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Zhang HG, McDermott G, Seyok T, Huang S, Dahal K, L'Yi S, Lea-Bonzel C, Stratton J, Weisenfeld D, Monach P, Raychaudhuri S, Yu KH, Cai T, Cui J, Hong C, Cai T, Liao KP. Identifying shared genetic architecture between rheumatoid arthritis and other conditions: a phenome-wide association study with genetic risk scores. EBioMedicine 2023; 92:104581. [PMID: 37121095 PMCID: PMC10173154 DOI: 10.1016/j.ebiom.2023.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/19/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) shares genetic variants with other autoimmune conditions, but existing studies test the association between RA variants with a pre-defined set of phenotypes. The objective of this study was to perform a large-scale, systemic screen to determine phenotypes that share genetic architecture with RA to inform our understanding of shared pathways. METHODS In the UK Biobank (UKB), we constructed RA genetic risk scores (GRS) incorporating human leukocyte antigen (HLA) and non-HLA risk alleles. Phenotypes were defined using groupings of International Classification of Diseases (ICD) codes. Patients with an RA code were excluded to mitigate the possibility of associations being driven by the diagnosis or management of RA. We performed a phenome-wide association study, testing the association between the RA GRS with phenotypes using multivariate generalized estimating equations that adjusted for age, sex, and first five principal components. Statistical significance was defined using Bonferroni correction. Results were replicated in an independent cohort and replicated phenotypes were validated using medical record review of patients. FINDINGS We studied n = 316,166 subjects from UKB without evidence of RA and screened for association between the RA GRS and n = 1317 phenotypes. In the UKB, 20 phenotypes were significantly associated with the RA GRS, of which 13 (65%) were immune mediated conditions including polymyalgia rheumatica, granulomatosis with polyangiitis (GPA), type 1 diabetes, and multiple sclerosis. We further identified a novel association in Celiac disease where the HLA and non-HLA alleles had strong associations in opposite directions. Strikingly, we observed that the non-HLA GRS was exclusively associated with greater risk of the validated conditions, suggesting shared underlying pathways outside the HLA region. INTERPRETATION This study replicated and identified novel autoimmune phenotypes verified by medical record review that share immune pathways with RA and may inform opportunities for shared treatment targets, as well as risk assessment for conditions with a paucity of genomic data, such as GPA. FUNDING This research was funded by the US National Institutes of Health (P30AR072577, R21AR078339, R35GM142879, T32AR007530) and the Harold and DuVal Bowen Fund.
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Affiliation(s)
- Harrison G Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Greg McDermott
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Thany Seyok
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sicong Huang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kumar Dahal
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clara Lea-Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jacklyn Stratton
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dana Weisenfeld
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul Monach
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Data Science, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kun-Hsing Yu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tianrun Cai
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA.
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Heneberg P, Kocková L, Čecháková M, Daňková P, Černá M. Autoimmunity-Associated PTPN22 Polymorphisms in Latent Autoimmune Diabetes of the Adult Differ from Those of Type 1 Diabetes Patients. Int Arch Allergy Immunol 2018; 177:57-68. [DOI: 10.1159/000489225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
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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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Fousteri G, Ippolito E, Ahmed R, Hamad ARA. Beta-cell Specific Autoantibodies: Are they Just an Indicator of Type 1 Diabetes? Curr Diabetes Rev 2017; 13:322-329. [PMID: 27117244 PMCID: PMC5266674 DOI: 10.2174/1573399812666160427104157] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/19/2016] [Accepted: 04/26/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Autoantibodies (AAbs) against islet autoantigens (AAgs) are used for type 1 diabetes (T1D) diagnosis and prediction. Islet-specific AAbs usually appear early in life and may fluctuate in terms of number and titer sometimes for over 20 years before T1D develops. Whereas their predictive power is high for pediatric subjects with high genetic risk who rapidly progress to multiple AAb positivity, they are less reliable for children with low genetic risk, single AAb positivity and slow disease progression. OBJECTIVE It is unknown how AAbs develop and whether they are involved in T1D pathogenesis. So far an increase in AAb number seems to only indicate AAg spreading and progression towards clinical T1D. The goal of this review is to shed light on the possible involvement of AAbs in T1D development. METHOD We thoroughly review the current literature and discuss possible mechanisms of AAb development and the roles they may play in disease pathogenesis. RESULTS Genetic and environmental factors instigate changes at the molecular and cellular levels that promote AAb development. Although direct involvement of AAbs in T1D is less clear, autoreactive B cells are clearly involved in various immune and autoimmune responses via antigen presentation, immunoregulation and cytokine production. CONCLUSION Our analysis suggests that understanding the mechanisms that lead to islet-specific AAb development and the diabetogenic processes that autoreactive B cells promote may uncover additional biomarkers and therapeutic targets.
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Affiliation(s)
- Georgia Fousteri
- Diabetes Research Institute (DRI), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Address correspondence to: Georgia Fousteri; ; tel: +39 02 2643 3184; Fax: +39 02 2643 7759
| | - Elio Ippolito
- Diabetes Research Institute (DRI), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rizwan Ahmed
- Department of Pathology and of Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Abdel Rahim A. Hamad
- Department of Pathology and of Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
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Prezioso G, Comegna L, Di Giulio C, Franchini S, Chiarelli F, Blasetti A. C1858T Polymorphism of Protein Tyrosine Phosphatase Non-receptor Type 22 (PTPN22): an eligible target for prevention of type 1 diabetes? Expert Rev Clin Immunol 2016; 13:189-196. [PMID: 27892782 DOI: 10.1080/1744666x.2017.1266257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION In type 1 diabetes (T1D), several genetic factors are associated to β-cell autoimmunity onset and clinical progression. HLA-genes play a major role in susceptibility and initiation of β-cell autoimmunity, whereas non-HLA genes may influence the destruction rate. Areas covered: Our review focuses on the possible role of the PTPN22 C1858 T variant as a prognostic factor, given its influence on disease variability. Moreover, we present the potential role of C1858 T as a target for tertiary prevention trials and new therapeutic strategies, such as the LYP inhibitors. We used PubMed for literature research; key words were 'PTPN22', 'C1858 T polymorphism', 'lymphoid-specific tyrosine phosphatase' and 'type 1 diabetes'. We selected publications between 2000 and 2016. Expert commentary: Current data suggest that PTPN22 can be a promising target for therapeutic interventions and identification of at-risk subjects in autoimmune diseases such as T1D.
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Affiliation(s)
- Giovanni Prezioso
- a Department of Pediatrics , 'G. D'Annunzio' University , Chieti , Italy
| | - Laura Comegna
- a Department of Pediatrics , 'G. D'Annunzio' University , Chieti , Italy
| | - Concetta Di Giulio
- a Department of Pediatrics , 'G. D'Annunzio' University , Chieti , Italy
| | - Simone Franchini
- a Department of Pediatrics , 'G. D'Annunzio' University , Chieti , Italy
| | | | - Annalisa Blasetti
- a Department of Pediatrics , 'G. D'Annunzio' University , Chieti , Italy
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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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Maziarz M, Hagopian W, Palmer JP, Sanjeevi CB, Kockum I, Breslow N, Lernmark Å. Non-HLA type 1 diabetes genes modulate disease risk together with HLA-DQ and islet autoantibodies. Genes Immun 2015; 16:541-51. [PMID: 26513234 PMCID: PMC4670274 DOI: 10.1038/gene.2015.43] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/16/2022]
Abstract
The possible interrelations between HLA-DQ, non-HLA single nucleotide polymorphisms (SNPs) and islet autoantibodies were investigated at clinical onset in 1-34 year old type 1 diabetes (T1D) patients (n=305) and controls (n=203). Among the non-HLA SNPs reported by the Type 1 Diabetes Genetics Consortium, 24% were supported in this Swedish replication set including that the increased risk of minor PTPN22 allele and high risk HLA was modified by GAD65 autoantibodies. The association between T1D and the minor AA+AC genotype in ERBB3 gene was stronger among IA-2 autoantibody-positive patients (comparison p=0.047). The association between T1D and the common insulin (AA) genotype was stronger among insulin autoantibody (IAA)-positive patients (comparison p=0.008). In contrast, the association between T1D and unidentified 26471 gene was stronger among IAA-negative (comparison p=0.049) and IA-2 autoantibody-negative (comparison p=0.052) patients. Finally, the association between IL2RA and T1D was stronger among IAA-positive than among IAA-negative patients (comparison p=0.028). These results suggest that the increased risk of T1D by non-HLA genes is often modified by both islet autoantibodies and HLA-DQ. The interactions between non-HLA genes, islet autoantibodies and HLA-DQ should be taken into account in T1D prediction studies as well as in prevention trials aimed at inducing immunological tolerance to islet autoantigens.
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Affiliation(s)
- M Maziarz
- Department of Biostatistics, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - W Hagopian
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| | - J P Palmer
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - C B Sanjeevi
- Department of Medicine, Karolinska Institute, Solna, Sweden
| | - I Kockum
- Department of Clinical Neurosciences, Karolinska Institute, Stockholm, Sweden
| | - N Breslow
- Department of Biostatistics, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Å Lernmark
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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Araujo DB, Skärstrand H, Barone B, Dantas JR, Kupfer R, Zajdenverg L, Milech A, Vaziri-Sani F, Oliveira JEPD, Rodacki M. Zinc transporter 8 autoantibodies in patients with type 1 diabetes from a multiethnic population and their first degree relatives. ACTA ACUST UNITED AC 2015; 58:737-43. [PMID: 25372583 DOI: 10.1590/0004-2730000003088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 06/29/2014] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Zinc transporter 8 autoantibodies (ZnT8A) have been poorly studied in non-Caucasian individuals. We aimed to investigate the prevalence of ZnT8 autoantibodies in patients with T1D and their first degree relatives (FDR) from a multiethnic population, as well as its relation with the insulin (INS) or the protein tyrosine phosphatase non-receptor 22 (PTPN22) gene polymorphisms. SUBJECTS AND METHODS ZnT8A were analyzed in sera from T1D patients (n = 72, mean age of 30.3 ± 11.4 years) of variable duration (15.7 ± 11.8 years) and their FDR (n = 78, mean age of 18.3 ± 9.1 years) by a triple mix Radioligand Binding Assay (RBA) for the ZnT8 autoantibody (ZnT8-RWQ) variants. SNP (single nucleotide polymorphism) for INS and PTPN22 were genotyped. RESULTS The prevalence of ZnT8A was higher in T1D patients than FDR, for ZnT8TripleA (24% vs. 4%,p = 0.001), ZnT8RA (24% vs. 4%, p < 0.001) and ZnT8QA (15% vs. 3%, p = 0.004). All FDR with ZnT8A (n = 3) had at least another positive antibody. Heterozygosis for PTPN22 was associated with a higher frequency of ZnT8TripleA (p = 0.039) and ZnT8RA (p = 0.038). CONCLUSIONS ZnT8A is observed in non-Caucasian patients with T1D, even years after the disease onset, as well as in their FDR. In those, there was an overlap between ZnT8A and other T1D antibodies. ZnT8A was associated with PTPN22 polymorphisms. Further longitudinal studies are necessary to elucidate the importance of these findings in the natural history of T1D patients with multiethnic background.
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Affiliation(s)
- Débora Batista Araujo
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Bianca Barone
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Joana Rodrigues Dantas
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosane Kupfer
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione, Rio de Janeiro, RJ, Brazil
| | - Lenita Zajdenverg
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adolpho Milech
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fariba Vaziri-Sani
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Melanie Rodacki
- Department of Nutrology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Törn C, Hadley D, Lee HS, Hagopian W, Lernmark Å, Simell O, Rewers M, Ziegler A, Schatz D, Akolkar B, Onengut-Gumuscu S, Chen WM, Toppari J, Mykkänen J, Ilonen J, Rich SS, She JX, Steck AK, Krischer J. Role of Type 1 Diabetes-Associated SNPs on Risk of Autoantibody Positivity in the TEDDY Study. Diabetes 2015; 64:1818-29. [PMID: 25422107 PMCID: PMC4407865 DOI: 10.2337/db14-1497] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
Abstract
The Environmental Determinants of Diabetes in the Young (TEDDY) study prospectively follows 8,677 children enrolled from birth who carry HLA-susceptibility genotypes for development of islet autoantibodies (IA) and type 1 diabetes (T1D). During the median follow-up time of 57 months, 350 children developed at least one persistent IA (GAD antibody, IA-2A, or micro insulin autoantibodies) and 84 of them progressed to T1D. We genotyped 5,164 Caucasian children for 41 non-HLA single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with T1D in the genome-wide association scan meta-analysis conducted by the Type 1 Diabetes Genetics Consortium. In TEDDY participants carrying high-risk HLA genotypes, eight SNPs achieved significant association to development of IA using time-to-event analysis (P < 0.05), whereof four were significant after adjustment for multiple testing (P < 0.0012): rs2476601 in PTPN22 (hazard ratio [HR] 1.54 [95% CI 1.27-1.88]), rs2292239 in ERBB3 (HR 1.33 [95% CI 1.14-1.55]), rs3184504 in SH2B3 (HR 1.38 [95% CI 1.19-1.61]), and rs1004446 in INS (HR 0.77 [0.66-0.90]). These SNPs were also significantly associated with T1D in particular: rs2476601 (HR 2.42 [95% CI 1.70-3.44]). Although genes in the HLA region remain the most important genetic risk factors for T1D, other non-HLA genetic factors contribute to IA, a first step in the pathogenesis of T1D, and the progression of the disease.
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Affiliation(s)
- Carina Törn
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - David Hadley
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL Division of Population Health Sciences and Education, St George's University of London, London, U.K
| | - Hye-Seung Lee
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL
| | | | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - Olli Simell
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO
| | - Anette Ziegler
- Department of Pediatrics, Diabetes Research Institute, Munich, Germany
| | - Desmond Schatz
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jorma Toppari
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Juha Mykkänen
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland Department of Clinical Microbiology, University of Eastern Finland, Kuopio, Finland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Georgia Regents University, Augusta, GA
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO
| | - Jeffrey Krischer
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL
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Pei Z, Chen X, Sun C, Du H, Wei H, Song W, Yang Y, Zhang M, Lu W, Cheng R, Luo F. A novel single nucleotide polymorphism in the protein tyrosine phosphatase N22 gene (PTPN22) is associated with Type 1 diabetes in a Chinese population. Diabet Med 2014; 31:219-26. [PMID: 24117662 DOI: 10.1111/dme.12331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/09/2013] [Accepted: 09/19/2013] [Indexed: 11/29/2022]
Abstract
AIMS To examine single nucleotide polymorphisms in the protein tyrosine phosphatase N22 gene (PTPN22) and to study their association with Type 1 diabetes in a Chinese cohort. METHODS Three hundred and sixty-four young patients with Type 1 diabetes and 719 healthy children were included in this case-controlled study. The genotypes of rs1217385, rs2488457 (-1123C>G), rs1217414, rs1217419, rs3765598 and rs2476601 (1858C>T) in the PTPN22 gene were determined using the SNaPshot method. Alleles, genotypes and haplotype frequencies were compared between patients with Type 1 diabetes and healthy control subjects. The association between single nucleotide polymorphisms and clinical traits/autoantibody status was also analysed. RESULTS The single nucleotide polymorphism, rs1217419, located in the second intron of the PTPN22 gene was associated with Type 1 diabetes (odds ratio 1.5, 95% CI 1.14-1.97, P = 0.003). An additional single nucleotide polymorphism, rs1217385, was also associated with Type 1 diabetes; however, the association was secondary to that of rs1217419. The previously reported single nucleotide polymorphism that is associated with Type 1 diabetes (-1123G>C) had only marginal association with Type 1 diabetes in our study. A marginal association was also identified between -1123G>C and glutamic acid decarboxylase autoantibody positivity in patients with Type 1 diabetes. There was no association between the single nucleotide polymorphism 1858C>T and Type 1 diabetes in our studied cohort. CONCLUSIONS Our study confirmed that PTPN22 is a gene that contributes to Type 1 diabetes susceptibility. The primary association occurs with single nucleotide polymorphism rs1217419 and there is clear heterogeneity of the association between PTPTN22 polymorphisms and Type 1 diabetes in a Chinese population compared with other populations.
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Affiliation(s)
- Z Pei
- Department of Pediatric Endocrinology and Inborn Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
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11
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Lempainen J, Härkönen T, Laine A, Knip M, Ilonen J. Associations of polymorphisms in non-HLA loci with autoantibodies at the diagnosis of type 1 diabetes: INS and IKZF4 associate with insulin autoantibodies. Pediatr Diabetes 2013; 14:490-6. [PMID: 23721563 DOI: 10.1111/pedi.12046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/17/2013] [Accepted: 04/04/2013] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE More than 50 loci outside the human leukocyte antigen (HLA) region have been confirmed to affect type 1 diabetes (T1D) risk but their effect on β-cell autoimmunity is poorly defined. We analyzed the association of 35 single nucleotide polymorphism (SNP) markers previously associated with T1D with the presence of disease-predictive autoantibodies at the time of T1D diagnosis. SUBJECTS AND METHODS The study cohort comprised 1554 children diagnosed with T1D before the age of 15 yr. The associations between various genotypes and positivity for antibodies against islet cells [islet cell antibodies (ICA)], insulin [insulin autoantibodies (IAA)], glutamic acid decarboxylase (GADA), islet antigen 2 (IA2A), and zinc transporter 8 (ZnT8A) were analyzed. RESULTS INS gene polymorphism rs689 and IKZF4 polymorphism (rs1701704) were strongly associated with IAA positivity at the time of T1D diagnosis (p = 0.000004 and 0.00044, respectively). The presence of the T1D-risk conferring INS AA genotype was associated with IAA. In contrast, the presence of the susceptible C allele of the IKZF4 marker was inversely associated with IAA. The INS and IKZF4 polymorphisms were not significantly associated with ICA, GADA, IA2A, or ZnT8A positivity. CONCLUSIONS Both INS and IKZF4 polymorphisms modified the probability of IAA positivity at time of T1D onset but the inverse association of IKZF4 risk allele with IAA suggests that the IKZF4 polymorphism is involved in a pathway of β-cell autoimmunity alternate to the route characterized by IAA and development of T1D in early childhood. The IKZF4 gene encodes Eos, which is implicated to play an important role in Treg programming where this gene might exert its influence on T1D risk.
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Affiliation(s)
- J Lempainen
- Immunogenetics Laboratory, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, University of Turku, Turku, Finland
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12
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Laine AP, Knip M, Ilonen J. Transmission disequilibrium analysis of 31 type 1 diabetes susceptibility loci in Finnish families. ACTA ACUST UNITED AC 2013; 82:35-42. [DOI: 10.1111/tan.12143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/23/2013] [Accepted: 05/17/2013] [Indexed: 01/13/2023]
Affiliation(s)
- A. P. Laine
- Immunogenetics Laboratory; University of Turku; Turku; Finland
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13
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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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14
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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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15
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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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16
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Liu J, Chen M, Li R, Yang F, Shi X, Zhu L, Wang HM, Yao W, Liu Q, Meng FG, Sun JP, Pang Q, Yu X. Biochemical and functional studies of lymphoid-specific tyrosine phosphatase (Lyp) variants S201F and R266W. PLoS One 2012; 7:e43631. [PMID: 22952725 PMCID: PMC3428364 DOI: 10.1371/journal.pone.0043631] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 07/23/2012] [Indexed: 11/21/2022] Open
Abstract
The Lymphoid specific tyrosine phosphatase (Lyp) has elicited tremendous research interest due to the high risk of its missense mutation R620W in a wide spectrum of autoimmune diseases. While initially characterized as a gain-of-function mutant, R620W was thought to lead to autoimmune diseases through loss-of-function in T cell signaling by a recent study. Here we investigate the biochemical characters and T cell signaling functions of two uncharacterized Lyp variants S201F and R266W, together with a previously characterized Lyp variant R263Q, which had reduced risk in several autoimmune diseases, including systemic lupus erythematosus (SLE), ulcerative colitis (UC) and rheumatoid arthritis (RA). Our kinetic and functional studies of R263Q polymorphism basically reproduced previous findings that it was a loss-of-function mutant. The other variant S201F reduced Lyp phosphatase activity moderately and decreased Lyp function in T cell slightly, while R266W severely impaired phosphatase activity and was a loss-of-function variant in T cell signaling. A combined kinetic and structure analysis suggests that the R266W variant may decrease its phosphatase activity through perturbing either the Q-loop or the WPD loop of Lyp. As both R266W and R263Q significantly change their phosphatase activity and T cell functions, future work could be considered to evaluate these mutants in a broader spectrum of autoimmune diseases.
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Affiliation(s)
- Jing Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Ming Chen
- The 309 Hospital of PLA, Beijing, China
| | - Rong Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan Yang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Xuanren Shi
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Lichao Zhu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Hong-Mei Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Wei Yao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan-Guo Meng
- Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Jin-Peng Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Qi Pang
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- * E-mail: (XY); (QP)
| | - Xiao Yu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- * E-mail: (XY); (QP)
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17
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Gabbay MAL, Sato MN, Duarte AJS, Dib SA. Serum titres of anti-glutamic acid decarboxylase-65 and anti-IA-2 autoantibodies are associated with different immunoregulatory milieu in newly diagnosed type 1 diabetes patients. Clin Exp Immunol 2012; 168:60-7. [PMID: 22385239 DOI: 10.1111/j.1365-2249.2011.04538.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Several studies correlated genetic background and pancreatic islet-cell autoantibody status (type and number) in type 1A diabetes mellitus (T1AD), but there are no data evaluating the relationship among these markers with serum cytokines, regulatory T cells and β cell function. This characterization has a potential importance with regard to T1AD patients' stratification and follow-up in therapeutic prevention. In this study we showed that peripheral sera cytokines [interleukin (IL)-12, IL-6, II-1β, tumour necrosis factor (TNF)-α, IL-10] and chemokines (CXCL10, CXCL8, CXCL9, CCL2) measured were significantly higher in newly diagnosed T1AD patients when compared to healthy controls (P < 0·001). Among T1AD, we found a positive correlation between CXCL10 and CCL-2 (r = 0·80; P = 0·000), IL-8 and TNF-α (r = 0·60; P = 0·000); IL-8 and IL-12 (r = 0·57; P = 0·001) and TNF-α and IL-12 (r = 0·93; P = 0·000). Glutamic acid decarboxylase-65 (GAD-65) autoantibodies (GADA) were associated negatively with CXCL10 (r = -0·45; P = 0·011) and CCL2 (r = -0·65; P = 0·000), while IA-2A showed a negative correlation with IL-10 (r = -0·38; P = 0·027). Human leucocyte antigen (HLA) DR3, DR4 or DR3/DR4 and PTPN22 polymorphism did not show any association with pancreatic islet cell antibodies or cytokines studied. In summary, our results revealed that T1AD have a proinflammatory cytokine profile compared to healthy controls and that IA-2A sera titres seem to be associated with a more inflammatory peripheral cytokine/chemokine profile than GADA. A confirmation of these data in the pre-T1AD phase could help to explain the mechanistic of the well-known role of IA-2A as a more specific marker of beta-cell damage than GADA during the natural history of T1AD.
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Affiliation(s)
- M Andrade Lima Gabbay
- Diabetes Center, Endocrinology Division, Department of Medicine, Federal University of São Paulo-Immunology Laboratory, Rua Pedro de Toledo 781/12, São Paulo, SP, Brazil.
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Lin WY, Lee WC. Improving power of genome-wide association studies with weighted false discovery rate control and prioritized subset analysis. PLoS One 2012; 7:e33716. [PMID: 22496761 PMCID: PMC3322139 DOI: 10.1371/journal.pone.0033716] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/16/2012] [Indexed: 02/06/2023] Open
Abstract
The issue of large-scale testing has caught much attention with the advent of high-throughput technologies. In genomic studies, researchers are often confronted with a large number of tests. To make simultaneous inference for the many tests, the false discovery rate (FDR) control provides a practical balance between the number of true positives and the number of false positives. However, when few hypotheses are truly non-null, controlling the FDR may not provide additional advantages over controlling the family-wise error rate (e.g., the Bonferroni correction). To facilitate discoveries from a study, weighting tests according to prior information is a promising strategy. A 'weighted FDR control' (WEI) and a 'prioritized subset analysis' (PSA) have caught much attention. In this work, we compare the two weighting schemes with systematic simulation studies and demonstrate their use with a genome-wide association study (GWAS) on type 1 diabetes provided by the Wellcome Trust Case Control Consortium. The PSA and the WEI both can increase power when the prior is informative. With accurate and precise prioritization, the PSA can especially create substantial power improvements over the commonly-used whole-genome single-step FDR adjustment (i.e., the traditional un-weighted FDR control). When the prior is uninformative (true disease susceptibility regions are not prioritized), the power loss of the PSA and the WEI is almost negligible. However, a caution is that the overall FDR of the PSA can be slightly inflated if the prioritization is not accurate and precise. Our study highlights the merits of using information from mounting genetic studies, and provides insights to choose an appropriate weighting scheme to FDR control on GWAS.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
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19
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Zhi D, Sun C, Sedimbi SK, Luo F, Shen S, Sanjeevi CB. Killer cell immunoglobulin-like receptor along with HLA-C ligand genes are associated with type 1 diabetes in Chinese Han population. Diabetes Metab Res Rev 2011; 27:872-7. [PMID: 22069276 DOI: 10.1002/dmrr.1264] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Killer cell immunoglobulin-like receptor (KIR) genes and their putative ligands human leukocyte antigen (HLA)-C genes have been associated with type 1 diabetes (T1D). We hypothesize that KIR genes and their ligands HLA-C genes are important in T1D aetiology. RESEARCH DESIGN AND METHODS KIR and HLA-C ligand genotyping was performed in 259 T1D patients and 262 healthy children. RESULTS No significant difference was observed in the distribution of KIR genes between T1D patients and healthy controls. However, frequency of HLA-C1 gene and HLA-C2 gene (marginal association) was higher in patient group. The combinations 2DL2-/HLA-C1+; 2DL3+/HLA-C1+; 2DS2-/HLAC1+ were positively associated with T1D. The combinations 2DL1+/HLA-C2-; 2DL2-/HLA-C1-; 2DL3+/HLA-C1-; 2DS2-/HLAC1- were found to be negatively associated with T1D. Among the genes we tested, a combination of HLA-C1 and -C2 conferred the strongest association with T1D and the strength of this association was higher than that of HLA-C1 alone. The frequencies of KIR 2DL1, 2DL2 and 2DL3 and HLA-C1 were higher in T1D patients positive for GAD65 autoantibody; frequency of KIR 2DS4 is higher in T1D patients positive for IA-2 autoantibody. The association between KIR/HLA-C gene and autoantibody status was not statistically significant after applying Bonferroni correction. CONCLUSION In our study of a Han population (East China), we found no direct association of KIR genes with T1D. However, a combination of HLA-C1 and -C2 showed a positive association with T1D. Different combinations of HLA-C and KIR showed positive and negative association with T1D.
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Affiliation(s)
- Dijing Zhi
- Department of Pediatric, Endocrinology and Inherited Metabolic Disease, Children's Hospital of Fudan University, Shanghai, China
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20
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Papadopoulou A, Lynch KF, Shaat N, Håkansson R, Ivarsson SA, Berntorp K, Agardh CD, Lernmark Å. Gestational diabetes mellitus is associated with TCF7L2 gene polymorphisms independent of HLA-DQB1*0602 genotypes and islet cell autoantibodies. Diabet Med 2011; 28:1018-27. [PMID: 21672010 PMCID: PMC3170100 DOI: 10.1111/j.1464-5491.2011.03359.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AIMS To test whether the TCF7L2 gene was associated with gestational diabetes, whether the association between TCF7L2 and gestational diabetes was independent of HLA-DQB1*0602 and islet cell autoantibodies, as well as maternal age, number of pregnancies, family history of diabetes and the HLA-DQB1 genotypes, and to test whether the distribution of HLA-DQB1 alleles was affected by country of birth. METHODS We genotyped the rs7903146, rs12255372 and rs7901695 single nucleotide polymorphisms of the TCF7L2 gene in 826 mothers with gestational diabetes and in 1185 healthy control subjects in the Diabetes Prediction in Skåne Study. The mothers were also typed for HLA-DQB1 genotypes and tested for islet cell autoantibodies against GAD65, insulinoma-associated antigen-2 and insulin. RESULTS The heterozygous genotypes CT, GT and TC of the rs7903146 (T is risk for Type 2 diabetes), rs12255372 (T is risk for Type 2 diabetes) and rs7901695 (C is risk for Type 2 diabetes), respectively, as well as the homozygous genotypes TT, TT and CC of the rs7903146, rs12255372 and rs7901695, respectively, were strongly associated with gestational diabetes (P < 0.0001). These associations remained statistically significant after adjusting for maternal age, number of pregnancies, family history of diabetes and HLA-DQ genotypes and were independent of the presence of islet cell autoantibodies. No interaction was observed between TCF7L2 and HLA-DQB1*0602, which was shown to be negatively associated with gestational diabetes in mothers born in Sweden (P = 0.010). CONCLUSIONS The TCF7L2 was associated with susceptibility for gestational diabetes independently of the presence of HLA-DQB1*0602 and islet cell autoantibodies and other factors such as maternal age, number of pregnancies, family history of diabetes and other HLA-DQ genotypes. The HLA-DQB1*0602 was negatively associated with gestational diabetes in mothers born in Sweden.
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Affiliation(s)
- A Papadopoulou
- Department of Clinical Sciences, Lund University, Malmö, Sweden.
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21
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Plagnol V, Howson JMM, Smyth DJ, Walker N, Hafler JP, Wallace C, Stevens H, Jackson L, Simmonds MJ, Bingley PJ, Gough SC, Todd JA. Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. PLoS Genet 2011; 7:e1002216. [PMID: 21829393 PMCID: PMC3150451 DOI: 10.1371/journal.pgen.1002216] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 06/17/2011] [Indexed: 02/06/2023] Open
Abstract
The genetic basis of autoantibody production is largely unknown outside of associations located in the major histocompatibility complex (MHC) human leukocyte antigen (HLA) region. The aim of this study is the discovery of new genetic associations with autoantibody positivity using genome-wide association scan single nucleotide polymorphism (SNP) data in type 1 diabetes (T1D) patients with autoantibody measurements. We measured two anti-islet autoantibodies, glutamate decarboxylase (GADA, n = 2,506), insulinoma-associated antigen 2 (IA-2A, n = 2,498), antibodies to the autoimmune thyroid (Graves') disease (AITD) autoantigen thyroid peroxidase (TPOA, n = 8,300), and antibodies against gastric parietal cells (PCA, n = 4,328) that are associated with autoimmune gastritis. Two loci passed a stringent genome-wide significance level (p<10−10): 1q23/FCRL3 with IA-2A and 9q34/ABO with PCA. Eleven of 52 non-MHC T1D loci showed evidence of association with at least one autoantibody at a false discovery rate of 16%: 16p11/IL27-IA-2A, 2q24/IFIH1-IA-2A and PCA, 2q32/STAT4-TPOA, 10p15/IL2RA-GADA, 6q15/BACH2-TPOA, 21q22/UBASH3A-TPOA, 1p13/PTPN22-TPOA, 2q33/CTLA4-TPOA, 4q27/IL2/TPOA, 15q14/RASGRP1/TPOA, and 12q24/SH2B3-GADA and TPOA. Analysis of the TPOA-associated loci in 2,477 cases with Graves' disease identified two new AITD loci (BACH2 and UBASH3A). Autoantibodies are important markers for autoimmune diseases such as type 1 diabetes and Graves' disease. However, little is known about the genetic factors that control their production. To improve our understanding of this genetic basis, we measured four autoantibodies in a collection of up to 8,300 type 1 diabetes cases plasma samples. We combined these measurements with genome-wide genotype data to conduct four independent genome-wide association studies. Two loci showed unequivocal evidence of autoantibody association: the FCRL3 locus and the ABO blood group locus. Variants in the FCRL3 gene have been previously associated with autoimmune diseases, but such associations have not been reported for ABO blood group genotypes. In addition, we found extensive overlap between type 1 diabetes and autoantibody loci, and these findings provide new information about the role of these risk variants. Lastly, we hypothesized that loci associated with thyroid autoantibodies are strong candidates for association with thyroid autoimmune disorders. We confirmed this hypothesis by genotyping these variants in an independent cohort of Graves' disease cases, and we found evidence for two new Graves' disease loci.
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Affiliation(s)
- Vincent Plagnol
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (VP); (JAT)
| | - Joanna M. M. Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Neil Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jason P. Hafler
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Chris Wallace
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Helen Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Laura Jackson
- University Hospitals Birmingham, Birmingham, United Kingdom
| | - Matthew J. Simmonds
- The Oxford Centre for Diabetes, Endocrinology, and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
| | | | - Polly J. Bingley
- School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Stephen C. Gough
- The Oxford Centre for Diabetes, Endocrinology, and Metabolism, Churchill Hospital, Headington, Oxford, United Kingdom
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (VP); (JAT)
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Crow MK. Type I interferon in organ-targeted autoimmune and inflammatory diseases. Arthritis Res Ther 2010; 12 Suppl 1:S5. [PMID: 21303493 PMCID: PMC2991778 DOI: 10.1186/ar2886] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A significant role for IFNα in the pathogenesis of systemic lupus erythematosus is well supported, and clinical trials of anti-IFNα monoclonal antibodies are in progress in this disease. In other autoimmune diseases characterized by substantial inflammation and tissue destruction, the role of type I interferons is less clear. Gene expression analysis of peripheral blood cells from patients with rheumatoid arthritis and multiple sclerosis demonstrate an interferon signature similar to but less intense than that seen in patients with lupus. In both of those diseases, presence of the interferon signature has been associated with more significant clinical manifestations. At the same time, evidence supports an anti-inflammatory and beneficial role of IFNβ locally in the joints of patients with rheumatoid arthritis and in murine arthritis models, and many patients with multiple sclerosis show a clinical response to recombinant IFNβ. As can also be proposed for type I diabetes mellitus, type I interferon appears to contribute to the development of autoimmunity and disease progression in multiple autoimmune diseases, while maintaining some capacity to control established disease - particularly at local sites of inflammation. Recent studies in both rheumatoid arthritis and multiple sclerosis suggest that quantification of type I interferon activity or target gene expression might be informative in predicting responses to distinct classes of therapeutic agents.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, Weill Cornell Medical College, 535 East 70th Street, New York, NY 10021, USA.
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