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Jiang P, Wang C, Zhang M, Tian Y, Zhao W, Xin J, Huang Y, Zhao Z, Sun W, Long J, Tang R, Qiu F, Shi X, Zhao Y, Zhu L, Dai N, Liu L, Wu X, Nie J, Jiang B, Shao Y, Gao Y, Yu J, Hu Z, Zang Z, Gong Y, Dai Y, Wang L, Ding N, Xu P, Chen S, Wang L, Xu J, Zhang L, Hong J, Qian R, Li H, Jiang X, Chen C, Tian W, Wu J, Jiang Y, Han C, Zhang K, Qiu H, Li L, Fan H, Chen L, Zhang J, Sun Z, Han X, Dai Z, Li E, Gershwin ME, Lian Z, Ma X, Seldin MF, Chen W, Wang M, Liu X. Differential regulation of JAK1 expression by ETS1 associated with predisposition to primary biliary cholangitis. J Genet Genomics 2023:S1673-8527(23)00140-6. [PMID: 37348755 DOI: 10.1016/j.jgg.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Peng Jiang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chan Wang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, Jiangsu 225009, China
| | - Mingming Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ye Tian
- Department of Radiology & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Weifeng Zhao
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Junyi Xin
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University School of Public Health, Nanjing, Jiangsu 210029, China
| | - Yexi Huang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhibin Zhao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Wenjuan Sun
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jie Long
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Ruqi Tang
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai 200001, China
| | - Fang Qiu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yi Zhao
- Department of Gastrointestinal Endoscopy, Eastern Hepatobiliary Surgery Hospital, Shanghai 201800, China
| | - Li Zhu
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Na Dai
- Department of Gastroenterology, Jiangsu University Affiliated Kunshan Hospital, Kunshan, Jiangsu 215300, China
| | - Lei Liu
- Department of Gastroenterology, Yixing People's Hospital, Yixin, Jiangsu 214200, China
| | - Xudong Wu
- Department of Gastroenterology, Yancheng First People's Hospital, Yancheng, Jiangsu 224005, China
| | - Jinshan Nie
- Department of Gastroenterology, Taicang First People's Hospital, Soochow University, Taicang, Jiangsu 215400, China
| | - Bo Jiang
- Department of Hepatology, Jingjiang Second People's Hospital, Jingjiang, Jiangsu 214500, China
| | - Youlin Shao
- Department of Hepatology, The Third People's Hospital of Changzhou, Changzhou, Jiangsu 213001, China
| | - Yueqiu Gao
- Department of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianjiang Yu
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, Jiangyin, Jiangsu 214400, China
| | - Zhigang Hu
- Department of Laboratory Medicine, Wuxi Children's Hospital, Wuxi, Jiangsu 214023, China
| | - Zhidong Zang
- Department of Hepatology, The Second Hospital of Nanjing, Southeast University, Nanjing, Jiangsu 210003, China
| | - Yuhua Gong
- Department of Laboratory Medicine, The Third People's Hospital of Zhenjiang, Zhenjiang, Jiangsu 212021, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214000, China
| | - Lan Wang
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Ningling Ding
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Ping Xu
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Sufang Chen
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Lu Wang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jing Xu
- Department of Clinical Laboratory, Southeast University ZhongDa Hospital, Nanjing, Jiangsu 210009, China
| | - Luyao Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Junyan Hong
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ruonan Qian
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hu Li
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xuan Jiang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Congwei Chen
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenyan Tian
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Jian Wu
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Yuzhang Jiang
- Department of Laboratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu 223300, China
| | - Chongxu Han
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Kui Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Hong Qiu
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Li Li
- Department of Clinical Laboratory, Southeast University ZhongDa Hospital, Nanjing, Jiangsu 210009, China
| | - Hong Fan
- Southeast University Medical College, Nanjing, Jiangsu 210009, China
| | - Liming Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of cancer, Department of biochemistry, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu 210023, China
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China; Southeast University Medical College, Nanjing, Jiangsu 210009, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhenhua Dai
- Section of Immunology & Joint Immunology Program, the Second Clinical Medical College of Guangzhou University of Chinese Medicine, and Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, Guangdong 510006, China
| | - Erguang Li
- Jiangsu Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, Jiangsu 210093, China
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Zhexiong Lian
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai 200001, China
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Weichang Chen
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China.
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University School of Public Health, Nanjing, Jiangsu 210029, China.
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China.
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to: "An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs" [J Hepatol 75 (2021) 572-581]. J Hepatol 2023; 78:883. [PMID: 36639314 DOI: 10.1016/j.jhep.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, USA
| | | | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, USA
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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Li Y, Li Z, Chen R, Lian M, Wang H, Wei Y, You Z, Zhang J, Li B, Li Y, Huang B, Chen Y, Liu Q, Lyu Z, Liang X, Miao Q, Xiao X, Wang Q, Fang J, Shi Y, Liu X, Seldin MF, Gershwin ME, Tang R, Ma X. A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression. Nat Commun 2023; 14:1732. [PMID: 36977669 PMCID: PMC10049997 DOI: 10.1038/s41467-023-37213-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Genome-wide association studies have identified 19p13.3 locus associated with primary biliary cholangitis (PBC). Here we aim to identify causative variant(s) and initiate efforts to define the mechanism by which the 19p13.3 locus variant(s) contributes to the pathogenesis of PBC. A genome-wide meta-analysis of 1931 PBC subjects and 7852 controls in two Han Chinese cohorts confirms the strong association between 19p13.3 locus and PBC. By integrating functional annotations, luciferase reporter assay and allele-specific chromatin immunoprecipitation, we prioritize rs2238574, an AT-Rich Interaction Domain 3A (ARID3A) intronic variant, as a potential causal variant at 19p13.3 locus. The risk allele of rs2238574 shows higher binding affinity of transcription factors, leading to an increased enhancer activity in myeloid cells. Genome-editing demonstrates the regulatory effect of rs2238574 on ARID3A expression through allele-specific enhancer activity. Furthermore, knock-down of ARID3A inhibits myeloid differentiation and activation pathway, and overexpression of the gene has the opposite effect. Finally, we find ARID3A expression and rs2238574 genotypes linked to disease severity in PBC. Our work provides several lines of evidence that a non-coding variant regulates ARID3A expression, presenting a mechanistic basis for association of 19p13.3 locus with the susceptibility to PBC.
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Affiliation(s)
- You Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Ruiling Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Min Lian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Hanxiao Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Yiran Wei
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Zhengrui You
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Jun Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Bo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Yikang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Bingyuan Huang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Yong Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Qiaoyan Liu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Zhuwan Lyu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Xueying Liang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Qi Miao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Xiao Xiao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Qixia Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - Jingyuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China
| | - YongYong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, China
| | - Michael F Seldin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA
| | - M Eric Gershwin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, CA, USA.
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China.
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, China.
- Institute of Aging & Tissue Regeneration, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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4
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Zuercher MD, Harvey DJ, Au LE, Shadyab AH, Nassir R, Robbins JA, Seldin MF, Garcia L. Genetic admixture and cardiovascular disease risk in postmenopausal Hispanic women. Int J Cardiol 2022; 367:99-104. [PMID: 35961613 PMCID: PMC10639166 DOI: 10.1016/j.ijcard.2022.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Hispanics are a heterogeneous population with differences in the prevalence of cardiovascular disease (CVD) and its related risk factors among ethnic sub-groups. This study evaluated the association of genetic admixture and CVD in self-identified Hispanic women from the Women's Health Initiative (WHI). METHODS Data came from the WHI Observational Study and the Clinical Trial Components conducted among postmenopausal women. The CVD outcomes included coronary heart disease (CHD) and stroke. The proportions of European (EUR), sub-Saharan African (AFR), and Amerindian (AMI) admixture were estimated using 92 ancestry-informative markers. Cox regression models were used to assess the relationship between genetic admixture and CVD adjusting for age, lifestyle risk factors, known risk factors, and neighborhood socioeconomic status. RESULTS Among 5195 participants EUR ancestry was associated with a lower CHD risk after adjusting for age (HR 0.41, p = 0.02), and in the fully adjusted model (HR 0.40, p = 0.03). AFR ancestry was associated with a higher CHD risk after adjusting for age (HR 2.91, p = 0.03), but it only showed a trend in in the fully adjusted model (HR 2.46, p = 0.10). AMI ancestry was not statistically significantly associated with CHD and none of the genetic admixture proportions were statistically significantly associated with stroke (p > 0.05). CONCLUSION EUR ancestry was associated with a lower risk of CHD in Hispanic women. This highlights the need to account for genetic admixture in future CVD studies to consider different heritage groups to understand the role that genetic, neighborhood socioeconomic status, and environmental factors contribute to CVD health disparities in Hispanic women.
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Affiliation(s)
| | | | - Lauren E Au
- University of California Davis, Davis, CA, United States
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, United States
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Quraa University, Saudi Arabia
| | - John A Robbins
- University of California Davis, Davis, CA, United States
| | | | - Lorena Garcia
- University of California Davis, Davis, CA, United States.
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5
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Li Y, Sun Y, Liu Y, Wang B, Li J, Wang H, Zhang H, Wang X, Han X, Lin Q, Zhou Y, Hu L, Song Y, Bao J, Gong L, Sun M, Yuan X, Zhang X, Lian M, Xiao X, Miao Q, Wang Q, Li KK, Du S, Ma A, Li Y, Xu J, Tang S, Shi J, Xu Y, Yang L, Zhang J, Huang Z, Zhou L, Cui Y, Seldin MF, Gershwin ME, Yan H, Zou Z, Zuo X, Tang R, Ma X. Genome-wide meta-analysis identifies susceptibility loci for autoimmune hepatitis type 1. Hepatology 2022; 76:564-575. [PMID: 35184318 DOI: 10.1002/hep.32417] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Autoimmune hepatitis (AIH) is a rare and chronic autoimmune liver disease. While genetic factors are believed to play a crucial role in the etiopathogenesis of AIH, our understanding of these genetic risk factors is still limited. In this study, we aimed to identify susceptibility loci to further understand the pathogenesis of this disease. APPROACH AND RESULTS We conducted a case-control association study of 1,622 Chinese patients with AIH type 1 and 10,466 population controls from two independent cohorts. A meta-analysis was performed to ascertain variants associated with AIH type 1. A single-nucleotide polymorphism within the human leukocyte antigen (HLA) region showed the strongest association with AIH (rs6932730: OR = 2.32; p = 9.21 × 10-73 ). The meta-analysis also identified two non-HLA loci significantly associated with AIH: CD28/CTLA4/ICOS on 2q33.3 (rs72929257: OR = 1.31; p = 2.92 × 10-9 ) and SYNPR on 3p14.2 (rs6809477: OR = 1.25; p = 5.48 × 10-9 ). In silico annotation, reporter gene assays, and CRISPR activation experiments identified a distal enhancer at 2q33.3 that regulated expression of CTLA4. In addition, variants near STAT1/STAT4 (rs11889341: OR = 1.24; p = 1.34 × 10-7 ), LINC00392 (rs9564997: OR = 0.81; p = 2.53 × 10-7 ), IRF8 (rs11117432: OR = 0.72; p = 6.10 × 10-6 ), and LILRA4/LILRA5 (rs11084330: OR = 0.65; p = 5.19 × 10-6 ) had suggestive association signals with AIH. CONCLUSIONS Our study identifies two novel loci (CD28/CTLA4/ICOS and SYNPR) exceeding genome-wide significance and suggests four loci as potential risk factors. These findings highlight the importance of costimulatory signaling and neuro-immune interaction in the pathogenesis of AIH.
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Affiliation(s)
- You Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ying Sun
- Department of Liver Disease, Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yanmin Liu
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Jia Li
- Tianjin Second People's Hospital, Tianjin Institute of Hepatology, Tianjin, China
| | - Hanxiao Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Haiping Zhang
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaoyi Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Xu Han
- Tianjin Second People's Hospital, Tianjin Institute of Hepatology, Tianjin, China
| | - Qiuxiang Lin
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Zhou
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Lilin Hu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhu Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Bao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Gong
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Mengying Sun
- Department of Gastroenterology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaoling Yuan
- Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinhe Zhang
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, ShenYang, China
| | - Min Lian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiao Xiao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Miao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qixia Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ke-Ke Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shiyu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Anlin Ma
- Department of infection disease, China-Japan Friendship Hospital, Beijing, China
| | - Yiling Li
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, ShenYang, China
| | - Jie Xu
- Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanhong Tang
- Department of Gastroenterology, The General Hospital of Western Theater Command, Chengdu, China
| | - Junping Shi
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital and Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, China
| | - Zuxiong Huang
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Michael F Seldin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, California, USA.,Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California, USA
| | - M Eric Gershwin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, California, USA
| | - Huiping Yan
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zhengsheng Zou
- Department of Liver Disease, Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Department of Pharmacy, China-Japan Friendship Hospital, Beijing, China
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
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6
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MA, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byun J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to 'An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs' [J Hepatol 2021;75(3):572-581]. J Hepatol 2022; 76:489. [PMID: 34895949 PMCID: PMC8935376 DOI: 10.1016/j.jhep.2021.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J. Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy,Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E. Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L. Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M. Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A. Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada,Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom,Corresponding author. Address: Academic Department of Medical Genetics, University of Cambridge, Box 238, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom.
| | - Canadian PBC ConsortiumSiminovitchKatherine A.252627HirschfieldGideon M.28MasonAndrew29VincentCatherine30XieGang31ZhangJinyi32Departments of Medicine, Immunology and Medical Sciences, University of Toronto, CanadaMount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, CanadaToronto General Research Institute, Toronto, Ontario, CanadaToronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, CanadaDept of Medicine, University of Alberta, Edmonton, Alberta, CanadaUniversite de Montreal Hospital Centre, Saint-Luc Hospital, Montreal, Quebec, CanadaLunenfeld Tanenbaum Research Institute, Toronto, CanadaLunenfeld Tanenbaum Research Institute, Toronto, Canada
| | - Chinese PBC ConsortiumTangRuqi33MaXiong33LiZhiqiang3435ShiYongyong3435Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, ChinaBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, ChinaAffiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, China
| | - Italian PBC Study GroupAffrontiAndrea36AlmasioPiero L.37AlvaroDomenico38AndreonePietro39AndriulliAngelo40AzzaroliFrancesco41BattezzatiPier Maria42BenedettiAntonio43BragazziMaria Consiglia44BrunettoMaurizia45BrunoSavino46CalvarusoVincenza47CardinaleVincenzo48CasellaGiovanni49CazzagonNora50CiaccioAntonio51CocoBarbara52ColliAgostino53ColloredoGuido54ColomboMassimo55ColomboSilvia56CristoferiLaura57CursaroCarmela58CrocèLory Saveria59CrosignaniAndrea60D’AmatoDaphne61DonatoFrancesca62EliaGianfranco63FabrisLuca64FagiuoliStefano65FerrariCarlo66FloreaniAnnarosa67GalliAndrea68GianniniEdoardo69GrattaglianoIgnazio70LamperticoPietro71LleoAna72MalinvernoFederica73MancusoClara74MarraFabio75MarzioniMarco76MassironiSara77MattaliaAlberto78MieleLuca79MilaniChiara80MoriniLorenzo81MoriscoFilomena82MuratoriLuigi83MuratoriPaolo84NiroGrazia A.85O’DonnellSarah86PicciottoAntonio87PortincasaPiero88RigamontiCristina89RoncaVincenzo90RosinaFloriano91SpinziGiancarlo92StrazzaboscoMario93TarocchiMirko94TiribelliClaudio95ToniuttoPierluigi96ValentiLuca97VinciMaria98ZuinMassimo99Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, ItalyGastroenterology & Hepatology Unit, Di.Bi.M.I.S., University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome; Eleonora Lorillard Spencer-Cenci Foundation, Rome, ItalyDepartment of Medical and Surgical Sciences, Bologna University, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDepartment of Medical and Surgical Sciences (DIMEC) University of Bologna, Bologna, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, ItalyUniversitàPolitecnica delle Marche, Ancona, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome, Rome, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, Ospedale Fatebene Fratelli e Oftalmico, Milan, ItalySezione di Gastroenterologia e Epatologia, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S.) University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Viale dell'Università37, 00185, Rome, ItalyMedical Department, Desio Hospital, Desio, ItalyDepartment of Surgery, Oncology and Gastroenterology, University of Padua, Padova, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, AO Provincia di Lecco, Lecco, ItalyDepartment of Internal Medicine, San Pietro Hospital, Bergamo, Ponte San Pietro, ItalyHumanitas Clinical and Research Center, IRCCS, Rozzano, ItalyTreviglio Hospital, Treviglio, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyHepatology Unit, Department of Medical and Surgical Sciences, University Hospital of Bologna, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalySan Paolo Hospital Medical School, Universitàdi Milano, Milan, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyFondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyUniversity of Padova, Padova, ItalyGastroenterologia Epatologia e Trapiantologia, Papa Giovanni XXIII Hospital, Bergamo, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyDepartment. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, ItalyUniversity of Florence, Florence, ItalyGastroenterology Unit, Department Internal Medicine, Policlinico San Martino, University of Genoa, Genoa, ItalyItalian College of General Practicioners, ASL Bari, ItalyDivision of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, ItalyDepartment of Biomedical Sciences, Humanitas University, Division of Internal Medicine and Hepatology, Department of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Via A. Manzoni 56, 20089 Rozzano (MI), ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Florence, Florence, ItalyUniversità Politecnica delle Marche, Ancona, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalySanta Croce Carle Hospital, Cuneo, ItalyInternal Medicine, Gastroenterology and Liver Unit, A. Gemelli Polyclinic, Sacro Cuore Catholic University, 20123 Rome, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyMagenta Hospital, Magenta, ItalyUniversity of Naples, Federico II, Naples, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Genoa, Genoa, ItalyDepartment of Interdisciplinary Medicine, University Medical School, Bari, ItalyDepartment of Translational Medicine, Universitàdel Piemonte Orientale UPO, 28100 Novara, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology & Hepatology, Center for Predictive Medicine, Gradenigo Hospital, Turin, ItalyAzienda Ospedaliera Valduce, Como, ItalyYale University, New Haven, Connecticut, USAUniversity of Florence, Florence, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalyUniversity of Udine, Udine, ItalyInternal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano, Department of Pathophysiology and Transplantation, Universitàdegli Studi di Milano, Milan, ItalyOspedale Niguarda, Milan, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, Italy
| | - Japan-PBC-GWAS ConsortiumNakamuraHitomi100AbiruSeigo100NagaokaShinya100KomoriAtsumasa100YatsuhashiHiroshi100IshibashiHiromi100ItoMasahiro100MigitaKiyoshi101OhiraHiromasa101KatsushimaShinji102NaganumaAtsushi102SugiKazuhiro102KomatsuTatsuji102MannamiTomohiko102MatsushitaKouki102YoshizawaKaname102MakitaFujio102NikamiToshiki102NishimuraHideo102KounoHiroshi102KounoHirotaka102OtaHajime102KomuraTakuya102NakamuraYoko102ShimadaMasaaki102HirashimaNoboru102KomedaToshiki102ArioKeisuke102NakamutaMakoto102YamashitaTsutomu102FurutaKiyoshi102KikuchiMasahiro102NaeshiroNoriaki102TakahashiHironao102ManoYutaka102TsunematsuSeiji102YabuuchiIwao102ShimadaYusuke102YamauchiKazuhiko102SugimotoRie102SakaiHironori102MitaEiji102KodaMasaharu102TsurutaSatoru102KamitsukasaHiroshi102SatoTakeaki102MasakiNaohiko102KobataTatsuro102FukushimaNobuyoshi102OharaYukio102MuroToyokichi102TakesakiEiichi102TakakiHitoshi102YamamotoTetsuo102KatoMichio102NagaokiYuko102HayashiShigeki102IshidaJinya102WatanabeYukio102KobayashiMasakazu102KogaMichiaki102SaoshiroTakeo102YaguraMichiyasu102HirataKeisuke102TanakaAtsushu103TakikawaHajime103ZeniyaMikio104AbeMasanori105OnjiMorikazu105KanekoShuichi106HondaMasao106AraiKuniaki106Arinaga-HinoTeruko107HashimotoEtsuko108TaniaiMakiko108UmemuraTakeji109JoshitaSatoru109NakaoKazuhiko110IchikawaTatsuki110ShibataHidetaka110YamagiwaSatoshi111SeikeMasataka112HondaKoichi112SakisakaShotaro113TakeyamaYasuaki113HaradaMasaru114SenjuMichio114YokosukaOsamu115KandaTatsuo115UenoYoshiyuki116KikuchiKentaro117EbinumaHirotoshi118HimotoTakashi119YasunamiMichio120MurataKazumoto121MizokamiMasashi121KawataKazuhito122ShimodaShinji123MiyakeYasuhiro124TakakiAkinobu124YamamotoKazuhide124HiranoKatsuji125IchidaTakafumi125IdoAkio126TsubouchiHirohito126ChayamaKazuaki127HaradaKenichi128NakanumaYasuni128MaeharaYoshihiko129TaketomiAkinobu129ShirabeKen129SoejimaYuji129MoriAkira130YagiShintaro130UemotoShinji130HEgawa131TanakaTomohiro132YamashikiNoriyo132TamuraSumito133SugawaraYasuhiro133KokudoNorihiro133Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, JapanDepartment of Gastroenterology and Rheumatic Diseases, Fukushima Medical University of Medicine, Fukushima, JapanHeadquaters of PBC Research in the NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Nagasaki, JapanDepartment of Medicine, Teikyo University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, JapanDepartment of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDivision of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, JapanDepartment of Medicine and Gastroenterology, Tokyo Women’s Medical University, Tokyo, JapanDepartment of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, JapanDepartment of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, JapanDivision of Gastroenterology and Hepatology,Niigata University Graduate School of Medical and Dental Sciences, Niigata, JapanFaculty of Medicine, Oita University, Oita, JapanDepartment of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, JapanThe Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, JapanDepartment of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, JapanDepartment of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, JapanDepartment of Internal Medicine, Teikyo University Mizonokuchi Hospital, Kawasaki, JapanDivision of Gastroenterology and Hepatology, Department of Internal Medicine, Keio Graduate School of Medicine, Tokyo, JapanDepartment of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, JapanDepartment of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasakin, JapanThe Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, JapanHepatology Division, Department of Internal Medicine II, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka JapanDepartment of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDepartment of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, JapanDepartment of Gastroenterology and Hepatology, Juntendo University Shizuoka Hospital, Shizuoka, JapanDepartment of Digestive and Lifestyle–Related Disease, Kagoshima University Graduate School of Medical and Dental Science, Kagoshima, JapanDepartment of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, JapanDepartment of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDepartment of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDivision of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, JapanDepartment of Surgery, Tokyo Women’s Medical University, Tokyo, JapanOrgan Transplantation Service, The University of Tokyo, Tokyo, JapanHepatobiliary and Pancreatic Surgery Division and Artificial Organ and Transplantation Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Japan
| | - US PBC ConsortiumJuranBrian D.134AtkinsonElizabeth J.135CheungAngela136de AndradeMariza137LazaridisKonstantinos N.138ChalasaniNaga139LuketicVel140OdinJoseph141ChopraKapil142BarasAris143HorowitzJulie143AbecasisGoncalo143CantorMichael143CoppolaGiovanni143EconomidesAris143LottaLuca A.143OvertonJohn D.143ReidJeffrey G.143ShuldinerAlan143BeechertChristina143ForsytheCaitlin143FullerErin D.143GuZhenhua143LattariMichael143LopezAlexander143OvertonJohn D.143SchleicherThomas D.143PadillaMaria Sotiropoulos143ToledoKarina143WidomLouis143WolfSarah E.143PradhanManasi143ManoochehriKia143UlloaRicardo H.143BaiXiaodong143BalasubramanianSuganthi143BarnardLeland143BlumenfeldAndrew143EomGisu143HabeggerLukas143HawesAlicia143KhalidShareef143ReidJeffrey G.143MaxwellEvan K.143SalernoWilliam143StaplesJeffrey C.143JonesMarcus B.143MitnaulLyndon J.143Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesIndiana University, Indiana, United StatesVirginia Commonwealth University, Virginia, United StatesIcahn School of Medicine, Mount Sinai, New York, United StatesUniversity of Pittsburgh, United StatesRegeneron, United States
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7
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Xu J, Zhang H, Wang C, Jiang P, Han C, Dai Y, Qiu F, Gong Y, Jiang Y, Xu P, Zhang M, Zhang L, Shi X, Chen S, Tian Y, Seldin MF, Gershwin ME, Liu X, Li L. Increased sensitivity of gp210 autoantibody detection using a newly designed gp210 antigen. J Immunol Methods 2021; 501:113211. [PMID: 34971632 DOI: 10.1016/j.jim.2021.113211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The detection of autoantibody to glycoprotein 210 (gp210 Ab) against a 15 amino-acid peptide epitope by enzyme-linked immunosorbent assay (ELISA) has been widely used in the diagnosis of primary biliary cholangitis (PBC). However, this small peptide antigen presents spatial limitations for antibody access, which reduces the sensitivity of autoantibody detection. A recombinant gp210 antigen was constructed for increased sensitivity in antibody detection is described here. METHODS The gp210 C terminal 18 amino acid coding sequence was ligated to the modified C-terminal 108 amino acid coding sequence of human serum albumin (mHSA108) and produced as a recombinant gp210 antigen mHSA108-gp210-C18. Measurements of gp210 Ab using the gp210 C-terminal 25 amino acid peptide (gp210-C25) and mHSA108-gp210-C18 by in-house ELISA were compared. ELISAs with mHSA108-gp210-C18 and commercial INOVA kit for gp210 Ab detection were also compared in PBC patients and healthy controls. The correlation between the two assays was analyzed and their efficiency in diagnosing was compared. RESULTS Of 86 PBC samples, 35 (40.70%) and 44 (52.33%) positive samples were detected for anti-gp210 Ab using gp210-C25 and mHSA108-gp210-C18, respectively. Of 252 samples from PBC, 114 (45.24%) were positive for mHSA108-gp210-C18 ELISA whereas 94 (37.3%) for commercial ELISA (INOVA). All positive samples detected with commercial ELISA kit were also tested positive in mHSA108-gp210-C18 ELISA. Among 374 patients with other autoimmune diseases, anti-gp210 Ab were detected by mHSA108-gp210-C18 ELISA in 0.95% systemic lupus erythematosus (SLE) patients (2/210), 13.04% rheumatoid arthritis (RA) patients (13/97), and 1.47% of Sjögren's Syndrome (SS) patients (1/67). CONCLUSIONS Compared to the gp210 peptide antigen, the sensitivity of the ELISA system using mHSA108-gp210-C18 antigen was improved. The novel gp210 antigen could be useful for screening patients known to be at increased risk of developing PBC.
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Affiliation(s)
- Jing Xu
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China; Department of Clinical Laboratory, ZhongDa Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Haoyi Zhang
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Chan Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, 136 Yangjiang Middle Road, Yangzhou, Jiangsu 225001, China
| | - Peng Jiang
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Chongxu Han
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, 98 Nantong West Road, Yangzhou, Jiangsu 225001, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, 1215 Guangrui Road, Wuxi, Jiangsu 214000, China
| | - Fang Qiu
- Department of Laboratory Medicine, The Forth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, China
| | - Yuhua Gong
- Department of Laboratory Medicine, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, Jiangsu 212021, China
| | - Yuzhang Jiang
- Department of Laboratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, 1 Huanghe West Road, Huai'an, Jiangsu 223300, China
| | - Ping Xu
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, 10 Guangqian Road, Suzhou, Jiangsu 215131, China
| | - Mingming Zhang
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Luyao Zhang
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Xingjuan Shi
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
| | - Sufang Chen
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, 10 Guangqian Road, Suzhou, Jiangsu 215131, China
| | - Ye Tian
- Department of Radiology, The Second Affiliated Hospital of Soochow University,1055 Sanxiang Road, Suzhou, Jiangsu 215004, China
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis School of Medicine, 4453 Tupper Hall, Davis, CA 95616, USA; Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, School of Medicine, Genome and Biomedical Sciences Facility Building, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616, USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, School of Medicine, Genome and Biomedical Sciences Facility Building, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616, USA
| | - Xiangdong Liu
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China.
| | - Li Li
- Institute of Life Sciences and Technology, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China; Department of Clinical Laboratory, ZhongDa Hospital, Southeast University, Nanjing, Jiangsu 210009, China.
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8
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. J Hepatol 2021; 75:572-581. [PMID: 34033851 PMCID: PMC8811537 DOI: 10.1016/j.jhep.2021.04.055] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUNDS & AIMS Primary biliary cholangitis (PBC) is a chronic liver disease in which autoimmune destruction of the small intrahepatic bile ducts eventually leads to cirrhosis. Many patients have inadequate response to licensed medications, motivating the search for novel therapies. Previous genome-wide association studies (GWAS) and meta-analyses (GWMA) of PBC have identified numerous risk loci for this condition, providing insight into its aetiology. We undertook the largest GWMA of PBC to date, aiming to identify additional risk loci and prioritise candidate genes for in silico drug efficacy screening. METHODS We combined new and existing genotype data for 10,516 cases and 20,772 controls from 5 European and 2 East Asian cohorts. RESULTS We identified 56 genome-wide significant loci (20 novel) including 46 in European, 13 in Asian, and 41 in combined cohorts; and a 57th genome-wide significant locus (also novel) in conditional analysis of the European cohorts. Candidate genes at newly identified loci include FCRL3, INAVA, PRDM1, IRF7, CCR6, CD226, and IL12RB1, which each play key roles in immunity. Pathway analysis reiterated the likely importance of pattern recognition receptor and TNF signalling, JAK-STAT signalling, and differentiation of T helper (TH)1 and TH17 cells in the pathogenesis of this disease. Drug efficacy screening identified several medications predicted to be therapeutic in PBC, some of which are well-established in the treatment of other autoimmune disorders. CONCLUSIONS This study has identified additional risk loci for PBC, provided a hierarchy of agents that could be trialled in this condition, and emphasised the value of genetic and genomic approaches to drug discovery in complex disorders. LAY SUMMARY Primary biliary cholangitis (PBC) is a chronic liver disease that eventually leads to cirrhosis. In this study, we analysed genetic information from 10,516 people with PBC and 20,772 healthy individuals recruited in Canada, China, Italy, Japan, the UK, or the USA. We identified several genetic regions associated with PBC. Each of these regions contains several genes. For each region, we used diverse sources of evidence to help us choose the gene most likely to be involved in causing PBC. We used these 'candidate genes' to help us identify medications that are currently used for treatment of other conditions, which might also be useful for treatment of PBC.
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Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan; Department of Hepatology, Nagasaki Graduate School of Biomedical Sciences, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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9
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Asselta R, Paraboschi EM, Gerussi A, Cordell HJ, Mells GF, Sandford RN, Jones DE, Nakamura M, Ueno K, Hitomi Y, Kawashima M, Nishida N, Tokunaga K, Nagasaki M, Tanaka A, Tang R, Li Z, Shi Y, Liu X, Xiong M, Hirschfield G, Siminovitch KA, Carbone M, Cardamone G, Duga S, Gershwin ME, Seldin MF, Invernizzi P. X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis. Gastroenterology 2021; 160:2483-2495.e26. [PMID: 33675743 PMCID: PMC8169555 DOI: 10.1053/j.gastro.2021.02.061] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies in primary biliary cholangitis (PBC) have failed to find X chromosome (chrX) variants associated with the disease. Here, we specifically explore the chrX contribution to PBC, a sexually dimorphic complex autoimmune disease. METHODS We performed a chrX-wide association study, including genotype data from 5 genome-wide association studies (from Italy, United Kingdom, Canada, China, and Japan; 5244 case patients and 11,875 control individuals). RESULTS Single-marker association analyses found approximately 100 loci displaying P < 5 × 10-4, with the most significant being a signal within the OTUD5 gene (rs3027490; P = 4.80 × 10-6; odds ratio [OR], 1.39; 95% confidence interval [CI], 1.028-1.88; Japanese cohort). Although the transethnic meta-analysis evidenced only a suggestive signal (rs2239452, mapping within the PIM2 gene; OR, 1.17; 95% CI, 1.09-1.26; P = 9.93 × 10-8), the population-specific meta-analysis showed a genome-wide significant locus in East Asian individuals pointing to the same region (rs7059064, mapping within the GRIPAP1 gene; P = 6.2 × 10-9; OR, 1.33; 95% CI, 1.21-1.46). Indeed, rs7059064 tags a unique linkage disequilibrium block including 7 genes: TIMM17B, PQBP1, PIM2, SLC35A2, OTUD5, KCND1, and GRIPAP1, as well as a superenhancer (GH0XJ048933 within OTUD5) targeting all these genes. GH0XJ048933 is also predicted to target FOXP3, the main T-regulatory cell lineage specification factor. Consistently, OTUD5 and FOXP3 RNA levels were up-regulated in PBC case patients (1.75- and 1.64-fold, respectively). CONCLUSIONS This work represents the first comprehensive study, to our knowledge, of the chrX contribution to the genetics of an autoimmune liver disease and shows a novel PBC-related genome-wide significant locus.
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Affiliation(s)
- Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, United Kingdom
| | - George F Mells
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - Richard N Sandford
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - David E Jones
- Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Nagasaki, Japan; Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan; Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhiqiang Li
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu, China
| | - Ma Xiong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Gideon Hirschfield
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Katherine A Siminovitch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | | | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy.
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10
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Wang C, Zheng X, Tang R, Han C, Jiang Y, Wu J, Shao Y, Gao Y, Yu J, Hu Z, Zang Z, Zhao Y, Dai N, Liu L, Wu X, Nie J, Jiang B, Lin M, Li L, Wei Y, Li Y, Gong Y, Dai Y, Wang L, Ding N, Xu P, Chen S, Jiang P, Wang L, Qiu F, Wu Q, Zhang M, Jawed R, Chen R, Zhang Y, Shi X, Zhu Z, Pei H, Huang L, Tian Y, Zhang K, Qiu H, Zhao W, Gershwin ME, Chen W, Seldin MF, Liu X, Ma X, Sun L. Fine mapping of the MHC region identifies major independent variants associated with Han Chinese primary biliary cholangitis. J Autoimmun 2019; 107:102372. [PMID: 31810856 DOI: 10.1016/j.jaut.2019.102372] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/03/2019] [Accepted: 11/14/2019] [Indexed: 02/08/2023]
Abstract
The genetic association of primary biliary cholangitis with major histocompatibility complex (MHC) has been widely confirmed among different ethnicities. To map specific MHC region variants associated with PBC in a Han Chinese cohort, we imputed HLA antigens and amino acids (AA) in 1126 PBC cases and 1770 healthy control subjects using a Han-MHC reference database. We demonstrate that HLA-DRB1 and/or HLA-DQB1 contributed the strongest signals, and that HLA-DPB1 was a separate independent locus. Regression analyses with classical HLA alleles indicate that HLA-DQB1*03:01 or HLA-DQβ1-Pro55, HLA-DPB1*17:01 or HLA-DPβ1-Asp84 and HLA-DRB1*08:03 could largely explain MHC association with PBC. Forward stepwise regression analyses with HLA amino acid variants localize the major signals to HLA-DRβ1-Ala74, HLA-DQβ1-Pro55 and HLA-DPβ1-Asp84. Electrostatic potential calculations implicated AA variations at HLA-DQβ1 position 55 and HLA-DPβ1 position 84 as critical to peptide binding properties. Furthermore, although several critical Han Chinese AA variants differed from those shown in European populations, the predicted effects on antigen binding are likely to be very similar or identical and underlie the major component of MHC association with PBC.
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Affiliation(s)
- Chan Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Xiaodong Zheng
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China, Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China, Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China, 218 Jixi Road, Hefei, Anhui, 230022, China
| | - Ruqi Tang
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, 145 Shandong Middle Road, Shanghai, 200001, China
| | - Chongxu Han
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, 98 Nantong West Road, Yangzhou, Jiangsu, 225001, China
| | - Yuzhang Jiang
- Department of Laboratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, 1 Huanghe West Road, Huai'an, Jiangsu, 223300, China
| | - Jian Wu
- Department of Rheumatology, First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, China
| | - Youlin Shao
- Department of Hepatology, The Third People's Hospital of Changzhou, 300 Lanling North Road, Changzhou, Jiangsu, 213001, China
| | - Yueqiu Gao
- Department of Liver Disease, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, China
| | - Jianjiang Yu
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, 163 Shoushan Road, Jiangyin, Jiangsu, 214400, China
| | - Zhigang Hu
- Department of Laboratory Medicine, Affiliated Wuxi People's Hospital of Nanjing Medical University, 299 Qingyang Road, Wuxi, Jiangsu, 214023, China
| | - Zhidong Zang
- Department of Hepatology, The Second Hospital of Nanjing, Southeast University, 1 Zhongfu Road, Nanjing, jiangsu, 210003, China
| | - Yi Zhao
- Department of Gastrointestinal Endoscopy, Eastern Hepatobiliary Surgery Hospital, 700 Moyu North Road, Shanghai, 201800, China
| | - Na Dai
- Department of Gastroenterology, Jiangsu University Affiliated Kunshan Hospital, 91 Qianjin West Road, Kunshan, Jiangsu, 215300, China
| | - Lei Liu
- Department of Gastroenterology, Yixing People's Hospital, 75 Tongzhenguan Road, Yixing, Jiangsu, 214200, China
| | - Xudong Wu
- Department of Gastroenterology, Yancheng First People's Hospital, 66 Renmin South Road, Yancheng, Jiangsu, 224005, China
| | - Jinshan Nie
- Department of Gastroenterology, Taicang First People's Hospital, Soochow University, 58 Changsheng South Road, Taicang, Jiangsu, 215400, China
| | - Bo Jiang
- Department of Hepatology, Jingjiang Second People's Hospital, 1 Chengxiqiao Jiangping Road, Jingjiang, Jiangsu, 214500, China
| | - Maosong Lin
- Department of Gastroenterology, Taizhou People's Hospital, 210 Yingchun Road, Taizhou, Jiangsu, 225300, China
| | - Li Li
- Department of Laboratory Medicine, Zhongda Hospital, Southeast University, 87 Dingjiaqiao Road, Nanjing, Jiangsu, 210009, China
| | - Yiran Wei
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, 145 Shandong Middle Road, Shanghai, 200001, China
| | - You Li
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, 145 Shandong Middle Road, Shanghai, 200001, China
| | - Yuhua Gong
- Department of Laboratory Medicine, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, Jiangsu, 212021, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, 1215 Guangrui Road, Wuxi, Jiangsu, 214000, China
| | - Lan Wang
- Department of Laboratory Medicine, The 81st Hospital of PLA, 34 Yanggongjing Nanjing, Jiangsu, 210002, China
| | - Ningling Ding
- Department of Hepatology, Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, 10 Guangqian Road, Suzhou, Jiangsu, 215131, China
| | - Ping Xu
- Department of Radiology, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu, 215004, China
| | - Sufang Chen
- Department of Hepatology, Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, 10 Guangqian Road, Suzhou, Jiangsu, 215131, China
| | - Peng Jiang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Lu Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Fang Qiu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Qiuyuan Wu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Mingming Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Rohil Jawed
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Ru Chen
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Yu Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China
| | - Zhen Zhu
- Department of Hepatology, The Third People's Hospital of Changzhou, 300 Lanling North Road, Changzhou, Jiangsu, 213001, China
| | - Hao Pei
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, 1215 Guangrui Road, Wuxi, Jiangsu, 214000, China
| | - Lihua Huang
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, 1215 Guangrui Road, Wuxi, Jiangsu, 214000, China
| | - Ye Tian
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China
| | - Kui Zhang
- Department of Hepatology, First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, China
| | - Hong Qiu
- Department of Laboratory Medicine, The 81st Hospital of PLA, 34 Yanggongjing Nanjing, Jiangsu, 210002, China
| | - Weifeng Zhao
- Department of Hepatology, First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, China
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility Building, 451 Health Sciences Drive, Suite 6510, Davis, CA, 95616, USA
| | - Weichang Chen
- Department of Gastroenterology, First Affiliated Hospital of Soochow University, 188 Shizi Road, Suzhou, Jiangsu, 215006, China
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis School of Medicine, 4327 Tupper Hall, Davis, CA, 95616, USA
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu, 210096, China.
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, 145 Shandong Middle Road, Shanghai, 200001, China.
| | - Liangdan Sun
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China, Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China, Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China, 218 Jixi Road, Hefei, Anhui, 230022, China.
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11
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Wang C, Zheng X, Jiang P, Tang R, Gong Y, Dai Y, Wang L, Xu P, Sun W, Wang L, Han C, Jiang Y, Wei Y, Zhang K, Wu J, Shao Y, Gao Y, Yu J, Hu Z, Zang Z, Zhao Y, Wu X, Dai N, Liu L, Nie J, Jiang B, Lin M, Li L, Li Y, Chen S, Shu L, Qiu F, Wu Q, Zhang M, Chen R, Jawed R, Zhang Y, Shi X, Zhu Z, Pei H, Huang L, Zhao W, Tian Y, Zhu X, Qiu H, Gershwin ME, Chen W, Seldin MF, Liu X, Sun L, Ma X. Genome-wide Association Studies of Specific Antinuclear Autoantibody Subphenotypes in Primary Biliary Cholangitis. Hepatology 2019; 70:294-307. [PMID: 30854688 PMCID: PMC6618054 DOI: 10.1002/hep.30604] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/03/2019] [Indexed: 02/05/2023]
Abstract
Anti-nuclear antibodies to speckled 100 kDa (sp100) and glycoprotein 210 (gp210) are specific serologic markers of primary biliary cholangitis (PBC) of uncertain/controversial clinical or prognostic significance. To study the genetic determinants associated with sp100 and gp210 autoantibody subphenotypes, we performed a genome-wide association analysis of 930 PBC cases based on their autoantibody status, followed by a replication study in 1,252 PBC cases. We confirmed single-nucleotide polymorphisms rs492899 (P = 3.27 × 10-22 ; odds ratio [OR], 2.90; 95% confidence interval [CI], 2.34-3.66) and rs1794280 (P = 5.78 × 10-28 ; OR, 3.89; 95% CI, 3.05-4.96) in the human major histocompatibility complex (MHC) region associated with the sp100 autoantibody. However, no genetic variant was identified as being associated with the gp210 autoantibody. To further define specific classical human leukocyte antigen (HLA) alleles or amino acids associated with the sp100 autoantibody, we imputed 922 PBC cases (211 anti-sp100-positive versus 711 negative cases) using a Han Chinese MHC reference database. Conditional analysis identified that HLA-DRβ1-Asn77/Arg74, DRβ1-Ser37, and DPβ1-Lys65 were major determinants for sp100 production. For the classical HLA alleles, the strongest association was with DRB1*03:01 (P = 1.51 × 10-9 ; OR, 2.97; 95% CI, 2.06-4.29). Regression analysis with classical HLA alleles identified DRB1*03:01, DRB1*15:01, DRB1*01, and DPB1*03:01 alleles can explain most of the HLA association with sp100 autoantibody. Conclusion: This study indicated significant genetic predisposition to the sp100 autoantibody, but not the gp210 autoantibody, subphenotype in PBC patients. Additional studies will be necessary to determine if these findings have clinical significance to PBC pathogenesis and/or therapeutics.
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Affiliation(s)
- Chan Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Xiaodong Zheng
- Department of DermatologyThe First Affiliated Hospital of Anhui Medical University, and Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China & Key Laboratory of Major Autoimmune Diseases, Anhui ProvinceHefeiChina
| | - Peng Jiang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Ruqi Tang
- Department of Gastroenterology and HepatologyShanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji HospitalShanghaiChina
| | - Yuhua Gong
- Department of Laboratory MedicineThe Third People's Hospital of ZhenjiangZhenjiangJiangsuChina
| | - Yaping Dai
- Department of Laboratory MedicineThe Fifth People's Hospital of WuxiWuxiJiangsuChina
| | - Lan Wang
- Department of Laboratory MedicineThe 81st Hospital of PLANanjingJiangsuChina
| | - Ping Xu
- Department of Laboratory MedicineThe Fifth People's Hospital of Suzhou, Soochow UniversitySuzhouJiangsuChina
| | - Wenjuan Sun
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Lu Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Chongxu Han
- Department of Laboratory MedicineSubei People's Hospital, Clinical Medical College, Yangzhou UniversityYangzhouJiangsuChina
| | - Yuzhang Jiang
- Department of Laboratory MedicineHuai'an First People's Hospital, Nanjing Medical UniversityHuai'anJiangsuChina
| | - Yiran Wei
- Department of Gastroenterology and HepatologyShanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji HospitalShanghaiChina
| | - Kui Zhang
- Department of Laboratory MedicineNanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical SchoolNanjingJiangsuChina
| | - Jian Wu
- Department of RheumatologyFirst Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Youlin Shao
- Department of HepatologyThe Third People's Hospital of ChangzhouChangzhouJiangsuChina
| | - Yueqiu Gao
- Department of Liver DiseasesShuguang Hospital, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Jianjiang Yu
- Department of Laboratory MedicineJiangyin People's Hospital, Southeast UniversityJiangyinJiangsuChina
| | - Zhigang Hu
- Department of Laboratory MedicineAffiliated Wuxi People's Hospital of Nanjing Medical UniversityWuxiJiangsuChina
| | - Zhidong Zang
- Department of HepatologyThe Second Hospital of Nanjing, Southeast UniversityNanjingJiangsuChina
| | - Yi Zhao
- Department of Gastrointestinal EndoscopyEastern Hepatobiliary Surgery HospitalShanghaiChina
| | - Xudong Wu
- Department of GastroenterologyYancheng First People's HospitalYanchengJiangsuChina
| | - Na Dai
- Department of GastroenterologyJiangsu University Affiliated Kunshan HospitalKunshanJiangsuChina
| | - Lei Liu
- Department of GastroenterologyYixing People's HospitalYixinJiangsuChina
| | - Jinshan Nie
- Department of GastroenterologyTaicang First People's Hospital, Soochow UniversityTaicangJiangsuChina
| | - Bo Jiang
- Department of HepatologyJingjiang Second People's HospitalJingjiangJiangsuChina
| | - Maosong Lin
- Department of GastroenterologyTaizhou People's HospitalTaizhouJiangsuChina
| | - Li Li
- Department of Laboratory MedicineZhongda Hospital, Southeast UniversityNanjingJiangsuChina
| | - You Li
- Department of Gastroenterology and HepatologyShanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji HospitalShanghaiChina
| | - Sufang Chen
- Department of Laboratory MedicineThe Fifth People's Hospital of Suzhou, Soochow UniversitySuzhouJiangsuChina
| | - Lixin Shu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Fang Qiu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Qiuyuan Wu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Mingming Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Ru Chen
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Rohil Jawed
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Yu Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Zhen Zhu
- Department of HepatologyThe Third People's Hospital of ChangzhouChangzhouJiangsuChina
| | - Hao Pei
- Department of Laboratory MedicineThe Fifth People's Hospital of WuxiWuxiJiangsuChina
| | - Lihua Huang
- Department of Laboratory MedicineThe Fifth People's Hospital of WuxiWuxiJiangsuChina
| | - Weifeng Zhao
- Department of GastroenterologyFirst Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Ye Tian
- Department of RadiologyThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Xiang Zhu
- Department of Laboratory MedicineThe Fifth People's Hospital of Suzhou, Soochow UniversitySuzhouJiangsuChina
| | - Hong Qiu
- Department of Laboratory MedicineThe 81st Hospital of PLANanjingJiangsuChina
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California at Davis School of MedicineDavisCA
| | - Weichang Chen
- Department of GastroenterologyFirst Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Michael F. Seldin
- Department of Biochemistry and Molecular MedicineUniversity of California at Davis School of MedicineDavisCA
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life SciencesSoutheast UniversityNanjingJiangsuChina
| | - Liangdan Sun
- Department of DermatologyThe First Affiliated Hospital of Anhui Medical University, and Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China & Key Laboratory of Major Autoimmune Diseases, Anhui ProvinceHefeiChina
| | - Xiong Ma
- Department of Gastroenterology and HepatologyShanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji HospitalShanghaiChina
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12
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Liaskou E, Jeffery L, Chanouzas D, Soskic B, Seldin MF, Harper L, Sansom D, Hirschfield GM. Genetic variation at the CD28 locus and its impact on expansion of pro-inflammatory CD28 negative T cells in healthy individuals. Sci Rep 2017; 7:7652. [PMID: 28794437 PMCID: PMC5550460 DOI: 10.1038/s41598-017-07967-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/05/2017] [Indexed: 12/13/2022] Open
Abstract
The CD28 locus is associated with susceptibility to a variety of autoimmune and immune-mediated inflammatory diseases including primary sclerosing cholangitis (PSC). Previously, we linked the CD28 pathway in PSC disease pathology and found that vitamin D could maintain CD28 expression. Here, we assessed whether the PSC-associated CD28 risk variant A (rs7426056) affects CD28 expression and T cell function in healthy individuals (n = 14 AA, n = 14 AG, n = 14 GG). Homozygotes for the PSC disease risk allele (AA) showed significantly lower CD28 mRNA expression ex-vivo than either GG or AG (p < 0.001) in total peripheral blood mononuclear cells. However, the CD28 risk variant alone was not sufficient to explain CD28 protein loss on CD4+ T cells. All genotypes responded equally to vitamin D as indicated by induction of a regulatory phenotype and an increased anti-inflammatory/pro-inflammatory cytokine ratio. A genotypic effect on response to TNFα stimuli was detected, which was inhibited by vitamin D. Together our results show: (a) an altered gene expression in carriers of the susceptible CD28 variant, (b) no differences in protein levels on CD4+ T cells, and (c) a protective effect of the variant upon CD28 protein loss on CD4+ T cells under inflammatory conditions.
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Affiliation(s)
- Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.,Centre for Rare Diseases, Institute of Translational Medicine, Birmingham Health Partners, University Hospitals Birmingham, Birmingham, UK
| | - Louisa Jeffery
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dimitrios Chanouzas
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Blagoje Soskic
- Institute of Immunity and Transplantation, University College London and Royal Free Hospital, London, NW3 2PF, UK
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, 95616, USA.,Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA, 95616, USA
| | - Lorraine Harper
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - David Sansom
- Institute of Immunity and Transplantation, University College London and Royal Free Hospital, London, NW3 2PF, UK
| | - Gideon M Hirschfield
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK. .,Centre for Rare Diseases, Institute of Translational Medicine, Birmingham Health Partners, University Hospitals Birmingham, Birmingham, UK.
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13
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Qiu F, Tang R, Zuo X, Shi X, Wei Y, Zheng X, Dai Y, Gong Y, Wang L, Xu P, Zhu X, Wu J, Han C, Gao Y, Zhang K, Jiang Y, Zhou J, Shao Y, Hu Z, Tian Y, Zhang H, Dai N, Liu L, Wu X, Zhao W, Zhang X, Zang Z, Nie J, Sun W, Zhao Y, Mao Y, Jiang P, Ji H, Dong Q, Li J, Li Z, Bai X, Li L, Lin M, Dong M, Li J, Zhu P, Wang C, Zhang Y, Jiang P, Wang Y, Jawed R, Xu J, Zhang Y, Wang Q, Yang Y, Yang F, Lian M, Jiang X, Xiao X, Li Y, Fang J, Qiu D, Zhu Z, Qiu H, Zhang J, Tian W, Chen S, Jiang L, Ji B, Li P, Chen G, Wu T, Sun Y, Yu J, Tang H, He M, Xia M, Pei H, Huang L, Qing Z, Wu J, Huang Q, Han J, Xie W, Sun Z, Guo J, He G, Eric Gershwin M, Lian Z, Liu X, Seldin MF, Liu X, Chen W, Ma X. A genome-wide association study identifies six novel risk loci for primary biliary cholangitis. Nat Commun 2017; 8:14828. [PMID: 28425483 PMCID: PMC5429142 DOI: 10.1038/ncomms14828] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/27/2017] [Indexed: 02/07/2023] Open
Abstract
Primary biliary cholangitis (PBC) is an autoimmune liver disease with a strong hereditary component. Here, we report a genome-wide association study that included 1,122 PBC cases and 4,036 controls of Han Chinese descent, with subsequent replication in a separate cohort of 907 PBC cases and 2,127 controls. Our results show genome-wide association of 14 PBC risk loci including previously identified 6p21 (HLA-DRA and DPB1), 17q12 (ORMDL3), 3q13.33 (CD80), 2q32.3 (STAT1/STAT4), 3q25.33 (IL12A), 4q24 (NF-κB) and 22q13.1 (RPL3/SYNGR1). We also identified variants in IL21, IL21R, CD28/CTLA4/ICOS, CD58, ARID3A and IL16 as novel PBC risk loci. These new findings and histochemical studies showing enhanced expression of IL21 and IL21R in PBC livers (particularly in the hepatic portal tracks) support a disease mechanism in which the deregulation of the IL21 signalling pathway, in addition to CD4 T-cell activation and T-cell co-stimulation are critical components in the development of PBC.
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Affiliation(s)
- Fang Qiu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ruqi Tang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Xianbo Zuo
- Department of Dermatology at No. 1 Hospital, Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230022, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yiran Wei
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Xiaodong Zheng
- Department of Dermatology at No. 1 Hospital, Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230022, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214005, China
| | - Yuhua Gong
- Department of Laboratory Medicine, The Third People's Hospital of Zhenjiang, Zhenjiang, Jiangsu 212005, China
| | - Lan Wang
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Ping Xu
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, Suzhou, Jiangsu 215007, China
| | - Xiang Zhu
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, Suzhou, Jiangsu 215007, China
| | - Jian Wu
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Chongxu Han
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Yueqiu Gao
- Department of Hepatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Kui Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Yuzhang Jiang
- Department of Laboratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu 223300, China
| | - Jianbo Zhou
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, Jiangyin, Jiangsu 214400, China
| | - Youlin Shao
- Department of Laboratory Medicine, The Third People's Hospital of Changzhou, Changzhou, Jiangsu 213000, China
| | - Zhigang Hu
- Department of Laboratory Medicine, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Ye Tian
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Haiyan Zhang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Na Dai
- Department of Gastroenterology, Jiangsu University affiliated Kunshan Hospital, Kunshan, Jiangsu 215300, China
| | - Lei Liu
- Department of Gastroenterology, Yixing People's Hospital, Yixing, Jiangsu 214200, China
| | - Xudong Wu
- Department of Gastroenterology, Yancheng First People's Hospital, Yancheng, Jiangsu 224005, China
| | - Weifeng Zhao
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Xiaomin Zhang
- Department of Laboratory Medicine, The University Hospital, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhidong Zang
- Department of Hepatology, The Second Hospital of Nanjing, Southeast University, Nanjing, Jiangsu 210003, China
| | - Jinshan Nie
- Department of Gastroenterology, Taicang First People's Hospital, Soochow University, Taicang, Jiangsu 215400, China
| | - Weihao Sun
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yi Zhao
- Department of Gastroenterology, Eastern Hepatobiliary Surgery Hospital, Shanghai 201805, China
| | - Yuan Mao
- Department of Immunology, Nanjing Kingmed Clinical Laboratory Co. Ltd. Nanjing, Jiangsu 210042, China
| | - Po Jiang
- Department of Hepatology, The Second People's Hospital of Jingjiang, Jingjiang, Jiangsu 214500, China
| | - Hualiang Ji
- Department of Gastroenterology, Hai'an People's Hospital, Nantong University Medical School, Hai'an, Jiangsu 226600, China
| | - Qing Dong
- Department of Laboratory Medicine, Suzhou Hospital of Traditional Chinese Medicine, Suzhou, Jiangsu 215009, China
| | - Junming Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zhenzhong Li
- Department of Paediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Xinli Bai
- Department of Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Li Li
- Department of Gastroenterology, Taizhou People's Hospital, Taizhou, Jiangsu 225300, China
| | - Maosong Lin
- Department of Hepatology, Traditional Chinese Medicine Hospital of Kunshan, Kunshan 215300, China
| | - Ming Dong
- Department of Genomics and Epigenomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinxin Li
- Department of Gerontology, Beijing Hospital, Beijing 100730, China
| | - Ping Zhu
- Department of Nutrition and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Chan Wang
- Division of Rheumatology, Allergy, and Clinical Immunology, Rowe Program in Genetics, University of California-Davis, Davis, California 95616, USA
| | - Yanqiu Zhang
- Department of Immunology, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Peng Jiang
- Department of Stomatology, The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yujue Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Rohil Jawed
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jing Xu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yu Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Qixia Wang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Yue Yang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Fan Yang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Min Lian
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Xiang Jiang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Xiao Xiao
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Yanmei Li
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Jingyuan Fang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Dekai Qiu
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
| | - Zhen Zhu
- Department of Laboratory Medicine, The Third People's Hospital of Changzhou, Changzhou, Jiangsu 213000, China
| | - Hong Qiu
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenyan Tian
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Sufang Chen
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Soochow University, Suzhou, Jiangsu 215007, China
| | - Ling Jiang
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Bing Ji
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Ping Li
- Department of Laboratory Medicine, The 81th Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Guochang Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Tianxue Wu
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Yan Sun
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Jianjiang Yu
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, Jiangyin, Jiangsu 214400, China
| | - Huijun Tang
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, Jiangyin, Jiangsu 214400, China
| | - Michun He
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Min Xia
- Department of Laboratory Medicine, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Hao Pei
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214005, China
| | - Lihua Huang
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214005, China
| | - Zhuye Qing
- Department of Immunology, Nanjing Kingmed Clinical Laboratory Co. Ltd. Nanjing, Jiangsu 210042, China
| | - Jianfang Wu
- Department of Hepatology, Traditional Chinese Medicine Hospital of Kunshan, Kunshan 215300, China
| | - Qinghai Huang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Junhai Han
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wei Xie
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhongsheng Sun
- Department of Genomics and Epigenomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Guo
- Department of Gerontology, Beijing Hospital, Beijing 100730, China
| | - Gengsheng He
- Department of Nutrition and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, Rowe Program in Genetics, University of California-Davis, Davis, California 95616, USA
| | - Zhexiong Lian
- Department of Immunology, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Xiang Liu
- Department of Stomatology, The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, China
| | - Michael F. Seldin
- Division of Rheumatology, Allergy, and Clinical Immunology, Rowe Program in Genetics, University of California-Davis, Davis, California 95616, USA
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Weichang Chen
- Department of Rheumatology, Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai 200001, China
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14
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Rothwell S, Cooper RG, Lundberg IE, Gregersen PK, Hanna MG, Machado PM, Herbert MK, Pruijn GJM, Lilleker JB, Roberts M, Bowes J, Seldin MF, Vencovsky J, Danko K, Limaye V, Selva-O'Callaghan A, Platt H, Molberg Ø, Benveniste O, Radstake TRDJ, Doria A, De Bleecker J, De Paepe B, Gieger C, Meitinger T, Winkelmann J, Amos CI, Ollier WE, Padyukov L, Lee AT, Lamb JA, Chinoy H. Immune-Array Analysis in Sporadic Inclusion Body Myositis Reveals HLA-DRB1 Amino Acid Heterogeneity Across the Myositis Spectrum. Arthritis Rheumatol 2017; 69:1090-1099. [PMID: 28086002 PMCID: PMC5516174 DOI: 10.1002/art.40045] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/10/2017] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Inclusion body myositis (IBM) is characterized by a combination of inflammatory and degenerative changes affecting muscle. While the primary cause of IBM is unknown, genetic factors may influence disease susceptibility. To determine genetic factors contributing to the etiology of IBM, we conducted the largest genetic association study of the disease to date, investigating immune-related genes using the Immunochip. METHODS A total of 252 Caucasian patients with IBM were recruited from 11 countries through the Myositis Genetics Consortium and compared with 1,008 ethnically matched controls. Classic HLA alleles and amino acids were imputed using SNP2HLA. RESULTS The HLA region was confirmed as the most strongly associated region in IBM (P = 3.58 × 10-33 ). HLA imputation identified 3 independent associations (with HLA-DRB1*03:01, DRB1*01:01, and DRB1*13:01), although the strongest association was with amino acid positions 26 and 11 of the HLA-DRB1 molecule. No association with anti-cytosolic 5'-nucleotidase 1A-positive status was found independent of HLA-DRB1*03:01. There was no association of HLA genotypes with age at onset of IBM. Three non-HLA regions reached suggestive significance, including the chromosome 3 p21.31 region, an established risk locus for autoimmune disease, where a frameshift mutation in CCR5 is thought to be the causal variant. CONCLUSION This is the largest, most comprehensive genetic association study to date in IBM. The data confirm that HLA is the most strongly associated region and identifies novel amino acid associations that may explain the risk in this locus. These amino acid associations differentiate IBM from polymyositis and dermatomyositis and may determine properties of the peptide-binding groove, allowing it to preferentially bind autoantigenic peptides. A novel suggestive association within the chromosome 3 p21.31 region suggests a role for CCR5.
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Affiliation(s)
| | | | - Ingrid E Lundberg
- Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Megan K Herbert
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, and Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - James B Lilleker
- University of Manchester, Manchester, UK, and Salford Royal NHS Foundation Trust, Salford, UK
| | | | - John Bowes
- University of Manchester, Manchester, UK
| | | | | | | | - Vidya Limaye
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | | | | | | | | | | | | | | | | | | | - Thomas Meitinger
- Technische Universität München, Munich, Germany, and Helmholtz Zentrum München, Neuherberg, Germany
| | - Juliane Winkelmann
- Technische Universität München, Munich, Germany, and Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | | | - Annette T Lee
- Feinstein Institute for Medical Research, Manhasset, New York
| | | | - Hector Chinoy
- Central Manchester University Hospitals NHS Foundation Trust, University of Manchester, Manchester, UK
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15
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Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev 2017; 26:126-135. [PMID: 27697780 PMCID: PMC5224974 DOI: 10.1158/1055-9965.epi-16-0106] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/30/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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Affiliation(s)
- Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - David J Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kimberly Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlisse Caga-Anan
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christopher A Haiman
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Tessier
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Daniel Vincent
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - François Bacot
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Stefanie Nelson
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Stephen Demetriades
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | | | | | - Judith L Forman
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Brüske-Hohlfeld
- Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lesley McGuffog
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karoline Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Katja Butterbach
- Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kraft
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Liesel FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Sara Lindström
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marjorie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew Berchuck
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Sylvie Laboissiere
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jack A Taylor
- Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sue K Park
- College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Hospital, New York, New York
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Rita Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California
- Department of Internal Medicine, University of California at Davis, Davis, California
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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16
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Li Y, Byun J, Cai G, Xiao X, Han Y, Cornelis O, Dinulos JE, Dennis J, Easton D, Gorlov I, Seldin MF, Amos CI. FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data. BMC Bioinformatics 2016; 17:122. [PMID: 26961892 PMCID: PMC4784403 DOI: 10.1186/s12859-016-0965-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/22/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Identifying subpopulations within a study and inferring intercontinental ancestry of the samples are important steps in genome wide association studies. Two software packages are widely used in analysis of substructure: Structure and Eigenstrat. Structure assigns each individual to a population by using a Bayesian method with multiple tuning parameters. It requires considerable computational time when dealing with thousands of samples and lacks the ability to create scores that could be used as covariates. Eigenstrat uses a principal component analysis method to model all sources of sampling variation. However, it does not readily provide information directly relevant to ancestral origin; the eigenvectors generated by Eigenstrat are sample specific and thus cannot be generalized to other individuals. RESULTS We developed FastPop, an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins. We demonstrate the use of FastPop using 2318 SNP markers selected from the genome based on high variability among European, Asian and West African (African) populations. We conducted an analysis of 505 Hapmap samples with European, African or Asian ancestry along with 19661 additional samples of unknown ancestry. The results from FastPop are highly consistent with those obtained by Structure across the 19661 samples we studied. The correlations of the results between FastPop and Structure are 0.99, 0.97 and 0.99 for European, African and Asian ancestry scores, respectively. Compared with Structure, FastPop is more efficient as it finished ancestry inference for 19661 samples in 16 min compared with 21-24 h required by Structure. FastPop also provided scores based on SNP weights so the scores of reference population can be applied to other studies provided the same set of markers are used. We also present application of the method for studying four continental populations (European, Asian, African, and Native American). CONCLUSIONS We developed an algorithm that can infer ancestries on data involving two or more intercontinental origins. It is efficient for analyzing large datasets. Additionally the PCA derived scores can be applied to multiple data sets to ensure the same ancestry analysis is applied to all studies.
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Affiliation(s)
- Yafang Li
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - Jinyoung Byun
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - Guoshuai Cai
- Department of Genetics, Dartmouth College, Hanover, NH, USA.
| | - Xiangjun Xiao
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - Younghun Han
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - Olivier Cornelis
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - James E Dinulos
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Cambridge University, Cambridge, UK.
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Cambridge University, Cambridge, UK.
| | - Ivan Gorlov
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
| | | | - Christopher I Amos
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA.
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17
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Tang R, Wei Y, Li Z, Chen H, Miao Q, Bian Z, Zhang H, Wang Q, Wang Z, Lian M, Yang F, Jiang X, Yang Y, Li E, Seldin MF, Gershwin ME, Liao W, Shi Y, Ma X. A Common Variant in CLDN14 is Associated with Primary Biliary Cirrhosis and Bone Mineral Density. Sci Rep 2016; 6:19877. [PMID: 26842849 PMCID: PMC4740766 DOI: 10.1038/srep19877] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/16/2015] [Indexed: 12/22/2022] Open
Abstract
Primary biliary cirrhosis (PBC), a chronic autoimmune liver disease, has been associated with increased incidence of osteoporosis. Intriguingly, two PBC susceptibility loci identified through genome-wide association studies are also involved in bone mineral density (BMD). These observations led us to investigate the genetic variants shared between PBC and BMD. We evaluated 72 genome-wide significant BMD SNPs for association with PBC using two European GWAS data sets (n = 8392), with replication of significant findings in a Chinese cohort (685 cases, 1152 controls). Our analysis identified a novel variant in the intron of the CLDN14 gene (rs170183, Pfdr = 0.015) after multiple testing correction. The three associated variants were followed-up in the Chinese cohort; one SNP rs170183 demonstrated consistent evidence of association in diverse ethnic populations (Pcombined = 2.43 × 10−5). Notably, expression quantitative trait loci (eQTL) data revealed that rs170183 was correlated with a decline in CLDN14 expression in both lymphoblastoid cell lines and T cells (Padj = 0.003 and 0.016, respectively). In conclusion, our study identified a novel PBC susceptibility variant that has been shown to be strongly associated with BMD, highlighting the potential of pleiotropy to improve gene discovery.
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Affiliation(s)
- Ruqi Tang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yiran Wei
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Qi Miao
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhaolian Bian
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Haiyan Zhang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Qixia Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhaoyue Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Min Lian
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Fan Yang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiang Jiang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yue Yang
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Enling Li
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA 95616, USA.,Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616, USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco School of Medicine, 1701 Dividadero Street, San Francisco, CA 94415, USA
| | - Yongyong Shi
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Xiong Ma
- State Key Laboratory for Oncogenes and Related Genes, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
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18
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Dong M, Li J, Tang R, Zhu P, Qiu F, Wang C, Qiu J, Wang L, Dai Y, Xu P, Gao Y, Han C, Wang Y, Wu J, Wu X, Zhang K, Dai N, Sun W, Zhou J, Hu Z, Liu L, Jiang Y, Nie J, Zhao Y, Gong Y, Tian Y, Ji H, Jiao Z, Jiang P, Shi X, Jawed R, Zhang Y, Huang Q, Li E, Wei Y, Xie W, Zhao W, Liu X, Zhu X, Qiu H, He G, Chen W, Seldin MF, Gershwin ME, Liu X, Ma X. Multiple genetic variants associated with primary biliary cirrhosis in a Han Chinese population. Clin Rev Allergy Immunol 2016; 48:316-21. [PMID: 25690649 DOI: 10.1007/s12016-015-8472-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Multiple genome-wide association studies of primary biliary cirrhosis (PBC) in both European and Japanese ancestries have shown significant associations of many genetic loci contributing to the susceptibility to PBC. Major differences in susceptibility loci between these two population groups were observed. In this study, we examined whether the most significant loci observed in either European and/or Japanese cohorts are associated with PBC in a Han Chinese population. In 1070 PBC patients and 1198 controls, we observed highly significant associations at CD80 (rs2293370, P = 2.67 × 10(-8)) and TNFSF15 (rs4979462, P = 3.86 × 10(-8)) and significant associations at 17q12-21 (rs9303277), PDGFB (rs715505), NF-κB1 (rs7665090), IL12RB2 (rs11209050), and STAT4 (rs7574865; all corrected P values <0.01). However, no association was observed for POU2AF1 (rs4938534), IL12A (rs485499 and rs2366408), IL7R (rs6897932), CXCR5 (rs715412), SOCS1 (rs725613), and TNFRSF1A (rs1800693). STAT4 (rs7574865) was strongly associated after additional control samples were analyzed. Our study is the first large-scale genetic analysis in a Han Chinese PBC cohort. These results do not only reflect that Han Chinese PBC patients share common genetic susceptibility genes with both their Japanese and European counterparts but also suggest a distinctly different genetic susceptibility profile.
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Affiliation(s)
- Ming Dong
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, 210096, Nanjing, Jiangsu, China
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19
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Seldin MF, Alkhairy OK, Lee AT, Lamb JA, Sussman J, Pirskanen-Matell R, Piehl F, Verschuuren JJGM, Kostera-Pruszczyk A, Szczudlik P, McKee D, Maniaol AH, Harbo HF, Lie BA, Melms A, Garchon HJ, Willcox N, Gregersen PK, Hammarstrom L. Genome-Wide Association Study of Late-Onset Myasthenia Gravis: Confirmation of TNFRSF11A and Identification of ZBTB10 and Three Distinct HLA Associations. Mol Med 2015; 21:769-781. [PMID: 26562150 DOI: 10.2119/molmed.2015.00232] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 01/05/2023] Open
Abstract
To investigate the genetics of late-onset myasthenia gravis (LOMG), we conducted a genome-wide association study imputation of>6 million single nucleotide polymorphisms (SNPs) in 532 LOMG cases (anti-acetylcholine receptor [AChR] antibody positive; onset age≥50 years) and 2,128 controls matched for sex and population substructure. The data confirm reported TNFRSF11A associations (rs4574025, P = 3.9 × 10-7, odds ratio [OR] 1.42) and identify a novel candidate gene, ZBTB10, achieving genome-wide significance (rs6998967, P = 8.9 × 10-10, OR 0.53). Several other SNPs showed suggestive significance including rs2476601 (P = 6.5 × 10-6, OR 1.62) encoding the PTPN22 R620W variant noted in early-onset myasthenia gravis (EOMG) and other autoimmune diseases. In contrast, EOMG-associated SNPs in TNIP1 showed no association in LOMG, nor did other loci suggested for EOMG. Many SNPs within the major histocompatibility complex (MHC) region showed strong associations in LOMG, but with smaller effect sizes than in EOMG (highest OR ~2 versus ~6 in EOMG). Moreover, the strongest associations were in opposite directions from EOMG, including an OR of 0.54 for DQA1*05:01 in LOMG (P = 5.9 × 10-12) versus 2.82 in EOMG (P = 3.86 × 10-45). Association and conditioning studies for the MHC region showed three distinct and largely independent association peaks for LOMG corresponding to (a) MHC class II (highest attenuation when conditioning on DQA1), (b) HLA-A and (c) MHC class III SNPs. Conditioning studies of human leukocyte antigen (HLA) amino acid residues also suggest potential functional correlates. Together, these findings emphasize the value of subgrouping myasthenia gravis patients for clinical and basic investigations and imply distinct predisposing mechanisms in LOMG.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, and Department of Medicine, University of California, Davis, California, United States of America
| | - Omar K Alkhairy
- Division of Clinical Immunology, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Annette T Lee
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York, United States of America
| | - Janine A Lamb
- Centre for Integrated Genomic Medical Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Jon Sussman
- Department of Neurology, Greater Manchester Neuroscience Centre, Manchester, United Kingdom
| | | | - Fredrik Piehl
- Department of Neurology, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | | | - Piotr Szczudlik
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - David McKee
- Department of Neurology, Greater Manchester Neuroscience Centre, Manchester, United Kingdom
| | - Angelina H Maniaol
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Arthur Melms
- Department of Neurology, Tübingen University Medical Center, Tübingen, Germany, and Neurologische Klinik, Universitàtsklinikum Erlangen, Erlangen, Germany
| | | | - Nicholas Willcox
- Nuffield Department of Clinical Neurosciences, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York, United States of America
| | - Lennart Hammarstrom
- Division of Clinical Immunology, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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20
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Abstract
Progress in defining the genetics of autoimmune disease has been dramatically enhanced by large scale genetic studies. Genome-wide approaches, examining hundreds or for some diseases thousands of cases and controls, have been implemented using high throughput genotyping and appropriate algorithms to provide a wealth of data over the last decade. These studies have identified hundreds of non-HLA loci as well as further defining HLA variations that predispose to different autoimmune diseases. These studies to identify genetic risk loci are also complemented by progress in gene expression studies including definition of expression quantitative trait loci (eQTL), various alterations in chromatin structure including histone marks, DNase I sensitivity, repressed chromatin regions as well as transcript factor binding sites. Integration of this information can partially explain why particular variations can alter proclivity to autoimmune phenotypes. Despite our incomplete knowledge base with only partial definition of hereditary factors and possible functional connections, this progress has and will continue to facilitate a better understanding of critical pathways and critical changes in immunoregulation. Advances in defining and understanding functional variants potentially can lead to both novel therapeutics and personalized medicine in which therapeutic approaches are chosen based on particular molecular phenotypes and genomic alterations.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA; Division of Rheumatology and Allergy, Department of Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA.
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21
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Iyengar SK, Sedor JR, Freedman BI, Kao WHL, Kretzler M, Keller BJ, Abboud HE, Adler SG, Best LG, Bowden DW, Burlock A, Chen YDI, Cole SA, Comeau ME, Curtis JM, Divers J, Drechsler C, Duggirala R, Elston RC, Guo X, Huang H, Hoffmann MM, Howard BV, Ipp E, Kimmel PL, Klag MJ, Knowler WC, Kohn OF, Leak TS, Leehey DJ, Li M, Malhotra A, März W, Nair V, Nelson RG, Nicholas SB, O’Brien SJ, Pahl MV, Parekh RS, Pezzolesi MG, Rasooly RS, Rotimi CN, Rotter JI, Schelling JR, Seldin MF, Shah VO, Smiles AM, Smith MW, Taylor KD, Thameem F, Thornley-Brown DP, Truitt BJ, Wanner C, Weil EJ, Winkler CA, Zager PG, Igo RP, Hanson RL, Langefeld CD. Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND). PLoS Genet 2015; 11:e1005352. [PMID: 26305897 PMCID: PMC4549309 DOI: 10.1371/journal.pgen.1005352] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/10/2015] [Indexed: 11/28/2022] Open
Abstract
Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD. Type 2 diabetes is the most common cause of severe kidney disease worldwide and diabetic kidney disease (DKD) associates with premature death. Individuals of non-European ancestry have the highest burden of type 2 DKD; hence understanding the causes of DKD remains critical to reducing health disparities. Family studies demonstrate that genes regulate the onset and progression of DKD; however, identifying these genes has proven to be challenging. The Family Investigation of Diabetes and Nephropathy consortium (FIND) recruited a large multi-ethnic collection of individuals with type 2 diabetes with and without kidney disease in order to detect genes associated with DKD. FIND discovered and replicated a DKD-associated genetic locus on human chromosome 6q25.2 (rs955333) between the SCAF8 and CNKSR genes. Findings were supported by significantly different expression of genes in this region from kidney tissue of subjects with, versus without DKD. The present findings identify a novel kidney disease susceptibility locus in individuals with type 2 diabetes which is consistent across subjects of differing ancestries. In addition, FIND results provide a rich catalogue of genetic variation in DKD patients for future research on the genetic architecture regulating this common and devastating disease.
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Affiliation(s)
- Sudha K. Iyengar
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - John R. Sedor
- Departments of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Departments of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail: (SKI); (JRS); (BIF)
| | - W. H. Linda Kao
- Department of Epidemiology and Medicine, John Hopkins University, Baltimore, Maryland, United States of America
| | - Matthias Kretzler
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Benjamin J. Keller
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Hanna E. Abboud
- Department of Medicine/Nephrology, The University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Sharon G. Adler
- Department of Medicine, Division of Nephrology and Hypertension, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Lyle G. Best
- Missouri Breaks Industries Research, Timber Lake, South Dakota, United States of America
| | - Donald W. Bowden
- Department of Biochemistry, Center for Human Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Allison Burlock
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Mary E. Comeau
- Center for Public Health Genomics and Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, United States of America
| | - Jeffrey M. Curtis
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Jasmin Divers
- Center for Public Health Genomics and Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, United States of America
| | - Christiane Drechsler
- University Hospital Würzburg, Renal Division and Comprehensive Heart Failure Center, Würzburg, Germany
| | - Ravi Duggirala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Robert C. Elston
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
| | - Eli Ipp
- Department of Medicine, Section of Diabetes and Metabolism, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Paul L. Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, United States of America
| | - Michael J. Klag
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - William C. Knowler
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Orly F. Kohn
- Department of Medicine, University of Chicago Medicine, Chicago, Illinois, United States of America
| | - Tennille S. Leak
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David J. Leehey
- Department of Medicine, Loyola School of Medicine, Maywood, Illinois, United States of America
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Alka Malhotra
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Winfried März
- Heidelberg University and Synlab Academy, University of Graz, Graz, Austria
| | - Viji Nair
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert G. Nelson
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Susanne B. Nicholas
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg, Russia, and Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America
| | - Madeleine V. Pahl
- Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Rulan S. Parekh
- Departments of Paediatrics and Medicine, Hospital for Sick Children, University Health Network and the University of Toronto, Toronto, Ontario, Canada
| | - Marcus G. Pezzolesi
- Department of Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rebekah S. Rasooly
- National Institute of Diabetes and Digestive Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, Bethesda, Maryland, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jeffrey R. Schelling
- Departments of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael F. Seldin
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, California, United States of America
| | - Vallabh O. Shah
- Department of Biochemistry & Molecular Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Adam M. Smiles
- Joslin Diabetes Center, Section on Genetics and Epidemiology, Boston, Massachusetts, United States of America
| | - Michael W. Smith
- National Human Genome Research Institute, Rockville, Maryland, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Farook Thameem
- Department of Medicine, The University of Texas Health Science Center, San Antonio, Texas, United States of America
| | | | - Barbara J. Truitt
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Christoph Wanner
- Department of Medicine, Division of Nephrology, University Hospital Würzburg, Würzburg, Germany
| | - E. Jennifer Weil
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Cheryl A. Winkler
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Philip G. Zager
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Robert P. Igo
- Department of Epidemiology & Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert L. Hanson
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, United States of America
| | - Carl D. Langefeld
- The Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, California, United States of America
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22
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Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJH, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JBA, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One 2015; 10:e0122271. [PMID: 25849893 PMCID: PMC4388675 DOI: 10.1371/journal.pone.0122271] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.
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Affiliation(s)
- Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine P. Liao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert R. Graham
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeffrey D. Greenberg
- New York University Hospital for Joint Diseases, New York, New York, United States of America
| | - Steve Eyre
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Jing Cui
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Lee
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Dimitrios A. Pappas
- Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
| | - Joel M. Kremer
- The Albany Medical College and The Center for Rheumatology, Albany, New York, United States of America
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Marieke J. H. Coenen
- Radboud university medical center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Barbara Franke
- Radboud University Medical Center, Donders Centre for Neurosciences, Department of Psychiatry and Human Genetics, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Xavier Mariette
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Corrine Richard-Miceli
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Helena Canhão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - João E. Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Niek de Vries
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P. Tak
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - J. Bart A. Crusius
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Michael T. Nurmohamed
- Amsterdam Rheumatology and Immunology Center, Department of Rheumatology, Reade, Amsterdam, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ted R. Mikuls
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yukinori Okada
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eli A. Stahl
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - David E. Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tracie L. Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda L. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Roman Kosoy
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Michael Ransom
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Tushar R. Bhangale
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Ward Ortmann
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Andrew Cagan
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Vivian Gainer
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Elizabeth W. Karlson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac Kohane
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Shawn N. Murphy
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, 18100, Spain
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
- Genetics Department, University Medical Center and Groningen University, Groningen, The Netherlands
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael F. Seldin
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Timothy Behrens
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
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23
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Robbins JA, Qi L, Garcia L, Younger JW, Seldin MF. Relationship of pain and ancestry in African American women. Eur J Pain 2015; 19:601-10. [PMID: 25752262 DOI: 10.1002/ejp.680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND African Americans are reported to be more sensitive to pain than European Americans. Pain sensitivity has been shown to be genetically linked in animal models and is likely to be in humans. METHODS Exactly, 11,239 self-identified African American post-menopausal women enrolled in the Women's Health Initiative had percentage African ancestry determined by ancestry informative markers, "Pain Construct" measurements and covariate information. They answered five questions about specific types and location of pain, such as joint, neck, low back, headache and urinary. They also answered two questions which were used to derive a "Pain Construct", a measure of general pain scored on a scale of 1-100. Associations were tested in linear regression models adjusting for age, self-reported medical conditions, neighbourhood socio-economic status, education and depression. RESULTS In the unadjusted model of the five specific types of pain measures, greater pain perception was associated with a higher proportion of African ancestry. However, some of the specific types of pain measures were no longer associated with African ancestry after adjustment for other study covariates. The Pain Construct was statistically significantly associated with African ancestry in both the unadjusted [β = -0.132, 95% confidence interval (CI) = -099 to -0.164; r = -0.075, 95% CI -0.056 to -0.093] and the adjusted models (β = -0.069 95% CI = -0.04 to -0.10). CONCLUSIONS Greater African ancestry was associated with higher levels of self-reported pain, although this accounted for only a minor fraction of the overall variation in the Pain Construct.
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Affiliation(s)
- J A Robbins
- Department of Internal Medicine, School of Medicine, University of California, Davis
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24
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Bykhovskaya Y, Seldin MF, Liu Y, Ransom M, Li X, Rabinowitz YS. Independent origin of c.57 C > T mutation in MIR184 associated with inherited corneal and lens abnormalities. Ophthalmic Genet 2014; 36:95-7. [PMID: 25373792 DOI: 10.3109/13816810.2014.977491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Seldin MF, Lasalle JM, Gershwin ME. Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front Immunol 2014; 5:128. [PMID: 24734033 PMCID: PMC3975093 DOI: 10.3389/fimmu.2014.00128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/13/2014] [Indexed: 01/12/2023] Open
Abstract
Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.
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Affiliation(s)
- Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
| | - Francesca Cavaciocchi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Ana Lleo
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | | | | | - Simone A Lombardi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria De Santis
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Francesca Meda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria Gabriella Raimondo
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Chiara Crotti
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Marco Folci
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Luca Zammataro
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Nancy Bach
- Mt. Sinai University , New York, NY , USA
| | - Shinji Shimoda
- Clinical Research Center, National Nagasaki Medical Center , Nagasaki , Japan
| | | | - Monica Miozzo
- Department of Pathophysiology and Transplantation, University of Milan , Milan , Italy ; Division of Pathology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Pietro Invernizzi
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | - Mauro Podda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Michelle R Martin
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA; Department of Internal Medicine, University of California at Davis, Davis, CA, USA
| | - Janine M Lasalle
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
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26
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Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Seldin MF, Lasalle JM, Gershwin ME. Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front Immunol 2014. [PMID: 24734033 PMCID: PMC4132258 DOI: 10.3389/fimmu.2014.00371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.
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Affiliation(s)
- Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
| | - Francesca Cavaciocchi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Ana Lleo
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | | | | | - Simone A Lombardi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria De Santis
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Francesca Meda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria Gabriella Raimondo
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Chiara Crotti
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Marco Folci
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Luca Zammataro
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Nancy Bach
- Mt. Sinai University , New York, NY , USA
| | - Shinji Shimoda
- Clinical Research Center, National Nagasaki Medical Center , Nagasaki , Japan
| | | | - Monica Miozzo
- Department of Pathophysiology and Transplantation, University of Milan , Milan , Italy ; Division of Pathology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Pietro Invernizzi
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | - Mauro Podda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Michelle R Martin
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA; Department of Internal Medicine, University of California at Davis, Davis, CA, USA
| | - Janine M Lasalle
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
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27
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Garcia L, Qi L, Singh K, Kosoy R, Nassir R, Fijalkowski N, Haan M, Robbins J, Seldin MF. Relationship between glaucoma and admixture in postmenopausal African American women. Ethn Dis 2014; 24:399-405. [PMID: 25417420 PMCID: PMC4500172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
OBJECTIVE To investigate the association between African admixture and glaucoma prevalence among African American women. DESIGN, SETTING, PARTICIPANTS Participants included 11616 African American women from the Women's Health Initiative Study (WHI) for whom admixture information was available and included 2548 who self-reported a diagnosis of glaucoma. MAIN OUTCOME MEASURES Glaucoma. RESULTS Significant association was observed between self-identified glaucoma status and admixture. However, this association was not significant in a model that included neighborhood socioeconomic status (NSES), hypertension, diabetes and body mass index (BMI). Self-identified glaucoma status was associated with diabetes that persisted after adjustment for admixture, NSES, hypertension, and BMI. Lower NSES was also associated with higher glaucoma risk but this association was marginal in the fully adjusted model and neither hypertension nor BMI showed association. When glaucoma status was limited to those reporting use or no use of appropriate ophthalmologic medication, no associations were observed in any of the models. CONCLUSION This study failed to find an independent association of glaucoma status and African admixture and these findings suggest that the higher frequency glaucoma in African Americans may be largely due to other factors.
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28
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Walsh KM, Amos CI, Wenzlaff AS, Gorlov IP, Sison JD, Wu X, Spitz MR, Hansen HM, Lu EY, Wei C, Zhang H, Chen W, Lloyd SM, Frazier ML, Bracci PM, Seldin MF, Wrensch MR, Schwartz AG, Wiencke JK. Association study of nicotinic acetylcholine receptor genes identifies a novel lung cancer susceptibility locus near CHRNA1 in African-Americans. Oncotarget 2013; 3:1428-38. [PMID: 23232035 PMCID: PMC3717803 DOI: 10.18632/oncotarget.746] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Studies in European and East Asian populations have identified lung cancer susceptibility loci in nicotinic acetylcholine receptor (nAChR) genes on chromosome 15q25.1 which also appear to influence smoking behaviors. We sought to determine if genetic variation in nAChR genes influences lung cancer susceptibly in African-Americans, and evaluated the association of these cancer susceptibility loci with smoking behavior. A total of 1308 African-Americans with lung cancer and 1241 African-American controls from three centers were genotyped for 378 single nucleotide polymorphisms (SNPs) spanning the sixteen human nAChR genes. Associations between SNPs and the risk of lung cancer were estimated using logistic regression, adjusted for relevant covariates. Seven SNPs in three nAChR genes were significantly associated with lung cancer at a strict Bonferroni-corrected level, including a novel association on chromosome 2 near the promoter of CHRNA1 (rs3755486: OR = 1.40, 95% CI = 1.18-1.67, P = 1.0 x 10-4). Association analysis of an additional 305 imputed SNPs on 2q31.1 supported this association. Publicly available expression data demonstrated that the rs3755486 risk allele correlates with increased CHRNA1 gene expression. Additional SNP associations were observed on 15q25.1 in genes previously associated with lung cancer, including a missense variant in CHRNA5 (rs16969968: OR = 1.60, 95% CI = 1.27-2.01, P = 5.9 x 10-5). Risk alleles on 15q25.1 also correlated with an increased number of cigarettes smoked per day among the controls. These findings identify a novel lung cancer risk locus on 2q31.1 which correlates with CHRNA1 expression and replicate previous associations on 15q25.1 in African-Americans.
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Affiliation(s)
- Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
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Aldrich MC, Selvin S, Wrensch MR, Sison JD, Hansen HM, Quesenberry CP, Seldin MF, Barcellos LF, Buffler PA, Wiencke JK. Socioeconomic status and lung cancer: unraveling the contribution of genetic admixture. Am J Public Health 2013; 103:e73-80. [PMID: 23948011 DOI: 10.2105/ajph.2013.301370] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos. METHODS We evaluated SES and genetic ancestry in a Northern California lung cancer case-control study (1998-2003) of African Americans and Latinos. Lung cancer case and control participants were frequency matched on age, gender, and race/ethnicity. We assessed case-control differences in individual admixture proportions using the 2-sample t test and analysis of covariance. Logistic regression models examined associations among genetic ancestry, socioeconomic characteristics, and lung cancer. RESULTS Decreased Amerindian ancestry was associated with higher education among Latino control participants and greater African ancestry was associated with decreased education among African lung cancer case participants. Education was associated with lung cancer among both Latinos and African Americans, independent of smoking, ancestry, age, and gender. Genetic ancestry was not associated with lung cancer among African Americans. CONCLUSIONS Findings suggest that socioeconomic factors may have a greater impact than genetic ancestry on lung cancer among African Americans. The genetic heterogeneity and recent dynamic migration and acculturation of Latinos complicate recruitment; thus, epidemiological analyses and findings should be interpreted cautiously.
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Affiliation(s)
- Melinda C Aldrich
- At the time of the study, Melinda C. Aldrich was with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Steve Selvin is with the Division of Biostatistics, School of Public Health, University of California, Berkeley. Margaret R. Wrensch, Helen M. Hansen, and John K. Wiencke are with the Department of Neurologic Surgery, University of California, San Francisco. Jennette D. Sison was with the Department of Neurologic Surgery, University of California, San Francisco. Charles P. Quesenberry Jr, is with the Division of Research, Kaiser Permanente, Oakland, CA. Michael F. Seldin is with the Departments of Biological Chemistry and Medicine, University of California, Davis. Lisa F. Barcellos and Patricia A. Buffler are with the Division of Epidemiology, School of Public Health, University of California, Berkeley
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Qi L, Nassir R, Kosoy R, Garcia L, Waetjen LE, Ochs-Balcom HM, Gass M, Robbins J, Seldin MF. Relationship between hysterectomy and admixture in African American women. Am J Obstet Gynecol 2013; 208:279.e1-7. [PMID: 23333549 DOI: 10.1016/j.ajog.2013.01.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/18/2012] [Accepted: 01/14/2013] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Most studies suggest that hysterectomies are more common in African American women than in other ethnic groups. To assess this ethnic surgical disparity in a novel way, our main goal was to determine whether admixture (the proportion of sub-Saharan African or European origin in individuals) is associated with hysterectomy frequency in African American women in the Women's Health Initiative. STUDY DESIGN In this retrospective study, we used ancestry informative single nucleotide polymorphisms to estimate admixture proportions in >10,000 African American women from the Women's Health Initiative. Logistic regression models were used to assess the association between admixture and self-reported history of hysterectomy with and without controls for relevant covariates. Multinomial logistic regression models were used to assess the association between admixture and self-reported age of hysterectomy. We also considered other potential risk factors (adiposity, hypertension, and education) for hysterectomy accounting for admixture. RESULTS African admixture was a strong risk factor after the adjustment for multiple covariates (odds ratio, 1.85; P < .0001). The admixture risk for hysterectomy was highest for those procedures that were performed in the 35-39 age range (odds ratio, 3.08; P < .0001) and least evident in oldest ages (≥45 years old). Our analyses also suggest that adiposity, hypertension, and education were associated independently with hysterectomy in this population group. CONCLUSION These results suggest that higher African admixture is associated with higher frequencies of hysterectomy and that genetic studies that specifically target African American women and diseases that are associated with hysterectomy may be especially useful in understanding the pathogenesis and underlying cause of this disparity in health outcome.
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Ochs-Balcom HM, Preus L, Wactawski-Wende J, Nie J, Johnson NA, Zakharia F, Tang H, Carlson C, Carty C, Chen Z, Hoffman T, Hutter CM, Jackson RD, Kaplan RC, Li L, Liu S, Neuhouser ML, Peters U, Robbins J, Seldin MF, Thornton TA, Thompson CL, Kooperberg C, Sucheston LE. Association of DXA-derived bone mineral density and fat mass with African ancestry. J Clin Endocrinol Metab 2013; 98:E713-7. [PMID: 23436924 PMCID: PMC3615193 DOI: 10.1210/jc.2012-3921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Both genes and environment have been implicated in determining the complex body composition phenotypes in individuals of European ancestry; however, few studies have been conducted in other race/ethnic groups. OBJECTIVE We conducted a genome-wide admixture mapping study in an attempt to localize novel genomic regions associated with genetic ancestry. SETTING/PARTICIPANTS We selected a sample of 842 African-American women from the Women's Health Initiative single nucleotide polymorphism (SNP) Health Association Resource for whom several dual-energy X-ray absorptiometry (DXA)-derived bone mineral density (BMD) and fat mass phenotypes were available. METHODS We derived both global and local ancestry estimates for each individual from Affymetrix 6.0 data and analyzed the correlation of DXA phenotypes with global African ancestry. For each phenotype, we examined the association of local genetic ancestry (number of African ancestral alleles at each marker) and each DXA phenotype at 570 282 markers across the genome in additive models with adjustment for important covariates. RESULTS We identified statistically significant correlations of whole-body fat mass, trunk fat mass, and all 6 measures of BMD with a proportion of African ancestry. Genome-wide (admixture) significance for femoral neck BMD was achieved across 2 regions ∼3.7 MB and 0.3 MB on chromosome 19q13; similarly, total hip and intertrochanter BMD were associated with local ancestry in these regions. Trunk fat was the most significant fat mass phenotype showing strong, but not genomewide significant associations on chromosome Xp22. CONCLUSIONS Our results suggest that genomic regions in postmenopausal African-American women contribute to variance in BMD and fat mass existence and warrant further study.
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Affiliation(s)
- Heather M Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, NY14214-8001, USA.
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Kar SP, Seldin MF, Chen W, Lu E, Hirschfield GM, Invernizzi P, Heathcote J, Cusi D, Gershwin ME, Siminovitch KA, Amos CI. Pathway-based analysis of primary biliary cirrhosis genome-wide association studies. Genes Immun 2013; 14:179-86. [PMID: 23392275 DOI: 10.1038/gene.2013.1] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genome-wide association studies (GWAS) have successfully identified several loci associated with primary biliary cirrhosis (PBC) risk. Pathway analysis complements conventional GWAS analysis. We applied the recently developed linear combination test for pathways to datasets drawn from independent PBC GWAS in Italian and Canadian subjects. Of the Kyoto Encyclopedia of Genes and Genomes and BioCarta pathways tested, 25 pathways in the Italian dataset (449 cases, 940 controls) and 26 pathways in the Canadian dataset (530 cases, 398 controls) were associated with PBC susceptibility (P<0.05). After correcting for multiple comparisons, only the eight most significant pathways in the Italian dataset had FDR <0.25 with tumor necrosis factor/stress-related signaling emerging as the top pathway (P=7.38 × 10⁻⁴, FDR=0.18). Two pathways, phosphatidylinositol signaling and hedgehog signaling, were replicated in both datasets (P<0.05), and subjected to two additional complementary pathway tests. Both pathway signals remained significant in the Italian dataset on modified gene set enrichment analysis (P<0.05). In both GWAS, variants nominally associated with PBC were significantly overrepresented in the phosphatidylinositol pathway (Fisher exact P<0.05). These results point to established and novel pathway-level associations with inherited predisposition to PBC that, on further independent replication and functional validation, may provide fresh insights into PBC etiology.
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Affiliation(s)
- S P Kar
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Richman IB, Taylor KE, Chung SA, Trupin L, Petri M, Yelin E, Graham RR, Lee A, Behrens TW, Gregersen PK, Seldin MF, Criswell LA. European genetic ancestry is associated with a decreased risk of lupus nephritis. ACTA ACUST UNITED AC 2013; 64:3374-82. [PMID: 23023776 DOI: 10.1002/art.34567] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE African Americans, East Asians, and Hispanics with systemic lupus erythematosus (SLE) are more likely to develop renal disease than are SLE patients of European descent. This study was undertaken to investigate whether European genetic ancestry protects against the development of lupus nephritis, with the aim of exploring the genetic and socioeconomic factors that might explain this effect. METHODS This was a cross-sectional study of SLE patients from a multiethnic case collection. Participants were genotyped for 126 single-nucleotide polymorphisms (SNPs) informative for ancestry. A subset of participants was also genotyped for 80 SNPs in 14 candidate genes for renal disease in SLE. Logistic regression was used to test the association between European ancestry and renal disease. Analyses were adjusted for continental ancestries, socioeconomic status (SES), and candidate genes. RESULTS Participants (n = 1,906) had, on average, 62.4% European, 15.8% African, 11.5% East Asian, 6.5% Amerindian, and 3.8% South Asian ancestry. Among the participants, 656 (34%) had renal disease. A 10% increase in the proportion of European ancestry estimated in each participant was associated with a 15% reduction in the odds of having renal disease, after adjustment for disease duration and sex (odds ratio 0.85, 95% confidence interval 0.82-0.87; P = 1.9 × 10(-30) ). Adjustment for other genetic ancestries, measures of SES, or SNPs in the genes most associated with renal disease (IRF5 [rs4728142], BLK [rs2736340], STAT4 [rs3024912], and HLA-DRB1*0301 and DRB1*1501) did not substantively alter this relationship. CONCLUSION European ancestry is protective against the development of renal disease in SLE, an effect that is independent of other genetic ancestries, candidate risk alleles, and socioeconomic factors.
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Walsh KM, Gorlov IP, Hansen HM, Wu X, Spitz MR, Zhang H, Lu EY, Wenzlaff AS, Sison JD, Wei C, Lloyd SM, Chen W, Frazier ML, Seldin MF, Bierut LJ, Bracci PM, Wrensch MR, Schwartz AG, Wiencke JK, Amos CI. Fine-mapping of the 5p15.33, 6p22.1-p21.31, and 15q25.1 regions identifies functional and histology-specific lung cancer susceptibility loci in African-Americans. Cancer Epidemiol Biomarkers Prev 2012; 22:251-60. [PMID: 23221128 DOI: 10.1158/1055-9965.epi-12-1007-t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies of European and East Asian populations have identified lung cancer susceptibility loci on chromosomes 5p15.33, 6p22.1-p21.31, and 15q25.1. We investigated whether these regions contain lung cancer susceptibly loci in African-Americans and refined previous association signals by using the reduced linkage disequilibrium observed in African-Americans. METHODS 1,308 African-American cases and 1,241 African-American controls from 3 centers were genotyped for 760 single-nucleotide polymorphisms (SNP) spanning 3 regions, and additional SNP imputation was carried out. Associations between polymorphisms and lung cancer risk were estimated using logistic regression, stratified by tumor histology where appropriate. RESULTS The strongest associations were observed on 15q25.1 in/near CHRNA5, including a missense substitution [rs16969968: OR, 1.57; 95% confidence interval (CI), 1.25-1.97; P, 1.1 × 10(-4)) and variants in the 5'-UTR. Associations on 6p22.1-p21.31 were histology specific and included a missense variant in BAT2 associated with squamous cell carcinoma (rs2736158: OR, 0.64; 95% CI, 0.48-0.85; P, 1.82 × 10(-3)). Associations on 5p15.33 were detected near TERT, the strongest of which was rs2735940 (OR, 0.82; 95% CI, 0.73-0.93; P, 1.1 × 10(-3)). This association was stronger among cases with adenocarcinoma (OR, 0.75; 95% CI, 0.65-0.86; P, 8.1 × 10(-5)). CONCLUSIONS Polymorphisms in 5p15.33, 6p22.1-p21.31, and 15q25.1 are associated with lung cancer in African-Americans. Variants on 5p15.33 are stronger risk factors for adenocarcinoma and variants on 6p21.33 associated only with squamous cell carcinoma. IMPACT Results implicate the BAT2, TERT, and CHRNA5 genes in the pathogenesis of specific lung cancer histologies.
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Affiliation(s)
- Kyle M Walsh
- Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Cente, San Francisco, CA, USA.
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Morris DL, Taylor KE, Fernando MMA, Nititham J, Alarcón-Riquelme ME, Barcellos LF, Behrens TW, Cotsapas C, Gaffney PM, Graham RR, Pons-Estel BA, Gregersen PK, Harley JB, Hauser SL, Hom G, Langefeld CD, Noble JA, Rioux JD, Seldin MF, Criswell LA, Vyse TJ. Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans. Am J Hum Genet 2012; 91:778-93. [PMID: 23084292 DOI: 10.1016/j.ajhg.2012.08.026] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/26/2012] [Accepted: 08/24/2012] [Indexed: 12/01/2022] Open
Abstract
We have performed a meta-analysis of the major-histocompatibility-complex (MHC) region in systemic lupus erythematosus (SLE) to determine the association with both SNPs and classical human-leukocyte-antigen (HLA) alleles. More specifically, we combined results from six studies and well-known out-of-study control data sets, providing us with 3,701 independent SLE cases and 12,110 independent controls of European ancestry. This study used genotypes for 7,199 SNPs within the MHC region and for classical HLA alleles (typed and imputed). Our results from conditional analysis and model choice with the use of the Bayesian information criterion show that the best model for SLE association includes both classical loci (HLA-DRB1(∗)03:01, HLA-DRB1(∗)08:01, and HLA-DQA1(∗)01:02) and two SNPs, rs8192591 (in class III and upstream of NOTCH4) and rs2246618 (MICB in class I). Our approach was to perform a stepwise search from multiple baseline models deduced from a priori evidence on HLA-DRB1 lupus-associated alleles, a stepwise regression on SNPs alone, and a stepwise regression on HLA alleles. With this approach, we were able to identify a model that was an overwhelmingly better fit to the data than one identified by simple stepwise regression either on SNPs alone (Bayes factor [BF] > 50) or on classical HLA alleles alone (BF > 1,000).
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Affiliation(s)
- David L Morris
- Divisions of Genetics and Molecular Medicine and Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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Gregersen PK, Kosoy R, Lee AT, Lamb J, Sussman J, McKee D, Simpfendorfer KR, Pirskanen-Matell R, Piehl F, Pan-Hammarstrom Q, Verschuuren JJGM, Titulaer MJ, Niks EH, Marx A, Ströbel P, Tackenberg B, Pütz M, Maniaol A, Elsais A, Tallaksen C, Harbo HF, Lie BA, Raychaudhuri S, de Bakker PIW, Melms A, Garchon HJ, Willcox N, Hammarstrom L, Seldin MF. Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08. Ann Neurol 2012; 72:927-35. [PMID: 23055271 DOI: 10.1002/ana.23691] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/18/2012] [Accepted: 06/13/2012] [Indexed: 01/20/2023]
Abstract
OBJECTIVE The objective of this study is to comprehensively define the genetic basis of early onset myasthenia gravis (EOMG). METHODS We have carried out a 2-stage genome-wide association study on a total of 649 North European EOMG patients. Cases were matched 1:4 with controls of European ancestry. We performed imputation and conditional analyses across the major histocompatibility complex, as well as in the top regions of association outside the human leukocyte antigen (HLA) region. RESULTS We observed the strongest association in the HLA class I region at rs7750641 (p = 1.2 × 10(-92) ; odds ratio [OR], 6.25). By imputation and conditional analyses, HLA-B*08 proves to be the major associated allele (p = 2.87 × 10(-113) ; OR, 6.41). In addition to the expected association with PTPN22 (rs2476601; OR, 1.71; p = 8.2 × 10(-10) ), an imputed coding variant (rs2233290) at position 151 (Pro→Ala) in the TNFAIP3-interacting protein 1, TNIP1, confers even stronger risk than PTPN22 (OR, 1.91; p = 3.2 × 10(-10) ). INTERPRETATION The association at TNIP1 in EOMG implies disease mechanisms involving ubiquitin-dependent dysregulation of NF-κB signaling. The localization of the major HLA signal to the HLA-B*08 allele suggests that CD8(+) T cells may play a key role in disease initiation or pathogenesis.
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Affiliation(s)
- Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY 11030, USA.
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Juran BD, Hirschfield GM, Invernizzi P, Atkinson EJ, Li Y, Xie G, Kosoy R, Ransom M, Sun Y, Bianchi I, Schlicht EM, Lleo A, Coltescu C, Bernuzzi F, Podda M, Lammert C, Shigeta R, Chan LL, Balschun T, Marconi M, Cusi D, Heathcote EJ, Mason AL, Myers RP, Milkiewicz P, Odin JA, Luketic VA, Bacon BR, Bodenheimer HC, Liakina V, Vincent C, Levy C, Franke A, Gregersen PK, Bossa F, Gershwin ME, deAndrade M, Amos CI, Lazaridis KN, Seldin MF, Siminovitch KA. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants. Hum Mol Genet 2012; 21:5209-21. [PMID: 22936693 DOI: 10.1093/hmg/dds359] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.
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Affiliation(s)
- Brian D Juran
- Center for Basic Research in Digestive Diseases, Mayo Clinic, Rochester, MN, USA
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Nassir R, Qi L, Kosoy R, Garcia L, Robbins J, Seldin MF. Relationship between gallbladder surgery and ethnic admixture in African American and Hispanic American women. Am J Gastroenterol 2012; 107:932-40. [PMID: 22415198 DOI: 10.1038/ajg.2012.46] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The objective of this study was to investigate whether differences in admixture in African American and Hispanic American adult women are associated with differences in gallbladder surgery. METHODS Gallbladder surgery history on entry to the Women's Health Initiative's (WHI) study was used as a dichotomous outcome measure for this study. The proportion of European, sub-Saharan African, and Amerindian (AMI) admixture was estimated for 10,841 African American and 4,620 Hispanic American women in WHI using 92 ancestry informative markers. Logistic regression analyses assessed the relationship between admixture and gallbladder surgery in WHI women (enrollment at ages >50, mean age 61 years) with or without adjusting for multiple covariates, including measures of adiposity, parity, alcohol use, and education. RESULTS There was a significant positive association between AMI admixture and the frequency of gallbladder surgery in Hispanic Americans. The odds ratio (OR) and 95% confidence intervals (CIs) for AMI admixture group was OR=2.97, CI=2.01-4.38, P<10(-4). Although there were strong positive associations with parity and adiposity, and negative associations with alcohol consumption and education, accounting for these covariates did not remove the admixture association (OR=2.46, CI=1.62-3.73). In contrast, the effect of African admixture was nearly indistinguishable from that of the European admixture, both of which were protective in the Hispanic American group, and African admixture had a marginal association with decreased gallbladder surgery in the African American group. Measures of adiposity were associated with increased risk for gallbladder surgery and remained significant after accounting for admixture and each of the other covariates. Education level and alcohol use were associated with decreased risk for gallbladder disease. However, after accounting for the other covariates these variably remained significant. CONCLUSIONS AMI admixture is strongly associated with gallbladder surgery in women, even after adjustment for selected risk factors for cholelithiasis. Additional studies to ascertain the specific genetic risk factors underlying these associations are warranted.
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Affiliation(s)
- Rami Nassir
- Department of Biochemistry and Molecular Medicine, University of California-Davis, USA
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Invernizzi P, Ransom M, Raychaudhuri S, Kosoy R, Lleo A, Shigeta R, Franke A, Bossa F, Amos CI, Gregersen PK, Siminovitch KA, Cusi D, de Bakker PIW, Podda M, Gershwin ME, Seldin MF. Classical HLA-DRB1 and DPB1 alleles account for HLA associations with primary biliary cirrhosis. Genes Immun 2012; 13:461-8. [PMID: 22573116 PMCID: PMC3423484 DOI: 10.1038/gene.2012.17] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Susceptibility to primary biliary cirrhosis (PBC) is strongly associated with HLA region polymorphisms. To determine if associations can be explained by classical HLA determinants we studied Italian 676 cases and 1440 controls with genotyped with dense single nucleotide polymorphisms (SNPs) for which classical HLA alleles and amino acids were imputed. Although previous genome-wide association studies and our results show stronger SNP associations near DQB1, we demonstrate that the HLA signals can be attributed to classical DRB1 and DPB1 genes. Strong support for the predominant role of DRB1 is provided by our conditional analyses. We also demonstrate an independent association of DPB1. Specific HLA-DRB1 genes (*08, *11 and *14) account for most of the DRB1 association signal. Consistent with previous studies, DRB1*08 (p = 1.59 × 10−11) was the strongest predisposing allele where as DRB1*11 (p = 1.42 × 10−10) was protective. Additionally DRB1*14 and the DPB1 association (DPB1*03:01) (p = 9.18 × 10−7) were predisposing risk alleles. No signal was observed in the HLA class 1 or class 3 regions. These findings better define the association of PBC with HLA and specifically support the role of classical HLA-DRB1 and DPB1 genes and alleles in susceptibility to PBC.
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Affiliation(s)
- P Invernizzi
- Department of Medicine, Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Davis, CA 95616, USA
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Qi L, Nassir R, Kosoy R, Garcia L, Curb JD, Tinker L, Howard BV, Robbins J, Seldin MF. Relationship between diabetes risk and admixture in postmenopausal African-American and Hispanic-American women. Diabetologia 2012; 55:1329-37. [PMID: 22322919 PMCID: PMC4430092 DOI: 10.1007/s00125-012-2486-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/11/2012] [Indexed: 12/23/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes is more prevalent in African-Americans (AFAs) and Hispanic-Americans (HAs) than in European-Americans. We assessed whether continental admixture was correlated with diabetes risk in these high-risk groups. METHODS We estimated the proportion of sub-Saharan African (AFR), Amerindian (AMI) and European admixture using 92 ancestry-informative marker genotypes in 16,476 AFA and HA women from the Women's Health Initiative. Cox regression models were used to examine the association between admixture and diabetes risk, with and without accounting for socioeconomic status (SES) and adiposity measurements. RESULTS AFR admixture was significantly associated with diabetes risk in AFA women when adjusting for entry age, neighbourhood SES and BMI or waist/hip ratio (WHR) (all p < 0.0001). In HA women, AMI admixture had significant associations with diabetes risk that remained significant after adjustment for SES and BMI (all p < 0.0005). In both AFAs and HAs, SES showed significant negative associations while BMI or WHR had significant positive associations with diabetes risk, with and without adjustment for genetic admixture. CONCLUSIONS/INTERPRETATION In AFAs, admixture, SES and BMI/WHR each independently contribute to diabetes risk after accounting for each of the other factors; in HAs, admixture, SES and BMI each independently contribute to diabetes risk after accounting for each of the other factors, whereas admixture is not significantly associated with diabetes risk after accounting for SES and WHR. The findings emphasise the importance of considering both genetic and environmental causes in the aetiology of type 2 diabetes.
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Affiliation(s)
- L Qi
- Department of Public Health Sciences, University of California, Davis, CA, USA
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Yao Z, Fanslow WC, Seldin MF, Rousseau AM, Painter SL, Comeau MR, Cohen JI, Spriggs MK. Herpesvirus saimiri encodes a new cytokine, IL-17, which binds to a novel cytokine receptor. J Immunol 2011; 187:4392-4402. [PMID: 22013205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Herpesvirus Saimiri gene 13 (HVS13) exhibits 57% identity with the predicted sequence of a T cell-derived molecule termed CTLA8. Recombinant HVS13 and CTLA8 stimulate transcriptional factor NF-kappaB activity and Interleukin-6 (IL-6) secretion in fibroblasts, and costimulate T cell proliferation. An HVS13.Fc fusion protein was used to isolate a cDNA encoding a novel receptor that also binds CTLA8. This receptor is unrelated to previously identified cytokine receptor families. A recombinant soluble receptor inhibited T cell proliferation and IL-2 production induced by PHA, concanavalin A (conA), and anti-TCR MAb. These results define CTLA8 and HVS13 as novel cytokines that bind to a novel cytokine receptor. We propose to call these molecules IL-17, vIL-17, and IL-17R, respectively.
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Affiliation(s)
- Zhengbin Yao
- Immunex Cororation, 51 University Street, Seattle, Washington 98101, USA
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Liu M, Rogers L, Cheng Q, Shao Y, Fernandez-Beros ME, Hirschhorn JN, Lyon HN, Gajdos ZKZ, Vedantam S, Gregersen P, Seldin MF, Bleck B, Ramasamy A, Hartikainen AL, Jarvelin MR, Kuokkanen M, Laitinen T, Eriksson J, Lehtimäki T, Raitakari OT, Reibman J. Genetic variants of TSLP and asthma in an admixed urban population. PLoS One 2011; 6:e25099. [PMID: 21966427 PMCID: PMC3178593 DOI: 10.1371/journal.pone.0025099] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 08/24/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Thymic stromal lymphopoietin (TSLP), an IL7-like cytokine produced by bronchial epithelial cells is upregulated in asthma and induces dendritic cell maturation supporting a Th2 response. Environmental pollutants, including tobacco smoke and diesel exhaust particles upregulate TSLP suggesting that TSLP may be an interface between environmental pollution and immune responses in asthma. Since asthma is prevalent in urban communities, variants in the TSLP gene may be important in asthma susceptibility in these populations. OBJECTIVES To determine whether genetic variants in TSLP are associated with asthma in an urban admixed population. METHODOLOGY AND MAIN RESULTS: Ten tag-SNPs in the TSLP gene were analyzed for association with asthma using 387 clinically diagnosed asthmatic cases and 212 healthy controls from an urban admixed population. One SNP (rs1898671) showed nominally significant association with asthma (odds ratio (OR) = 1.50; 95% confidence interval (95% CI): 1.09-2.05, p = 0.01) after adjusting for age, BMI, income, education and population stratification. Association results were consistent using two different approaches to adjust for population stratification. When stratified by smoking status, the same SNP showed a significantly increased risk associated with asthma in ex-smokers (OR = 2.00, 95% CI: 1.04-3.83, p = 0.04) but not significant in never-smokers (OR = 1.34; 95% CI: 0.93-1.94, p = 0.11). Haplotype-specific score test indicated that an elevated risk for asthma was associated with a specific haplotype of TSLP involving SNP rs1898671 (OR = 1.58, 95% CI: 1.10-2.27, p = 0.01). Association of this SNP with asthma was confirmed in an independent large population-based cohort consortium study (OR = 1.15, 95% CI: 1.07-1.23, p = 0.0003) and the results stratified by smoking status were also validated (ex-smokers: OR = 1.21, 95% CI: 1.08-1.34, p = 0.003; never-smokers: OR = 1.06, 95% CI: 0.94-1.17, p = 0.33). CONCLUSIONS Genetic variants in TSLP may contribute to asthma susceptibility in admixed urban populations with a gene and environment interaction.
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Affiliation(s)
- Mengling Liu
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Linda Rogers
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Qinyi Cheng
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Yongzhao Shao
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Maria Elena Fernandez-Beros
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Joel N. Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Helen N. Lyon
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Zofia K. Z. Gajdos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Sailaja Vedantam
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Peter Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Michael F. Seldin
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California, United States of America
| | - Bertram Bleck
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Adaikalavan Ramasamy
- Respiratory Epidemiology and Public Health, Imperial College, London, United Kingdom
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences, Obstetrics and Gynecology, Institute of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College, London, United Kingdom
| | - Mikko Kuokkanen
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Oulu, Finland
| | - Tarja Laitinen
- Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital and University of Turku, Turku, Finland
| | - Johan Eriksson
- National Institute for Health and Welfare, Finland Department of General Practice and Primary Health Care, University of Helsinki, Finland Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland Folkhalsan Research Centre, Helsinki, Finland Vasa Central Hospital, Vasa, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Medicine, University of Turku and Department of Clinical Physiology, Turku University Hospital, Turku, Finland
| | - Joan Reibman
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, United States of America
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
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Amos CI, Wang LE, Lee JE, Gershenwald JE, Chen WV, Fang S, Kosoy R, Zhang M, Qureshi AA, Vattathil S, Schacherer CW, Gardner JM, Wang Y, Bishop DT, Barrett JH, MacGregor S, Hayward NK, Martin NG, Duffy DL, Mann GJ, Cust A, Hopper J, Brown KM, Grimm EA, Xu Y, Han Y, Jing K, McHugh C, Laurie CC, Doheny KF, Pugh EW, Seldin MF, Han J, Wei Q. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Hum Mol Genet 2011; 20:5012-23. [PMID: 21926416 DOI: 10.1093/hmg/ddr415] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We performed a multistage genome-wide association study of melanoma. In a discovery cohort of 1804 melanoma cases and 1026 controls, we identified loci at chromosomes 15q13.1 (HERC2/OCA2 region) and 16q24.3 (MC1R) regions that reached genome-wide significance within this study and also found strong evidence for genetic effects on susceptibility to melanoma from markers on chromosome 9p21.3 in the p16/ARF region and on chromosome 1q21.3 (ARNT/LASS2/ANXA9 region). The most significant single-nucleotide polymorphisms (SNPs) in the 15q13.1 locus (rs1129038 and rs12913832) lie within a genomic region that has profound effects on eye and skin color; notably, 50% of variability in eye color is associated with variation in the SNP rs12913832. Because eye and skin colors vary across European populations, we further evaluated the associations of the significant SNPs after carefully adjusting for European substructure. We also evaluated the top 10 most significant SNPs by using data from three other genome-wide scans. Additional in silico data provided replication of the findings from the most significant region on chromosome 1q21.3 rs7412746 (P = 6 × 10(-10)). Together, these data identified several candidate genes for additional studies to identify causal variants predisposing to increased risk for developing melanoma.
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Affiliation(s)
- Christopher I Amos
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Chen Z, Qi L, Beck TJ, Robbins J, Wu G, Lewis CE, Cauley JA, Wright NC, Seldin MF. Stronger bone correlates with African admixture in African-American women. J Bone Miner Res 2011; 26:2307-16. [PMID: 21590740 PMCID: PMC7401709 DOI: 10.1002/jbmr.430] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Osteoporosis affects all populations, but the risk for low bone density and fracture varies greatly by self-reported race and ethnicity. In this article, the relationship between measured percent African admixture and hip structural geometry, estimated from the hip structural analysis (HSA) program, was examined in a subcohort of the Women's Health Initiative (WHI). The study sample included 793 African-American women and 8559 non-Hispanic white women. All the participants were postmenopausal, between the ages of 50 and 79 years, at the time of recruitment and were followed for up to 9 years. Bone density and hip geometry were assessed using dual-energy X-ray absorptiometry. African admixture was measured for African Americans using genetic ancestry informative markers. Multiple regression and mixed-effects models were used for cross-sectional and longitudinal analyses, respectively. Covariates assessed from questionnaires and physical measurements were included in the analysis to control for possible confounding effects. The study results show significant correlations between percent of African admixture and HSA assessments. In comparison with non-Hispanic white women, significantly greater bone strength, as indicated by higher hip bone mineral density and stronger hip geometry, in women with higher African admixture was observed. However, women with higher percent African admixture had larger reductions in bone strength than non-Hispanic white women during the follow-up.
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Affiliation(s)
- Zhao Chen
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA.
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Abstract
Admixed populations such as African Americans and Hispanic Americans are often medically underserved and bear a disproportionately high burden of disease. Owing to the diversity of their genomes, these populations have both advantages and disadvantages for genetic studies of complex phenotypes. Advances in statistical methodologies that can infer genetic contributions from ancestral populations may yield new insights into the aetiology of disease and may contribute to the applicability of genomic medicine to these admixed population groups.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, USA.
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Bronson PG, Goldstein BA, Ramsay PP, Beckman KB, Noble JA, Lane JA, Seldin MF, Kelly JA, Harley JB, Moser KL, Gaffney PM, Behrens TW, Criswell LA, Barcellos LF. The rs4774 CIITA missense variant is associated with risk of systemic lupus erythematosus. Genes Immun 2011; 12:667-71. [PMID: 21614020 DOI: 10.1038/gene.2011.36] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The major histocompatibility complex (MHC) class II transactivator gene (CIITA) encodes an important transcription factor required for human leukocyte antigens (HLA) class II MHC-restricted antigen presentation. MHC genes, including the HLA class II DRB1*03:01 allele, are strongly associated with systemic lupus erythematosus (SLE). Recently the rs4774 CIITA missense variant (+1632G/C) was reported to be associated with susceptibility to multiple sclerosis. In the current study, we investigated CIITA, DRB1*03:01 and risk of SLE using a multi-stage analysis. In stage 1, 9 CIITA variants were tested in 658 cases and 1363 controls (N=2021). In stage 2, rs4774 was tested in 684 cases and 2938 controls (N=3622). We also performed a meta-analysis of the pooled 1342 cases and 4301 controls (N=5643). In stage 1, rs4774(*)C was associated with SLE (odds ratio (OR)=1.24, 95% confidence interval (95% CI)=1.07-1.44, P=4.2 × 10(-3)). Similar results were observed in stage 2 (OR=1.16, 95% CI=1.02-1.33, P=8.5 × 10(-3)) and the meta-analysis of the combined data set (OR=1.20, 95% CI=1.09-1.33, P(meta)=2.5 × 10(-4)). In all three analyses, the strongest evidence for association between rs4774(*)C and SLE was present in individuals who carried at least one copy of DRB1*03:01 (P(meta)=1.9 × 10(-3)). Results support a role for CIITA in SLE, which appears to be stronger in the presence of DRB1*03:01.
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Affiliation(s)
- P G Bronson
- Division of Epidemiology, Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, CA 94720-7356, USA
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Kosoy R, Ransom M, Chen H, Marconi M, Macciardi F, Glorioso N, Gregersen PK, Cusi D, Seldin MF. Evidence for malaria selection of a CR1 haplotype in Sardinia. Genes Immun 2011; 12:582-8. [PMID: 21593778 DOI: 10.1038/gene.2011.33] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Complement receptor 1 (CR1) levels have been associated with malarial susceptibility and/or severity of the disease in different population groups, and CR1 is a receptor for Plasmodium falciparum. In this study, multiple CR1 single-nucleotide polymorphisms (SNPs) showed strong evidence of population differentiation between Sardinian and other European ethnic groups. Cross population algorithms comparing haplotype structure and differences in haplotype and allele frequency distribution provided additional support for natural selection of CR1 in Sardinia. The predominant Sardinian CR1 haplotype included SNPs that are associated with decreased CR1 levels in Europeans and other population groups. Previous studies have shown that the SNPs within the dominant Sardinian haplotype have a significantly higher frequency in a malaria endemic compared with non-endemic regions in India. Together with the historical evidence of the prevalence of malaria in Sardinia, these data support the role of malaria leading to positive selection of this CR1 haplotype in Sardinia.
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Affiliation(s)
- R Kosoy
- Department of Biochemistry and Molecular Medicine, Rowe Program in Human Genetics, University of California, Davis, CA 95616, USA
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Tanaka A, Invernizzi P, Ohira H, Kikuchi K, Nezu S, Kosoy R, Seldin MF, Gershwin ME, Takikawa H. Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort. ACTA ACUST UNITED AC 2011; 78:65-8. [PMID: 21506939 DOI: 10.1111/j.1399-0039.2011.01684.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To examine the genetics of susceptibility to primary biliary cirrhosis (PBC), genome-wide association studies GWAS have been performed in patients of European ancestry and have shown the significant associations of IL12-related pathways, SPIB, IRF5-TNPO3, and 17q12-21. We tested whether these findings could be extended to a Japanese cohort, 303 Japanese PBC and 298 controls. We failed to detect significant associations at IL12A (rs574808, rs1075498) and IL12RB2 (rs3790567). There was no genetic variance at IRF5-TNPO3 (rs10488631) in Japanese. A single nucleotide polymorphism (SNP) at SPIB (rs3745516) reached nominal significance, but the corrected P value did not reach significance. For the 17q12-21 region, two SNPs had nominally significant associations [GSDMB (rs2305480, P = 0.022) and ZPBP2 (rs11557467, P = 0.021)] and we noted a significant P value at a SNP in IKZF3 (rs939327, P = 0.0024, P(c) = 0.017) after correction for multiple comparisons. Thus, these results indicate a haplotype on 17q12-21 with a similar association in Japanese and European PBC.
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Affiliation(s)
- A Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan.
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Nassir R, Qi L, Kosoy R, Garcia L, Allison M, Ochs-Balcom HM, Tylavsky F, Manson JE, Shigeta R, Robbins J, Seldin MF. Relationship between adiposity and admixture in African-American and Hispanic-American women. Int J Obes (Lond) 2011; 36:304-13. [PMID: 21487399 PMCID: PMC3137678 DOI: 10.1038/ijo.2011.84] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Objective To investigate whether differences in admixture in African American (AFA) and Hispanic American (HA) adult women are associated with adiposity and adipose distribution. Design The proportion of European, sub– Saharan African and Amerindian admixture was estimated for AFA and HA women in the Women's Heath Initiative using 92 ancestry informative markers. Analyses assessed the relationship between admixture and adiposity indices. Subjects 11712 AFA and 5088 HA self– identified post– menopausal women. Results There was a significant positive association between body mass index (BMI) and African admixture when BMI was considered as a continuous variable, and age, education, physical activity, parity, family income and smoking were included covariates (p < 10− 4). A dichotomous model (upper and lower BMI quartiles) showed that African admixture was associated with a high odds ratio [OR = 3.27 (for 100% admixture compared to 0% admixture), 95% confidence interval (CI) 2.08 – 5.15]. For HA there was no association between BMI and admixture. In contrast, when waist to hip ratio (WHR) was used as a measure of adipose distribution, there was no significant association between WHR and admixture in AFA but there was a strong association in HA (p<10− 4; OR Amerindian admixture = 5.93, CI = 3.52 – 9.97). Conclusion These studies show that 1) African admixture is associated with BMI in AFA women; 2) Amerindian admixture is associated with WHR but not BMI in HA women; and 3) it may be important to consider different measurements of adiposity and adipose distribution in different ethnic population groups.
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Affiliation(s)
- R Nassir
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95616, USA
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Stephensen CB, Armstrong P, Newman JW, Pedersen TL, Legault J, Schuster GU, Kelley D, Vikman S, Hartiala J, Nassir R, Seldin MF, Allayee H. ALOX5 gene variants affect eicosanoid production and response to fish oil supplementation. J Lipid Res 2011; 52:991-1003. [PMID: 21296957 DOI: 10.1194/jlr.p012864] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to determine whether 5-lipoxygenase (ALOX5) gene variants associated with cardiovascular disease affect eicosanoid production by monocytes. The study was a randomized, double-masked, parallel intervention trial with fish oil (5.0 g of fish oil daily, containing 2.0 g of eicosapentaenoic acid [EPA] and 1.0 g of docosahexaenoic acid [DHA]) or placebo oil (5.0 g of corn/soy mixture). A total of 116 subjects (68% female, 20-59 years old) of African American ancestry enrolled, and 98 subjects completed the study. Neither ALOX5 protein nor arachidonic acid-derived LTB4, LTD4, and LTE4 varied by genotype, but 5-hydroxyeicosatetraenoate (5-HETE), 6-trans-LTB4, 5-oxo-ETE, 15-HETE, and 5,15-diHETE levels were higher in subjects homozygous for the ALOX5 promoter allele containing five Sp1 element tandem repeats ("55" genotype) than in subjects with one deletion (d) (three or four repeats) and one common ("d5" genotype) allele or with two deletion ("dd") alleles. The EPA-derived metabolites 5-HEPE and 15-HEPE and the DHA-derived metabolite 17-HDoHE had similar associations with genotype and increased with supplementation; 5-HEPE and 15-HEPE increased, and 5-oxo-ETE decreased to a greater degree in the 55 than in the other genotypes. This differential eicosanoid response is consistent with the previously observed interaction of these variants with dietary intake of omega-3 fatty acids in predicting cardiovascular disease risk.
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Affiliation(s)
- Charles B Stephensen
- Western Human Nutrition Research Center, US Department of Agriculture, Davis, CA 95616, USA.
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