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Zhang L, Qiu L, Wu J, Qi Y, Gao X, He C, Qi R, Wang H, Yao X, Zhu H, Li Y, Hao S, Lu Q, Long H, Lian S, Zhu W, Zhang H, Lai W, Su X, Lu R, Guo Z, Li J, Li M, Liu Q, Wang H, He L, Nong X, Li F, Li Y, Yao C, Xu J, Tang H, Wang D, Li Z, Yu H, Xiao S, An J, Pu X, Yu S, Zhang J, Chen X, Wang H, Huang W, Chen H, Xiao T. GWAS of Chronic Spontaneous Urticaria Reveals Genetic Overlap with Autoimmune Diseases, Not Atopic Diseases. J Invest Dermatol 2023; 143:67-77.e15. [PMID: 35933036 DOI: 10.1016/j.jid.2022.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/03/2022] [Accepted: 07/09/2022] [Indexed: 02/08/2023]
Abstract
Although chronic spontaneous urticaria (CSU) is a common disease, GWASs of CSU are lacking. We aimed to identify susceptibility SNPs by performing a GWAS in Chinese Han adults with CSU. The discovery cohort included 430 CSU cases and 482 healthy controls. The GWAS findings were validated in 800 CSU cases and 900 healthy controls. Genetic, functional enrichment, and bioinformatic analyses of genome-wide significant SNPs were performed to assess the association between CSU and autoimmunity or atopy. Five genome-wide significant SNPs were identified: rs434124/LILRA3, rs61986182/IGHG1/2, rs73075571/TDGF1, rs9378141/HLA-G, and rs3789612/PTPN22. The first four SNPs were in linkage disequilibrium with autoimmune-related diseases‒associated SNPs and were cis-expression quantitative trait loci in immune cells. The five SNPs-annotated genes were significantly enriched in immune processes. Higher polygenic risk scores and allele frequencies of rs3789612∗T, rs9378141∗C, and rs73075571∗G were significantly associated with autoimmune-related CSU phenotypes, including positive antithyroglobulin IgG, positive anti-FcεRIα IgG, total IgE <40 IU/ml, and positive antithyroid peroxidase IgG but not with atopic or allergic sensitized CSU phenotypes. This GWAS of CSU identifies five risk loci and reveals that CSU shares genetic overlap with autoimmune diseases and that genetic factors predisposing to CSU mainly manifest through associations with autoimmune traits.
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Affiliation(s)
- Liming Zhang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Li Qiu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Jian Wu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Yumeng Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xinghua Gao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Chundi He
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ruiqun Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Hexiao Wang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hong Zhu
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yuzhen Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Siyu Hao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hai Long
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shi Lian
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Zhu
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Haiping Zhang
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Lai
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiangyang Su
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Rongbiao Lu
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zaipei Guo
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Jingyi Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Quanzhong Liu
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huiping Wang
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiang Nong
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fuqiu Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Yang Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Chunli Yao
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Hui Tang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Duoqin Wang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Zhenlu Li
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Huiqian Yu
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shengxiang Xiao
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Jingang An
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xiongming Pu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Shirong Yu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Xue Chen
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Haifeng Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Hongduo Chen
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ting Xiao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China.
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Brian BF, Sjaastad FV, Freedman TS. SH3-domain mutations selectively disrupt Csk homodimerization or PTPN22 binding. Sci Rep 2022; 12:5875. [PMID: 35393453 PMCID: PMC8989918 DOI: 10.1038/s41598-022-09589-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
The kinase Csk is the primary negative regulator of the Src-family kinases (SFKs, e.g., Lck, Fyn, Lyn, Hck, Fgr, Blk, Yes), phosphorylating a tyrosine on the SFK C-terminal tail that mediates autoinhibition. Csk also binds phosphatases, including PTPN12 (PTP-PEST) and immune-cell PTPN22 (LYP/Pep), which dephosphorylate the SFK activation loop to promote autoinhibition. Csk-binding proteins (e.g., CBP/PAG1) oligomerize within membrane microdomains, and high local concentration promotes Csk function. Purified Csk homodimerizes in solution through an interface that overlaps the phosphatase binding footprint. Here we demonstrate that Csk can homodimerize in Jurkat T cells, in competition with PTPN22 binding. We designed SH3-domain mutations in Csk that selectively impair homodimerization (H21I) or PTPN22 binding (K43D) and verified their kinase activity in solution. Disruption of either interaction in cells, however, decreased the negative-regulatory function of Csk. Csk W47A, a substitution previously reported to block PTPN22 binding, had a secondary effect of impairing homodimerization. Csk H21I and K43D will be useful tools for dissecting the protein-specific drivers of autoimmunity mediated by the human polymorphism PTPN22 R620W, which impairs interaction with Csk and with the E3 ubiquitin ligase TRAF3. Future investigations of Csk homodimer activity and phosphatase interactions may reveal new facets of SFK regulation in hematopoietic and non-hematopoietic cells.
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Affiliation(s)
- Ben F Brian
- Graduate Program in Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, MN, 55455, USA.,Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94170, USA
| | - Frances V Sjaastad
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Cardiac Rhythm Management, Medtronic, Mounds View, MN, 55112, USA
| | - Tanya S Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Autoimmune Diseases Research, University of Minnesota, Minneapolis, MN, 55455, USA.
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Khanbarari F, Ghasemi N, Vakili M, Samadi M. Association of the single nucleotide polymorphism C1858T of the PTPN22 gene with unexplained recurrent pregnancy loss: A case-control study. Int J Reprod Biomed 2021; 19:873-880. [PMID: 34805727 PMCID: PMC8595908 DOI: 10.18502/ijrm.v19i10.9819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/12/2020] [Accepted: 05/25/2021] [Indexed: 11/29/2022] Open
Abstract
Background Lymphoid-tyrosine-phosphatase which is encoded by the protein tyrosine phosphatase non-receptor 22 (PTPN22) gene plays a pivotal role in the regulation of immune responses by dephosphorylating several signaling intermediates of immune cells. Objective Since a balanced immune response has been shown to be important during pregnancy, the purpose of this research was to compare the frequency of the PTPN22 C1858T polymorphism in women with unexplained recurrent pregnancy loss (URPL) vs. in a control group for the first time. Materials and Methods Genomic DNA from 200 individuals with URPL and 200 individuals without URPL (the control group) at the infertility center in Yazd, Iran was isolated using the salting-out method. The PTPN22 C1858T polymorphism of the two groups was analyzed using polymerase chain reaction-restriction fragment length polymorphism. Genotype frequencies in the women with URPL and the fertile control group were compared using the Chi-square test. Results There were significant differences in the frequency of the PTPN22 1858T polymorphism in the URPL individuals vs. the healthy controls, i.e. 32.0% and 21.5%, respectively (p = 0.01). Conclusion Our findings suggest that the PTPN22 1858T polymorphism could play a role in recurrent pregnancy loss. Therefore, genotyping of the mentioned polymorphism can help clinicians to predict the probable risk of URPL.
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Affiliation(s)
- Fateme Khanbarari
- Immunology Department, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Nasrin Ghasemi
- Abortion Research Center, Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmood Vakili
- Health Monitoring Research Center, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Morteza Samadi
- Abortion Research Center, Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Oh EH, Shin JH, Kim HS, Cho JW, Choi SY, Choi KD, Rhee JK, Lee S, Lee C, Choi JH. Rare Variants of Putative Candidate Genes Associated With Sporadic Meniere's Disease in East Asian Population. Front Neurol 2020; 10:1424. [PMID: 32038468 PMCID: PMC6987317 DOI: 10.3389/fneur.2019.01424] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives: The cause of Meniere's disease (MD) is unclear but likely involves genetic and environmental factors. The aim of this study was to investigate the genetic basis underlying MD by screening putative candidate genes for MD. Methods: Sixty-eight patients who met the diagnostic criteria for MD of the Barany Society were included. We performed targeted gene sequencing using next generation sequencing (NGS) panel composed of 45 MD-associated genes. We identified the rare variants causing non-synonymous amino acid changes, stop codons, and insertions/deletions in the coding regions, and excluded the common variants with minor allele frequency >0.01 in public databases. The pathogenicity of the identified variants was analyzed by various predictive tools and protein structural modeling. Results: The average read depth for the targeted regions was 1446.3-fold, and 99.4% of the targeted regions were covered by 20 or more reads, achieving the high quality of the sequencing. After variant filtering, annotation, and interpretation, we identified a total of 15 rare heterozygous variants in 12 (17.6%) sporadic patients. Among them, four variants were detected in familial MD genes (DTNA, FAM136A, DPT), and the remaining 11 in MD-associated genes (PTPN22, NFKB1, CXCL10, TLR2, MTHFR, SLC44A2, NOS3, NOTCH2). Three patients had the variants in two or more genes. All variants were not detected in our healthy controls (n = 100). No significant differences were observed between patients with and without a genetic variant in terms of sex, mean age of onset, bilaterality, the type of MD, and hearing threshold at diagnosis. Conclusions: Our study identified rare variants of putative candidate genes in some of MD patients. The genes were related to the formation of inner ear structures, the immune-associated process, or systemic hemostasis derangement, suggesting the multiple genetic predispositions in the development of MD.
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Affiliation(s)
- Eun Hye Oh
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University School of Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jin-Hong Shin
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University School of Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Hyang-Sook Kim
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University School of Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jae Wook Cho
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University School of Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Seo Young Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Kwang-Dong Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Je-Keun Rhee
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
| | - Seowhang Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Sciences and Technology, Ulsan, South Korea
| | - Changwook Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Sciences and Technology, Ulsan, South Korea
| | - Jae-Hwan Choi
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University School of Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
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Mustelin T, Bottini N, Stanford SM. The Contribution of PTPN22 to Rheumatic Disease. Arthritis Rheumatol 2019; 71:486-495. [PMID: 30507064 PMCID: PMC6438733 DOI: 10.1002/art.40790] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022]
Abstract
One of the unresolved questions in modern medicine is why certain individuals develop a disorder such as rheumatoid arthritis (RA) or lupus, while others do not. Contemporary science indicates that genetics is partly responsible for disease development, while environmental and stochastic factors also play a role. Among the many genes that increase the risk of autoimmune conditions, the risk allele encoding the W620 variant of protein tyrosine phosphatase N22 (PTPN22) is shared between multiple rheumatic diseases, suggesting that it plays a fundamental role in the development of immune dysfunction. Herein, we discuss how the presence of the PTPN22 risk allele may shape the signs and symptoms of these diseases. Besides the emerging clarity regarding how PTPN22 tunes T and B cell antigen receptor signaling, we discuss recent discoveries of important functions of PTPN22 in myeloid cell lineages. Taken together, these new insights reveal important clues to the molecular mechanisms of prevalent diseases like RA and lupus and may open new avenues for the development of personalized therapies that spare the normal function of the immune system.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, 750 Republican Street, Room E507, Seattle, WA 99108, phone (206) 616-6130,
| | - Nunzio Bottini
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, MC0656, La Jolla, CA 92093-0656, phone (858) 246-2398 (N.B.) and (858) 246-2397 (S.M.S.), (N.B.) and (S.M.S.)
| | - Stephanie M. Stanford
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, MC0656, La Jolla, CA 92093-0656, phone (858) 246-2398 (N.B.) and (858) 246-2397 (S.M.S.), (N.B.) and (S.M.S.)
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