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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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Al-Awadhi AM, Haider MZ, Sukumaran J, Hasan EAH, Bartella YA. The Protein Tyrosine Phosphatase Non-receptor Type N22 (PTPN22) Gene Functional Polymorphism (1858T) is not Associated with Rheumatoid Arthritis in Kuwaiti Patients. Open Rheumatol J 2021. [DOI: 10.2174/1874312902115010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Rheumatoid Arthritis (RA) is a chronic disorder characterized by an inflammation of synovial tissue in joints resulting in pain, deformities and affects the quality of life. The gene for protein tyrosine phosphatase non-receptor type 22 (PTPN22) encodes a lymphoid specific phosphatase (LYP), which serves as a negative regulator of T lymphocyte activation and is associated with a number of autoimmune/chronic diseases in various ethnic groups.
Objective:
This study was undertaken to investigate an association between PTPN22 gene functional polymorphism (C1858T; rs2476601) and rheumatoid arthritis (RA) in Kuwaiti Arabs. The frequency of this candidate locus was compared between Kuwaiti RA patients and the controls and with that reported from other populations.
Methods:
The study was carried out in 191 Kuwaiti RA patients and 214 healthy controls. The diagnosis of RA was carried out according to the guidelines of the American College of Rheumatology (ACR). The genotypes of PTPN22 gene (C1858T) polymorphism were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by DNA sequence analysis in RA patients and controls.
Results:
The TT genotype of PTPN22 gene functional polymorphism C1858T was found in 2/191 (1%) in RA patients compared to 2/214 (1%) in the controls (P = 1.0). In contrast, heterozygous CT genotype was detected in 3/191 (1.57%) RA patients compared to 32/214 (14.9%) in the controls. The CC genotype was detected in 186/191 (97.38%), RA patients while it was detected in 180/214 (84.1%) of the controls. The two RA patients who carried the homozygous variant (TT) genotype were both positive for rheumatoid factor (RF) and did not have any extra-articular manifestations. Amongst the Kuwaiti RA patients, 27% had a family history of RA. No correlation was found between the activity/severity of the disease and PTPN22 gene polymorphism genotypes.
Conclusion:
This study did not find an association between the PTPN22 gene functional polymorphism (C1858T) and clinical manifestation and activity/severity of RA in Kuwaiti Arabs. This is in sharp contrast to previous reports from Caucasian and some other populations in which a positive association of PTPN22 gene (C1858T) polymorphism with genetic susceptibility to RA has been reported.
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3
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Genetic approaches for the diagnosis and treatment of rheumatoid arthritis through personalized medicine. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abbasifard M, Imani D, Bagheri-Hosseinabadi Z. PTPN22 gene polymorphism and susceptibility to rheumatoid arthritis (RA): Updated systematic review and meta-analysis. J Gene Med 2020; 22:e3204. [PMID: 32333475 DOI: 10.1002/jgm.3204] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/13/2020] [Accepted: 04/12/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Several genome-wide association studies have revealed a genetic background with respect to susceptibility to rheumatoid arthritis (RA). Although several individual case-control studies have evaluated the role of protein tyrosine phosphatase non-receptor 22 (PTPN22) gene rs2476601 single nucleotide polymorphism (SNP) in conferring a risk for RA, the results have been conflicting. Hence, this meta-analysis was aimed to provide a solution for this issue. METHODS To search for studies assessing the association between the PTPN22 gene rs2476601 SNP and the risk of RA, a systematic search was conducted in the main databases, including PubMed, Scopus and Web of Science, prior to December 2019. The odds ratio (OR) and corresponding 95% confidence interval (CI) was calculated to assess the possibility of association risk. RESULTS The literature search identified 52 case-control studies. The pooled analysis detected significant positive association of rs2476601 in all genetic models, including dominant model (OR = 1.69, 95% CI = 1.55-1.84, P < 0.001), recessive model (OR = 2.50, 95% CI = 2.06-3.05, P < 0.001), allelic model (OR = 1.80, 95% CI = 1.60-2.2, P < 0.001), TT versus CC model (OR = 2.79, 95% CI = 2.28-3.41, P < 0.001) and CT versus CC model (OR = 1.59, 95% CI = 1.50-1.67, P < 0.001). Analyses based on population stratification indicated that rs2476601 SNP strongly increased the risk of RA in Caucasians and Africans under all genotype models. CONCLUSIONS This meta-analysis reports that the PTPN22 gene rs2476601 SNP increases RA risk, especially in Caucasians and Africans.
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Affiliation(s)
- Mitra Abbasifard
- Department of internal Medicine, Ali-Ibn Abi-Talib hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Rheumatology Research Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Danyal Imani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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El Fotoh WMMA, El Razek Midan DA, El Shalakany AH. Role of C1858T Polymorphism of Lymphoid Tyrosine Phosphatase in Egyptian Children and Adolescents with Type 1 Diabetes. Curr Diabetes Rev 2019; 16:73-79. [PMID: 29984661 DOI: 10.2174/1573399814666180709102533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 06/25/2018] [Accepted: 07/03/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Type 1 Diabetes Mellitus (T1DM) is a multifactorial autoimmune disease. The Protein Tyrosine Phosphatase Non-receptor 22 (PTPN22) gene is an important negative regulator of signal transduction through the T-cell Receptors (TCR). A PTPN22 polymorphism, C1858T, has been found to be a risk determinant for several autoimmune diseases, including T1DM, in different populations. OBJECTIVE The present study was aimed to analyze a possible association between the C1858T polymorphism in Egyptian children with T1DM. METHODS This case-control study included 240 children divided evenly between T1DM patients and controls. The PTPN22 C1858T polymorphism was genotyped using polymerase chain reaction with Restriction Fragment Length Polymorphism (RFLP). RESULTS Both the 1858CΤ and 1858ΤΤ genotypes and the 1858T allele were found more frequently in patients (32.5% and 18.7%, respectively) than in controls (10% and 5.0%, respectively), P=0.013 and P=0.007, respectively. Among females, the 1858T allele was more common in patients (18%) than in controls (2.6%), P=0.014. CONCLUSION These findings suggest that the PTPN22 1858T allele could be a T1DM susceptibility factor in the Egyptian population and that it might play a different role in susceptibility to T1DM according to gender in T1DM patients.
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Smigoc Schweiger D, Goricar K, Hovnik T, Mendez A, Bratina N, Brecelj J, Vidan-Jeras B, Battelino T, Dolzan V. Dual Role of PTPN22 but Not NLRP3 Inflammasome Polymorphisms in Type 1 Diabetes and Celiac Disease in Children. Front Pediatr 2019; 7:63. [PMID: 30915320 PMCID: PMC6422865 DOI: 10.3389/fped.2019.00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/18/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic polymorphisms in genes coding for inflammasome components nucleotide-binding oligomerization domain leucine rich repeat and pyrin domain-containing protein 3 (NLRP3) and caspase recruitment domain-containing protein 8 (CARD8) have been associated with autoinflammatory and autoimmune diseases. On the other hand several studies suggested that NLRP3 inflammasome contributes to maintenance of gastrointestinal immune homeostasis and that activation of NLRP3 is regulated by protein tyrosine phosphatase non-receptor 22 (PTPN22). PTPN22 polymorphism was implicated in the risk for various autoimmune diseases including type 1 diabetes (T1D) but not for celiac disease (CD). The aim of our study was to evaluate the role of inflammasome related polymorphisms in subjects with either T1D or CD as well as in subjects affected by both diseases. We examined PTPN22 rs2476601 (p.Arg620Trp), NLRP3 rs35829419 (p.Gln705Lys), and CARD8 rs2043211 (p.Cys10Ter) in 66 subjects with coexisting T1D and CD, 65 subjects with T1D who did not develop CD, 67 subjects diagnosed only with CD and 127 healthy unrelated Slovenian individuals. All results were adjusted for clinical characteristic and human leukocyte antigen (HLA) risk. PTPN22 rs2476601 allele was significantly more frequent among subjects with T1D (Padj = 0.001) and less frequent in subjects with CD (Padj = 0.039) when compared to controls. In patients with coexisting T1D and CD this variant was significantly less frequent compared to T1D group (Padj = 0.010). Protective effect on CD development in individuals with T1D was observed only within the low risk HLA group. On the other hand, we found no association of NLRP3 rs35829419 and CARD8 rs2043211 with the development of T1D, CD or both diseases together. In conclusion PTPN22 rs2476601polymorphism was significantly associated with the risk of developing T1D in Slovenian population, while no associations of proinflammatory NLRP3 and CARD8 polymorphisms with T1D and CD were observed. Interestingly, the same PTPN22 variant protected from CD. We hypothesize that this effect may be mediated through the NLRP3 inflammasome activation.
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Affiliation(s)
- Darja Smigoc Schweiger
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katja Goricar
- Pharmacogenetics Laboratory, Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Tinka Hovnik
- Unit of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Andrijana Mendez
- Tissue Typing Centre, Blood Transfusion Center of Slovenia, Ljubljana, Slovenia
| | - Natasa Bratina
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Brecelj
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Department of Gastroenterology, Hepatology and Nutrition, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Blanka Vidan-Jeras
- Tissue Typing Centre, Blood Transfusion Center of Slovenia, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Vita Dolzan
- Pharmacogenetics Laboratory, Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Ljubljana, Slovenia
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Alswat KA, Nasr A, Al Dubayee MS, Talaat IM, Alsulaimani AA, Mohamed IAA, Allam G. The Potential Role of PTPN-22 C1858T Gene Polymorphism in the Pathogenesis of Type 1 Diabetes in Saudi Population. Immunol Invest 2018; 47:521-533. [PMID: 29611765 DOI: 10.1080/08820139.2018.1458109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent investigations have reported an association between protein tyrosine phosphatase non-receptor type-22 (PTPN-22) gene polymorphism and susceptibility to the development of type 1 diabetes (T1D) in some populations and not in others. In this study, we aimed to investigate the association of PTPN-22 C1858T polymorphism with T1D in Saudi children. METHODS A cohort of 372 type 1 diabetic children and 372 diabetes-free subjects was enrolled in the current investigation. The PTPN-22 C1858T polymorphism was identified using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS Our data showed that the frequency of CT and TT genotypes of PTPN-22 C1858T was higher in T1D children (17.7% and 4.3%, respectively) compared to healthy controls (4.8% and 1.6%, respectively), and both genotypes were statistically associated with T1D patients (OR = 4.4, 95% CI: 2.55-7.58, p < 0.001; and OR = 3.2, 95% CI: 1.23-8.28, p = 0.017, respectively). Moreover, the 1858T allele was significantly associated with T1D patients compared to the C allele (OR = 3.2, 95% CI: 1.59-6.88, p < 0.001). In addition, the T allele was significantly associated with elevated levels of HbA1c, anti-GAD, and anti-insulin antibodies (p < 0.001) and a lower concentration of C-peptide (p < 0.001) in T1D children. CONCLUSION The data presented here suggests that the T allele of PTPN-22 C1858T polymorphism might be a risk factor for T1D development in Saudi children.
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Affiliation(s)
- Khaled A Alswat
- a Department of Internal Medicine , College of Medicine, Taif University , Taif , Saudi Arabia.,b Diabetic Center , Prince Mansour Military Community Hospital , Taif , Saudi Arabia
| | - Amre Nasr
- c King Saud bin Abdulaziz University for Health Sciences , Riyadh , Saudi Arabia.,d King Abdullah International Medical Research Center KAIMRC , Riyadh , Saudi Arabia
| | - Mohammed S Al Dubayee
- c King Saud bin Abdulaziz University for Health Sciences , Riyadh , Saudi Arabia.,d King Abdullah International Medical Research Center KAIMRC , Riyadh , Saudi Arabia.,e King Abdulaziz Medical City , Saudi Arabia
| | - Iman M Talaat
- f Department of Pediatrics, Faculty of Medicine , Ain Shams University , Cairo , Egypt
| | - Adnan A Alsulaimani
- b Diabetic Center , Prince Mansour Military Community Hospital , Taif , Saudi Arabia.,g Department of Pediatrics , College of Medicine, Taif University , Taif , Saudi Arabia
| | - Imad A A Mohamed
- h Department of Microbiology, Faculty of Veterinary Medicine , Zagazig University , Sharkia , Egypt.,i Department of Microbiology and Immunology , College of Medicine, Taif University , Taif , Saudi Arabia
| | - Gamal Allam
- i Department of Microbiology and Immunology , College of Medicine, Taif University , Taif , Saudi Arabia.,j Immunology Section, Department of Zoology, Faculty of Science , Beni-Suef University , Beni-Suef , Egypt
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Aflatounian M, Rezaei A, Sadr M, Saghazadeh A, Elhamian N, Sadeghi H, Motevasselian F, Farahmand F, Fallahi G, Motamed F, Najafi M, Rezaei N. Association of PTPN22 Single Nucleotide Polymorphisms with Celiac Disease. Fetal Pediatr Pathol 2017; 36:195-202. [PMID: 28481156 DOI: 10.1080/15513815.2017.1290725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Celiac disease is a chronic autoimmune disease in which gene-environment interactions cause the immune system to unfavorably react to naturally gluten-containing foods. PTPN22 plays a crucial role in regulating the function of various cells of the immune system, particularly T cells. Polymorphisms of the PTPN22 gene have been associated with many autoimmune diseases. The present genetic association study was conducted to investigate the possible associations between PTPNTT single nucleotide polymorphisms (SNPs) and celiac disease in an Iranian population. MATERIALS AND METHODS The study population consisted of 45 patients with celiac disease and 93 healthy controls. The study genotyped five SNPs of the PTPN22 gene: rs12760457, rs1310182, rs1217414, rs33996649, and rs2476601. RESULTS AND CONCLUSIONS Control and patient groups did not differ on the genotype distribution of four of five investigated SNPs in the PTPN22 gene, for example, rs12760457, rs2476601, rs1217414, and rs33996649. The only investigated PTPN22 variant, which could be associated with CD, was rs1310182. A significant increase in the carriage of the T allele of rs1310182 in CD patients was observed (OR (95% CI) = 11.42 (5.41, 24.1), p value < 0.0001). The TT genotype of this SNP was significantly associated with celiac disease. Our study suggests that the rs1310182 SNP of PTPN22 gene may be a predisposing factor of celiac disease in the Iranian population. Further studies are required to investigate the issue in other racial and ethnic subgroups.
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Affiliation(s)
- Majid Aflatounian
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Arezou Rezaei
- b Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Maryam Sadr
- c Molecular Immunology Research Center, Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Amene Saghazadeh
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Nazanin Elhamian
- b Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Hengameh Sadeghi
- c Molecular Immunology Research Center, Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | | | - Fatemeh Farahmand
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | | | - Farzaneh Motamed
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Mehri Najafi
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran
| | - Nima Rezaei
- a Children's Medical Center, Tehran University of Medical Sciences , Tehran , Iran.,d Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN) , Tehran , Iran
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Raslan HM, Attia HR, Salama I, Ibrahim MH, Hassan EM, El Hussieny MS, El Menyawi MM, Amr KS. Association of PTPN22 1858C→T polymorphism, HLA-DRB1 shared epitope and autoantibodies with rheumatoid arthritis. Rheumatol Int 2016; 36:1167-75. [PMID: 27324632 DOI: 10.1007/s00296-016-3511-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/14/2016] [Indexed: 02/05/2023]
Abstract
To assess impact of PTPN22 1858C→T polymorphism, HLA shared epitope and autoantibodies on susceptibility and severity of rheumatoid arthritis (RA). A total of 150 RA patients and 150 controls were included in the study. Anti-cyclic citrullinated peptide (anti-CCP) and rheumatoid factor isotypes (IgG, IgM and IgA) were assayed by ELISA. PTPN22 1858C→T polymorphism was performed by RFLP analysis and HLA-DRB1 genotyping by PCR-SSP analysis. Single-view, anteroposterior radiographs of the hands and feet were obtained on all RA patients. The results showed association of PTPN22 1858 T allele with RA (OR = 2.3, 95 % CI 1.5-3.5) and bone erosion (OR = 2.9, 95 % CI 1.1-7.6). The associations increased with the combination of positive autoantibodies, HLA-DRB1 SE with PTPN22 1858 T allele carriage. The highest association was with the combination with anti-CCP antibodies (OR = 47.3, 95 % CI 10.9-204.4 for RA and OR = 69.4, 95 % CI 15.8-305.5 for erosion p < 0.001). Combination of PTPN22 1858 T allele carriage with negative RF isotypes or with absence HLA-DRB1 SE showed no significant association with RA. The presence of PTPN22 1858C→T polymorphism with HLA SE and autoantibodies increases risk of RA development and erosive disease.
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Affiliation(s)
- Hala M Raslan
- Internal Medicine Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt.
| | - Hanaa R Attia
- Clinical and Chemical Pathology Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
| | - Iman Salama
- Community Medicine Research Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
| | - Mona Hamed Ibrahim
- Clinical and Chemical Pathology Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
| | - Eman Mahmoud Hassan
- Clinical and Chemical Pathology Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
| | - Mohamed S El Hussieny
- Biological Anthropology Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
| | - Manal M El Menyawi
- Internal Medicine Department, Kasr Al Aini Hospital, Kasr Al Aini street, Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetic Department, National Research Centre, El Buhouth street 2311, Dokki, Egypt
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Abbasi Z, Kazemi Nezhad SR, Pourmahdi-Broojeni M, Rajaei E. Association of PTPN22 rs2476601 Polymorphism with Rheumatoid Arthritis and Celiac Disease in Khuzestan Province, Southwestern Iran. IRANIAN BIOMEDICAL JOURNAL 2016; 21:61-6. [PMID: 27215233 PMCID: PMC5141256 DOI: 10.6091/.21.1.61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background: Single-nucleotide polymorphism (SNP) rs2476601 within protein tyrosine phosphatase non-receptor type 22 gene (PTPN22) has been shown to be a risk factor for different autoimmune diseases. This study explored the association of 1858 C/T SNP with rheumatoid arthritis (RA) and celiac disease (CD) in a region covering south-west of Iran. Methods: Totally, 52 patients with CD, 120 patients with RA, and 120 healthy subjects were selected. The samples were genotyped for the rs2476601 in PTPN22 gene using the tetra-amplification refractory mutation system polymerase chain reaction. Results: The frequency of +1858T risk allele was significantly increased in both RA (P=0.021, OR=2.56, 95%CI=1.19-5.47) and CD (P=0.002, OR=3.87, 95%CI=1.68-8.95) patients, as compared to the control group. However, no association was found between the +1858C/T PTPN22 gene SNP and the anti-cyclic citrullinated peptide and rheumatoid factor positivity in RA patients. Conclusions: PTPN22 gene could play a crucial role in people’s susceptibility to certain autoimmune diseases.
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Affiliation(s)
- Zahra Abbasi
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Mahdi Pourmahdi-Broojeni
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Iran
| | - Elham Rajaei
- Department of Internal Medicine, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Blasetti A, Di Giulio C, Tumini S, Provenzano M, Rapino D, Comegna L, Prezioso G, Chiuri R, Franchini S, Chiarelli F, Stuppia L. Role of the C1858T polymorphism of protein tyrosine phosphatase non-receptor type 22 (PTPN22) in children and adolescents with type 1 diabetes. THE PHARMACOGENOMICS JOURNAL 2016; 17:186-191. [DOI: 10.1038/tpj.2016.6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/24/2015] [Accepted: 01/20/2016] [Indexed: 01/18/2023]
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Nabi G, Akhter N, Wahid M, Bhatia K, Mandal RK, Dar SA, Jawed A, Haque S. Meta-analysis reveals PTPN22 1858C/T polymorphism confers susceptibility to rheumatoid arthritis in Caucasian but not in Asian population. Autoimmunity 2016; 49:197-210. [PMID: 26763276 DOI: 10.3109/08916934.2015.1134514] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The PTPN22 1858C/T polymorphism is associated with rheumatoid arthritis (RA). However, reports from the Asian populations are conflicting in nature and lacks consensus. The aim of our study was to evaluate the association between the PTPN22 1858C/T polymorphism and RA in Asian and Caucasian subjects by carrying out a meta-analysis of Asian and Caucasian data. A total of 27 205 RA cases and 27 677 controls were considered in the present meta-analysis involving eight Asian and 35 Caucasian studies. The pooled odds ratios (ORs) were performed for the allele, dominant, and recessive genetic model. No statistically significant association was found between the PTPN22 1858C/T polymorphism and risk of RA in Asian population (allele genetic model: OR = 1.217, 95% confidence interval (CI) = 0.99-1.496, p value 0.061; dominant genetic model: OR = 1.238, 95% CI = 0.982-1.562, p value 0.071; recessive genetic model: OR = 1.964, 95% CI = 0.678-5.693, p value 0.213). A significant association with risk of RA in Caucasian population suggesting that T-- allele does confer susceptibility to RA in this subgroup was observed (allele genetic model: OR = 1.638, 95% CI = 1.574-1.705, p value < 0.0001; dominant genetic model: OR = 1.67, 95% CI = 1.598-1.745, p value < 0.0001; recessive genetic model: OR = 2.65, 95% CI = 2.273-3.089, p value < 0.0001). The PTPN22 1858C/T polymorphism is not associated with RA risk in Asian populations. However, our meta-analysis confirms that the PTPN22 1858C/T polymorphism is associated with RA susceptibility in Caucasians.
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Affiliation(s)
- Gowher Nabi
- a Molecular Genetics Laboratory, Department of Medical Lab Technology, College of Applied Medical Sciences, Jazan University , Jazan , Saudi Arabia
| | - Naseem Akhter
- b Department of Laboratory Medicine , Faculty of Applied Medical Sciences, Albaha University , Albaha , Saudi Arabia
| | - Mohd Wahid
- c Research and Scientific Studies Unit , College of Nursing & Allied Health Sciences, Jazan University , Jazan , Saudi Arabia , and
| | - Kanchan Bhatia
- d Department of Biological Sciences , Rabigh College of Science and Arts, King Abdulaziz University , Rabigh , Jeddah , Saudi Arabia
| | - Raju Kumar Mandal
- c Research and Scientific Studies Unit , College of Nursing & Allied Health Sciences, Jazan University , Jazan , Saudi Arabia , and
| | - Sajad Ahmad Dar
- c Research and Scientific Studies Unit , College of Nursing & Allied Health Sciences, Jazan University , Jazan , Saudi Arabia , and
| | - Arshad Jawed
- c Research and Scientific Studies Unit , College of Nursing & Allied Health Sciences, Jazan University , Jazan , Saudi Arabia , and
| | - Shafiul Haque
- c Research and Scientific Studies Unit , College of Nursing & Allied Health Sciences, Jazan University , Jazan , Saudi Arabia , and
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13
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Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, Chiavacci RM, Kim CE, Wang F, Snyder J, Richie MD, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Russell RK, Wilson DC, Silverberg MS, Annese V, Lie BA, Punaro M, Dubinsky MC, Monos DS, Strisciuglio C, Staiano A, Miele E, Kugathasan S, Ellis JA, Munro JE, Sullivan KE, Wise CA, Chapel H, Cunningham-Rundles C, Grant SFA, Orange JS, Sleiman PMA, Behrens EM, Griffiths AM, Satsangi J, Finkel TH, Keinan A, Prak ETL, Polychronakos C, Baldassano RN, Li H, Keating BJ, Hakonarson H. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nat Med 2015; 21:1018-27. [PMID: 26301688 PMCID: PMC4863040 DOI: 10.1038/nm.3933] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 07/23/2015] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases.
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Affiliation(s)
- Yun R Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jin Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sihai D Zhao
- Department of Biostatistics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan P Bradfield
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frank D Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - S Melkorka Maggadottir
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cuiping Hou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Debra J Abrams
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Diana Chang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
- Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Feng Gao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Yiran Guo
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher J Cardinale
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marina Bakay
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dong Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Charlly Kao
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly A Thomas
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Haijun Qiu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rosetta M Chiavacci
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cecilia E Kim
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fengxiang Wang
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James Snyder
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marylyn D Richie
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Øystein Førre
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lee A Denson
- Division of Gastroenterology, The Center for Inflammatory Bowel Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Susan D Thompson
- Divison of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mara L Becker
- Division of Rheumatology, Children's Mercy Hospitals and Clinics, Kansas City, Missouri, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah School of Medicine and Primary Children's Medical Center, Salt Lake City, Utah, USA
| | - Anna Latiano
- Division of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elena Perez
- Division of Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Elena Resnick
- Institute of Immunology and Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Yorkhill Hospital for Sick Children, Glasgow, Scotland, UK
| | - David C Wilson
- Paediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, University of Edinburgh, Ediburgh, UK
| | - Mark S Silverberg
- Mount Sinai Hospital IBD Centre, University of Toronto, Toronto, Ontario, Canada
| | - Vito Annese
- Unit of Gastroenterology, Department of Medical and Surgical Specialties, Careggi University Hospital, Florence, Italy
| | - Benedicte A Lie
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marilynn Punaro
- Department of Rheumatology, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Pediatric IBD Center, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dimitri S Monos
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caterina Strisciuglio
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Annamaria Staiano
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta, Atlanta, Georgia, USA
| | - Justine A Ellis
- Genes, Environment and Complex Disease, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Jane E Munro
- Pediatric Rheumatology Unit, Royal Children's Hospital, Parkville, Victoria, Australia
- Arthritis and Rheumatology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Helen Chapel
- Department of Clinical Immunology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Struan F A Grant
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jordan S Orange
- Section of Immunology, Allergy, and Rheumatology, Department of Pediatric Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward M Behrens
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anne M Griffiths
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Jack Satsangi
- Gastrointestinal Unit, Division of Medical Sciences, School of Molecular and Clinical Medicine, University of Edinburgh, Edinburgh, UK
| | - Terri H Finkel
- Department of Pediatrics, Nemours Children's Hospital, Orlando, Florida, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
- Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Eline T Luning Prak
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Constantin Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University Health Centre Research Institute, Montréal, Québec, Canada
| | - Robert N Baldassano
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongzhe Li
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J Keating
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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14
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Worthington J, Eyre S. Principles of genetic epidemiology. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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Almasi S, Aliparasti MR, Yazdchi-Marandi L, Aliasgarzadeh A, Sioofy-Khojine A, Mesri A, Zamani F. Analysis of PTPN22 C1858T gene polymorphism in cases with type 1 diabetes of Azerbaijan, Northwest Iran. Cell Immunol 2014; 292:14-8. [DOI: 10.1016/j.cellimm.2014.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
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Yarwood A, Huizinga TWJ, Worthington J. The genetics of rheumatoid arthritis: risk and protection in different stages of the evolution of RA. Rheumatology (Oxford) 2014; 55:199-209. [PMID: 25239882 DOI: 10.1093/rheumatology/keu323] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 11/13/2022] Open
Abstract
There is now a general consensus that RA has a spectrum of disease stages that can begin many years before the onset of clinical symptoms. It is widely thought that understanding the complex interplay between genetics and environment, and their role in pathogenesis, is essential in gaining further insight into the mechanisms that drive disease development and progression. More than 100 genetic susceptibility loci have now been identified for RA through studies that have focused on patients with established RA compared with healthy controls. Studying the early preclinical phases of disease will provide valuable insights into the biological events that precede disease and could potentially identify biomarkers to predict disease onset and future therapeutic targets. In this review we will cover recent advances in the knowledge of genetic and environmental risk factors and speculate on how these factors may influence the transition from one stage of disease to another.
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Affiliation(s)
- Annie Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Stopford Building, University of Manchester, Manchester, UK
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands and
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Stopford Building, University of Manchester, Manchester, UK, NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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17
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The role of PTPN22 C1858T gene polymorphism in diabetes mellitus type 1: first evaluation in Greek children and adolescents. BIOMED RESEARCH INTERNATIONAL 2013; 2013:721604. [PMID: 23936838 PMCID: PMC3727122 DOI: 10.1155/2013/721604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/27/2013] [Accepted: 06/20/2013] [Indexed: 12/25/2022]
Abstract
Type 1 diabetes mellitus (T1DM) is an autoimmune multifactorial disease. Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene encodes lymphoid-specific tyrosine phosphatase (Lyp), an inhibitor of T cell activation. PTPN22 C1858T polymorphism was associated with T1DM in populations of Caucasian origin. The aim of this study was the investigation for the first time of the association of PTPN22 C1858T polymorphism with T1DM in Greek population. We studied 130 children and adolescents with T1DM and 135 healthy individuals of Greek origin. The polymorphism was genotyped using polymerase chain reaction with restriction fragment length polymorphism. C1858T and T1858T genotypes as well as 1858T allele were found more frequently in patients (10.8% and 5.8%, resp.) than in healthy individuals (5.9% and 3.0%, resp.) but at non statistically significant level. There was no statistically significant association found with gender, age at diagnosis, severity of onset, history of Hashimoto thyroiditis or family history of T1DM. Increased frequency of 1858T allele in patients than in controls, implying a probable association, agrees with results of similar studies on other populations. The inability to find a statistically significant difference is probably due to the decreased frequency of minor allele in Greek population, indicating the need for a larger sample.
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Abstract
Genetic studies in immune-mediated diseases have yielded a large number of disease-associated loci. Here we review the progress being made in 12 such diseases, for which 199 independently associated non-HLA loci have been identified by genome-wide association studies since 2007. It is striking that many of the loci are not unique to a single disease but shared between different immune-mediated diseases. The challenge now is to understand how the unique and shared genetic factors can provide insight into the underlying disease biology. We annotated disease-associated variants using the Encyclopedia of DNA Elements (ENCODE) database and demonstrate that, of the predisposing disease variants, the majority have the potential to be regulatory. We also demonstrate that many of these variants affect the expression of nearby genes. Furthermore, we summarize results from the Immunochip, a custom array, which allows a detailed comparison between five of the diseases that have so far been analyzed using this platform.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands;
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19
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Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. ACTA ACUST UNITED AC 2013; 65:571-81. [PMID: 23233247 DOI: 10.1002/art.37801] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/15/2012] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The significance of non-rheumatoid arthritis (RA) autoantibodies in patients with RA is unclear. The aim of this study was to assess associations of autoantibodies with autoimmune risk alleles and with clinical diagnoses from the electronic medical records (EMRs) among RA cases and non-RA controls. METHODS Data on 1,290 RA cases and 1,236 non-RA controls of European genetic ancestry were obtained from the EMRs of 2 large academic centers. The levels of anti-citrullinated protein antibodies (ACPAs), antinuclear antibodies (ANAs), anti-tissue transglutaminase antibodies (AGTAs), and anti-thyroid peroxidase (anti-TPO) antibodies were measured. All subjects were genotyped for autoimmune risk alleles, and the association between number of autoimmune risk alleles present and number of types of autoantibodies present was studied. A phenome-wide association study (PheWAS) was conducted to study potential associations between autoantibodies and clinical diagnoses among RA cases and non-RA controls. RESULTS The mean ages were 60.7 years in RA cases and 64.6 years in non-RA controls. The proportion of female subjects was 79% in each group. The prevalence of ACPAs and ANAs was higher in RA cases compared to controls (each P < 0.0001); there were no differences in the prevalence of anti-TPO antibodies and AGTAs. Carriage of higher numbers of autoimmune risk alleles was associated with increasing numbers of autoantibody types in RA cases (P = 2.1 × 10(-5)) and non-RA controls (P = 5.0 × 10(-3)). From the PheWAS, the presence of ANAs was significantly associated with a diagnosis of Sjögren's/sicca syndrome in RA cases. CONCLUSION The increased frequency of autoantibodies in RA cases and non-RA controls was associated with the number of autoimmune risk alleles carried by an individual. PheWAS of EMR data, with linkage to laboratory data obtained from blood samples, provide a novel method to test for the clinical significance of biomarkers in disease.
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Affiliation(s)
- Katherine P Liao
- Brigham and Women's Hospital, 75 Francis Street, PBB-B3, Boston, MA 02115, USA.
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Wang XF, Chen ZX, Shao YC, Ma YS, Zhang F, Zhang L, Fu D, Xia Q. Population-based and family-based studies on the protein tyrosine phosphatase non-receptor 22 gene polymorphism and type 1 diabetes: A meta-analysis. Gene 2013; 517:191-6. [DOI: 10.1016/j.gene.2012.12.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/25/2012] [Accepted: 12/19/2012] [Indexed: 10/27/2022]
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21
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Xuan C, Lun LM, Zhao JX, Wang HW, Zhu BZ, Yu S, Liu Z, He GW. PTPN22 gene polymorphism (C1858T) is associated with susceptibility to type 1 diabetes: a meta-analysis of 19,495 cases and 25,341 controls. Ann Hum Genet 2013; 77:191-203. [PMID: 23438410 DOI: 10.1111/ahg.12016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 12/05/2012] [Indexed: 12/30/2022]
Abstract
The protein tyrosine phosphatase N22 (PTPN22) gene C1858T polymorphism has been reported to be associated with susceptibility to type 1 diabetes (T1D) in relatively small sample sizes. This study aimed at investigating the pooled association by carrying out a meta-analysis on the published studies. The Medline, EBSCO, and BIOSIS databases were searched to identify eligible studies published in English before June 2012. The association was assessed by odds ratio (OR) with 95% confidence intervals (CI). The presence of heterogeneity and publication bias was explored by using meta-regression analysis and Begg's test, respectively. A total of 28 studies were involved in this meta-analysis. Across all populations, significant associations were found between the PTPN22 C1858T polymorphism and susceptibility to T1D under genotypic (TT vs. CC [OR = 3.656, 95% CI: 3.139-4.257], CT vs. CC [OR = 1.968, 95% CI: 1.683-2.300]), recessive (OR = 3.147, 95% CI: 2.704-3.663), and dominant models (OR = 1.957, 95% CI: 1.817-2.108). In ethnicity- and sex-stratified analyses, similar associations were found among Caucasians and within Caucasian male and female strata. The meta-analysis results suggest that the PTPN22 C1858T polymorphism was associated with susceptibility to T1D among the Caucasian population, and males who carried the -1858T allele were more susceptible to T1D than females.
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Affiliation(s)
- Chao Xuan
- Department of Clinical Laboratory, The Affiliated Hospital of Medical College, Qingdao University, Qingdao 266101, P.R China
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Song GG, Bae SC, Kim JH, Lee YH. The PTPN22 C1858T polymorphism and rheumatoid arthritis: a meta-analysis. Rheumatol Int 2013; 33:1991-9. [PMID: 23370857 DOI: 10.1007/s00296-013-2679-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 01/19/2013] [Indexed: 11/30/2022]
Abstract
The aim of this study was to determine whether the protein tyrosine phosphatase nonreceptor 22 (PTPN22) C1858T polymorphism confers susceptibility to rheumatoid arthritis (RA) in populations with different ethnicities. MEDLINE database and manual search were utilized to identify articles in which the PTPN22 polymorphism was determined in RA patients and controls. A meta-analysis was conducted on the associations between the PTPN22 C1858T polymorphism and RA using (1) allelic contrast and (2) dominant model. A total of 30 separate comparisons involving 17,961 RA patients and 18,611 controls were considered in this meta-analysis. Meta-analysis showed an association between the T allele and RA in all subjects (OR = 1.490, 95% CI = 1.332-1.668, P < 1.0 × 10(-9)). After stratification by ethnicity, analysis indicated that the T allele was significantly associated with RA in Europeans and in Non-Europeans (OR = 1.423, 95% CI = 1.260-1.605, P = 1.0 × 10(-8); OR = 1.902, 95% CI = 1.488-2.430, P = 2.8 × 10(-8)). Meta-analysis of the CT + TT genotype showed the same result patterns as that shown by the PTPN22 C1858T polymorphism T allele. Furthermore, a direct comparison between rheumatoid factor (RF)-positive and RF-negative subjects revealed a significant association with the T allele in RA patients with RF, but not in subjects without RF (OR = 1.561, 95% CI = 1.373-1.775, P < 1.0 × 10(-9)). This meta-analysis confirms that the PTPN22 C1858T polymorphism is associated with RA susceptibility in different ethnic groups, especially in Europeans, and the PTPN22 C1858T polymorphism T allele is significantly more prevalent in RF-positive patents than in RF-negative patients.
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Affiliation(s)
- Gwan Gyu Song
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 126-1 ga, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-705, Korea
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23
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Meta-analysis reveals an association of PTPN22 C1858T with autoimmune diseases, which depends on the localization of the affected tissue. Genes Immun 2012; 13:641-52. [DOI: 10.1038/gene.2012.46] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Meta-analysis of the family-based association between the PTPN22 C1858T polymorphism and Type 1 diabetes. Mol Biol Rep 2012; 40:211-5. [DOI: 10.1007/s11033-012-2051-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 10/02/2012] [Indexed: 02/02/2023]
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Pradhan VD, Dalvi H, Parsannavar D, Rajadhyaksha A, Patwardhan M, Ghosh K. Study of PTPN22 1858C/T polymorphism in rheumatoid arthritis patients from Western India. INDIAN JOURNAL OF RHEUMATOLOGY 2012. [DOI: 10.1016/j.injr.2012.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Tang S, Peng W, Wang C, Tang H, Zhang Q. Association of the PTPN22 gene (+1858C/T, -1123G/C) polymorphisms with type 1 diabetes mellitus: a systematic review and meta-analysis. Diabetes Res Clin Pract 2012; 97:446-52. [PMID: 22572103 DOI: 10.1016/j.diabres.2012.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/28/2012] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVE A meta-analysis was conducted to evaluate the association of PTPN22 gene (+1858C/T -1123G/C) polymorphism with T1DM susceptibility. METHODS Electronic databases were used to identify published studies before September 2011. We adopted the most appropriate genetic model. The combined odds ratio (OR) with 95% confidence interval (95% CI) was calculated to estimate the strength of the association in a fixed or random effect model. Heterogeneity and publication bias were also assessed. RESULTS Totally, 25 case-control studies including 8613 T1DM cases and 10,133 healthy controls (24 studies containing 8129 cases and 9641 controls for PTPN22 +1858C/T, 5 studies including 1460 cases and 1609 controls for PTPN22 -1123G/C) were identified as eligible and analyzed. The most appropriate co-dominant model was adopted. A significant association of PTPN22 +1858C/T gene polymorphism was found in overall population. When stratified by race, significance was observed in Europe and America, but not in Asia. We did not detect any association for PTPN22 -1123G/C polymorphism. CONCLUSIONS Our study indicated that T1DM is associated with PTPN22 +1858C/T gene polymorphism, and targeting this promoter polymorphism should be dependent on ethnicity. Whether -1123G/C polymorphism is a susceptibility locus for T1DM, further studies with well-designed among different ethnicity populations are required.
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Affiliation(s)
- Songtao Tang
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Peng H, Zhou M, Xu WD, Xu K, Zhai Y, Li R, Wang W, Zhang YJ, Liu SS, Pan HF, Ye DQ. Association of PTPN22 C1858T polymorphism and type 1 diabetes: a meta-analysis. Immunol Invest 2012; 41:484-96. [PMID: 22429252 DOI: 10.3109/08820139.2012.664226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recently, protein tyrosine phosphatase nonreceptor 22 (PTPN22) C1858T polymorphism has been identified as a susceptibile gene for type 1 diabetes (T1D), but studies are inconsistence, In order to assess the association between PTPN22C1858T polymorphism and T1D based on different ethnicities, a meta-analysis was performed, including 26 studies, total of 16,240 patients and 17,997 controls. Meta-analysis was performed on T versus C, T/T+T/C versus C/C (dominant model) and T/T versus T/C+C/C (recessive model) in a fixed/random effects model. The results indicated an association between the PTPN22 C1858T polymorphism and T1D in all subjects. The overall odds ratio (OR) of T versus C using the fixed effects model was 1.948 (95% CI = 1.859∼2.041, P < 0.001). After stratification by ethnicity, analysis revealed that the PTPN22 C1858T polymorphism T allele was significantly associated with T1D in Europeans, Americans (OR = 1.946, 95% CI = 1.852~2.045, P < 0.001; OR = 1.946, 95% CI = 1.690~2.242, P < 0.001, respectively). Meta-analysis of the T/T+T/C genotype and the T/T genotypes showed the same results as that shown by the PTPN22 C1858T polymorphism T allele. This meta-analysis suggests a possible association between the PTPN22 C1858T polymorphism and T1D, especially in European and American populations.
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Affiliation(s)
- Hui Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, PR China
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Need for Clarification of Data in the Recent Meta-analysis About 1858 C/T Polymorphism of the Protein Tyrosine Phosphatase Nonreceptor 22 Gene and Rheumatoid Arthritis Risk. Arch Med Res 2012; 43:170-1; author reply 172. [DOI: 10.1016/j.arcmed.2012.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/01/2012] [Indexed: 11/22/2022]
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Association between the CTLA-4 +49 A/G polymorphism and susceptibility to rheumatoid arthritis: a meta-analysis. Mol Biol Rep 2011; 39:5599-605. [DOI: 10.1007/s11033-011-1364-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 12/12/2011] [Indexed: 10/14/2022]
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Totaro MC, Tolusso B, Napolioni V, Faustini F, Canestri S, Mannocci A, Gremese E, Bosello SL, Alivernini S, Ferraccioli G. PTPN22 1858C>T polymorphism distribution in Europe and association with rheumatoid arthritis: case-control study and meta-analysis. PLoS One 2011; 6:e24292. [PMID: 21949702 PMCID: PMC3174938 DOI: 10.1371/journal.pone.0024292] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/03/2011] [Indexed: 11/20/2022] Open
Abstract
Objective The PTPN22 rs2476601 polymorphism is associated with rheumatoid arthritis (RA); nonetheless, the association is weaker or absent in some southern European populations. The aim of the study was to evaluate the association between the PTPN22 rs2476601 polymorphism and RA in Italian subjects and to compare our results with those of other European countries, carrying out a meta-analysis of European data. Methods A total of 396 RA cases and 477 controls, all of Italic ancestry, were genotyped for PTPN22 rs2476601 polymorphism. Patients were tested for autoantibodies positivity. The meta-analysis was performed on 23 selected studies. Results The PTPN22 T1858 allele was significantly more frequent in RA patients compared to controls (5.7% vs. 3.7%, p = 0.045). No clear relationship arose with the autoantibodies tested. The 1858T allele frequency in Italian RA patients was lower than the one described in northern European populations and similar to the frequency found in Spain, Turkey, Greece, Tunisia. A clear-cut North-South gradient arose from the analysis. Conclusions The PTPN22 T1858 allele is associated with RA in the Italian population. A North-South gradient of the allele frequency seems to exist in Europe, with a lower prevalence of the mutation in the Mediterranean area.
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Affiliation(s)
- Michele Ciro Totaro
- Division of Rheumatology, Catholic University of the Sacred Heart, Rome, Italy
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The association between the PTPN22 C1858T polymorphism and rheumatoid arthritis: a meta-analysis update. Mol Biol Rep 2011; 39:3453-60. [DOI: 10.1007/s11033-011-1117-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 06/20/2011] [Indexed: 12/19/2022]
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Abstract
The study of complex genetics in autoimmune diseases has progressed at a tremendous pace over the last 4 years, as a direct result of the enormous gains made by genome wide association studies (GWAS). Novel genetic findings are continuously being reported alongside the rapid development of genetic technologies, sophisticated statistical analysis, and larger sample collections. It is now becoming clear that multiple genes contribute to disease risk in many complex genetic disorders including rheumatoid arthritis (RA) and that there are common genetic risk factors that underlie a spectrum of autoimmune diseases. This review details the current genetic landscape of RA, and describes what GWAS has taught us in terms of missing heritability, subsets of disease, existence of genetic heterogeneity, and shared autoimmune risk loci. Finally, this review addresses the initial challenges faced in translating the wealth of genetic findings into determining the biological mechanisms that contribute to the relationship between genotype and phenotype. Unraveling the mechanism of how genes directly influence the cause of RA will lead to a better understanding of the disease and will ultimately have a direct clinical impact, informing the development of new therapies that can be utilized in the treatment of RA.
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Affiliation(s)
- Kate McAllister
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Stephen Eyre
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Gisela Orozco
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
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Eerligh P, van Lummel M, Zaldumbide A, Moustakas AK, Duinkerken G, Bondinas G, Koeleman BPC, Papadopoulos GK, Roep BO. Functional consequences of HLA-DQ8 homozygosity versus heterozygosity for islet autoimmunity in type 1 diabetes. Genes Immun 2011; 12:415-27. [PMID: 21562577 DOI: 10.1038/gene.2011.24] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human leukocyte antigen (HLA) class II haplotypes are established risk factors in type 1 diabetes (T1D). The heterozygous DQ2/8 genotype confers the highest risk, whereas the DQ6/8 genotype is protective. We hypothesized that DQ2/8 trans-molecules composed of α and β chains from DQ2 and DQ8 express unique β-cell epitopes, whereas DQ6 may interfere with peptide binding to DQ8. Here we show that a single insulin epitope (InsB13-21) within the T1D prototype antigenic InsB6-22 peptide can bind to both cis- and trans-dimers, although these molecules display different peptide binding patterns. DQ6 binds a distinct insulin epitope (InsB6-14). The phenotype of DQ8-restricted T cells from a T1D patient changed from proinflammatory to anti-inflammatory in the presence of DQ6. Our data provide new insights into both susceptible and protective mechanism of DQ, where protecting HLA molecules bind autoantigens in a different (competing) binding register leading to 'epitope stealing', thereby inducing a regulatory, rather than a pathogenic immune response.
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Affiliation(s)
- P Eerligh
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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Burn GL, Svensson L, Sanchez-Blanco C, Saini M, Cope AP. Why is PTPN22 a good candidate susceptibility gene for autoimmune disease? FEBS Lett 2011; 585:3689-98. [PMID: 21515266 DOI: 10.1016/j.febslet.2011.04.032] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/13/2011] [Accepted: 04/13/2011] [Indexed: 10/18/2022]
Abstract
The PTPN22 locus is one of the strongest risk factors outside of the major histocompatability complex that associates with autoimmune diseases. PTPN22 encodes lymphoid protein tyrosine phosphatase (Lyp) which is expressed exclusively in immune cells. A single base change in the coding region of this gene resulting in an arginine to tryptophan amino acid substitution within a polyproline binding motif associates with type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosis, Hashimotos thyroiditis, Graves disease, Addison's disease, Myasthenia Gravis, vitiligo, systemic sclerosis juvenile idiopathic arthritis and psoriatic arthritis. Here, we review the current understanding of the PTPN22 locus from a genetic, geographical, biochemical and functional perspective.
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Affiliation(s)
- Garth L Burn
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King's College School of Medicine, King's College London, UK.
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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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Worthington J. Genetic factors in rheumatic disease. Rheumatology (Oxford) 2011. [DOI: 10.1016/b978-0-323-06551-1.00014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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37
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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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Huang JJ, Qiu YR, Li HX, Sun DH, Yang J, Yang CL. A PTPN22 promoter polymorphism -1123G>C is associated with RA pathogenesis in Chinese. Rheumatol Int 2010; 32:767-71. [PMID: 21193990 DOI: 10.1007/s00296-010-1705-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 11/28/2010] [Indexed: 01/15/2023]
Abstract
The minor allele of the non-synonymous single nucleotide polymorphism (SNP) +1858C>T within the PTPN22 gene has now been unequivocally confirmed as conferring susceptibility to RA in population from Europe and America, but not in population from Asia. The aim of this study was to jointly address and integrate these separate findings to further elucidate the association between the PTPN22 gene and RA in Chinese Hans of Guangdong province. Four hundred and ninety-four cases with RA and 496 healthy controls were randomly selected, their SNPs at position -1123G>C (rs2488457), +1858C>T (rs2476601), +788G>A (rs33996649), and rs1310182 were genotyped using PCR-RFLP, followed by agarose gel electrophoresis. +1858C>T (rs2476601) and +788G>A (rs33996649) are not polymorphic in Chinese Hans. Meanwhile, our result reveals that the degree of association between the promoter polymorphism, -1123G>C and RA, was analogous to that observed in Japanese reports (odds ratio [OR] = 1.517, 95% CI = [1.154-1.995], P = 0.003). Expression study also indicated a tendency for association between -1123G>C and PTPN22 gene expression. Our study underpins that the promoter polymorphism, -1123G/C, may be a causal SNP for RA in Asian.
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Affiliation(s)
- Jian-Jun Huang
- Department of Clinical Laboratory, Nanfang Hospital, Southern Medical University, 510515 Guangzhou, China
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D'Silva KJ, Zamora MB, Gerlach J, Schwartz KA. Increased representation of the PTPN22 mutation in patients with immune thrombocytopenia. J Thromb Haemost 2010; 8:2076-8. [PMID: 20553389 DOI: 10.1111/j.1538-7836.2010.03954.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Lins TC, Vieira RG, Grattapaglia D, Pereira RW. Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases. Autoimmunity 2010; 43:308-16. [PMID: 20166877 DOI: 10.3109/08916930903405883] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The rs2476601-T allele at the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene has been consistently associated with several autoimmune diseases in European-derived populations. However, little is known about the allele and haplotype frequency distributions in PTPN22 among populations derived from other ethnic groups. In the present study, the allele and haplotype frequency distributions of six single nucleotide polymorphisms (SNPs) in the PTPN22 gene were compared among Brazilian populations and HapMap phase 3 dataset. A total of 10 different population samples were evaluated. Additionally, in admixed populations, individual genetic ancestries were estimated for Native American, African, and European contributions. Estimated individual ancestries were used as quantitative traits in a conditional approach for single-marker and haplotype-specific regression analyses. It was shown that several SNPs and haplotypes have different frequencies among different ethnic populations. Individual genetic ancestries were not associated with the rs2476601-T allele, but were associated with PTPN22 haplotypes in Brazilian, Mexican, and African-American admixed populations. Our results suggest caution in the interpretation of results found in association studies involving PTPN22 polymorphisms in admixed populations. Correction for stratification generated by admixture should be mandatory to minimize or avoid chances of spurious association.
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Affiliation(s)
- Tulio C Lins
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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Plant D, Flynn E, Mbarek H, Dieudé P, Cornelis F, Arlestig L, Dahlqvist SR, Goulielmos G, Boumpas DT, Sidiropoulos P, Johansen JS, Ørnbjerg LM, Hetland ML, Klareskog L, Filer A, Buckley CD, Raza K, Witte T, Schmidt RE, Worthington J. Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers. Ann Rheum Dis 2010; 69:1548-53. [PMID: 20498205 PMCID: PMC2938898 DOI: 10.1136/ard.2009.121020] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Genetic factors have a substantial role in determining development of rheumatoid arthritis (RA), and are likely to account for 50–60% of disease susceptibility. Genome-wide association studies have identified non-human leucocyte antigen RA susceptibility loci which associate with RA with low-to-moderate risk. Objectives To investigate recently identified RA susceptibility markers using cohorts from six European countries, and perform a meta-analysis including previously published results. Methods 3311 DNA samples were collected from patients from six countries (UK, Germany, France, Greece, Sweden and Denmark). Genotype data or DNA samples for 3709 controls were collected from four countries (not Sweden or Denmark). Eighteen single nucleotide polymorphisms (SNPs) were genotyped using Sequenom MassArray technology. Samples with a >95% success rate and only those SNPs with a genotype success rate of >95% were included in the analysis. Scandinavian patient data were pooled and previously published Swedish control data were accessed as a comparison group. Meta-analysis was used to combine results from this study with all previously published data. Results After quality control, 3209 patients and 3692 controls were included in the study. Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs4810485 (CD40), rs5029937 (6q23), rs10760130 (TRAF1/C5) and rs7574865 (STAT4)) were significantly associated with RA by meta-analysis. All 18 markers were associated with RA when previously published studies were incorporated in the analysis. Data from this study increased the significance for association with RA and nine markers. Conclusions In a large European RA cohort further evidence for the association of 18 markers with RA development has been obtained.
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Affiliation(s)
- Darren Plant
- arc-Epidemiology Unit, Stopford Building, The University of Manchester, Manchester M13 9PT, UK.
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The association between the PTPN22 1858C>T variant and type 1 diabetes depends on HLA risk and GAD65 autoantibodies. Genes Immun 2010; 11:406-15. [PMID: 20445565 DOI: 10.1038/gene.2010.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The single nucleotide polymorphism 1858C>T in the PTPN22 gene is associated with type 1 diabetes (T1D) in several populations. Earlier reports have suggested that the association may be modified by human leukocyte antigen (HLA), as well as by islet autoantibodies. In a large case-control study of Swedish incident T1D patients and controls, 0-34 years of age, we tested whether the odds ratio (OR) measure of association was dependent on HLA or autoantibodies against the islet autoantigens glutamic acid decarboxylase 65 kDa autoantibodies (GADA), insulin, islet antigen-2, or islet cell. The association between the carrier status of 1858C>T allele in PTPN22 (PTPN22(CT+TT)) and T1D was modified by HLA. In addition, in GADA-positive T1D, the OR was 2.83 (2.00, 3.99), whereas in GADA-negative T1D, the OR was 1.41 (0.98, 2.04) (P for comparison=0.007). The OR of association between PTPN22(CT+TT) and GADA-positive T1D declined with increasing HLA-risk category from 6.12 to 1.54 (P=0.003); no such change was detected in GADA-negative T1D (P=0.722) (P for comparison=0.001). However, the absolute difference in risk between PTPN22(CC) and PTPN22(CT+TT) subjects with high-risk HLA was five times higher than that for subjects with low-risk HLA. We hypothesize that the altered T-cell function because of the PTPN22(1858C>T) polymorphism is exclusively associated with GADA-positive T1D at diagnosis.
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Orozco G, Barton A. Update on the genetic risk factors for rheumatoid arthritis. Expert Rev Clin Immunol 2010; 6:61-75. [PMID: 20383892 DOI: 10.1586/eci.09.72] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rheumatoid arthritis (RA) is a complex disease, meaning that multiple genetic variants, environmental factors and random events interact to trigger pathological pathways. Although many of these etiological factors have not yet been identified, recent groundbreaking advances have expanded our knowledge about the genetic factors that contribute to RA. Here, we review the most recent findings on the genetic risk factors for RA. First, we give an overview of the genetics of RA and briefly describe the susceptibility loci discovered prior to the availability of genome-wide association studies (GWAS). Second, we focus on the newly discovered RA loci that have arisen from GWAS in populations of European ancestry. Through these studies, the number of established RA susceptibility loci has now grown to 13. Third, we discuss several important issues emerging from GWAS, such as ethnic heterogeneity and shared autoimmunity risk loci. Finally, we discuss what still needs to be accomplished before a more complete picture of the genetic risk to RA can be attained.
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Affiliation(s)
- Gisela Orozco
- Arthritis Research Campaign Epidemiology Unit, The University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Oxford Road, Manchester M13 9PT, UK.
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Morgan AR, Han DY, Huebner C, Lam WJ, Fraser AG, Ferguson LR. PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population. ACTA ACUST UNITED AC 2010; 76:119-25. [PMID: 20403149 DOI: 10.1111/j.1399-0039.2010.01493.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent genome-wide association studies have provided evidence for the involvement of the genes PTPN2 and PTPN22 in the pathogenesis of Crohn's disease (CD). We investigated whether genetic variants in these genes were associated with CD in a New Zealand population. Single-nucleotide polymorphisms (SNPs) rs2542151 (PTPN2) and rs2476601 (PTPN22) were genotyped in 315 CD cases and 481 controls. In this sample, we were able to confirm an association between CD and PTPN2 (genotypic P = 0.019 and allelic P = 0.011), and phenotypic analysis showed an association of this SNP with late age at first diagnosis, inflammatory and penetrating CD behaviour, requirement of bowel resection and being a smoker at diagnosis. There was no evidence for an association with PTPN22.
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Affiliation(s)
- A R Morgan
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
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O'Rielly DD, Rahman P. Pharmacogenetics of rheumatoid arthritis: Potential targets from susceptibility genes and present therapies. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2010; 3:15-31. [PMID: 23226040 PMCID: PMC3513198 DOI: 10.2147/pgpm.s5012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Indexed: 01/29/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic heterogeneous autoimmune disorder of unknown etiology resulting in inflammation in the synovium, cartilage, and bone. Genetic factors play an important role in susceptibility to RA as the heritability of RA is between 50% and 60%, with the human leukocyte antigen (HLA) locus accounting for at least 30% of overall genetic risk. Outside the major histocompatibility complex (MHC) region, six additional risk loci have been identified and validated including PTPN22, STAT4, PADI4, CTLA4, TNFAIP3-OLIG3, and TRAF1/C5. Genetic factors are also important in RA pharmacotherapy due to the gene-dependent activity of enzymes involved in the pharmacokinetics and/or pharmacodynamics of RA medications. Indeed, there is great variability in drug efficacy as well as adverse events associated with any anti-rheumatic therapy and genetics is thought to contribute significantly to this inter-individual variability in response. This review will summarize the genetic factors that have been implicated in the pathogenesis of RA, and how these determinants may factor into the potential pharmacogenetics of this disease. We will also review the therapeutic agents that are currently being utilized or presently being evaluated in the treatment of RA, along with potential pharmacogenetic markers that have been proposed for such medications.
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Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Chagastelles PC, Romitti M, Trein MR, Bandinelli E, Tschiedel B, Nardi NB. Association between the 1858T allele of the protein tyrosine phosphatase nonreceptor type 22 and type 1 diabetes in a Brazilian population. ACTA ACUST UNITED AC 2010; 76:144-8. [PMID: 20331840 DOI: 10.1111/j.1399-0039.2010.01480.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 1858T allele of the protein tyrosine phosphatase nonreceptor 22 (PTPN22) gene has been associated to diabetes in different populations. We investigated a possible relationship between this polymorphism and type 1 diabetes in a cohort of Brazilian patients. A significantly higher frequency of the 1858T allele was observed in diabetic patients (n = 211) than in control individuals (n = 241). Additionally, the heterozygote genotype was also increased in the diabetic group. No association was observed between the PTPN22 T allele and gender, or between T carriers and age of onset of T1D. This work describes for the first time a strong association of the 1858T allele with type 1 diabetes in a Brazilian population, reinforcing the role of this variant as an important susceptibility factor for this disease.
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Affiliation(s)
- P C Chagastelles
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Stanford SM, Mustelin TM, Bottini N. Lymphoid tyrosine phosphatase and autoimmunity: human genetics rediscovers tyrosine phosphatases. Semin Immunopathol 2010; 32:127-36. [PMID: 20204370 DOI: 10.1007/s00281-010-0201-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 01/28/2010] [Indexed: 01/22/2023]
Abstract
A relatively large number of protein tyrosine phosphatases (PTPs) are known to regulate signaling through the T cell receptor (TCR). Recent human genetics studies have shown that several of these PTPs are encoded by major autoimmunity genes. Here, we will focus on the lymphoid tyrosine phosphatase (LYP), a critical negative modulator of TCR signaling encoded by the PTPN22 gene. The functional analysis of autoimmune-associated PTPN22 genetic variants suggests that genetic variability of TCR signal transduction contributes to the pathogenesis of autoimmunity in humans.
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Affiliation(s)
- Stephanie M Stanford
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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Sfar I, Aleya WB, Mouelhi L, Aouadi H, Rhomdhane TB, Makhlouf M, Ayed-Jendoubi S, Gargaoui H, Najjar T, Abdallah TB, Ayed K, Gorgi Y. Lymphoid tyrosine phosphatase R620W variant and inflammatory bowel disease in Tunisia. World J Gastroenterol 2010; 16:479-83. [PMID: 20101775 PMCID: PMC2811802 DOI: 10.3748/wjg.v16.i4.479] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the possible association between PTPN22 (R620W) gene polymorphism and inflammatory bowel disease (IBD).
METHODS: One hundred and sixty-four patients with IBD [105 Crohn’s disease (CD) and 59 ulcerative colitis (UC)] and 100 healthy controls were recruited. Genotyping of the PTPN22 gene 1858C→T polymorphism was performed by restriction fragment length polymorphism-polymerase chain reaction with RsaI digestion.
RESULTS: The genotypic and allelic frequencies of (R620W) PTPN22 gene polymorphism reveal a significant association of the PTPN22 620-W allele with IBD, compared to the healthy control group (OR: 17.81, 95% CI: 4.18-21.86, P = 0.00001). Nevertheless, no difference in this polymorphism was found between CD and UC patients. No significant association was found between the frequencies of genotypes of the PTPN22 gene with either the clinical features such as sex, age, age at disease onset, and extent of colitis, or the production of serological markers (anti-Saccharomyces cerevisiae antibody in CD and perinuclear anti-neutrophil cytoplasmic antibody in UC).
CONCLUSION: These observations confirm the association of IBD susceptibility with the PTPN22 1858T (620-W) allele in Tunisian patients.
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Howson JMM, Walker NM, Smyth DJ, Todd JA. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. Genes Immun 2009; 10 Suppl 1:S74-84. [PMID: 19956106 PMCID: PMC2810493 DOI: 10.1038/gene.2009.96] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In recent years the pace of discovery of genetic associations with type I diabetes (T1D) has accelerated, with the total number of confirmed loci, including the major histocompatibility complex (MHC) region, reaching 43. However, much of the deciphering of the associations at these, and the established T1D loci, has yet to be performed in sufficient numbers of samples or with sufficient markers. Here, 257 single-nucleotide polymorphisms (SNPs) have been genotyped in 19 candidate genes (INS, PTPN22, IL2RA, CTLA4, IFIH1, SUMO4, VDR, PAX4, OAS1, IRS1, IL4, IL4R, IL13, IL12B, CEACAM21, CAPSL, Q7Z4c4(5Q), FOXP3, EFHB) in 2300 affected sib-pair families and tested for association with T1D as part of the Type I Diabetes Genetics Consortium's candidate gene study. The study had approximately 80% power at alpha=0.002 and a minor allele frequency of 0.2 to detect an effect with a relative risk (RR) of 1.20, which drops to just 40% power for a RR of 1.15. At the INS gene, rs689 (-23 HphI) was the most associated SNP (P=3.8 x 10(-31)), with the estimated RR=0.57 (95% confidence interval, 0.52-0.63). In addition, rs689 was associated with age-at-diagnosis of T1D (P=0.001), with homozygosity for the T1D protective T allele, delaying the onset of T1D by approximately 2 years in these families. At PTPN22, rs2476601 (R620W), in agreement with previous reports, was the most significantly associated SNP (P=6.9 x 10(-17)), with RR=1.55 (1.40-1.72). Evidence for association with T1D was observed for the IFIH1 SNP, rs1990760 (P=7.0 x 10(-4)), with RR=0.88 (0.82-0.95) and the CTLA4 SNP rs1427676 (P=0.0005), with RR=1.14 (1.06-1.23). In contrast, no convincing evidence of association was obtained for SUMO4, VDR, PAX4, OAS1, IRS1, IL4, IL4R, IL13, IL12B, CEACAM21 or CAPSL gene regions (http://www.T1DBase.org).
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Affiliation(s)
- J M M Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK.
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Barton A, Worthington J. Genetic susceptibility to rheumatoid arthritis: An emerging picture. ACTA ACUST UNITED AC 2009; 61:1441-6. [DOI: 10.1002/art.24672] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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