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Huang HYR, Wireko AA, Miteu GD, Khan A, Roy S, Ferreira T, Garg T, Aji N, Haroon F, Zakariya F, Alshareefy Y, Pujari AG, Madani D, Papadakis M. Advancements and progress in juvenile idiopathic arthritis: A Review of pathophysiology and treatment. Medicine (Baltimore) 2024; 103:e37567. [PMID: 38552102 PMCID: PMC10977530 DOI: 10.1097/md.0000000000037567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Juvenile idiopathic arthritis (JIA) is a chronic clinical condition characterized by arthritic features in children under the age of 16, with at least 6 weeks of active symptoms. The etiology of JIA remains unknown, and it is associated with prolonged synovial inflammation and structural joint damage influenced by environmental and genetic factors. This review aims to enhance the understanding of JIA by comprehensively analyzing relevant literature. The focus lies on current diagnostic and therapeutic approaches and investigations into the pathoaetiologies using diverse research modalities, including in vivo animal models and large-scale genome-wide studies. We aim to elucidate the multifactorial nature of JIA with a strong focus towards genetic predilection, while proposing potential strategies to improve therapeutic outcomes and enhance diagnostic risk stratification in light of recent advancements. This review underscores the need for further research due to the idiopathic nature of JIA, its heterogeneous phenotype, and the challenges associated with biomarkers and diagnostic criteria. Ultimately, this contribution seeks to advance the knowledge and promote effective management strategies in JIA.
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Affiliation(s)
- Helen Ye Rim Huang
- Faculty of Medicine and Health Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Goshen David Miteu
- School of Biosciences, Biotechnology, University of Nottingham, Nottingham, UK
- Department of Biochemistry, Caleb University Lagos, Lagos, Nigeria
| | - Adan Khan
- Kent and Medway Medical School, Canterbury, Kent, UK
| | - Sakshi Roy
- School of Medicine, Queen’s University Belfast, Belfast, Northern Ireland, UK
| | - Tomas Ferreira
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Tulika Garg
- Government Medical College and Hospital Chandigarh, Chandigarh, India
| | - Narjiss Aji
- Faculty of Medicine and Pharmacy of Rabat, Rabat, Morocco
| | - Faaraea Haroon
- Faculty of Public Health, Health Services Academy, Islamabad, Pakistan
| | - Farida Zakariya
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Yasir Alshareefy
- School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Anushka Gurunath Pujari
- Faculty of Medicine and Health Science, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Kinesiology, Faculty of Science, McMaster University, Hamilton, Ontario, Canada
| | - Djabir Madani
- UCD Lochlann Quinn School of Business and Sutherland School of Law, University College Dublin, Dublin, Ireland
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Wuppertal, Germany
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Pang H, Lin J, Luo S, Huang G, Li X, Xie Z, Zhou Z. The missing heritability in type 1 diabetes. Diabetes Obes Metab 2022; 24:1901-1911. [PMID: 35603907 PMCID: PMC9545639 DOI: 10.1111/dom.14777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022]
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disease characterized by an absolute deficiency of insulin. It affects more than 20 million people worldwide and imposes an enormous financial burden on patients. The underlying pathogenic mechanisms of T1D are still obscure, but it is widely accepted that both genetics and the environment play an important role in its onset and development. Previous studies have identified more than 60 susceptible loci associated with T1D, explaining approximately 80%-85% of the heritability. However, most identified variants confer only small increases in risk, which restricts their potential clinical application. In addition, there is still a so-called 'missing heritability' phenomenon. While the gap between known heritability and true heritability in T1D is small compared with that in other complex traits and disorders, further elucidation of T1D genetics has the potential to bring novel insights into its aetiology and provide new therapeutic targets. Many hypotheses have been proposed to explain the missing heritability, including variants remaining to be found (variants with small effect sizes, rare variants and structural variants) and interactions (gene-gene and gene-environment interactions; e.g. epigenetic effects). In the following review, we introduce the possible sources of missing heritability and discuss the existing related knowledge in the context of T1D.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
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Lim CK, Bronson PG, Varade J, Behrens TW, Hammarström L. STXBP6 and B3GNT6 Genes are Associated With Selective IgA Deficiency. Front Genet 2022; 12:736235. [PMID: 34976003 PMCID: PMC8718598 DOI: 10.3389/fgene.2021.736235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Immunoglobulin A Deficiency (IgAD) is a polygenic primary immune deficiency, with a strong genetic association to the human leukocyte antigen (HLA) region. Previous genome-wide association studies (GWAS) have identified five non-HLA risk loci (IFIH1, PVT1, ATG13-AMBRA1, AHI1 and CLEC16A). In this study, we investigated the genetic interactions between different HLA susceptibility haplotypes and non-MHC genes in IgAD. To do this, we stratified IgAD subjects and healthy controls based on HLA haplotypes (N = 10,993), and then performed GWAS to identify novel genetic regions contributing to IgAD susceptibility. After replicating previously published HLA risk haplotypes, we compared individuals carrying at least one HLA risk allele (HLA-B*08:01-DRB1*03:01-DQB1*02:01 or HLA-DRB1*07:01-DQB1*02:02 or HLA-DRB1*01-DQB1*05:01) with individuals lacking an HLA risk allele. Subsequently, we stratified subjects based on the susceptibility alleles/haplotypes and performed gene-based association analysis using 572,856 SNPs and 24,125 genes. A significant genome-wide association in STXBP6 (rs4097492; p = 7.63 × 10-9) was observed in the cohort carrying at least one MHC risk allele. We also identified a significant gene-based association for B3GNT6 (P Gene = 2.1 × 10-6) in patients not carrying known HLA susceptibility alleles. Our findings indicate that the etiology of IgAD differs depending on the genetic background of HLA susceptibility haplotypes.
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Affiliation(s)
- Che Kang Lim
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University, Hospital Huddinge, Stockholm, Sweden.,Department Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Paola G Bronson
- RED OMNI Human Genetics, Genentech, South San Francisco, CA, United States
| | - Jezabel Varade
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University, Hospital Huddinge, Stockholm, Sweden.,Biomedical Research Center (CINBIO) Singular Research Center, University of Vigo, Vigo, Spain
| | | | - Lennart Hammarström
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University, Hospital Huddinge, Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,BGI-Shenzhen, Shenzhen, China
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Abou El Ella SS, Tawfik MA, Mohammed ZS, Barseem NF. PTPN22 gene and IL2RA rs11594656, rs2104286 gene variants: additional insights of polygenic single-nucleotide polymorphisms’ pattern among Egyptian children with type 1 diabetes. EGYPTIAN PEDIATRIC ASSOCIATION GAZETTE 2021. [DOI: 10.1186/s43054-021-00079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Type 1 diabetes mellitus (T1D) results from environmental and genetic factors.
We aimed to investigate the distribution of PTPN22, IL2RA rs11594656, and rs2104286 variants and its association with T1D in children.
A case-control study conducted on 100 diabetic patients and 100 control children. PTPN22 gene, IL2RA rs11594656, and rs2104286 polymorphisms study were done by PCR followed by restriction fragment length polymorphism (RFLP) assay.
Results
T allele of PTPN22 gene was presented more frequently 47% in patient group versus 30% in controls, while C allele was 53% in the diabetic group versus 70% in controls showing a statistically significant difference between patient and control groups. Similarly, TT 1858 genotype was found in higher frequency with a statistically significant difference in favor of T1D patients (p = 0.038), OR (CI 95% 3.16 (1.28–7.09).
For IL2RA rs11594656 polymorphism, the frequency of TT, TA, and AA in patients at percentages of 20%, 60%, and 20% versus 4%, 60%, and 36% in controls respectively showed significant difference (p = 0.045). Also, T allele was detected more in patients group as evidenced by p = 0.059, OR (95% CI) of 2.38(1.49–6.12). Whereas, IL2RA rs2104286 polymorphism revealed a difference of otherwise non-statistical significance (p = 0.091). Those who harbored homozygous pattern of both IL2RA polymorphisms frequently had DKA and high mean HbA1C values.
Conclusion
PTPN22 (C1858T) and IL2RA rs11594656 polymorphisms increased the risk of T1DM development, while IL2RA rs2104286 polymorphism did not display any significant association among children with T1D. Having more than one risk allele could affect progression and control of T1D.
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Guo X. JS-MA: A Jensen-Shannon Divergence Based Method for Mapping Genome-Wide Associations on Multiple Diseases. Front Genet 2020; 11:507038. [PMID: 33193597 PMCID: PMC7662082 DOI: 10.3389/fgene.2020.507038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Taking advantage of the high-throughput genotyping technology of Single Nucleotide Polymorphism (SNP), Genome-Wide Association Studies (GWASs) have been successfully implemented for defining the relative role of genes and the environment in disease risk, assisting in enabling preventative and precision medicine. However, current multi-locus-based methods are insufficient in terms of computational cost and discrimination power to detect statistically significant interactions with different genetic effects on multifarious diseases. Statistical tests for multi-locus interactions (≥2 SNPs) raise huge analytical challenges because computational cost increases exponentially as the growth of the cardinality of SNPs in an interaction module. In this paper, we develop a simple, fast, and powerful method, named JS-MA, based on Jensen-Shannon divergence and agglomerative hierarchical clustering, to detect the genome-wide multi-locus interactions associated with multiple diseases. From the systematical simulation, JS-MA is more powerful and efficient compared with the state-of-the-art association mapping tools. JS-MA was applied to the real GWAS datasets for two common diseases, i.e., Rheumatoid Arthritis and Type 1 Diabetes. The results showed that JS-MA not only confirmed recently reported, biologically meaningful associations, but also identified novel multi-locus interactions. Therefore, we believe that JS-MA is suitable and efficient for a full-scale analysis of multi-disease-related interactions in the large GWASs.
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Affiliation(s)
- Xuan Guo
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, United States
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Kraus AU, Penna-Martinez M, Shoghi F, Seidl C, Meyer G, Badenhoop K. HLA-DQB1 Position 57 Defines Susceptibility to Isolated and Polyglandular Autoimmunity in Adults: Interaction With Gender. J Clin Endocrinol Metab 2019; 104:1907-1916. [PMID: 30590628 DOI: 10.1210/jc.2018-01621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/18/2018] [Indexed: 02/05/2023]
Abstract
CONTEXT Autoimmune endocrinopathies result from environmental triggers on the genetic background of risk alleles, especially HLA-DR and HLA-DQ with alanine (Ala) in HLA-DQB1 position 57 (Ala57), whereas amino acid Asp57 is protective. OBJECTIVES Differentiate the effects of HLA-DQB1 amino acid variants at position 57 in adult patients with isolated endocrinopathies and autoimmune polyglandular syndrome type 2 (APS-2) compared with healthy controls in relation to gender. SETTING University Hospital Frankfurt, Frankfurt, Germany. PARTICIPANTS Two hundred seventy-eight patients with APS-2 and 1373 patients with isolated endocrinopathies: [type 1 diabetes (T1D), n = 867], Addison disease (AD, n = 185), autoimmune thyroiditis (AIT, n = 321) and 526 healthy controls. RESULTS Homozygous HLA-DQB1 Ala57 was more frequent in polyglandular T1D/AIT (OR 11.7, Pc = 3 × 10-7) and AD/AIT (OR 4.0, Pc = 3 × 10-7), as well as in isolated T1D (OR 9.7, Pc = 3 × 10-7) and AD (OR 3.1, Pc = 3 × 10-7). Heterozygous HLA-DQB1 57 Ala/non-Ala was increased in women with isolated AD and polyglandular AD/AIT (both OR 1.7, Pc= 0.02) whereas the same amino acid variant was overrepresented in men with T1D compared with women (OR 1.6, Pc = 0.004). The amino acid Ala57 was more frequent (OR 2.0, Pc = 0.02) and the amino acid Asp57 was much more rare (OR 0.4, Pc = 0.007) in the APS-2 cohort T1D/AIT than in AD/AIT. CONCLUSION HLA-DQB1 confers strong susceptibility by Ala57 homozygosity and protection by non-Ala57, both in adult isolated and polyglandular diseases. Frequencies of HLA-DQB1 amino acids differentiate between APS-2 T1D/AIT and AD/AIT. HLA-DQB1 Ala57 heterozygous women are at increased risk for AD or AIT, whereas men were found to have an increased susceptibility for T1D.
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Affiliation(s)
- Anna U Kraus
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Frankfurt, Germany
| | - Marissa Penna-Martinez
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Frankfurt, Germany
| | - Firouzeh Shoghi
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Frankfurt, Germany
| | - Christian Seidl
- Institute of Transfusion Medicine and Immunohematology, Department of Transplantation Immunology and Immunogenetics, University Hospital Frankfurt, Frankfurt, Germany
| | - Gesine Meyer
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Frankfurt, Germany
| | - Klaus Badenhoop
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Frankfurt, Germany
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Lei ZX, Chen WJ, Liang JQ, Wang YJ, Jin L, Xu C, Kang XJ. The association between rs2476601 polymorphism in PTPN22 gene and risk of alopecia areata: A meta-analysis of case-control studies. Medicine (Baltimore) 2019; 98:e15448. [PMID: 31096440 PMCID: PMC6531179 DOI: 10.1097/md.0000000000015448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The single nucleotide polymorphism (SNP) rs2476601 of the protein tyrosine phosphatase, nonreceptor type 22 (PTPN22) gene has been presented to implicate in the pathogenesis of alopecia areata (AA) in a few association investigations with limited sample size and inconsistent conclusions. METHODS The aim of the current meta-analysis was to assess and synthesize the presently available data on the connection between rs2476601 and AA vulnerability. Six electronic databases, including EMBASE, PubMed, Web of Science, the Cochrane Library, Wanfang data, and the China National Knowledge Infrastructure database (CNKI), were systematically retrieved for relevant observational studies published previous to November 2018. Total odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were analyzed to evaluate the correlation between PTPN22 polymorphism and AA. Risk of bias was estimated according to the Newcastle-Ottawa Scale (NOS). Sensitivity analyses were carried out using the RevMan 5.3 software. RESULTS In general, 5 case-control studies including 1129 AA patients and 1702 healthy control individuals were obtained for this meta-analysis. The pooled results suggested that rs2476601 SNP was significantly associated with AA susceptibility under allelic model (C vs T, OR = 0.77, 95% CI, 0.64-0.92, P = .003) and recessive model (CC vs CT + TT, OR = 0.73, 95% CI, 0.60-0.88, P = .001). CONCLUSION On the basis of the results of the current research, the rs2476601 polymorphism of PTPN22 gene is significantly correlated with AA susceptibility. The C-allele and CC-genotype carriers at this locus have a lower risk of AA.
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Affiliation(s)
- Zi-Xian Lei
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
- Xinjiang Medical University, Urumqi, China
| | - Wen-Jing Chen
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
- Xinjiang Medical University, Urumqi, China
| | - Jun-Qin Liang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
| | - Yan-Jun Wang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
- Xinjiang Medical University, Urumqi, China
| | - Lan Jin
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
- Xinjiang Medical University, Urumqi, China
| | - Chen Xu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
- Xinjiang Medical University, Urumqi, China
| | - Xiao-Jing Kang
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang
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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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Haider MZ, Rasoul MA, Al-Mahdi M, Al-Kandari H, Dhaunsi GS. Association of protein tyrosine phosphatase non-receptor type 22 gene functional variant C1858T, HLA-DQ/DR genotypes and autoantibodies with susceptibility to type-1 diabetes mellitus in Kuwaiti Arabs. PLoS One 2018; 13:e0198652. [PMID: 29924845 PMCID: PMC6010291 DOI: 10.1371/journal.pone.0198652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/11/2018] [Indexed: 12/18/2022] Open
Abstract
The incidence of type-1 Diabetes Mellitus (T1DM) has increased steadily in Kuwait during recent years and it is now considered amongst the high-incidence countries. An interaction between susceptibility genes, immune system mediators and environmental factors predispose susceptible individuals to T1DM. We have determined the prevalence of protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene functional variant (C1858T; R620W, rs2476601), HLA-DQ and DR alleles and three autoantibodies in Kuwaiti children with T1DM to evaluate their impact on genetic predisposition of the disease. This study included 253 Kuwaiti children with T1DM and 214 ethnically matched controls. The genotypes of PTPN22 gene functional variant C1858T (R620W; rs2476601) were detected by PCR-RFLP method and confirmed by DNA sequencing. HLA-DQ and DR alleles were determined by sequence-specific PCR. Three autoantibodies were detected in the T1DM patients using radio-immunoassays. A significant association was detected between the variant genotype of the PTPN22 gene (C1858T, rs2476601) and T1DM in Kuwaiti Arabs. HLA-DQ2 and DQ8 alleles showed a strong association with T1DM. In T1DM patients which carried the variant TT-genotype of the PTPN22 gene, 93% had at least one DQ2 allele and 60% carried either a DQ2 or a DQ8 allele. Amongst the DR alleles, the DR3-DRB5, DR3-3, DR3-4 and DR4-4 showed a strong association with T1DM. Majority of T1DM patients who carried homozygous variant (TT) genotype of the PTPN22 gene had either DR3-DRB5 or DRB3-DRB4 genotypes. In T1DM patients who co-inherited the high risk HLA DQ, DR alleles with the variant genotype of PTPN22 gene, the majority were positive for three autoantibodies. Our data demonstrate that the variant T-allele of the PTPN22 gene along with HLA-DQ2 and DQ8 alleles constitute significant determinants of genetic predisposition of T1DM in Kuwaiti children.
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Affiliation(s)
- Mohammad Z. Haider
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Majedah A. Rasoul
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Department of Pediatrics, Adan Hospital, Al-Adan, Kuwait
| | - Maria Al-Mahdi
- Department of Pediatrics, Adan Hospital, Al-Adan, Kuwait
| | | | - Gursev S. Dhaunsi
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Medical Laboratories, Mubarak Al-Kabeer Hospital, Jabriya, Kuwait
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11
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Varade J, Wang N, Lim CK, Zhang T, Zhang Y, Liu X, Piehl F, Matell R, Cao H, Xu X, Hammarström L. Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis. J Autoimmun 2018; 88:43-49. [DOI: 10.1016/j.jaut.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 01/16/2023]
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Chen YG, Mathews CE, Driver JP. The Role of NOD Mice in Type 1 Diabetes Research: Lessons from the Past and Recommendations for the Future. Front Endocrinol (Lausanne) 2018; 9:51. [PMID: 29527189 PMCID: PMC5829040 DOI: 10.3389/fendo.2018.00051] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For more than 35 years, the NOD mouse has been the primary animal model for studying autoimmune diabetes. During this time, striking similarities to the human disease have been uncovered. In both species, unusual polymorphisms in a major histocompatibility complex (MHC) class II molecule confer the most disease risk, disease is caused by perturbations by the same genes or different genes in the same biological pathways and that diabetes onset is preceded by the presence of circulating autoreactive T cells and autoantibodies that recognize many of the same islet antigens. However, the relevance of the NOD model is frequently challenged due to past failures translating therapies from NOD mice to humans and because the appearance of insulitis in mice and some patients is different. Nevertheless, the NOD mouse remains a pillar of autoimmune diabetes research for its usefulness as a preclinical model and because it provides access to invasive procedures as well as tissues that are rarely procured from patients or controls. The current article is focused on approaches to improve the NOD mouse by addressing reasons why immune therapies have failed to translate from mice to humans. We also propose new strategies for mixing and editing the NOD genome to improve the model in ways that will better advance our understanding of human diabetes. As proof of concept, we report that diabetes is completely suppressed in a knock-in NOD strain with a serine to aspartic acid substitution at position 57 in the MHC class II Aβ. This supports that similar non-aspartic acid substitutions at residue 57 of variants of the human class II HLA-DQβ homolog confer diabetes risk.
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Affiliation(s)
- Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - John P. Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- *Correspondence: John P. Driver,
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A haplotypic variant at the IRGM locus and rs11747270 are related to the susceptibility for chronic periodontitis. Inflamm Res 2017; 67:129-138. [PMID: 28983640 DOI: 10.1007/s00011-017-1101-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE AND DESIGN Immunity-regulated GTPase M (IRGM) plays a critical role in the defense against intracellular bacteria by regulating autophagy formation. This direct genetic association study aimed to determine whether variants at the IRGM genetic locus are associated with chronic periodontitis. MATERIALS AND SUBJECTS Using PCR and melting curve analysis 390 periodontitis patients and 770 healthy controls have been genotyped regarding six polymorphisms in the IRGM gene (rs13361189, rs10065172, rs4958847, rs1000113, rs11747270, rs931058). RESULTS Frequency distribution of alleles and genotypes for the six polymorphisms were not significantly different between the periodontitis and the control group. Also following stratification according to gender and smoking no significant linkage was found for any of the IRGM variants with periodontitis. Analysis of a subsample of patients revealed a significant association for rs11747270 with severe periodontitis (p = 0.003). Pairwise linkage analysis revealed one block composed of rs13361189, rs10065172, rs4958847, rs1000113 and 11747270 with strong or even complete linkage disequilibrium (r 2 > 0.9). Four haplotypes showed a frequency of > 1%, among which the haplotype C-T-A-T-G was significantly associated with chronic periodontitis (p = 0.0051; OR 4.66, 95% CI 1.41-15.42). CONCLUSIONS One rare haplotype of the IRGM locus is significantly associated with chronic periodontitis in a German cohort.
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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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Mladkova N, Kiryluk K. Genetic Complexities of the HLA Region and Idiopathic Membranous Nephropathy. J Am Soc Nephrol 2017; 28:1331-1334. [PMID: 28396523 DOI: 10.1681/asn.2017030283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Nikol Mladkova
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
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Abbasi F, Soltani S, Saghazadeh A, Soltaninejad E, Rezaei A, Zare Bidoki A, Bahrami T, Amirzargar AA, Rezaei N. PTPN22 Single-Nucleotide Polymorphisms in Iranian Patients with Type 1 Diabetes Mellitus. Immunol Invest 2017; 46:409-418. [DOI: 10.1080/08820139.2017.1288239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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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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Abstract
Autophagy has broad functions in immunity, ranging from cell-autonomous defence to coordination of complex multicellular immune responses. The successful resolution of infection and avoidance of autoimmunity necessitates efficient and timely communication between autophagy and pathways that sense the immune environment. The recent literature indicates that a variety of immune mediators induce or repress autophagy. It is also becoming increasingly clear that immune signalling cascades are subject to regulation by autophagy, and that a return to homeostasis following a robust immune response is critically dependent on this pathway. Importantly, examples of non-canonical forms of autophagy in mediating immunity are pervasive. In this article, the progress in elucidating mechanisms of crosstalk between autophagy and inflammatory signalling cascades is reviewed. Improved mechanistic understanding of the autophagy machinery offers hope for treating infectious and inflammatory diseases.
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Affiliation(s)
- Ken Cadwell
- grid.137628.90000 0004 1936 8753and the Department of Microbiology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, 10016 New York USA
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19
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Verma MK, Sobha K. Understanding the major risk factors in the beginning and the progression of rheumatoid arthritis: current scenario and future prospects. Inflamm Res 2015; 64:647-59. [DOI: 10.1007/s00011-015-0843-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 12/19/2022] Open
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Abstract
BACKGROUND Many aspects of autoimmune disease are not well understood, including the specificities of autoimmune targets, and patterns of co-morbidity and cross-heritability across diseases. Prior work has provided evidence that somatic mutation caused by gene conversion and deletion at segmentally duplicated loci is relevant to several diseases. Simple tandem repeat (STR) sequence is highly mutable, both somatically and in the germ-line, and somatic STR mutations are observed under inflammation. RESULTS Protein-coding genes spanning STRs having markers of mutability, including germ-line variability, high total length, repeat count and/or repeat similarity, are evaluated in the context of autoimmunity. For the initiation of autoimmune disease, antigens whose autoantibodies are the first observed in a disease, termed primary autoantigens, are informative. Three primary autoantigens, thyroid peroxidase (TPO), phogrin (PTPRN2) and filaggrin (FLG), include STRs that are among the eleven longest STRs spanned by protein-coding genes. This association of primary autoantigens with long STR sequence is highly significant (p<3.0x10(-7)). Long STRs occur within twenty genes that are associated with sixteen common autoimmune diseases and atherosclerosis. The repeat within the TTC34 gene is an outlier in terms of length and a link with systemic lupus erythematosus is proposed. CONCLUSIONS The results support the hypothesis that many autoimmune diseases are triggered by immune responses to proteins whose DNA sequence mutates somatically in a coherent, consistent fashion. Other autoimmune diseases may be caused by coherent somatic mutations in immune cells. The coherent somatic mutation hypothesis has the potential to be a comprehensive explanation for the initiation of many autoimmune diseases.
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Affiliation(s)
- Kenneth Andrew Ross
- Department of Computer Science, Columbia University, New York, New York, United States of America
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21
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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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22
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Bottini N, Peterson EJ. Tyrosine phosphatase PTPN22: multifunctional regulator of immune signaling, development, and disease. Annu Rev Immunol 2013; 32:83-119. [PMID: 24364806 DOI: 10.1146/annurev-immunol-032713-120249] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inheritance of a coding variant of the protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene is associated with increased susceptibility to autoimmunity and infection. Efforts to elucidate the mechanisms by which the PTPN22-C1858T variant modulates disease risk revealed that PTPN22 performs a signaling function in multiple biochemical pathways and cell types. Capable of both enzymatic activity and adaptor functions, PTPN22 modulates signaling through antigen and innate immune receptors. PTPN22 plays roles in lymphocyte development and activation, establishment of tolerance, and innate immune cell-mediated host defense and immunoregulation. The disease-associated PTPN22-R620W variant protein is likely involved in multiple stages of the pathogenesis of autoimmunity. Establishment of a tolerant B cell repertoire is disrupted by PTPN22-R620W action during immature B cell selection, and PTPN22-R620W alters mature T cell responsiveness. However, after autoimmune attack has initiated tissue injury, PTPN22-R620W may foster inflammation through modulating the balance of myeloid cell-produced cytokines.
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Affiliation(s)
- Nunzio Bottini
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037;
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Evidence of stage- and age-related heterogeneity of non-HLA SNPs and risk of islet autoimmunity and type 1 diabetes: the diabetes autoimmunity study in the young. Clin Dev Immunol 2013; 2013:417657. [PMID: 24367383 PMCID: PMC3866813 DOI: 10.1155/2013/417657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/10/2013] [Accepted: 09/23/2013] [Indexed: 11/24/2022]
Abstract
Previously, we examined 20 non-HLA SNPs for association with islet autoimmunity (IA) and/or progression to type 1 diabetes (T1D). Our objective was to investigate fourteen additional non-HLA T1D candidate SNPs for stage- and age-related heterogeneity in the etiology of T1D. Of 1634 non-Hispanic white DAISY children genotyped, 132 developed IA (positive for GAD, insulin, or IA-2 autoantibodies at two or more consecutive visits); 50 IA positive children progressed to T1D. Cox regression was used to analyze risk of IA and progression to T1D in IA positive children. Restricted cubic splines were used to model SNPs when there was evidence that risk was not constant with age. C1QTNF6 (rs229541) predicted increased IA risk (HR: 1.57, CI: 1.20–2.05) but not progression to T1D (HR: 1.13, CI: 0.75–1.71). SNP (rs10517086) appears to exhibit an age-related effect on risk of IA, with increased risk before age 2 years (age 2 HR: 1.67, CI: 1.08–2.56) but not older ages (age 4 HR: 0.84, CI: 0.43–1.62). C1QTNF6 (rs229541), SNP (rs10517086), and UBASH3A (rs3788013) were associated with development of T1D. This prospective investigation of non-HLA T1D candidate loci shows that some SNPs may exhibit stage- and age-related heterogeneity in the etiology of T1D.
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Stankov K, Benc D, Draskovic D. Genetic and epigenetic factors in etiology of diabetes mellitus type 1. Pediatrics 2013; 132:1112-22. [PMID: 24190679 DOI: 10.1542/peds.2013-1652] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Diabetes mellitus type 1 (T1D) is a complex disease resulting from the interplay of genetic, epigenetic, and environmental factors. Recent progress in understanding the genetic basis of T1D has resulted in an increased recognition of childhood diabetes heterogeneity. After the initial success of family-based linkage analyses, which uncovered the strong linkage and association between HLA gene variants and T1D, genome-wide association studies performed with high-density single-nucleotide polymorphism genotyping platforms provided evidence for a number of novel loci, although fine mapping and characterization of these new regions remains to be performed. T1D is one of the most heritable common diseases, and among autoimmune diseases it has the largest range of concordance rates in monozygotic twins. This fact, coupled with evidence of various epigenetic modifications of gene expression, provides convincing proof of the complex interplay between genetic and environmental factors. In T1D, epigenetic phenomena, such as DNA methylation, histone modifications, and microRNA dysregulation, have been associated with altered gene expression. Increasing epidemiologic and experimental evidence supports the role of genetic and epigenetic alterations in the etiopathology of diabetes. We discuss recent results related to the role of genetic and epigenetic factors involved in development of T1D.
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Affiliation(s)
- Karmen Stankov
- Clinical Centre of Vojvodina, Medical Faculty, University of Novi Sad, Hajduk Veljkova 1, 21000 Novi Sad, Serbia.
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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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26
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Martínez-Pérez B, de la Torre-Díez I, López-Coronado M. Mobile health applications for the most prevalent conditions by the World Health Organization: review and analysis. J Med Internet Res 2013; 15:e120. [PMID: 23770578 PMCID: PMC3713954 DOI: 10.2196/jmir.2600] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/30/2013] [Accepted: 05/08/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND New possibilities for mHealth have arisen by means of the latest advances in mobile communications and technologies. With more than 1 billion smartphones and 100 million tablets around the world, these devices can be a valuable tool in health care management. Every aid for health care is welcome and necessary as shown by the more than 50 million estimated deaths caused by illnesses or health conditions in 2008. Some of these conditions have additional importance depending on their prevalence. OBJECTIVE To study the existing applications for mobile devices exclusively dedicated to the eight most prevalent health conditions by the latest update (2004) of the Global Burden of Disease (GBD) of the World Health Organization (WHO): iron-deficiency anemia, hearing loss, migraine, low vision, asthma, diabetes mellitus, osteoarthritis (OA), and unipolar depressive disorders. METHODS Two reviews have been carried out. The first one is a review of mobile applications in published articles retrieved from the following systems: IEEE Xplore, Scopus, ScienceDirect, Web of Knowledge, and PubMed. The second review is carried out by searching the most important commercial app stores: Google play, iTunes, BlackBerry World, Windows Phone Apps+Games, and Nokia's Ovi store. Finally, two applications for each condition, one for each review, were selected for an in-depth analysis. RESULTS Search queries up to April 2013 located 247 papers and more than 3673 apps related to the most prevalent conditions. The conditions in descending order by the number of applications found in literature are diabetes, asthma, depression, hearing loss, low vision, OA, anemia, and migraine. However when ordered by the number of commercial apps found, the list is diabetes, depression, migraine, asthma, low vision, hearing loss, OA, and anemia. Excluding OA from the former list, the four most prevalent conditions have fewer apps and research than the final four. Several results are extracted from the in-depth analysis: most of the apps are designed for monitoring, assisting, or informing about the condition. Typically an Internet connection is not required, and most of the apps are aimed for the general public and for nonclinical use. The preferred type of data visualization is text followed by charts and pictures. Assistive and monitoring apps are shown to be frequently used, whereas informative and educational apps are only occasionally used. CONCLUSIONS Distribution of work on mobile applications is not equal for the eight most prevalent conditions. Whereas some conditions such as diabetes and depression have an overwhelming number of apps and research, there is a lack of apps related to other conditions, such as anemia, hearing loss, or low vision, which must be filled.
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Affiliation(s)
- Borja Martínez-Pérez
- University of Valladolid, Department of Signal Theory and Communications, and Telematics Engineering., University of Valladolid, Valladolid, Spain.
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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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28
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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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Driver JP, Chen YG, Mathews CE. Comparative genetics: synergizing human and NOD mouse studies for identifying genetic causation of type 1 diabetes. Rev Diabet Stud 2012; 9:169-87. [PMID: 23804259 DOI: 10.1900/rds.2012.9.169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Although once widely anticipated to unlock how human type 1 diabetes (T1D) develops, extensive study of the nonobese diabetic (NOD) mouse has failed to yield effective treatments for patients with the disease. This has led many to question the usefulness of this animal model. While criticism about the differences between NOD and human T1D is legitimate, in many cases disease in both species results from perturbations modulated by the same genes or different genes that function within the same biological pathways. Like in humans, unusual polymorphisms within an MHC class II molecule contributes the most T1D risk in NOD mice. This insight supports the validity of this model and suggests the NOD has been improperly utilized to study how to cure or prevent disease in patients. Indeed, clinical trials are far from administering T1D therapeutics to humans at the same concentration ranges and pathological states that inhibit disease in NOD mice. Until these obstacles are overcome it is premature to label the NOD mouse a poor surrogate to test agents that cure or prevent T1D. An additional criticism of the NOD mouse is the past difficulty in identifying genes underlying T1D using conventional mapping studies. However, most of the few diabetogenic alleles identified to date appear relevant to the human disorder. This suggests that rather than abandoning genetic studies in NOD mice, future efforts should focus on improving the efficiency with which diabetes susceptibility genes are detected. The current review highlights why the NOD mouse remains a relevant and valuable tool to understand the genes and their interactions that promote autoimmune diabetes and therapeutics that inhibit this disease. It also describes a new range of technologies that will likely transform how the NOD mouse is used to uncover the genetic causes of T1D for years to come.
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Affiliation(s)
- John P Driver
- Department of Animal Science, University of Florida, Gainesville, FL 32610, USA
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Howson JMM, Cooper JD, Smyth DJ, Walker NM, Stevens H, She JX, Eisenbarth GS, Rewers M, Todd JA, Akolkar B, Concannon P, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Pociot F, Rich SS. Evidence of gene-gene interaction and age-at-diagnosis effects in type 1 diabetes. Diabetes 2012; 61:3012-7. [PMID: 22891215 PMCID: PMC3478521 DOI: 10.2337/db11-1694] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The common genetic loci that independently influence the risk of type 1 diabetes have largely been determined. Their interactions with age-at-diagnosis of type 1 diabetes, sex, or the major susceptibility locus, HLA class II, remain mostly unexplored. A large collection of more than 14,866 type 1 diabetes samples (6,750 British diabetic individuals and 8,116 affected family samples of European descent) were genotyped at 38 confirmed type 1 diabetes-associated non-HLA regions and used to test for interaction of association with age-at-diagnosis, sex, and HLA class II genotypes using regression models. The alleles that confer susceptibility to type 1 diabetes at interleukin-2 (IL-2), IL2/4q27 (rs2069763) and renalase, FAD-dependent amine oxidase (RNLS)/10q23.31 (rs10509540), were associated with a lower age-at-diagnosis (P = 4.6 × 10⁻⁶ and 2.5 × 10⁻⁵, respectively). For both loci, individuals carrying the susceptible homozygous genotype were, on average, 7.2 months younger at diagnosis than those carrying the protective homozygous genotypes. In addition to protein tyrosine phosphatase nonreceptor type 22 (PTPN22), evidence of statistical interaction between HLA class II genotypes and rs3087243 at cytotoxic T-lymphocyte antigen 4 (CTLA4)/2q33.2 was obtained (P = 7.90 × 10⁻⁵). No evidence of differential risk by sex was obtained at any loci (P ≥ 0.01). Statistical interaction effects can be detected in type 1 diabetes although they provide a relatively small contribution to our understanding of the familial clustering of the disease.
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Affiliation(s)
- Joanna M M Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Department of Medical Genetics, University of Cambridge, Cambridge, UK.
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Abstract
The immune system is tasked with defending the host from a wide array of pathogens and environmental insults. When uncontrolled, this endeavor may lead to off-target reactivity to self-tissues resulting in multiple autoimmune diseases including type 1 diabetes (T1D). This multifactorial disease process involves over 40 susceptibility genes and is influenced by poorly characterized environmental factors. While many questions regarding the pathogenesis of the disease process remain, it has become increasingly clear that the progression to disease results from a breakdown in the processes that maintain peripheral immune tolerance. The end result of this process is localized tissue inflammation, islet dysfunction, and ultimately the destruction of pancreatic β cells due to concomitant defects in innate and adaptive immune responses. A number of immunomodulatory intervention trials have now been conducted in patients at risk for or with recent onset T1D, often with the goal of restoring immune tolerance by inducing regulatory T cells (Tregs). Unfortunately, many of these trials have fallen short of inducing persistent immune regulation. This shortfall has led to additional efforts to more directly shift the balance from destructive effector T cell (Teff) responses to favor Tregs, including the use of autologous Treg cell therapy. In this review we will discuss key concepts related to the use of autologous Treg cell therapy for the treatment of T1D. Among these topics, we will discuss the notions of genetic control of Treg activity, Treg cellular plasticity, and requirements for antigen-specificity.
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Affiliation(s)
- James A Thompson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Espinoza JL, Takami A, Onizuka M, Morishima Y, Fukuda T, Kodera Y, Akiyama H, Miyamura K, Mori T, Nakao S. Recipient PTPN22 -1123 C/C genotype predicts acute graft-versus-host disease after HLA fully matched unrelated bone marrow transplantation for hematologic malignancies. Biol Blood Marrow Transplant 2012; 19:240-6. [PMID: 23025987 DOI: 10.1016/j.bbmt.2012.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/20/2012] [Indexed: 01/13/2023]
Abstract
PTPN22 is a critical negative regulator of T cell responses. Its promoter gene variant (rs2488457, -1123G>C) has been reported to be associated with autoimmune diseases. This study analyzed the impact of the PTPN22 variant on transplantation outcomes in a cohort of 663 patients who underwent unrelated HLA-matched bone marrow transplantation (BMT) for hematologic malignancies through the Japan Marrow Donor Program. The recipient C/C genotype versus the recipient G/G genotype resulted in a lower incidence of grade II-IV acute graft-versus-host disease (hazard ratio [HR], 0.50; 95% confidence interval [CI], 0.29-0.85; P = .01), as well as a higher incidence of relapse (HR, 1.78; 95% CI, 1.10-2.90; P = .02), as demonstrated on multivariate analysis. In patients with high-risk disease, the recipient C/C genotype was associated with significantly worse overall survival rates than the recipient G/G genotype (HR, 1.60; 95% CI, 1.02-2.51; P = .04), whereas this effect was absent in patients with standard-risk disease. In addition, the donor G/C genotype was associated with a lower incidence of relapse (HR, 0.58; 95% CI, 0.40-0.85), which did not influence survival. Our findings suggest that PTPN22 genotyping could be useful in predicting prognoses and creating therapeutic strategies for improving the final outcomes of allogeneic BMT.
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Affiliation(s)
- J Luis Espinoza
- Department of Hematology and Oncology, Kanazawa University Hospital, Kanazawa, Japan
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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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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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Lee HS, Kang J, Yang S, Kim D, Park Y. Susceptibility influence of a PTPN22 haplotype with thyroid autoimmunity in Koreans. Diabetes Metab Res Rev 2011; 27:878-82. [PMID: 22069277 DOI: 10.1002/dmrr.1265] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Considerable amount of evidences in the Caucasians have suggested the association of a missense single-nucleotide polymorphism (SNP) in the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene (rs2476601) with several autoimmune diseases including autoimmune thyroid diseases (AITD) and type 1 diabetes (T1D). As the SNP was reported to be non-polymorphic in Asians, we attempt to explore an association of PTPN22 without restricting to the rs2476601 with AITD or T1D in Korean population. METHODS We studied 389 T1D, 212 AITD (84 Graves' disease and 128 Hashimoto's thyroiditis) patients and 225 controls. In addition to the rs2476601, we selected five testing SNPs spanning 58 kb over the PTPN22 gene using the previous resequencing data and International HapMap Project. RESULTS We found that neither alleles, genotypes among all five SNPs, nor reconstructed haplotypes of five SNPs were associated with T1D. Interestingly, a minor allele of a SNP (rs12730735) and a haplotype (GGCTT) showed significant association with the susceptibility of AITD, especially with that of Hashimoto's thyroiditis (p<0.01). CONCLUSIONS These results indicate that the PTPN22 gene polymorphism independent of the SNP rs2476601 might be a supplementary risk factor to AITD, but not in T1D in Koreans, contradicting a major contributory influence of the PTPN22 gene in explaining common mechanism underlying multiple autoimmune diseases.
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Affiliation(s)
- Hye-Soon Lee
- Department of Internal Medicine and Bioengineering, Hanyang University College of Medicine and Engineering, and Hanyang University Hospital, Seoul, Korea
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36
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Polychronakos C, Li Q. Understanding type 1 diabetes through genetics: advances and prospects. Nat Rev Genet 2011; 12:781-92. [PMID: 22005987 DOI: 10.1038/nrg3069] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Starting with early crucial discoveries of the role of the major histocompatibility complex, genetic studies have long had a role in understanding the biology of type 1 diabetes (T1D), which is one of the most heritable common diseases. Recent genome-wide association studies (GWASs) have given us a clearer picture of the allelic architecture of genetic susceptibility to T1D. Fine mapping and functional studies are gradually revealing the complex mechanisms whereby immune self-tolerance is lost, involving multiple aspects of adaptive immunity. The triggering of these events by dysregulation of the innate immune system has also been implicated by genetic evidence. Finally, genetic prediction of T1D risk is showing promise of use for preventive strategies.
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Affiliation(s)
- Constantin Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Québec, Canada H3H 1P3. Constantin.
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Martín JE, Alizadeh BZ, González-Gay MA, Balsa A, Pascual-Salcedo D, González-Escribano MF, Rodriguez-Rodriguez L, Fernández-Gutiérrez B, Raya E, Coenen MJH, van Riel P, Radstake TRDJ, Kvien TK, Viken MK, Lie BA, Koeleman BPC, Martín J. Evidence for PTPN22 R620W polymorphism as the sole common risk variant for rheumatoid arthritis in the 1p13.2 region. J Rheumatol 2011; 38:2290-6. [PMID: 21965649 DOI: 10.3899/jrheum.110361] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The PTPN22 rs2476601 genetic variant has been associated with rheumatoid arthritis (RA) and other autoimmune diseases. Some reports suggest that this single-nucleotide polymorphism (SNP) may not be the only causal variant in the region of PTPN22. Our aim was to identify new independent RA-associated common gene variants in the PTPN22 region. METHODS We analyzed Wellcome Trust Case-Control Consortium genome-wide association study data for associations in the 397.2 kb PTPN22 region and selected 9 associated SNP (with p < 5 × 10(-3)) for replication and dependence analysis. The replication cohorts comprised 2857 patients with RA and 2994 controls from Spain, Netherlands, and Norway. RESULTS We found that 6 of the 9 selected SNP were associated in the Spanish cohort. Of these, 4 were also associated in the Dutch and Norwegian cohorts, and all 6 were associated with RA in the combined analysis. Conditional analyses showed that none of these associations was independent of rs2476601. CONCLUSION The SNP rs2476601 located in the PTPN22 gene is the sole common genetic variant associated with RA in the 1p13.2 region, suggesting that neighbor genes of PTPN22 do not have a major influence in RA.
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Affiliation(s)
- Jose-Ezequiel Martín
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Parque Tecnologico de Ciencias de la Salud, Granada, Spain.
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Wang N, Shen N, Vyse TJ, Anand V, Gunnarson I, Sturfelt G, Rantapää-Dahlqvist S, Elvin K, Truedsson L, Andersson BA, Dahle C, Örtqvist E, Gregersen PK, Behrens TW, Hammarström L. Selective IgA deficiency in autoimmune diseases. Mol Med 2011; 17:1383-96. [PMID: 21826374 PMCID: PMC3321806 DOI: 10.2119/molmed.2011.00195] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 12/12/2022] Open
Abstract
Selective immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in Caucasians. It has previously been suggested to be associated with a variety of concomitant autoimmune diseases. In this review, we present data on the prevalence of IgAD in patients with Graves disease (GD), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), celiac disease (CD), myasthenia gravis (MG) and rheumatoid arthritis (RA) on the basis of both our own recent large-scale screening results and literature data. Genetic factors are important for the development of both IgAD and various autoimmune disorders, including GD, SLE, T1D, CD, MG and RA, and a strong association with the major histocompatibility complex (MHC) region has been reported. In addition, non-MHC genes, such as interferon-induced helicase 1 (IFIH1) and c-type lectin domain family 16, member A (CLEC16A), are also associated with the development of IgAD and some of the above diseases. This indicates a possible common genetic background. In this review, we present suggestive evidence for a shared genetic predisposition between these disorders.
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Affiliation(s)
- Ning Wang
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Nan Shen
- Department of Rheumatology, Renji Hospital, JiaoTong University School of Medicine, Shanghai, China
| | - Timothy J Vyse
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Vidya Anand
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Iva Gunnarson
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Gunnar Sturfelt
- Department of Rheumatology, Lund University Hospital, Lund, Sweden
| | | | - Kerstin Elvin
- Unit of Clinical Immunology, Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lennart Truedsson
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Sweden
| | | | - Charlotte Dahle
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Örtqvist
- Department of Woman and Child Health, Astrid Lindgren Children’s Hospital, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Timothy W Behrens
- Division of Immunology, Tissue Growth & Repair, Biomarker Discovery and Human Genetics, Genentech, South San Francisco, California, United States of America
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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Weinstock C, Matheis N, Barkia S, Haager MC, Janson A, Marković A, Bux J, Kahaly GJ. Autoimmune polyglandular syndrome type 2 shows the same HLA class II pattern as type 1 diabetes. ACTA ACUST UNITED AC 2011; 77:317-24. [PMID: 21388354 DOI: 10.1111/j.1399-0039.2011.01634.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autoimmune polyglandular syndrome (APS) type 2 is defined by the manifestation of at least two autoimmune endocrine diseases. Only few data exist on genetic associations of APS type 2. In this controlled study, 98 patients with APS type 2, 96 patients with type 1 diabetes (T1D), and 92 patients with autoimmune thyroid disease, both as a single autoimmune endocrinopathy, were tested for association with alleles of the human leukocyte antigen (HLA) class II loci DRB1, DQA1, and DQB1. Patients with APS type 2 had significantly more often the alleles DRB1*03 (P(c) < 0.0001), DRB1*04 (P(c) < 0.000005), DQA1*03 (P(c) < 0.0001), and DQB1*02 (P(c) < 0.05), when compared with controls. Less frequent in APS were DRB1*15 (P(c) < 0.05), DQA1*01 (P(c) < 0.0005), and DQB1*05 (P(c) < 0.005). With regard to frequency and linkage of these alleles, the susceptible haplotypes DRB1*0301-DQA1*0501-DQB1*0201 and DRB1*0401/04-DQA1*0301-DQB1*0302 were deduced. Protective haplotypes in this study were DRB1*1501-DQA1*0102-DQB1*0602 and DRB1*0101-DQA1*0101-DQB1*0501. Comparing APS patients with vs without AD, no significant differences regarding HLA class II alleles were noted in our collective. Patients with T1D as a singular disease had the same susceptible and protective HLA alleles and haplotypes. The prevalence of DRB1*03 and DRB1*04 in APS patients was not because of the presence of diabetes, as the APS type 2 patients without diabetes had the same allele distribution. In conclusion, these data suggest a common immunogenetic pathomechanism for T1D and APS type 2, which might be different from the immunogenetic pathomechanism of other autoimmune endocrine disease.
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Affiliation(s)
- C Weinstock
- German Red Cross Blood Service West, Hagen, Germany.
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Stranger BE, Stahl EA, Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics 2011; 187:367-83. [PMID: 21115973 PMCID: PMC3030483 DOI: 10.1534/genetics.110.120907] [Citation(s) in RCA: 361] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Enormous progress in mapping complex traits in humans has been made in the last 5 yr. There has been early success for prevalent diseases with complex phenotypes. These studies have demonstrated clearly that, while complex traits differ in their underlying genetic architectures, for many common disorders the predominant pattern is that of many loci, individually with small effects on phenotype. For some traits, loci of large effect have been identified. For almost all complex traits studied in humans, the sum of the identified genetic effects comprises only a portion, generally less than half, of the estimated trait heritability. A variety of hypotheses have been proposed to explain why this might be the case, including untested rare variants, and gene-gene and gene-environment interaction. Effort is currently being directed toward implementation of novel analytic approaches and testing rare variants for association with complex traits using imputed variants from the publicly available 1000 Genomes Project resequencing data and from direct resequencing of clinical samples. Through integration with annotations and functional genomic data as well as by in vitro and in vivo experimentation, mapping studies continue to characterize functional variants associated with complex traits and address fundamental issues such as epistasis and pleiotropy. This review focuses primarily on the ways in which genome-wide association studies (GWASs) have revolutionized the field of human quantitative genetics.
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Affiliation(s)
- Barbara E Stranger
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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CHEN RONG, BUTTE ATULJ. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2011:231-42. [PMID: 21121051 PMCID: PMC3732491 DOI: 10.1142/9789814335058_0025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Personal genome resequencing has provided promising lead to personalized medicine. However, due to the limited samples and the lack of case/control design, current interpretation of personal genome sequences has been mainly focused on the identification and functional annotation of the DNA variants that are different from the reference genome. The reference genome was deduced from a collection of DNAs from anonymous individuals, some of whom might be carriers of disease risk alleles. We queried the reference genome against a large high-quality disease-SNP association database and found 3,556 disease-susceptible variants, including 15 rare variants. We assessed the likelihood ratio for risk for the reference genome on 104 diseases and found high risk for type 1 diabetes (T1D) and hypertension. We further demonstrated that the risk of T1D was significantly higher in the reference genome than those in a healthy patient with a whole human genome sequence. We found that the high T1D risk was mainly driven by a R260W mutation in PTPN22 in the reference genome. Therefore, we recommend that the disease-susceptible variants in the reference genome should be taken into consideration and future genome sequences should be interpreted with curated and predicted disease-susceptible loci to assess personal disease risk.
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Affiliation(s)
- RONG CHEN
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305-5479, USA
| | - ATUL J. BUTTE
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305-5479, USA
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Strange A, Capon F, Spencer CCA, Knight J, Weale ME, Allen MH, Barton A, Band G, Bellenguez C, Bergboer JGM, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Cork MJ, Corvin A, Deloukas P, Dilthey A, Duncanson A, Edkins S, Estivill X, Fitzgerald O, Freeman C, Giardina E, Gray E, Hofer A, Hüffmeier U, Hunt SE, Irvine AD, Jankowski J, Kirby B, Langford C, Lascorz J, Leman J, Leslie S, Mallbris L, Markus HS, Mathew CG, McLean WHI, McManus R, Mössner R, Moutsianas L, Naluai AT, Nestle FO, Novelli G, Onoufriadis A, Palmer CNA, Perricone C, Pirinen M, Plomin R, Potter SC, Pujol RM, Rautanen A, Riveira-Munoz E, Ryan AW, Salmhofer W, Samuelsson L, Sawcer SJ, Schalkwijk J, Smith CH, Ståhle M, Su Z, Tazi-Ahnini R, Traupe H, Viswanathan AC, Warren RB, Weger W, Wolk K, Wood N, Worthington J, Young HS, Zeeuwen PLJM, Hayday A, Burden AD, Griffiths CEM, Kere J, Reis A, McVean G, Evans DM, Brown MA, Barker JN, Peltonen L, Donnelly P, Trembath RC. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 2010; 42:985-90. [PMID: 20953190 PMCID: PMC3749730 DOI: 10.1038/ng.694] [Citation(s) in RCA: 786] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 08/31/2010] [Indexed: 02/08/2023]
Abstract
To identify new susceptibility loci for psoriasis, we undertook a genome-wide association study of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls. We identified associations at eight previously unreported genomic loci. Seven loci harbored genes with recognized immune functions (IL28RA, REL, IFIH1, ERAP1, TRAF3IP2, NFKBIA and TYK2). These associations were replicated in 9,079 European samples (six loci with a combined P < 5 × 10⁻⁸ and two loci with a combined P < 5 × 10⁻⁷). We also report compelling evidence for an interaction between the HLA-C and ERAP1 loci (combined P = 6.95 × 10⁻⁶). ERAP1 plays an important role in MHC class I peptide processing. ERAP1 variants only influenced psoriasis susceptibility in individuals carrying the HLA-C risk allele. Our findings implicate pathways that integrate epidermal barrier dysfunction with innate and adaptive immune dysregulation in psoriasis pathogenesis.
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Wan Taib WR, Smyth DJ, Merriman ME, Dalbeth N, Gow PJ, Harrison AA, Highton J, Jones PBB, Stamp L, Steer S, Todd JA, Merriman TR. The PTPN22 locus and rheumatoid arthritis: no evidence for an effect on risk independent of Arg620Trp. PLoS One 2010; 5:e13544. [PMID: 20975833 PMCID: PMC2958827 DOI: 10.1371/journal.pone.0013544] [Citation(s) in RCA: 13] [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: 06/05/2010] [Accepted: 09/29/2010] [Indexed: 11/22/2022] Open
Abstract
Objectives The Trp620 allotype of PTPN22 confers susceptibility to rheumatoid arthritis (RA) and certain other classical autoimmune diseases. There has been a report of other variants within the PTPN22 locus that alter risk of RA; protective haplotype ‘5’, haplotype group ‘6–10’ and susceptibility haplotype ‘4’, suggesting the possibility of other PTPN22 variants involved in the pathogenesis of RA independent of R620W (rs2476601). Our aim was to further investigate this possibility. Methods A total of 4,460 RA cases and 4,481 controls, all European, were analysed. Single nucleotide polymorphisms rs3789607, rs12144309, rs3811021 and rs12566340 were genotyped over New Zealand (NZ) and UK samples. Publically-available Wellcome Trust Case Control Consortium (WTCCC) genotype data were used. Results The protective effect of haplotype 5 was confirmed (rs3789607; (OR = 0.91, P = 0.016), and a second protective effect (possibly of haplotype 6) was observed (rs12144309; OR = 0.90, P = 0.021). The previously reported susceptibility effect of haplotype 4 was not replicated; instead a protective effect was observed (rs3811021; OR = 0.85, P = 1.4×10−5). Haplotypes defined by rs3789607, rs12144309 and rs3811021 coalesced with the major allele of rs12566340 within the adjacent BFK (B-cell lymphoma 2 (BCL2) family kin) gene. We, therefore, tested rs12566340 for association with RA conditional on rs2476601; there was no evidence for an independent effect at rs12566340 (P = 0.76). Similarly, there was no evidence for an independent effect at rs12566340 in type 1 diabetes (P = 0.85). Conclusions We have no evidence for a common variant additional to rs2476601 within the PTPN22 locus that influences the risk of RA. Arg620Trp is almost certainly the single common causal variant.
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Affiliation(s)
- Wan R. Wan Taib
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Peter J. Gow
- Department of Rheumatology, Middlemore Hospital, Auckland, New Zealand
| | | | - John Highton
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Peter B. B. Jones
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Sophia Steer
- Department of Rheumatology, Kings College London School of Medicine at Guy's, King's and St. Thomas', London, United Kingdom
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Tony R. Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- * E-mail:
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Martín JE, Alizadeh BZ, González-Gay MA, Balsa A, Pascual-Salcedo D, Fernández-Gutiérrez B, Raya E, Franke L, van't Slot R, Coenen MJH, van Riel P, Radstake TRDJ, Koeleman BPC, Martín J. Identification of the oxidative stress-related gene MSRA as a rheumatoid arthritis susceptibility locus by genome-wide pathway analysis. ACTA ACUST UNITED AC 2010; 62:3183-90. [DOI: 10.1002/art.27648] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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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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Qu HQ, Bradfield JP, Li Q, Kim C, Frackelton E, Grant SFA, Hakonarson H, Polychronakos C. In silico replication of the genome-wide association results of the Type 1 Diabetes Genetics Consortium. Hum Mol Genet 2010; 19:2534-8. [PMID: 20378605 DOI: 10.1093/hmg/ddq133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recently, the Type 1 Diabetes Genetics Consortium (T1DGC) reported 22 novel type 1 diabetes (T1D)-associated loci identified by meta-analysis of three genome-wide association studies (GWASs) with a case-control design. However, the association of 10 of these 22 reported loci was not confirmed in the T1DGC family cohort (P > 0.1). To address concerns about potential bias from population stratification, this study aims to replicate the association in three independent GWAS cohorts, one of which was based on the stratification-proof transmission disequilibrium analysis. Three European-descent population samples were included in this study: 483 cases and both parents, a case-control cohort of 514 cases and 2027 controls, and an additional cohort of 1078 cases and 341 controls from the dbGaP database. Among the 22 SNPs reported by the T1DGC, we had high-quality genotypes for 15; the remaining were imputed. T1D association was replicated in seven loci after Bonferroni correction for 22 independent hypotheses. An additional eight loci had nominal (one-sided) significance of P < 0.1 in the same direction, giving a false discovery rate of 3.35%. The genetic susceptibility conferred by non-HLA loci in our family cohort with one affected offspring was higher than the T1DGC multiplex families. Reciprocally, the frequency of strongly predisposing HLA alleles in the multiplex families was higher. This study replicated T1D association with at least as many of these novel loci as expected from the power of our sample size, thus supporting the validity of the new discoveries.
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Affiliation(s)
- Hui-Qi Qu
- Department of Pediatrics, McGill University, Montreal, QC, Canada H4H 2P4
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Fraser HI, Dendrou CA, Healy B, Rainbow DB, Howlett S, Smink LJ, Gregory S, Steward CA, Todd JA, Peterson LB, Wicker LS. Nonobese diabetic congenic strain analysis of autoimmune diabetes reveals genetic complexity of the Idd18 locus and identifies Vav3 as a candidate gene. THE JOURNAL OF IMMUNOLOGY 2010; 184:5075-84. [PMID: 20363978 DOI: 10.4049/jimmunol.0903734] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have used the public sequencing and annotation of the mouse genome to delimit the previously resolved type 1 diabetes (T1D) insulin-dependent diabetes (Idd)18 interval to a region on chromosome 3 that includes the immunologically relevant candidate gene, Vav3. To test the candidacy of Vav3, we developed a novel congenic strain that enabled the resolution of Idd18 to a 604-kb interval, designated Idd18.1, which contains only two annotated genes: the complete sequence of Vav3 and the last exon of the gene encoding NETRIN G1, Ntng1. Targeted sequencing of Idd18.1 in the NOD mouse strain revealed that allelic variation between NOD and C57BL/6J (B6) occurs in noncoding regions with 138 single nucleotide polymorphisms concentrated in the introns between exons 20 and 27 and immediately after the 3' untranslated region. We observed differential expression of VAV3 RNA transcripts in thymocytes when comparing congenic mouse strains with B6 or NOD alleles at Idd18.1. The T1D protection associated with B6 alleles of Idd18.1/Vav3 requires the presence of B6 protective alleles at Idd3, which are correlated with increased IL-2 production and regulatory T cell function. In the absence of B6 protective alleles at Idd3, we detected a second T1D protective B6 locus, Idd18.3, which is closely linked to, but distinct from, Idd18.1. Therefore, genetic mapping, sequencing, and gene expression evidence indicate that alteration of VAV3 expression is an etiological factor in the development of autoimmune beta-cell destruction in NOD mice. This study also demonstrates that a congenic strain mapping approach can isolate closely linked susceptibility genes.
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Affiliation(s)
- Heather I Fraser
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge
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Wu J, Devlin B, Ringquist S, Trucco M, Roeder K. Screen and clean: a tool for identifying interactions in genome-wide association studies. Genet Epidemiol 2010; 34:275-85. [PMID: 20088021 PMCID: PMC2915560 DOI: 10.1002/gepi.20459] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Epistasis could be an important source of risk for disease. How interacting loci might be discovered is an open question for genome-wide association studies (GWAS). Most researchers limit their statistical analyses to testing individual pairwise interactions (i.e., marginal tests for association). A more effective means of identifying important predictors is to fit models that include many predictors simultaneously (i.e., higher-dimensional models). We explore a procedure called screen and clean (SC) for identifying liability loci, including interactions, by using the lasso procedure, which is a model selection tool for high-dimensional regression. We approach the problem by using a varying dictionary consisting of terms to include in the model. In the first step the lasso dictionary includes only main effects. The most promising single-nucleotide polymorphisms (SNPs) are identified using a screening procedure. Next the lasso dictionary is adjusted to include these main effects and the corresponding interaction terms. Again, promising terms are identified using lasso screening. Then significant terms are identified through the cleaning process. Implementation of SC for GWAS requires algorithms to explore the complex model space induced by the many SNPs genotyped and their interactions. We propose and explore a set of algorithms and find that SC successfully controls Type I error while yielding good power to identify risk loci and their interactions. When the method is applied to data obtained from the Wellcome Trust Case Control Consortium study of Type 1 Diabetes it uncovers evidence supporting interaction within the HLA class II region as well as within Chromosome 12q24.
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Affiliation(s)
- Jing Wu
- Department of Statistics Carnegie Mellon University Pittsburgh, PA 15213
| | - Bernie Devlin
- Department of Psychiatry University of Pittsburgh School of Medicine Pittsburgh, PA 15213
| | - Steven Ringquist
- Division of Immunogenetics Department of Pediatrics Children’s Hospital of Pittsburgh of UPMC Pittsburgh, PA 15201
| | - Massimo Trucco
- Division of Immunogenetics Department of Pediatrics Children’s Hospital of Pittsburgh of UPMC Pittsburgh, PA 15201
| | - Kathryn Roeder
- Department of Statistics Carnegie Mellon University Pittsburgh, PA 15213
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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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Pierce BL, Ahsan H. Genetic susceptibility to type 2 diabetes is associated with reduced prostate cancer risk. Hum Hered 2010; 69:193-201. [PMID: 20203524 DOI: 10.1159/000289594] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 12/18/2009] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE To examine the collective effects of type 1 (T1D) and type 2 diabetes (T2D) risk alleles on prostate cancer (PCa) risk. METHODS Using data on 14 and 18 single nucleotide polymorphisms (SNPs) that effect T1D and T2D risk, respectively, we generated risk scores (a 'risk allele count' and a 'genetic relative risk') for both T1D and T2D for 1,171 non-Hispanic white, PSA-screened PCa cases and 1,101 matched controls from the Cancer Genetic Markers of Susceptibility study. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for associations between the diabetes risk scores and PCa risk. RESULTS Both T2D risk scores, but neither T1D score, showed an inverse association with PCa (p < 0.01). These associations remained significant after excluding HNF1B SNP rs4430796 (a known PCa risk factor) from the analysis. The highest quartile of the T2D allele count (>20 risk alleles) was associated with reduced PCa risk (OR = 0.77; CI: 0.60-0.99) compared to the lowest category (<17 risk alleles). CONCLUSIONS These results suggest that individuals with increased genetic susceptibility to T2D have decreased risk for PCa. This association is consistent with the observation that individuals with T2D are at decreased risk for PCa; however, data on T2D status was not available for this analysis.
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Affiliation(s)
- Brandon L Pierce
- Department of Health Studies, The University of Chicago, Chicago, IL 60637, USA.
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