLA-DRB1 as well as within other HLA loci that contribute to disease risk. In addition, more than 100 common variants in non-HLA loci have been implicated in disease susceptibility. Genetic factors are involved not only in the development of RA, but also with various disease subphenotypes, including production and circulating levels of autoantibodies and joint destruction. The major current challenge is to integrate these new data into a precise understanding of disease pathogenesis, including the critical cell types and molecular networks involved as well as interactions with environmental factors. We predict that delineating the functional effects of genetic variants is likely to drive new diagnostic and therapeutic approaches to the disease.
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Affiliation(s)
- Chikashi Terao
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142; .,Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto 606-8501, Japan;
| | - Soumya Raychaudhuri
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142; .,Institute of Inflammation and Repair, University of Manchester, M15 6SZ Manchester, United Kingdom.,Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, SE-171 76 Stockholm, Sweden
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030;
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Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes. Sci Rep 2015; 5:16972. [PMID: 26593880 PMCID: PMC4655331 DOI: 10.1038/srep16972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
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Seldin MF, Alkhairy OK, Lee AT, Lamb JA, Sussman J, Pirskanen-Matell R, Piehl F, Verschuuren JJGM, Kostera-Pruszczyk A, Szczudlik P, McKee D, Maniaol AH, Harbo HF, Lie BA, Melms A, Garchon HJ, Willcox N, Gregersen PK, Hammarstrom L. Genome-Wide Association Study of Late-Onset Myasthenia Gravis: Confirmation of TNFRSF11A and Identification of ZBTB10 and Three Distinct HLA Associations. Mol Med 2015; 21:769-781. [PMID: 26562150 DOI: 10.2119/molmed.2015.00232] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 01/05/2023] Open
Abstract
To investigate the genetics of late-onset myasthenia gravis (LOMG), we conducted a genome-wide association study imputation of>6 million single nucleotide polymorphisms (SNPs) in 532 LOMG cases (anti-acetylcholine receptor [AChR] antibody positive; onset age≥50 years) and 2,128 controls matched for sex and population substructure. The data confirm reported TNFRSF11A associations (rs4574025, P = 3.9 × 10-7, odds ratio [OR] 1.42) and identify a novel candidate gene, ZBTB10, achieving genome-wide significance (rs6998967, P = 8.9 × 10-10, OR 0.53). Several other SNPs showed suggestive significance including rs2476601 (P = 6.5 × 10-6, OR 1.62) encoding the PTPN22 R620W variant noted in early-onset myasthenia gravis (EOMG) and other autoimmune diseases. In contrast, EOMG-associated SNPs in TNIP1 showed no association in LOMG, nor did other loci suggested for EOMG. Many SNPs within the major histocompatibility complex (MHC) region showed strong associations in LOMG, but with smaller effect sizes than in EOMG (highest OR ~2 versus ~6 in EOMG). Moreover, the strongest associations were in opposite directions from EOMG, including an OR of 0.54 for DQA1*05:01 in LOMG (P = 5.9 × 10-12) versus 2.82 in EOMG (P = 3.86 × 10-45). Association and conditioning studies for the MHC region showed three distinct and largely independent association peaks for LOMG corresponding to (a) MHC class II (highest attenuation when conditioning on DQA1), (b) HLA-A and (c) MHC class III SNPs. Conditioning studies of human leukocyte antigen (HLA) amino acid residues also suggest potential functional correlates. Together, these findings emphasize the value of subgrouping myasthenia gravis patients for clinical and basic investigations and imply distinct predisposing mechanisms in LOMG.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, and Department of Medicine, University of California, Davis, California, United States of America
| | - Omar K Alkhairy
- Division of Clinical Immunology, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Annette T Lee
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York, United States of America
| | - Janine A Lamb
- Centre for Integrated Genomic Medical Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Jon Sussman
- Department of Neurology, Greater Manchester Neuroscience Centre, Manchester, United Kingdom
| | | | - Fredrik Piehl
- Department of Neurology, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | | | - Piotr Szczudlik
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - David McKee
- Department of Neurology, Greater Manchester Neuroscience Centre, Manchester, United Kingdom
| | - Angelina H Maniaol
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Arthur Melms
- Department of Neurology, Tübingen University Medical Center, Tübingen, Germany, and Neurologische Klinik, Universitàtsklinikum Erlangen, Erlangen, Germany
| | | | - Nicholas Willcox
- Nuffield Department of Clinical Neurosciences, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York, United States of America
| | - Lennart Hammarstrom
- Division of Clinical Immunology, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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18
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Gichohi-Wainaina WN, Melse-Boonstra A, Feskens EJ, Demir AY, Veenemans J, Verhoef H. Tumour necrosis factor allele variants and their association with the occurrence and severity of malaria in African children: a longitudinal study. Malar J 2015; 14:249. [PMID: 26088606 PMCID: PMC4474355 DOI: 10.1186/s12936-015-0767-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/07/2015] [Indexed: 12/16/2022] Open
Abstract
Background Tumour necrosis factor (TNF) is central to the immune response to Plasmodium infection. Its plasma concentration is influenced by allele variants in the promoter region of TNF. The study’s objectives were to assess TNF allele variants (TNF−1031, TNF−308): (1) modulation of malaria rates in young Tanzanian children; (2) modulation of the severity of malaria as indicated by haemoglobin concentrations at the time of presentation with febrile episodes; and (3) the association between Plasmodium infection and haemoglobin concentration in symptomless parasite carriers. Methods Data from a placebo-controlled trial in which 612 Tanzanian children aged 6–60 months with height-for-age z-score in the range −3 SD to 1.5 SD was utilised. Those with Plasmodium infection at baseline were treated with artemether-lumefantrine. An episode of malaria was predefined as current Plasmodium infection with an inflammatory response (axillary temperature ≥37.5°C or whole blood C-reactive protein concentration ≥8 mg/L) in children reported sick. Linkage disequilibrium (LD) pattern assessment as well as haplotype analysis was conducted using HAPLOVIEW. Cox regression models used in the primary analysis accounted for multiple episodes per child. Results Genotyping of 94.9% (581/612) children for TNF−1031 (TNF−1031T>C); allele frequency was 0.39. Corresponding values for rs1800629 (TNF−308G>A) were 95.4% (584/612) and 0.17. Compared to the wild type genotype (TT), malaria rates were increased in the TNF−1031CC genotype (hazard ratio, HR [95% CI]: 1.41 [1.01‒1.97] and 1.31 [0.97‒1.76] for crude analysis and adjusting for pre-specified baseline factors, respectively) but decreased in those with the TNF−308AA genotype (corresponding HR: 0.13 [0.02‒0.63] and 0.16 [0.04‒0.67]). These associations were weaker when analysing first episodes of malaria (P value −0.59 and 0.38, respectively). No evidence that allele variants of TNF−1031 and TNF−308 affected haemoglobin concentration at first episode of malaria, or that they modified the association between Plasmodium infection and haemoglobin concentrations at baseline was observed. Conclusion In this cohort of Tanzanian children, the TNF−1031CC genotype was associated with increased rates of malarial episodes, whereas the TNF−308AA genotype was associated with decreased rates.
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Affiliation(s)
| | - Alida Melse-Boonstra
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands.
| | - Edith J Feskens
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands.
| | - Ayse Y Demir
- Laboratory for Clinical Chemistry, Meander Medical Centre, Amersfoort, The Netherlands.
| | - Jacobien Veenemans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands.
| | - Hans Verhoef
- Cell Biology and Immunology Group, Wageningen University, Wageningen, The Netherlands. .,Medical Research Council (MRC) International Nutrition Group, London School of Hygiene & Tropical Medicine, London, UK. .,Medical Research Council (MRC), Keneba, The Gambia.
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van Steenbergen HW, Raychaudhuri S, Rodríguez-Rodríguez L, Rantapää-Dahlqvist S, Berglin E, Toes REM, Huizinga TWJ, Fernández-Gutiérrez B, Gregersen PK, van der Helm-van Mil AHM. Association of valine and leucine at HLA-DRB1 position 11 with radiographic progression in rheumatoid arthritis, independent of the shared epitope alleles but not independent of anti-citrullinated protein antibodies. Arthritis Rheumatol 2015; 67:877-86. [PMID: 25580908 DOI: 10.1002/art.39018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/30/2014] [Indexed: 01/29/2023]
Abstract
OBJECTIVE For decades it has been known that the HLA-DRB1 shared epitope (SE) alleles are associated with an increased risk of development and progression of rheumatoid arthritis (RA). Recently, the following variations in the peptide-binding grooves of HLA molecules that predispose to RA development have been identified: Val and Leu at HLA-DRB1 position 11, Asp at HLA-B position 9, and Phe at HLA-DPB1 position 9. This study was undertaken to investigate whether these variants are also associated with radiographic progression in RA, independent of SE and anti-citrullinated protein antibody (ACPA) status. METHODS A total of 4,911 radiograph sets from 1,878 RA patients included in the Leiden Early Arthritis Clinic (The Netherlands), Umeå (Sweden), Hospital Clinico San Carlos-Rheumatoid Arthritis (Spain), and National Data Bank for Rheumatic Diseases (US) cohorts were studied. HLA was imputed using single-nucleotide polymorphism data from an Immunochip, and the amino acids listed above were tested in relation to radiographic progression per cohort using an additive model. Results from the 4 cohorts were combined in inverse-variance weighted meta-analyses using a fixed-effects model. Analyses were conditioned on SE and ACPA status. RESULTS Val and Leu at HLA-DRB1 position 11 were associated with more radiographic progression (meta-analysis P = 5.11 × 10(-7)); this effect was independent of SE status (meta-analysis P = 0.022) but not independent of ACPA status. Phe at HLA-DPB1 position 9 was associated with more severe radiographic progression (meta-analysis P = 0.024), though not independent of SE status. Asp at HLA-B position 9 was not associated with radiographic progression. CONCLUSION Val and Leu at HLA-DRB1 position 11 conferred a risk of a higher rate of radiographic progression independent of SE status but not independent of ACPA status. These findings support the relevance of these amino acids at position 11.
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Anti-citrullinated peptide autoantibodies, human leukocyte antigen shared epitope and risk of future rheumatoid arthritis: a nested case-control study. Arthritis Res Ther 2013; 15:R159. [PMID: 24286474 PMCID: PMC3953952 DOI: 10.1186/ar4342] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/02/2013] [Indexed: 01/13/2023] Open
Abstract
Introduction The aim of this study was to characterize anti-citrullinated peptide antibody (ACPA) serostatus in pre-clinical rheumatoid arthritis (RA) with and without Human Leukocyte Antigen-Shared Epitope (HLA-SE) alleles. Methods We identified 192 women in the Nurses’ Health Study cohorts with blood samples obtained 4 months to 17 years prior to medical record-confirmed RA diagnosis. Three controls were selected matched on age, cohort, menopausal status and post-menopausal hormone use. Reactivities to 18 ACPAs were measured using a custom BioPlex platform. We used conditional logistic regression to calculate the relative risk (RR) of RA for any ACPA-positive and peptide-specific ACPA-positive and examined RRs by time between blood draw and RA onset. Measures of multiplicative and additive interaction between any ACPA-positive and HLA-SE were calculated. Results All ACPAs by peptide groups were significantly associated with RA risk, RRs ranged from 4.7 to 11.7. The association between ACPA and RA varied over time with the strongest association in those with blood draw less than 5 years before onset (RR 17.0 [95% CI 5.8 to 53.7]) and no association 10 or more years prior to onset (RR 1.4 [95% CI 0.5 to 4.3]). Individuals with both HLA-SE and any ACPA-positive had the highest risk of RA. HLA-SE-positive RA cases showed reactivity to more ACPA types than HLA-SE negative (χ2 test for trend, P = 0.01). Conclusions There is increasing ACPA reactivity up to 10 years before RA onset with the strongest association within 5 years of RA onset. The magnitude of the response to ACPAs, in combination with the presence of HLA-SE, is most important for identifying those individuals with the highest risk of RA.
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HLA-C alleles confer risk for anti-citrullinated peptide antibody-positive rheumatoid arthritis independent of HLA-DRB1 alleles. Rheumatology (Oxford) 2013; 52:1973-82. [DOI: 10.1093/rheumatology/ket252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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22
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Clinical features and independent predictors in the further development of rheumatoid arthritis in undifferentiated arthritis. Rheumatol Int 2013; 33:2827-32. [DOI: 10.1007/s00296-013-2799-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/06/2013] [Indexed: 11/26/2022]
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Shimane K, Kochi Y, Suzuki A, Okada Y, Ishii T, Horita T, Saito K, Okamoto A, Nishimoto N, Myouzen K, Kubo M, Hirakata M, Sumida T, Takasaki Y, Yamada R, Nakamura Y, Kamatani N, Yamamoto K. An association analysis of HLA-DRB1 with systemic lupus erythematosus and rheumatoid arthritis in a Japanese population: effects of *09:01 allele on disease phenotypes. Rheumatology (Oxford) 2013; 52:1172-82. [DOI: 10.1093/rheumatology/kes427] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Montes A, Perez-Pampin E, Calaza M, Gomez-Reino JJ, Gonzalez A. Association of anti-citrullinated vimentin and anti-citrullinated α-enolase antibodies with subsets of rheumatoid arthritis. ACTA ACUST UNITED AC 2013; 64:3102-10. [PMID: 22674012 DOI: 10.1002/art.34569] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To determine whether the anti-citrullinated vimentin peptide 60-75 (anti-Cit-vimentin) and the immunodominant anti-citrullinated α-enolase peptide 1 (anti-CEP-1) antibodies are associated with subsets of patients with rheumatoid arthritis (RA) independently of the associations between anti-cyclic citrullinated peptide (anti-CCP) antibodies and clinical features of RA. METHODS The 3 antibody types were quantified by enzyme-linked immunosorbent assay (ELISA) in serum samples from 521 patients with RA and 173 healthy controls of Spanish ancestry. Genotypes for HLA-DRB1 alleles and rs2476601 in PTPN22 were available for these patients and controls plus an additional 106 healthy controls. A combined analysis of the 3 antibodies was conducted using stratified contingency tables and logistic regression models. RESULTS A differential, particularly strong, and independent association was observed between the presence of anti-Cit-vimentin antibodies and the presence of shared epitope (SE) alleles, specifically in patients carrying 2 SE alleles, and between the presence of anti- Cit-vimentin antibodies and the prevalence of joint erosion. Associations were observed between anti-CEP-1 positivity and the presence of HLA-DRB1 and PTPN22 risk alleles and their additive interaction. These associations were not accounted for by the anti-CCP status. CONCLUSION Our results indicate that the 2 antibodies against citrullinated peptides analyzed in this study add specific information beyond that obtained with the anti-CCP status. They define subgroups of patients with RA in which genetic factors have different weight and there is an observed difference in the prevalence of erosions.
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Affiliation(s)
- Ariana Montes
- Instituto de Investigacion Sanitaria and Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
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Toonen EJM, Barrera P, Fransen J, de Brouwer APM, Eijsbouts AM, Miossec P, Marotte H, Scheffer H, van Riel PLCM, Franke B, Coenen MJH. Meta-analysis identified the TNFA -308G > A promoter polymorphism as a risk factor for disease severity in patients with rheumatoid arthritis. Arthritis Res Ther 2012; 14:R264. [PMID: 23217265 PMCID: PMC3674610 DOI: 10.1186/ar4110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/30/2012] [Indexed: 12/12/2022] Open
Abstract
Introduction The goal of this study is to investigate whether the -308G > A promoter polymorphism in the tumor necrosis factor alpha (TNFA) gene is associated with disease severity and radiologic joint damage in a large cohort of patients with rheumatoid arthritis (RA). Methods A long-term observational early RA inception cohort (n = 208) with detailed information about disease activity and radiologic damage after 3, 6 and 9 years of disease was genotyped for the TNFA -308G > A promoter polymorphism (rs1800629). A longitudinal regression analysis was performed to assess the effect of genotype on RA disease severity and joint damage. Subsequently, a meta-analysis, including all publically available data, was performed to further test the association between joint erosions and the TNFA polymorphism. To learn more about the mechanism behind the effect of the polymorphism, RNA isolated from peripheral blood from RA patients (n = 66) was used for TNFA gene expression analysis by quantitative PCR. Results Longitudinal regression analysis with correction for gender and disease activity showed a significant difference in total joint damage between GG and GA+AA genotype groups (P = 0.002), which was stable over time. The meta-analysis, which included 2,053 patients, confirmed an association of the genetic variant with the development of erosions (odds ratio 0.78, 95% CI 0.62, 0.98). No significant differences in TNFA gene expression were observed for the different genotypes, confirming earlier findings in healthy individuals. Conclusions Our data confirm that the TNFA -308G > A promoter polymorphism is associated with joint damage in patients with RA. This is not mediated by differences in TNFA gene expression between genotypes.
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Jacob N, Jacob CO. Genetics of rheumatoid arthritis: an impressionist perspective. Rheum Dis Clin North Am 2012; 38:243-57. [PMID: 22819082 DOI: 10.1016/j.rdc.2012.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rheumatoid arthritis (RA) is the most common rheumatic disease. The genetic basis of RA is supported through the identification of more than 30 susceptibility genetic variants. Each of these genes individually makes only a slight contribution to the risk of disease. Moreover, there is significant disparity in the genetic variants associated with different RA subgroups and patient ethnicities, which emphasizes the intricate nature of the disease's pathogenesis, and the complexities involved in large-scale genetic studies. This review evaluates critically the recent literature on the genetic contribution to RA and assesses the methodology used to identify these risk alleles.
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Affiliation(s)
- Noam Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue HMR 703, Los Angeles, CA 90033, USA.
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A genome-wide homozygosity association study identifies runs of homozygosity associated with rheumatoid arthritis in the human major histocompatibility complex. PLoS One 2012; 7:e34840. [PMID: 22536334 PMCID: PMC3335047 DOI: 10.1371/journal.pone.0034840] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 03/08/2012] [Indexed: 12/02/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disorder with a polygenic mode of inheritance. This study examined the hypothesis that runs of homozygosity (ROHs) play a recessive-acting role in the underlying RA genetic mechanism and identified RA-associated ROHs. Ours is the first genome-wide homozygosity association study for RA and characterized the ROH patterns associated with RA in the genomes of 2,000 RA patients and 3,000 normal controls of the Wellcome Trust Case Control Consortium. Genome scans consistently pinpointed two regions within the human major histocompatibility complex region containing RA-associated ROHs. The first region is from 32,451,664 bp to 32,846,093 bp (−log10(p)>22.6591). RA-susceptibility genes, such as HLA-DRB1, are contained in this region. The second region ranges from 32,933,485 bp to 33,585,118 bp (−log10(p)>8.3644) and contains other HLA-DPA1 and HLA-DPB1 genes. These two regions are physically close but are located in different blocks of linkage disequilibrium, and ∼40% of the RA patients' genomes carry these ROHs in the two regions. By analyzing homozygote intensities, an ROH that is anchored by the single nucleotide polymorphism rs2027852 and flanked by HLA-DRB6 and HLA-DRB1 was found associated with increased risk for RA. The presence of this risky ROH provides a 62% accuracy to predict RA disease status. An independent genomic dataset from 868 RA patients and 1,194 control subjects of the North American Rheumatoid Arthritis Consortium successfully validated the results obtained using the Wellcome Trust Case Control Consortium data. In conclusion, this genome-wide homozygosity association study provides an alternative to allelic association mapping for the identification of recessive variants responsible for RA. The identified RA-associated ROHs uncover recessive components and missing heritability associated with RA and other autoimmune diseases.
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Hu HJ, Jin EH, Yim SH, Yang SY, Jung SH, Shin SH, Kim WU, Shim SC, Kim TG, Chung YJ. Common variants at the promoter region of the APOM confer a risk of rheumatoid arthritis. Exp Mol Med 2012; 43:613-21. [PMID: 21844665 DOI: 10.3858/emm.2011.43.11.068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Although the genetic component in the etiology of rheumatoid arthritis (RA) has been consistently suggested, many novel genetic loci remain to uncover. To identify RA risk loci, we performed a genome-wide association study (GWAS) with 100 RA cases and 600 controls using Affymetrix SNP array 5.0. The candidate risk locus (APOM gene) was re-sequenced to discover novel promoter and coding variants in a group of the subjects. Replication was performed with the independent case-control set comprising of 578 RAs and 711 controls. Through GWAS, we identified a novel SNP associated with RA at the APOM gene in the MHC class III region on 6p21.33 (rs805297, odds ratio (OR) = 2.28, P = 5.20 × 10-7). Three more polymorphisms were identified at the promoter region of the APOM by the re-sequencing. For the replication, we genotyped the four SNP loci in the independent case-control set. The association of rs805297 identified by GWAS was successfully replicated (OR = 1.40, P = 6.65 × 10-5). The association became more significant in the combined analysis of discovery and replication sets (OR = 1.56, P = 2.73 × 10-10). The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA.
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Affiliation(s)
- Hae Jin Hu
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine Seoul 137-701, Korea
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Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, Alfredsson L, Padyukov L, Klareskog L, Worthington J, Siminovitch KA, Bae SC, Plenge RM, Gregersen PK, de Bakker PI. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet 2012; 44:291-6. [PMID: 22286218 PMCID: PMC3288335 DOI: 10.1038/ng.1076] [Citation(s) in RCA: 659] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/12/2011] [Indexed: 12/16/2022]
Abstract
The genetic association of the major histocompatibility complex (MHC) to rheumatoid arthritis risk has commonly been attributed to alleles in HLA-DRB1. However, debate persists about the identity of the causal variants in HLA-DRB1 and the presence of independent effects elsewhere in the MHC. Using existing genome-wide SNP data in 5,018 individuals with seropositive rheumatoid arthritis (cases) and 14,974 unaffected controls, we imputed and tested classical alleles and amino acid polymorphisms in HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1 and HLA-DRB1, as well as 3,117 SNPs across the MHC. Conditional and haplotype analyses identified that three amino acid positions (11, 71 and 74) in HLA-DRβ1 and single-amino-acid polymorphisms in HLA-B (at position 9) and HLA-DPβ1 (at position 9), which are all located in peptide-binding grooves, almost completely explain the MHC association to rheumatoid arthritis risk. This study shows how imputation of functional variation from large reference panels can help fine map association signals in the MHC.
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Affiliation(s)
- Soumya Raychaudhuri
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Cynthia Sandor
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eli A. Stahl
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jan Freudenberg
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Xiaoming Jia
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet at Karolinska University Hospital Solna, Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet at Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Katherine A. Siminovitch
- Department of Medicine, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Robert M. Plenge
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY USA
| | - Paul I.W. de Bakker
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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Bergamaschi S, Morato E, Bazzo M, Neves F, Fialho S, Castro G, Zimmermann A, Pereira I. Tumor markers are elevated in patients with rheumatoid arthritis and do not indicate presence of cancer. Int J Rheum Dis 2011; 15:179-82. [PMID: 22462421 DOI: 10.1111/j.1756-185x.2011.01671.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM To investigate serum levels of tumor markers in patients with rheumatoid arthritis (RA) and their association with disease activity or the presence of cancer. METHOD We performed an observational cohort study including 100 patients with RA and control subjects. Serum levels of tumor markers carcinoembryonic antigen (CEA), cancer antigen (CA) 125, CA 19-9 and CA 15-3 were evaluated along with clinical and laboratorial RA data. Association tests between tumor markers levels and RA disease activity parameters were performed. Patients with abnormal tests were submitted to further investigation, including chest X-ray, colonoscopy, abdominal ultrasonography, upper gastrointestinal endoscopy and mammography, depending on the type of tumor marker that was elevated. RESULTS Patients with RA had high levels of CEA and CA 19-9 more frequently than controls (P < 0.05). No correlation was found between tumor markers and RA disease activity assessed by the Disease Activity Score 28. Two neoplasms were found, but only one was related to high tumor marker (an ovarian carcinoma with high CA 125 levels). CONCLUSION High tumor markers were frequently found in RA patients, even with controlled disease and were not related to actual cancer. Therefore, small increases of these markers in RA cases probably do not warrant a search for an occult neoplasm.
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Affiliation(s)
- Samuel Bergamaschi
- Medicine, Universidade Federal de Santa Catarina, Florianopolis, SC, Brazil
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Vignal CM, Bansal AT, Balding DJ. Using Penalised Logistic Regression to Fine Map HLA Variants for Rheumatoid Arthritis. Ann Hum Genet 2011; 75:655-64. [DOI: 10.1111/j.1469-1809.2011.00670.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang N, Shen N, Vyse TJ, Anand V, Gunnarson I, Sturfelt G, Rantapää-Dahlqvist S, Elvin K, Truedsson L, Andersson BA, Dahle C, Örtqvist E, Gregersen PK, Behrens TW, Hammarström L. Selective IgA deficiency in autoimmune diseases. Mol Med 2011; 17:1383-96. [PMID: 21826374 PMCID: PMC3321806 DOI: 10.2119/molmed.2011.00195] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 12/12/2022] Open
Abstract
Selective immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in Caucasians. It has previously been suggested to be associated with a variety of concomitant autoimmune diseases. In this review, we present data on the prevalence of IgAD in patients with Graves disease (GD), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), celiac disease (CD), myasthenia gravis (MG) and rheumatoid arthritis (RA) on the basis of both our own recent large-scale screening results and literature data. Genetic factors are important for the development of both IgAD and various autoimmune disorders, including GD, SLE, T1D, CD, MG and RA, and a strong association with the major histocompatibility complex (MHC) region has been reported. In addition, non-MHC genes, such as interferon-induced helicase 1 (IFIH1) and c-type lectin domain family 16, member A (CLEC16A), are also associated with the development of IgAD and some of the above diseases. This indicates a possible common genetic background. In this review, we present suggestive evidence for a shared genetic predisposition between these disorders.
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Affiliation(s)
- Ning Wang
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Nan Shen
- Department of Rheumatology, Renji Hospital, JiaoTong University School of Medicine, Shanghai, China
| | - Timothy J Vyse
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Vidya Anand
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Iva Gunnarson
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Gunnar Sturfelt
- Department of Rheumatology, Lund University Hospital, Lund, Sweden
| | | | - Kerstin Elvin
- Unit of Clinical Immunology, Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lennart Truedsson
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Sweden
| | | | - Charlotte Dahle
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Örtqvist
- Department of Woman and Child Health, Astrid Lindgren Children’s Hospital, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Timothy W Behrens
- Division of Immunology, Tissue Growth & Repair, Biomarker Discovery and Human Genetics, Genentech, South San Francisco, California, United States of America
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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Safra N, Pedersen NC, Wolf Z, Johnson EG, Liu HW, Hughes AM, Young A, Bannasch DL. Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations. Vet J 2011; 189:220-6. [PMID: 21741283 DOI: 10.1016/j.tvjl.2011.06.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The dog leukocyte antigen (DLA) system contains many of the functional genes of the immune system, thereby making it a candidate region for involvement in immune-mediated disorders. A number of studies have identified associations between specific DLA class II haplotypes and canine immune hemolytic anemia, thyroiditis, immune polyarthritis, type I diabetes mellitus, hypoadrenocorticism, systemic lupus erythematosus-related disease complex, necrotizing meningoencephalitis (NME) and anal furunculosis. These studies have relied on sequencing approximately 300 bases of exon 2 of each of the DLA class II genes: DLA-DRB1, DLA-DQA1 and DLA-DQB1. In the present study, an association (odds ratio=4.29) was identified by this method between Weimaraner dogs with hypertrophic osteodystrophy (HOD) and DLA-DRB1∗01501. To fine map the association with HOD, a genotyping assay of 126 coding single nucleotide polymorphisms (SNPs) from across the entire DLA, spanning a region of 2.5 Mb (3,320,000-5,830,000) on CFA12, was developed and tested on Weimaraners with HOD, as well as two additional breeds with diseases associated with DLA class II: Nova Scotia duck tolling retrievers with hypoadrenocorticism and Pug dogs with NME. No significant associations were found between Weimaraners with HOD or Nova Scotia duck tolling retrievers with hypoadrenocorticism and SNPs spanning the DLA region. In contrast, significant associations were found with NME in Pug dogs, although the associated region extended beyond the class II genes. By including a larger number of genes from a larger genomic region, a SNP genotyping assay was generated that provides coverage of the extended DLA region and may be useful in identifying and fine mapping DLA associations in dogs.
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Affiliation(s)
- N Safra
- School of Veterinary Medicine, University of California, Davis, USA.
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Epidemiología genética de la artritis reumatoide: ¿qué esperar de América Latina? BIOMEDICA 2011. [DOI: 10.7705/biomedica.v26i4.326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Orozco G, Barton A, Eyre S, Ding B, Worthington J, Ke X, Thomson W. HLA-DPB1-COL11A2 and three additional xMHC loci are independently associated with RA in a UK cohort. Genes Immun 2011; 12:169-75. [PMID: 21293383 DOI: 10.1038/gene.2010.57] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aim of this study was to investigate the complex association pattern of the extended major histocompatibility complex (xMHC) region with rheumatoid arthritis (RA) susceptibility to identify effects independent of HLA-DRB1. A total of 1804 RA cases and 1474 controls were included. High-resolution HLA-DRB1 typing was performed. Subjects were genotyped for 1546 single-nucleotide polymorphisms (SNPs) using Affymetrix GeneChip 500 K (Santa Clara, CA, USA) as part of the Wellcome Trust Case Control Consortium Study. Statistical analysis was carried out using PLINK. To avoid confounding by RA-associated HLA-DRB1 alleles, we analyzed xMHC SNPs using a data set with pairwise matching of cases and controls on DRB1 genotypes. A total of 594 case-control pairs with identical DRB1 genotypes were identified. After this adjustment, 104 SNPs remained significantly associated with RA (P<0.05), suggesting that additional RA loci independent of HLA-DRB1 can be found in the xMHC region. Of these, four loci showed the strongest associations with RA (P<0.005): ZNF391, the olfactory receptor (OR) gene cluster, C6orf26-RDBP and HLA-DPB1-COL11A2. An additional locus mapping to the BTN (butyrophilin) cluster showed independent association with RA in anti-cyclic citrullinated peptide-positive patients exclusively. We have validated the previously described independent association of the HLA-DPB1-COL11A2 locus with RA. In addition, association with three novel independent RA loci in the xMHC region (ZNF391, OR2H1 and C6orf26-RDBP) has been detected.
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Affiliation(s)
- G Orozco
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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The rheumatoid joint. Rheumatology (Oxford) 2011. [DOI: 10.1016/b978-0-323-06551-1.00091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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The contribution of genetic factors to rheumatoid arthritis. Rheumatology (Oxford) 2011. [DOI: 10.1016/b978-0-323-06551-1.00086-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Alter A, Grant A, Abel L, Alcaïs A, Schurr E. Leprosy as a genetic disease. Mamm Genome 2010; 22:19-31. [PMID: 20936290 DOI: 10.1007/s00335-010-9287-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 09/01/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Andrea Alter
- Research Institute of the McGill University Health Centre, McGill Centre for the Study of Host Resistance, Department of Medicine, McGill University, Montreal, QC, Canada
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Zhang R, Sun P, Jiang Y, Chen Z, Huang C, Zhang X, Zhang R. Genome-wide haplotype association analysis and gene prioritization identify CCL3 as a risk locus for rheumatoid arthritis. Int J Immunogenet 2010; 37:273-8. [PMID: 20518837 DOI: 10.1111/j.1744-313x.2010.00920.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disease caused by a complex interaction of multiple genetic variants and environmental factors. The association between RA and genetic susceptibility loci has been observed in many different populations, and most studies have focused on univariate analyses of single nucleotide polymorphisms. We performed a genome-wide haplotype association study and prioritized RA-related genes within 100 kb in either direction of significant haplotypes (P < 0.0001), based on their similarity to known RA susceptibility genes. The results showed that the chemokine CCL3 was associated with susceptibility to RA. A haplotype that located CCL3 on chromosome 17q12 had significant correlation with RA (P = 7.56E-05), and the global similarity score of CCL3 was ranked in the top of all RA-related genes, excluding known susceptibility genes (P = 8.42E-07). Our findings provide further evidence for the potential importance of the chemokine CCL3 in RA, and will facilitate the further understanding of its role in immunological regulation and the pathogenesis of RA.
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Affiliation(s)
- R Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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Briggs FBS, Ramsay PP, Madden E, Norris JM, Holers VM, Mikuls TR, Sokka T, Seldin MF, Gregersen PK, Criswell LA, Barcellos LF. Supervised machine learning and logistic regression identifies novel epistatic risk factors with PTPN22 for rheumatoid arthritis. Genes Immun 2010; 11:199-208. [PMID: 20090771 DOI: 10.1038/gene.2009.110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Investigating genetic interactions (epistasis) has proven difficult despite the recent advances of both laboratory methods and statistical developments. With no 'best' statistical approach available, combining several analytical methods may be optimal for detecting epistatic interactions. Using a multi-stage analysis that incorporated supervised machine learning and methods of association testing, we investigated epistatic interactions with a well-established genetic factor (PTPN22 1858T) in a complex autoimmune disease (rheumatoid arthritis (RA)). Our analysis consisted of four principal stages: Stage I (data reduction)-identifying candidate chromosomal regions in 292 affected sibling pairs, by predicting PTPN22 concordance using multipoint identity-by-descent probabilities and a supervised machine learning algorithm (Random Forests); Stage II (extension analysis)-testing detailed genetic data within candidate chromosomal regions for epistasis with PTPN22 1858T in 677 cases and 750 controls using logistic regression; Stage III (replication analysis)-confirmation of epistatic interactions in 947 cases and 1756 controls; Stage IV (combined analysis)-a pooled analysis including all 1624 RA cases and 2506 control subjects for final estimates of effect size. A total of seven replicating epistatic interactions were identified. SNP variants within CDH13, MYO3A, CEP72 and near WFDC1 showed significant evidence for interaction with PTPN22, affecting susceptibility to RA.
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Amos CI, Chen WV, Seldin MF, Remmers EF, Taylor KE, Criswell LA, Lee AT, Plenge RM, Kastner DL, Gregersen PK. Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data. BMC Proc 2009; 3 Suppl 7:S2. [PMID: 20018009 PMCID: PMC2795916 DOI: 10.1186/1753-6561-3-s7-s2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
For Genetic Analysis Workshop 16 Problem 1, we provided data for genome-wide association analysis of rheumatoid arthritis. Single-nucleotide polymorphism (SNP) genotype data were provided for 868 cases and 1194 controls that had been assayed using an Illumina 550 k platform. In addition, phenotypic data were provided from genotyping DRB1 alleles, which were classified according to the rheumatoid arthritis shared epitope, levels of anti-cyclic citrullinated peptide, and levels of rheumatoid factor IgM. Several questions could be addressed using the data, including analysis of genetic associations using single SNPs or haplotypes, as well as gene-gene and genetic analysis of SNPs for qualitative and quantitative factors.
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Affiliation(s)
- Christopher I Amos
- Departments of Epidemiology and Biomathematics, University of Texas, MD Anderson Cancer Center, 1155 Pressler Street, Houston, Texas 77030, USA.
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Taylor KE, Criswell LA. Conditional analysis of the major histocompatibility complex in rheumatoid arthritis. BMC Proc 2009; 3 Suppl 7:S36. [PMID: 20018027 PMCID: PMC2795934 DOI: 10.1186/1753-6561-3-s7-s36] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We performed a whole-genome association study of rheumatoid arthritis susceptibility using Illumina 550k single-nucleotide polymorphism (SNP) genotypes of 868 cases and 1194 controls from the North American Rheumatoid Arthritis Consortium (NARAC). Structured association analysis with adjustment for potential population stratification yielded 200 SNPs with p < 1 x 10-8 for association with RA, all of which were on chromosome 6 in a 2.7-Mb region of the major histocompatibility complex (MHC). Given the extensive linkage equilibrium in the region and known risk of HLA-DRB1 alleles, we then applied conditional analyses to ascertain independent signals for RA susceptibility among these 200 candidate SNPs. Conditional analyses incorporating risk categories of the HLA-DRB1 "shared epitope" revealed three SNPs having independent associations with RA (conditional p < 0.001). This supports the presence of significant effects on RA susceptibility in the MHC in addition to the shared epitope.
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Affiliation(s)
- Kimberly E Taylor
- The Rosalind Russell Medical Research Center for Arthritis, University of California San Francisco, 374 Parnassus Ave, San Francisco, California 94143 USA.
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Lemire M. On the association between rheumatoid arthritis and classical HLA class I and class II alleles predicted from single-nucleotide polymorphism data. BMC Proc 2009; 3 Suppl 7:S33. [PMID: 20018024 PMCID: PMC2795931 DOI: 10.1186/1753-6561-3-s7-s33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Using single-nucleotide polymorphisms (SNPs), we sought to predict classical class I and class II human leukocyte antigen (HLA) alleles, and test for their associations with rheumatoid arthritis (RA) in the North American Rheumatoid Arthritis Consortium sample of cases and controls, genotyped on the Illumina HumanHap550 BeadChip. We use publicly available databases of SNP data and HLA data to find SNPs or SNP-haplotypes to be used as surrogates for each HLA allele. To reduce the confounding effects of linkage disequilibrium with the HLA-DRB1 locus, we tested for the association conditional on the presence or absence of a shared epitope allele on the same haplotype as the target HLA allele. Using SNP surrogates, we find that components of the DQ8 serotype (DQA1*0301:DQB1*0302) are associated with RA, irrespective of the presence or absence of a shared epitope allele on their respective haplotypes. Knowledge of the haplotype structure in the HLA region is still necessary for better interpretation of the results.
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Affiliation(s)
- Mathieu Lemire
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, MaRS Centre, South Tower, Toronto, ON M5G0A3 Canada.
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Cho S, Kim H, Oh S, Kim K, Park T. Elastic-net regularization approaches for genome-wide association studies of rheumatoid arthritis. BMC Proc 2009; 3 Suppl 7:S25. [PMID: 20018015 PMCID: PMC2795922 DOI: 10.1186/1753-6561-3-s7-s25] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current trend in genome-wide association studies is to identify regions where the true disease-causing genes may lie by evaluating thousands of single-nucleotide polymorphisms (SNPs) across the whole genome. However, many challenges exist in detecting disease-causing genes among the thousands of SNPs. Examples include multicollinearity and multiple testing issues, especially when a large number of correlated SNPs are simultaneously tested. Multicollinearity can often occur when predictor variables in a multiple regression model are highly correlated, and can cause imprecise estimation of association. In this study, we propose a simple stepwise procedure that identifies disease-causing SNPs simultaneously by employing elastic-net regularization, a variable selection method that allows one to address multicollinearity. At Step 1, the single-marker association analysis was conducted to screen SNPs. At Step 2, the multiple-marker association was scanned based on the elastic-net regularization. The proposed approach was applied to the rheumatoid arthritis (RA) case-control data set of Genetic Analysis Workshop 16. While the selected SNPs at the screening step are located mostly on chromosome 6, the elastic-net approach identified putative RA-related SNPs on other chromosomes in an increased proportion. For some of those putative RA-related SNPs, we identified the interactions with sex, a well known factor affecting RA susceptibility.
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Affiliation(s)
- Seoae Cho
- Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St, 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.
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Okada Y, Yamada R, Suzuki A, Kochi Y, Shimane K, Myouzen K, Kubo M, Nakamura Y, Yamamoto K. Contribution of a haplotype in the HLA region to antiâcyclic citrullinated peptide antibody positivity in rheumatoid arthritis, independently of HLAâDRB1. ACTA ACUST UNITED AC 2009; 60:3582-90. [DOI: 10.1002/art.24939] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Vandiedonck C, Knight JC. The human Major Histocompatibility Complex as a paradigm in genomics research. BRIEFINGS IN FUNCTIONAL GENOMICS & PROTEOMICS 2009; 8:379-94. [PMID: 19468039 PMCID: PMC2987720 DOI: 10.1093/bfgp/elp010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became the first genomic region to be entirely re-sequenced for common haplotypes, while studies mapping gene expression phenotypes across the genome have strongly implicated variation in the MHC. This review shows how the MHC continues to provide new insights and remains in the vanguard of contemporary research in human genomics.
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Affiliation(s)
- Claire Vandiedonck
- Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, UK.
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Santiago JL, Li W, Lee A, Martinez A, Chandrasekaran A, Fernandez-Arquero M, Khalili H, de la Concha EG, Urcelay E, Gregersen PK. Localization of Type 1 Diabetes susceptibility in the ancestral haplotype 18.2 by high density SNP mapping. Genomics 2009; 94:228-32. [PMID: 19591919 DOI: 10.1016/j.ygeno.2009.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 02/19/2009] [Accepted: 06/17/2009] [Indexed: 10/20/2022]
Abstract
Previous studies have suggested that the ancestral haplotype 18.2 (AH18.2) carries additional susceptibility gene to Type 1 Diabetes (T1D) on the Major Histocompatibility Complex (MHC). We analyzed 10 DR3/TNFa1b5 homozygous subjects in order to establish the conservation of the AH18.2 and then compared this conserved region with other DR3 haplotype, the AH8.1. The Illumina's HumanHap550 Bead chip was used to perform an extensive genotyping of the MHC region. The AH18.2 was highly conserved between DDR1 and HLA-DQA1 genes; therefore most probably the second susceptibility gene is located within this region. We can exclude the region centromeric to HLA-DRA gene and telomeric to DDR1 gene. A comparison between the AH18.2 and AH8.1 haplotypes showed that 233 SNPs were different in the aforementioned conserved region. These data suggest that the 1.65 Mb MHC region between DDR1 and HLA-DRA genes is likely to carry additional susceptibility alleles for T1D on the AH18.2 haplotype.
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Affiliation(s)
- Jose Luis Santiago
- Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA.
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Brown M, Newton J, Harney SM, Wordsworth P. Challenges in mapping non-HLA-DRB1 major histocompatibility genes in rheumatoid arthritis: comment on the article by Vignal et al. ARTHRITIS AND RHEUMATISM 2009; 60:2207-2208. [PMID: 19565502 DOI: 10.1002/art.24624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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