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Pasha U, Nisar H, Nisar H, Abid R, Ashraf NM, Sadaf S. Molecular Dynamic Simulations Unravel the Underlying Impact of Missense Mutation in Autoimmunity Gene PTPN22 on Predisposition to Rheumatoid Arthritis. J Interferon Cytokine Res 2023; 43:121-132. [PMID: 36811459 DOI: 10.1089/jir.2022.0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Genetic mutations in various proteins have been implicated with increased risk or severity of rheumatoid arthritis (RA) in different population groups. In the present case-control study, we have investigated the risk association of single nucleotide mutations present in some of the highly reported anti-inflammatory proteins and/or cytokines, with RA susceptibility in the Pakistani subjects. The study involves 310 ethnically and demographically similar participants from whom blood samples were taken and processed for DNA extraction. Through extensive data mining, 5 hotspot mutations reported in 4 genes, that is, interleukin (IL)-4 (-590; rs2243250), IL-10 (-592; rs1800872), IL-10 (-1082; rs1800896), PTPN22 (C1858T; rs2476601), and TNFAIP3 (T380G; rs2230926), were selected for RA susceptibility analyses using genotyping assays. The results demonstrated the association of only 2 DNA variants [rs2243250 (odds ratio, OR = 2.025, 95% confidence interval, CI = 1.357-3.002, P = 0.0005 Allelic) and rs2476601 (OR = 4.25, 95% CI = 1.569-11.55, P = 0.004 Allelic)] with RA susceptibility in the local population. The former single nucleotide mutation was nonfunctional, whereas the latter, residing in the exonic region of a linkage-proven autoimmunity gene PTPN22, was involved in R620→W620 substitution. Comparative molecular dynamic simulations and free-energy calculations revealed a radical impact on the geometry/confirmation of key functional moieties in the mutant protein leading to a rather weak binding of W620 variant with the interacting receptor (SRC kinase). The interaction imbalance and binding instabilities provide convincing clues about the insufficient inhibition of T cell activation and/or ineffective clearance of autoimmune clones-a hallmark of several autoimmune disorders. In conclusion, the present research describes the association of 2 hotspot mutations in IL-4 promoter and PTPN22 gene with RA susceptibility in the Pakistani study cohort. It also details how a functional mutation in PTPN22 impacts the overall protein geometry, charge, and/or receptor interactions to contribute to RA susceptibility.
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Affiliation(s)
- Usman Pasha
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Haseeb Nisar
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Hajira Nisar
- Emergency and Out Patient Department, Ali Fatima Hospital, Lahore, Pakistan
| | - Rizwan Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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Ali Y, Khan S, Chen Y, Farooqi N, Islam ZU, Akhtar M, Aamir, Aman A, Shah AA, Jamal M, Jalil F. Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort. Genet Res (Camb) 2021; 2021:5544198. [PMID: 34104118 PMCID: PMC8147531 DOI: 10.1155/2021/5544198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is one of the complex diseases with the involvement of the genetic as well as environmental factors in its onset and severity. Different genome-wide association and candidate gene studies have shown the role of several genetic variants in multiple loci/genes with ethnical and geographical variations. This study was designed to detect the association of a single-nucleotide polymorphism (SNP) rs10865035 in the AFF3 gene with the genetic background of rheumatoid arthritis (RA) in the Pakistani cohort. A total of 703 individuals, including 409 RA patients and 294 healthy controls, were genotyped using TaqMan assay and Tri primer ARMS-PCR (amplification-refractory mutation system-polymerase chain reaction) methods. The association of rs10865035 with the RA was statistically determined using different models. Interestingly, besides the homozygous recessive model (G/G vs. A/G + A/A) (OR = 1.693(1.06-2.648); P = 0.025), all other models, which included the codominant (χ 2 = 5.169; P = 0.075), homozygous dominant (A/A vs. G/G + A/G) (OR = 0.867 (0.636-1.187); P = 0.41), heterozygous (A/G vs. A/A + GG) (OR = 0.491 (0.667-1.215); P = 0.49), and additive model (OR = 0.826 (0.665-1.027); P = 0.08) showed insignificant distribution of the genotypes among the cases and controls. These findings suggest that the AFF3 gene (rs10865035) has no significant role in the onset of RA in the Pakistani population.
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Affiliation(s)
- Yasir Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suleman Khan
- Lady Ready Hospital, MTI Peshawar, Peshawar, Pakistan
| | - Yangchao Chen
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Pakistan
| | - Nadia Farooqi
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Zia-Ul Islam
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Aamir
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Aisha Aman
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, Dubinsky M, Brant SR, Silverberg M, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D’Amato M, McGovern DP, Cho JH, Rioux JD, Xavier RJ, Daly MJ. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 2011; 43:1066-73. [PMID: 21983784 PMCID: PMC3378381 DOI: 10.1038/ng.952] [Citation(s) in RCA: 576] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 08/31/2011] [Indexed: 02/08/2023]
Abstract
More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10(-16), odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.
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Affiliation(s)
- Manuel A. Rivas
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Melissa Beaudoin
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Agnes Gardet
- Gastrointenstinal Unit, Center for the Study of the Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Yashoda Sharma
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - Clarence K. Zhang
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - Gabrielle Boucher
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Stephan Ripke
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Schittenhelmstr. 12, D-24105 Kiel, Germany
| | - Noel Burtt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tim Fennell
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrew Kirby
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anna Latiano
- Unit of Gastroenterology, IRCCS - Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Philippe Goyette
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Todd Green
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jonas Halfvarson
- Örebro University Hospital, Department of Medicine and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Talin Haritunians
- The Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - Finny Kuruvilla
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Clarus Ventures, Cambridge, MA, USA
| | - Caroline Lagacé
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Benjamin Neale
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ken Sin Lo
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Phil Schumm
- Department of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Leif Törkvist
- Karolinska Institutet, Department of Clinical Science Intervention and Technology, Stockholm, Sweden
| | | | | | - Marla Dubinsky
- The Pedriatic IBD Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Steven R. Brant
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark Silverberg
- Mount Sinai Hospital Inflammatory Bowel Disease Centre, University of Toronto, Toronto, Ontario, Canada
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David Altshuler
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Guillaume Lettre
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Andre Franke
- Institute of Clinical Molecular Biology, Schittenhelmstr. 12, D-24105 Kiel, Germany
| | - Mauro D’Amato
- Karolinska Institutet, Department of Biosciences and Nutrition, Stockholm, Sweden
| | - Dermot P.B. McGovern
- The Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Judy H. Cho
- Keck Biotechnology Resource Laboratory and Yale School of Medicine, New Haven, Connecticut, USA
| | - John D. Rioux
- Université de Montréal and Research Centre, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Ramnik J. Xavier
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gastrointenstinal Unit, Center for the Study of the Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Zhu J, Zhang D, Wu F, He F, Liu X, Wu L, Zhou B, Liu J, Lu F, Liu J, Luo R, Long W, Yang M, Ma S, Wu X, Shi Y, Wu T, Lin Y, Yang J, Yuan G, Yang Z. Single nucleotide polymorphisms at the TRAF1/C5 locus are associated with rheumatoid arthritis in a Han Chinese population. BMC MEDICAL GENETICS 2011; 12:53. [PMID: 21492465 PMCID: PMC3094270 DOI: 10.1186/1471-2350-12-53] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 04/14/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genetic variants in TRAF1C5 and PTPN22 genes have been shown to be significantly associated with arthritis rheumatoid in Caucasian populations. This study investigated the association between single nucleotide polymorphisms (SNPs) in TRAF1/C5 and PTPN22 genes and rheumatoid arthritis (RA) in a Han Chinese population. We genotyped SNPs rs3761847 and rs7021206 at the TRAF1/C5 locus and rs2476601 SNP in the PTPN22 gene in a Han Chinese cohort composed of 576 patients with RA and 689 controls. The concentrations of anti-cyclic citrullinated peptide antibodies (CCP) and rheumatoid factor (RF) were determined for all affected patients. The difference between the cases and the controls was compared using χ2 analysis. RESULTS Significant differences in SNPs rs3761847 and rs7021206 at TRAF1/C5 were observed between the case and control groups in this cohort; the allelic p-value was 0.0018 with an odds ratio of 1.28 for rs3761847 and 0.005 with an odds ratio of 1.27 for rs7021206. This significant association between rs3761847 and RA was independent of the concentrations of anti-CCP and RF. No polymorphism of rs2476601 was observed in this cohort. CONCLUSIONS We first demonstrated that genetic variants at the TRAF1/C5 locus are significantly associated with RA in Han Chinese, suggesting that TRAF1/C5 may play a role in the development of RA in this population, which expands the pathogenesis role of TRAF1/C5 in a different ethnicity.
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Affiliation(s)
- Jing Zhu
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Dinging Zhang
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Fengxia Wu
- Institute of Rheumatology and Immunology, Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fei He
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xiaoqi Liu
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Lijun Wu
- Department of Rheumatology, People's Hospital of Xin Jiang Uygur Autonomous Region, Urumchi, Xin Jiang, China
| | - Bin Zhou
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jianping Liu
- Institute of Rheumatology and Immunology, Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fang Lu
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jian Liu
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ruijun Luo
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Wubin Long
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Minghui Yang
- Institute of Rheumatology and Immunology, Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shi Ma
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xiaodan Wu
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yi Shi
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Tong Wu
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ying Lin
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jiyun Yang
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Guohua Yuan
- Institute of Rheumatology and Immunology, Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Zhenglin Yang
- Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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Lorentzen AR, Smestad C, Lie BA, Oturai AB, Akesson E, Saarela J, Myhr KM, Vartdal F, Celius EG, Sørensen PS, Hillert J, Spurkland A, Harbo HF. The SH2D2A gene and susceptibility to multiple sclerosis. J Neuroimmunol 2008; 197:152-8. [PMID: 18554728 DOI: 10.1016/j.jneuroim.2008.04.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 04/25/2008] [Accepted: 04/29/2008] [Indexed: 01/16/2023]
Abstract
We previously reported an association between the SH2D2A gene encoding TSAd and multiple sclerosis (MS). Here a total of 2128 Nordic MS patients and 2004 controls were genotyped for the SH2D2A promoter GA repeat polymorphism and rs926103 encoding a serine to asparagine substitution at amino acid position 52 in TSAd. The GA(16)-rs926103()A haplotype was associated with MS in Norwegians (OR 1.4, P=0.04). A similar trend was observed among Danes. In the independent Norwegian, Danish and Swedish sample sets the GA(16) allele showed a combined OR of 1.13, P=0.05. Thus, the present study shows that the SH2D2A gene may contribute to susceptibility to MS.
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Affiliation(s)
- Aslaug R Lorentzen
- Department of Neurology, University of Oslo, Oslo, Norway; Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway.
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Deeks SG, Walker BD. Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. Immunity 2007; 27:406-16. [PMID: 17892849 DOI: 10.1016/j.immuni.2007.08.010] [Citation(s) in RCA: 538] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chronic viral infections can appear in two very different forms: those that are typically immunologically contained after acute symptomatic infection, such as Epstein-Barr virus (EBV), and those that predictably lead to persistent viremia and progressive clinical disease. Human immunodeficiency virus (HIV) infection is typical of the latter and has resulted in more than 20 million deaths worldwide. Here we review a remarkable subset of persons infected with HIV who are able to achieve long-term control of viremia and avoid immunodeficiency without the need for antiviral therapy. We review the contributing role of host genetic factors, innate and adaptive immune responses, and viral factors that may contribute to this phenotype. These individuals indicate that as with other potentially pathogenic chronic viral infections, the human immune system is able to fully control HIV and prevent HIV-associated disease, at least in some individuals. Further understanding of the mechanisms whereby this occurs should yield critical insights for prophylactic and therapeutic antiviral interventions.
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Affiliation(s)
- Steven G Deeks
- University of California, San Francisco, and San Francisco General Hospital, San Francisco, CA 94110, USA
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7
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Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, Ding B, Liew A, Khalili H, Chandrasekaran A, Davies LR, Li W, Tan AK, Bonnard C, Ong RT, Thalamuthu A, Pettersson S, Liu C, Tian C, Chen WV, Carulli JP, Beckman EM, Altshuler D, Alfredsson L, Criswell LA, Amos CI, Seldin MF, Kastner DL, Klareskog L, Gregersen PK. TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med 2007; 357:1199-209. [PMID: 17804836 PMCID: PMC2636867 DOI: 10.1056/nejmoa073491] [Citation(s) in RCA: 611] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Rheumatoid arthritis has a complex mode of inheritance. Although HLA-DRB1 and PTPN22 are well-established susceptibility loci, other genes that confer a modest level of risk have been identified recently. We carried out a genomewide association analysis to identify additional genetic loci associated with an increased risk of rheumatoid arthritis. METHODS We genotyped 317,503 single-nucleotide polymorphisms (SNPs) in a combined case-control study of 1522 case subjects with rheumatoid arthritis and 1850 matched control subjects. The patients were seropositive for autoantibodies against cyclic citrullinated peptide (CCP). We obtained samples from two data sets, the North American Rheumatoid Arthritis Consortium (NARAC) and the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA). Results from NARAC and EIRA for 297,086 SNPs that passed quality-control filters were combined with the use of Cochran-Mantel-Haenszel stratified analysis. SNPs showing a significant association with disease (P<1x10(-8)) were genotyped in an independent set of case subjects with anti-CCP-positive rheumatoid arthritis (485 from NARAC and 512 from EIRA) and in control subjects (1282 from NARAC and 495 from EIRA). RESULTS We observed associations between disease and variants in the major-histocompatibility-complex locus, in PTPN22, and in a SNP (rs3761847) on chromosome 9 for all samples tested, the latter with an odds ratio of 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10(-14)). The SNP is in linkage disequilibrium with two genes relevant to chronic inflammation: TRAF1 (encoding tumor necrosis factor receptor-associated factor 1) and C5 (encoding complement component 5). CONCLUSIONS A common genetic variant at the TRAF1-C5 locus on chromosome 9 is associated with an increased risk of anti-CCP-positive rheumatoid arthritis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter K. Gregersen
- The authors' affiliations are listed in the Appendix. Address reprint requests to Dr. Gregersen at the Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, or at
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8
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Goyette P, Labbé C, Trinh TT, Xavier RJ, Rioux JD. Molecular pathogenesis of inflammatory bowel disease: genotypes, phenotypes and personalized medicine. Ann Med 2007; 39:177-99. [PMID: 17457716 DOI: 10.1080/07853890701197615] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC), also known as inflammatory bowel diseases (IBD), are characterized by chronic inflammation of the gastrointestinal tract. IBD is among the few complex diseases for which several genomic regions and specific genes have been identified and confirmed in multiple replication studies. We will review the different loci implicated in disease risk in the context of three proposed mechanisms leading to chronic inflammation of the gut mucosa: 1) deregulation of the innate immune response to enteric microflora or pathogens; 2) increased permeability across the epithelial barrier; and 3) defective regulation of the adaptive immune system. As our knowledge of genetic variation, analytical approaches and technology improves, additional genetic risk factors are expected to be identified. With the identification of novel risk variants, additional pathophysiological mechanisms are likely to emerge. The resulting discoveries will further our molecular understanding of IBD, potentially leading to improved disease classification and rational drug design. Moreover, these approaches and tools can be applied in the context of variable drug response with the goal of providing more personalized clinical management of patients with IBD.
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Affiliation(s)
- Philippe Goyette
- Université de Montréal, Department of Medicine, Montréal, Québec, Canada
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9
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Abstract
PURPOSE OF REVIEW Pediatric arthritis is a heterogeneous group of chronic arthropathies that are influenced by complex genetic and perhaps environmental factors. Interacting genetic traits may one day be identified that provide the basis for predicting disease risk and other characteristics such as course, age of onset, and disease severity. The purpose of this review is to describe the recent progress towards identifying the multiple genes related to pediatric arthritis and understand how they relate to each other and to disease pathology. RECENT FINDINGS Candidate gene studies are by far the most widely reported type of genetic studies to date for juvenile arthritis with only one genome-wide screen for juvenile rheumatoid/idiopathic arthritis published. Particular attention is paid to studies of candidate genes with potential immunological roles and those associated with other forms of autoimmunity. SUMMARY Genomic studies may perhaps one day provide information to allow future classification systems of childhood arthritis to include molecular biomarkers as a complement to clinical observations, as well as understand how these genes or proteins relate to each other and to disease pathogenesis.
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Affiliation(s)
- James D Phelan
- William S. Rowe Division of Rheumatology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
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10
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