1
|
Zhou XJ, Tsoi LC, Hu Y, Patrick MT, He K, Berthier CC, Li Y, Wang YN, Qi YY, Zhang YM, Gan T, Li Y, Hou P, Liu LJ, Shi SF, Lv JC, Xu HJ, Zhang H. Exome Chip Analyses and Genetic Risk for IgA Nephropathy among Han Chinese. Clin J Am Soc Nephrol 2021; 16:213-224. [PMID: 33462083 PMCID: PMC7863642 DOI: 10.2215/cjn.06910520] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/11/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVES IgA nephropathy is the most common form of primary GN worldwide. The evidence of geographic and ethnic differences, as well as familial aggregation of the disease, supports a strong genetic contribution to IgA nephropathy. Evidence for genetic factors in IgA nephropathy comes also from genome-wide association patient-control studies. However, few studies have systematically evaluated the contribution of coding variation in IgA nephropathy. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We performed a two-stage exome chip-based association study in 13,242 samples, including 3363 patients with IgA nephropathy and 9879 healthy controls of Han Chinese ancestry. Common variant functional annotation, gene-based low-frequency variants analysis, differential mRNA expression, and gene network integration were also explored. RESULTS We identified three non-HLA gene regions (FBXL21, CCR6, and STAT3) and one HLA gene region (GABBR1) with suggestive significance (Pmeta <5×10-5) in single-variant associations. These novel non-HLA variants were annotated as expression-associated single-nucleotide polymorphisms and were located in enhancer regions enriched in histone marks H3K4me1 in primary B cells. Gene-based low-frequency variants analysis suggests CFB as another potential susceptibility gene. Further combined expression and network integration suggested that the five novel susceptibility genes, TGFBI, CCR6, STAT3, GABBR1, and CFB, were involved in IgA nephropathy. CONCLUSIONS Five novel gene regions with suggestive significance for IgA nephropathy were identified and shed new light for further mechanism investigation.
Collapse
Affiliation(s)
- Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kevin He
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
- Kidney Epidemiology and Cost Center, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Celine C. Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Yanming Li
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas
| | - Yan-na Wang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Yuan-yuan Qi
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Yue-miao Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Ting Gan
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Yang Li
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Ping Hou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Li-jun Liu
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Su-fang Shi
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Ji-cheng Lv
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Hu-ji Xu
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, People’s Republic of China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, People’s Republic of China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, People’s Republic of China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People’s Republic of China
- Research Units of Diagnosis and Treatment of Immune-Mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| |
Collapse
|
2
|
González-Serna D, Ortiz-Fernández L, Vargas S, García A, Raya E, Fernández-Gutierrez B, López-Longo FJ, Balsa A, González-Álvaro I, Narvaez J, Gómez-Vaquero C, Sabio JM, García-Portales R, González-Escribano MF, Tolosa C, Carreira P, Kiemeney L, Coenen MJH, Witte T, Schneider M, González-Gay MÁ, Martín J. Association of a rare variant of the TNFSF13B gene with susceptibility to Rheumatoid Arthritis and Systemic Lupus Erythematosus. Sci Rep 2018; 8:8195. [PMID: 29844438 PMCID: PMC5974315 DOI: 10.1038/s41598-018-26573-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
A rare variant (BAFF-var) of the tumor necrosis factor superfamily 13b (TNFSF13B) gene has been recently associated with multiple sclerosis (MS) and systemic lupus erythematosus (SLE). The aim of this study was to investigate the association between TNFSF13B BAFF-var and susceptibility to rheumatoid arthritis (RA) and replicate that association in SLE. 6,218 RA patients, 2,575 SLE patients and 4,403 healthy controls from three different countries were included in the study. TNFSF13B BAFF-var was genotyped using TaqMan allelic discrimination assay. PLINK software was used for statistical analyses. TNFSF13B BAFF-var was significantly associated with RA (p = 0.015, OR = 1.21, 95% CI = 1.03-1.41) in the Spanish cohort. A trend of association was observed in the Dutch (p = 0.115) and German (p = 0.228) RA cohorts. A meta-analysis of the three RA cohorts included in this study revealed a statistically significant association (p = 0.002, OR = 1.24, 95% CI = 1.10-1.38). In addition, TNFSF13B BAFF-var was significantly associated with SLE in the Spanish (p = 0.001, OR = 1.41, 95% CI = 1.14-1.74) and the German cohorts (p = 0.030, OR = 1.86, 95% CI = 1.05-3.28), with a statistically significant p-value obtained in the meta-analysis (p = 0.0002, OR = 1.46, 95% CI = 1.09-2.32). The results obtained confirm the known association of TNFSF13B BAFF-var with SLE and, for the first time, demonstrate that this variant contributes to susceptibility to RA.
Collapse
Affiliation(s)
| | | | - Sofía Vargas
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Antonio García
- Rheumatology Department, Hospital Virgen de las Nieves, Granada, Spain
| | - Enrique Raya
- Systemic Autoimmune Diseases Unit, Hospital Campus de la Salud, Granada, Spain
| | | | | | - Alejandro Balsa
- Rheumatology Department, Instituto de Investigación Hospital Universitario La Paz (IDIPAZ), Madrid, Spain
| | - Isidoro González-Álvaro
- Rheumatology Department, Instituto de Investigación del Hospital de La Princesa (IIS-IP), Madrid, Spain
| | - Javier Narvaez
- Rheumatology Service, Hospital Universitario de Bellvitge, Barcelona, Spain
| | | | - José Mario Sabio
- Systemic Autoimmune Diseases Unit, Department of Internal Medicine, Hospital Virgen de las Nieves, Granada, Spain
| | | | | | - Carles Tolosa
- Department of Internal Medicine, Hospital Parc Taulí, Sabadell, Spain
| | - Patricia Carreira
- Rheumatology Service, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Lambertus Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Marieke J H Coenen
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Torsten Witte
- Department for Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Matthias Schneider
- Policlinic and Hiller Research Unit for Rheumatology, UKD, Heinrich-Heine-University Dusseldorf, Dusseldorf, Germany
| | - Miguel Ángel González-Gay
- Epidemiology, Genetics and Atherosclerosis Research Group on Systemic Inflammatory Diseases IDIVAL, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
| |
Collapse
|