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Liu X, Song Y, Wan L, Du R. Knowledge, Attitudes, and Practices Among Patients with Systemic Lupus Erythematosus Toward Disease Management and Biologic Therapy. J Multidiscip Healthc 2024; 17:937-947. [PMID: 38455274 PMCID: PMC10918590 DOI: 10.2147/jmdh.s444619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/19/2024] [Indexed: 03/09/2024] Open
Abstract
Background This study aims to investigate the knowledge, attitudes, and practices (KAP) among patients with systemic lupus erythematosus (SLE) toward disease management and biologic therapy. Methods This cross-sectional study was conducted between April 20, 2023, and May 5, 2023, among patients with SLE at Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology. A self-designed questionnaire was developed to collect demographic information of SLE patients and assess their KAP. Results A total of 463 SLE patients participated. The mean scores for knowledge, attitudes, and practices were 8.52 ± 2.36 (possible range: 0-11), 39.40 ± 3.38 (possible range: 11-55), and 27.10 ± 6.29 (possible range: 8-40), respectively. The path analysis demonstrated a significant and positive association between knowledge and attitudes, as indicated by a path coefficient of 0.455 (p < 0.001), and a significant and positive relationship between knowledge and practices, with a path coefficient of 0.709 (p < 0.001). Conclusion Patients with SLE exhibited insufficient knowledge, negative attitudes, and poor practices.
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Affiliation(s)
- Xiaojing Liu
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - You Song
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Limin Wan
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Rong Du
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
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2
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Zhang Y, Hou G, Shen N. Non-coding DNA variants for risk in lupus. Best Pract Res Clin Rheumatol 2024:101937. [PMID: 38429183 DOI: 10.1016/j.berh.2024.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/03/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is a multifactorial autoimmune disease that arises from a dynamic interplay between genetics and environmental triggers. The advent of sophisticated genomics technology has catalyzed a shift in our understanding of disease etiology, spotlighting the pivotal role of non-coding DNA variants in SLE pathogenesis. In this review, we present a comprehensive examination of the non-coding variants associated with SLE, shedding light on their role in influencing disease risk and progression. We discuss the latest methodological advancements that have been instrumental in the identification and functional characterization of these genomic elements, with a special focus on the transformative power of CRISPR-based gene-editing technologies. Additionally, the review probes into the therapeutic opportunities that arise from modulating non-coding regions associated with SLE. Through an exploration of the complex network of non-coding DNA, this review aspires to decode the genetic puzzle of SLE and set the stage for groundbreaking gene-based therapeutic interventions and the advancement of precision medicine strategies tailored to SLE management.
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Affiliation(s)
- Yutong Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
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3
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Zhang C, Qin Q, Li Y, Zheng X, Chen W, Zhen Q, Li B, Wang W, Sun L. Multifactor dimensionality reduction reveals the effect of interaction between ERAP1 and IFIH1 polymorphisms in psoriasis susceptibility genes. Front Genet 2022; 13:1009589. [PMID: 36425068 PMCID: PMC9679141 DOI: 10.3389/fgene.2022.1009589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/18/2022] [Indexed: 09/18/2023] Open
Abstract
Background: Psoriasis is a common immune-mediated hyperproliferative skin dysfunction with known genetic predisposition. Gene-gene interaction (e.g., between HLA-C and ERAP1) in the psoriasis context has been reported in various populations. As ERAP1 has been recognized as a psoriasis susceptibility gene and plays a critical role in antigen presentation, we performed this study to identify interactions between ERAP1 and other psoriasis susceptibility gene variants. Methods: We validated psoriasis susceptibility gene variants in an independent cohort of 5,414 patients with psoriasis and 5,556 controls. Multifactor dimensionality reduction (MDR) analysis was performed to identify the interaction between variants significantly associated with psoriasis in the validation cohort and ERAP1 variants. We then conducted a meta-analysis of those variants with datasets from exome sequencing, target sequencing, and validation analyses and used MDR to identify the best gene-gene interaction model, including variants that were significant in the meta-analysis and ERAP1 variants. Results: We found that 19 of the replicated variants were identified with p < 0.05 and detected six single-nucleotide polymorphisms of psoriasis susceptibility genes in the meta-analysis. MDR analysis revealed that the best predictive model was that between the rs27044 polymorphism of ERAP1 and the rs7590692 polymorphism of IFIH1 (cross-validation consistency = 9/10, test accuracy = 0.53, odds ratio = 1.32 (95% CI, 1.09-1.59), p < 0.01). Conclusion: Our findings suggest that the interaction between ERAP1 and IFIH1 affects the development of psoriasis. This hypothesis needs to be tested in basic biological studies.
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Affiliation(s)
- Chang Zhang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Qin Qin
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Yuanyuan Li
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Qi Zhen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Bao Li
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Wenjun Wang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Liangdan Sun
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
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4
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Cui M, Wang C, Shen Q, Ren H, Li L, Li S, Song Z, Lin W, Zhang R. Integrative analysis of omics summary data reveals putative mechanisms linked to different cell populations in systemic lupus erythematosus. Genomics 2022; 114:110435. [PMID: 35878812 DOI: 10.1016/j.ygeno.2022.110435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/15/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex disease involving many interactions at the molecular level, the details of which remain unclear. Here, we demonstrated an analytical paradigm of prioritizing genes and regulatory elements based on GWAS loci at the single-cell levels. Our initial step was to apply TWMR to identify causal genes and causal methylation sites in SLE. Based on the eQTL, LD and mQTL, we calculated the correlation between these genes and methylation sites. Next, we separately used gene expression and DNAm as exposure variables and outcome variables to analyze the regulatory mechanisms. We identified two mediating modes for SLE: 1) transcription mediation model and 2) epigenetic mediation model. Further, using single-cell RNA sequencing data, we revealed the cell subclusters associated with these mechanisms. Our identification of the mechanisms of SLE in different cell populations is of great significance for understanding the heterogeneity of disease in different cell populations.
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Affiliation(s)
- Mintian Cui
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Qi Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Hongbiao Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Liangshuang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Wenbo Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
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5
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Xu Q, Zheng X, Mao Y, Chen W, Chen S, Zhang H, Zhen Q, Li B, Yong L, Ge H, Yu Y, Zhang R, Cao L, Cheng H, Wang W, Sun L. Gene interaction analysis of psoriasis in Chinese Han population. Mol Genet Genomic Med 2022; 10:e1858. [PMID: 35352505 PMCID: PMC9034666 DOI: 10.1002/mgg3.1858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/10/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background/aims Psoriasis is a chronic immune‐mediated inflammatory skin disease characterized by excessive proliferation of keratinocytes. It has a strong genetic predisposition; gene‐gene interactions are important genetic models for common diseases. In this study, we explore pair‐wise interactions among SNPs contributing to psoriasis susceptibility. Methods We first performed gene interactions with exome‐sequencing, next, we analyzed gene interactions combining the exome sequencing data with the targeted sequencing data. After we sequenced HLA region, we analyzed gene interactions including HLA regions and non‐HLA regions. Results We found interactions between HLA regions were significant. We observed significant interactions between HLA‐C*06:02 and rs118179173 (snp31443520; p = 8.21 × 10−20, OR = 0.22) and between HLA‐C*06:02 and HLA‐B:AA67 (p = 1.22 × 10−12, OR = 0.45). Conclusion This study provides evidence that HLA is the most important susceptibility region on the risk of psoriasis and interactions that occur in this region are still significant.
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Affiliation(s)
- Qiongqiong Xu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yiwen Mao
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Shirui Chen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Hui Zhang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qi Zhen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Bao Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liang Yong
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Huiyao Ge
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yafen Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Ruixue Zhang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Lu Cao
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Hui Cheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Wenjun Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liangdan Sun
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Medical University, Anhui Provincial Institute of Translational Medicine, Hefei, China.,Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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6
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Tian X, Li M, Wang Q, Zhao J, Zeng X. The Challenges and Future Perspective for the Management of Systemic Lupus Erythematosus in China: A Concise Annual Report of 2020. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:38-44. [PMID: 36467018 PMCID: PMC9524811 DOI: 10.2478/rir-2022-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Xinping Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science and Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science and Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science and Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science and Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science and Technology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
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7
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The genetic architecture of primary biliary cholangitis. Eur J Med Genet 2021; 64:104292. [PMID: 34303876 DOI: 10.1016/j.ejmg.2021.104292] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/03/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022]
Abstract
Primary biliary cholangitis (PBC) is a rare autoimmune disease of the liver affecting the small bile ducts. From a genetic point of view, PBC is a complex trait and several genetic and environmental factors have been called in action to explain its etiopathogenesis. Similarly to other complex traits, PBC has benefited from the introduction of genome-wide association studies (GWAS), which identified many variants predisposing or protecting toward the development of the disease. While a progressive endeavour toward the characterization of candidate loci and downstream pathways is currently ongoing, there is still a relatively large portion of heritability of PBC to be revealed. In addition, genetic variation behind progression of the disease and therapeutic response are mostly to be investigated yet. This review outlines the state-of-the-art regarding the genetic architecture of PBC and provides some hints for future investigations, focusing on the study of gene-gene interactions, the application of whole-genome sequencing techniques, and the investigation of X chromosome that can be helpful to cover the missing heritability gap in PBC.
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8
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Nam SW, Lee KS, Yang JW, Ko Y, Eisenhut M, Lee KH, Shin JI, Kronbichler A. Understanding the genetics of systemic lupus erythematosus using Bayesian statistics and gene network analysis. Clin Exp Pediatr 2021; 64:208-222. [PMID: 32683804 PMCID: PMC8103040 DOI: 10.3345/cep.2020.00633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
The publication of genetic epidemiology meta-analyses has increased rapidly, but it has been suggested that many of the statistically significant results are false positive. In addition, most such meta-analyses have been redundant, duplicate, and erroneous, leading to research waste. In addition, since most claimed candidate gene associations were false-positives, correctly interpreting the published results is important. In this review, we emphasize the importance of interpreting the results of genetic epidemiology meta-analyses using Bayesian statistics and gene network analysis, which could be applied in other diseases.
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Affiliation(s)
- Seoung Wan Nam
- Department of Rheumatology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kwang Seob Lee
- Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Korea
| | - Michael Eisenhut
- Department of Pediatrics, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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9
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Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 2021; 12:1611. [PMID: 33712590 PMCID: PMC7955039 DOI: 10.1038/s41467-021-21854-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE. Thousands of genetic variants have been associated with lupus, but causal variants and mechanisms are unknown. Here, the authors combine a massively parallel reporter assay with genome-wide ChIP experiments to identify risk variants with allelic enhancer activity mediated through transcription factor binding.
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10
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Ludwig-Słomczyńska AH, Seweryn MT, Kapusta P, Pitera E, Mantaj U, Cyganek K, Gutaj P, Dobrucka Ł, Wender-Ożegowska E, Małecki MT, Wołkow PP. The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes. Mol Med 2021; 27:6. [PMID: 33472578 PMCID: PMC7818927 DOI: 10.1186/s10020-020-00266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Clinical data suggest that BMI and gestational weight gain (GWG) are strongly interconnected phenotypes; however, the genetic basis of the latter is rather unclear. Here we aim to find genes and genetic variants which influence BMI and/or GWG. METHODS We have genotyped 316 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays. The GIANT, ARIC and T2D-GENES summary statistics were used for TWAS (performed with PrediXcan) in adipose tissue. Next, the analysis of association of imputed expression with BMI in the general and diabetic cohorts (Analysis 1 and 2) or GWG (Analysis 3 and 4) was performed, followed by variant association analysis (1 Mb around identified loci) with the mentioned phenotypes. RESULTS In Analysis 1 we have found 175 BMI associated genes and 19 variants (p < 10-4) which influenced GWG, with the strongest association for rs11465293 in CCL24 (p = 3.18E-06). Analysis 2, with diabetes included in the model, led to discovery of 1812 BMI associated loci and 207 variants (p < 10-4) influencing GWG, with the strongest association for rs9690213 in PODXL (p = 9.86E-07). In Analysis 3, among 648 GWG associated loci, 2091 variants were associated with BMI (FDR < 0.05). In Analysis 4, 7 variants in GWG associated loci influenced BMI in the ARIC cohort. CONCLUSIONS Here, we have shown that loci influencing BMI might have an impact on GWG and GWG associated loci might influence BMI, both in the general and T1DM cohorts. The results suggest that both phenotypes are related to insulin signaling, glucose homeostasis, mitochondrial metabolism, ubiquitinoylation and inflammatory responses.
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Affiliation(s)
| | - Michał T Seweryn
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Przemysław Kapusta
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Ewelina Pitera
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Urszula Mantaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Cyganek
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Gutaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Łucja Dobrucka
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
| | - Ewa Wender-Ożegowska
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej T Małecki
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł P Wołkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland.
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11
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Cheng Y, Meng Y, Li S, Cao D, Ben S, Qin C, Hua L, Cheng G. Genetic variants in the cholesterol biosynthesis pathway genes and risk of prostate cancer. Gene 2021; 774:145432. [PMID: 33444688 DOI: 10.1016/j.gene.2021.145432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/06/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022]
Abstract
Previous studies have found the relationship between cholesterol biosynthesis pathway genes and the risk or prognosis of prostate cancer (PCa), while there is no definite evidence that genetic variants in the cholesterol biosynthesis pathway gene is related to PCa risk. Consequently, we performed this study to explore the associations of single-nucleotide polymorphisms (SNPs) in the cholesterol biosynthesis pathway with PCa risk. We systematically evaluated the association of SNPs in 21 cholesterol biosynthesis pathway genes with the risk of PCa using the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial database using a logistic regression model. Gene expression data of PCa from Gene Expression Omnibus (GEO) datasets and the Cancer Genome Atlas (TCGA) database were applied for mRNA expression analysis. The TCGA database was used to perform expression quantitative trait loci (eQTL) analysis. The interaction between demographic factors and SNPs was analyzed using two-by-four tables. We found T allele of rs67415672 in HMGCS1 is a significant protective allele of PCa [adjusted odds ratio (OR) = 0.90, 95% confidence interval (CI) = 0.83-0.97, P = 4.16 × 10-3]. Moreover, rs67415672 was an eQTL for HMGCS1 (P = 2.23 × 10-6). The expression of HMGCS1 significantly decreased in PCa primary tumors than that in normal tissues. These findings indicated that the HMGCS1 rs67415672 might be possible functional susceptibility loci for PCa.
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Affiliation(s)
- Yifei Cheng
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yixuan Meng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dongliang Cao
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chao Qin
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lixin Hua
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Gong Cheng
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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12
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Zhang F, Wang YF, Zhang Y, Lin Z, Cao Y, Zhang H, Liu ZY, Morris DL, Sheng Y, Cui Y, Zhang X, Vyse TJ, Lau YL, Yang W, Chen Y. Independent Replication on Genome-Wide Association Study Signals Identifies IRF3 as a Novel Locus for Systemic Lupus Erythematosus. Front Genet 2020; 11:600. [PMID: 32719713 PMCID: PMC7348047 DOI: 10.3389/fgene.2020.00600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a genetically complex autoimmune disease. Despite the significant progress made in identifying susceptibility genes for SLE, the genetic architecture of the disease is far from being understood. In this study, we set to replicate a number of suggestive association signals found in genome-wide association studies (GWASs) in additional independent cohorts. Replication studies were performed on Han Chinese cohorts from Hong Kong and Anhui, involving a total of 2,269 cases and 5,073 controls. We identified a missense variant in IRF3 (rs7251) reaching genome-wide significance through a joint analysis of GWAS and replication data (OR = 0.876, P = 4.40E-08). A significant correlation was observed between rs7251 and lupus nephritis (LN) by subphenotype stratification (OR = 0.785, P = 0.0128). IRF3 is a key molecule in type I interferon production upon nucleic acid antigen stimulations and may inhibit regulatory T cell differentiation. Further elucidation of the mechanism of this association could help us better understand the pathogenesis of SLE.
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Affiliation(s)
- Feixia Zhang
- Department of Pediatrics, Union Hospital Affiliated to Fujian Medical University, Fuzhou, China
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong.,Shenzhen Futian Hospital for Rheumatic Disease, Shenzhen, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zhiming Lin
- Department of Rheumatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yujie Cao
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Zhong-Yi Liu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - David L Morris
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - Yujun Sheng
- Department of Dermatology, No.1 Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Yong Cui
- Department of Dermatology, No.1 Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Xuejun Zhang
- Department of Dermatology, No.1 Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yanhui Chen
- Department of Pediatrics, Union Hospital Affiliated to Fujian Medical University, Fuzhou, China
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13
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Watanabe A, Inoue N, Watanabe M, Yamamoto M, Ozaki H, Hidaka Y, Iwatani Y. Increases of CD80 and CD86 Expression on Peripheral Blood Cells and their Gene Polymorphisms in Autoimmune Thyroid Disease. Immunol Invest 2019; 49:191-203. [DOI: 10.1080/08820139.2019.1688343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ayano Watanabe
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naoya Inoue
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka, Japan
| | - Mikio Watanabe
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Mayu Yamamoto
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Haruka Ozaki
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoh Hidaka
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka, Japan
| | - Yoshinori Iwatani
- Department of Biomedical Informatics Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
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14
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Mo X, Guo Y, Qian Q, Fu M, Lei S, Zhang Y, Zhang H. Mendelian randomization analysis revealed potential causal factors for systemic lupus erythematosus. Immunology 2019; 159:279-288. [PMID: 31670388 DOI: 10.1111/imm.13144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/13/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified many loci for systemic lupus erythematosus (SLE). However, identification of functionally relevant genes remains a challenge. The aim of this study was to highlight potential causal genes for SLE in the GWAS loci. By applying Mendelian randomization (MR) methods, such as summary data-based MR (SMR), generalized SMR and MR pleiotropy residual sum and outlier, we identified DNA methylations in 15 loci and mRNA expression of 21 genes that were causally associated with SLE. The identified genes enriched in 14 specific KEGG pathways (e.g. SLE, viral carcinogenesis) and two GO terms (interferon-γ-mediated signaling pathway and innate immune response). Among the identified genes, UBE2L3 and BLK variants were significantly associated with UBE2L3 and BLK methylations and gene expressions, respectively. UBE2L3 was up-regulated in SLE patients in several types of immune cells. Methylations (e.g. cg06850285) and mRNA expression of UBE2L3 were causally associated with SLE. Methylation site cg09528494 and mRNA expression of BLK were causally associated with SLE. BLK single nucleotide polymorphisms that were significantly associated with SLE were strongly associated with plasma cathepsin B level. Deep analysis identified that plasma cathepsin B level was causally associated with SLE. In summary, this study identified hundreds of DNA methylations and genes as potential risk factors for SLE. Genetic variants in UBE2L3 gene might affect SLE by influencing gene expression. Genetic variants in BLK gene might affect SLE by influencing BLK gene expression and plasma cathepsin B protein level.
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Affiliation(s)
- Xingbo Mo
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.,Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, China.,Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Yufan Guo
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiyu Qian
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.,Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Mengzhen Fu
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Shufeng Lei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.,Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, China
| | - Yonghong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.,Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Huan Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.,Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
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15
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Wang PH, Fung SY, Gao WW, Deng JJ, Cheng Y, Chaudhary V, Yuen KS, Ho TH, Chan CP, Zhang Y, Kok KH, Yang W, Chan CP, Jin DY. A novel transcript isoform of STING that sequesters cGAMP and dominantly inhibits innate nucleic acid sensing. Nucleic Acids Res 2019; 46:4054-4071. [PMID: 29547894 PMCID: PMC5934658 DOI: 10.1093/nar/gky186] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/01/2018] [Indexed: 02/06/2023] Open
Abstract
STING is a core adaptor in innate nucleic acid sensing in mammalian cells, on which different sensing pathways converge to induce type I interferon (IFN) production. Particularly, STING is activated by 2'3'-cGAMP, a cyclic dinucleotide containing mixed phosphodiester linkages and produced by cytoplasmic DNA sensor cGAS. Here, we reported on a novel transcript isoform of STING designated STING-β that dominantly inhibits innate nucleic acid sensing. STING-β without transmembrane domains was widely expressed at low levels in various human tissues and viral induction of STING-β correlated inversely with IFN-β production. The expression of STING-β declined in patients with lupus, in which type I IFNs are commonly overproduced. STING-β suppressed the induction of IFNs, IFN-stimulated genes and other cytokines by various immunostimulatory agents including cyclic dinucleotides, DNA, RNA and viruses, whereas depletion of STING-β showed the opposite effect. STING-β interacted with STING-α and antagonized its antiviral function. STING-β also interacted with TBK1 and prevented it from binding with STING-α, TRIF or other transducers. In addition, STING-β bound to 2'3'-cGAMP and impeded its binding with and activation of STING-α, leading to suppression of IFN-β production. Taken together, STING-β sequesters 2'3'-cGAMP second messenger and other transducer molecules to inhibit innate nucleic acid sensing dominantly.
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Affiliation(s)
- Pei-Hui Wang
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wei-Wei Gao
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jian-Jun Deng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yun Cheng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Vidyanath Chaudhary
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ting-Hin Ho
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ching-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yan Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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16
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Wang YF, Lau YL, Yang W. Genetic studies on systemic lupus erythematosus in East Asia point to population differences in disease susceptibility. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:262-268. [PMID: 30897304 DOI: 10.1002/ajmg.c.31696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with extreme clinical heterogeneity and significant differences between populations. East Asian populations are known to have higher prevalence and more severe clinical manifestations for SLE than Europeans. The difference could be the result of genetic and environmental factors, and the interactions between them. Thus, identifying genetic associations from diverse populations provides an opportunity to better understand the genetic architecture of this heterogeneous disease. It is also necessary to elucidate population differences and to apply the findings in future stratified treatment of the disease, with ethnicity likely a major factor to consider. Indeed, it has shown that there are significant differences between East Asians and European populations in several genetic loci for SLE. Genetic studies on SLE are very active in East Asian countries and there have been close collaborations among scientists in this region. Here, we document some work done in this region on SLE genetic research and discuss the aspect of population differences.
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Affiliation(s)
- Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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17
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Wang PH, Ye ZW, Deng JJ, Siu KL, Gao WW, Chaudhary V, Cheng Y, Fung SY, Yuen KS, Ho TH, Chan CP, Zhang Y, Kok KH, Yang W, Chan CP, Jin DY. Inhibition of AIM2 inflammasome activation by a novel transcript isoform of IFI16. EMBO Rep 2018; 19:embr.201845737. [PMID: 30104205 DOI: 10.15252/embr.201845737] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
Mouse p202 is a disease locus for lupus and a dominant-negative inhibitor of AIM2 inflammasome activation. A human homolog of p202 has not been identified so far. Here, we report a novel transcript isoform of human IFI16-designated IFI16-β, which has a domain architecture similar to that of mouse p202. Like p202, IFI16-β contains two HIN domains, but lacks the pyrin domain. IFI16-β is ubiquitously expressed in various human tissues and cells. Its mRNA levels are also elevated in leukocytes of patients with lupus, virus-infected cells, and cells treated with interferon-β or phorbol ester. IFI16-β co-localizes with AIM2 in the cytoplasm, whereas IFI16-α is predominantly found in the nucleus. IFI16-β interacts with AIM2 to impede the formation of a functional AIM2-ASC complex. In addition, IFI16-β sequesters cytoplasmic dsDNA and renders it unavailable for AIM2 sensing. Enforced expression of IFI16-β inhibits the activation of AIM2 inflammasome, whereas knockdown of IFI16-β augments interleukin-1β secretion triggered by dsDNA but not dsRNA Thus, cytoplasm-localized IFI16-β is functionally equivalent to mouse p202 that exerts an inhibitory effect on AIM2 inflammasome.
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Affiliation(s)
- Pei-Hui Wang
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zi-Wei Ye
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jian-Jun Deng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wei-Wei Gao
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Vidyanath Chaudhary
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yun Cheng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ting-Hin Ho
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ching-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yan Zhang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wanling Yang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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18
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Association of TNFAIP3 and TNIP1 polymorphisms with systemic lupus erythematosus risk: A meta-analysis. Gene 2018; 668:155-165. [PMID: 29783072 DOI: 10.1016/j.gene.2018.05.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/12/2018] [Accepted: 05/16/2018] [Indexed: 02/01/2023]
Abstract
OBJECT With the development of GWAS, both TNFAIP3 and TNIP1 were revealed to be susceptibility genes of SLE. However, some other studies revealed no association between TNFAIP3, TNIP1 and SLE susceptibility. In order to estimate such association more precisely and systemically, a meta-analysis was conducted. METHOD Studies on the association between TNFAIP3 rs2230926, TNIP1 rs7708392 and SLE risk were carefully selected via searching 3 databases (Pubmed, Embase, and Web of Science). A fixed- or random-effect model was used according to the heterogeneity, and a subgroup analysis by ethnicity was also performed. RESULTS 26 studies from 18 articles involving a total of 21,372 patients and 30,165 controls were analyzed for TNFAIP3 rs2230926. A significant association between the minor G allele of TNFAIP3 rs2230926 and SLE risk was found via a random-effect model (OR = 1.643, 95% CI = (1.462, 1.847), p < 0.01). In the subgroup analysis by ethnicity, significant correlations were also found in all Caucasians, Asians, and Africans (OR = 1.675, 95% CI = (1.353, 2.074), p < 0.01; OR = 1.738, 95% CI = (1.557, 1.940), p < 0.01; OR = 1.324, 95% CI = (1.029, 1.704), p < 0.05). As for TNIP1 rs7708392, 21 studies from 12 articles involving 24,716 cases and 32,200 controls were analyzed. A significant association of the minor C allele of TNIP1 rs7708392 and SLE risk was found via a random-effect model (OR = 1.247, 95% CI = (1.175, 1.323), p < 0.01). In the subgroup analysis by ethnicity, significant correlations were found in Caucasians, and Africans (OR = 1.317, 95% CI = (1.239, 1.401), p < 0.01; OR = 1.210, 95% CI = (1.108, 1.322), p < 0.01). However, there was no significant association in Asians (OR = 1.122, 95% CI = (0.953, 1.321), p > 0.05). CONCLUSION The minor G allele of TNFAIP3 rs2230926 was associated with increased risk of SLE in all Caucasians, Asians, and Africans. The minor C allele of TNIP1 rs7708392 was associated with the increased risk of SLE in Caucasians and Africans, while it was not associated with SLE susceptibility in Asians.
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19
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Pamuk ON, Gurkan H, Pamuk GE, Tozkır H, Duymaz J, Yazar M. BLK pathway-associated rs13277113 GA genotype is more frequent in SLE patients and associated with low gene expression and increased flares. Clin Rheumatol 2016; 36:103-109. [PMID: 27864698 DOI: 10.1007/s10067-016-3475-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 11/04/2016] [Indexed: 02/02/2023]
Abstract
We aimed to evaluate the relationship between some important genetic variations and expressions of these genes in our SLE population. We also determined their association with clinical parameters. Eighty-four SLE patients (79 F, 5 M) and 105 healthy controls (98 F, 7 M) were included in the study. rs13277113, rs2736340, rs7829816, rs6983130, rs2613310, and rs704853 polymorphisms, gene expressions of Src family kinases (Blk, Hck, Lck, and Lyn), and Syk kinases (Syk, ZAP70) were studied by real-time PCR. The heterozygous genotypic pattern (GA) for rs13277113 polymorphism was more frequent in patients with SLE when compared to that in controls (48.8 vs. 31.4%, p = 0.035). Other genotype variants were similar in SLE patients and controls. In the SLE group, the heterozygous genotype for rs13277113 was significantly less frequent in active SLE patients (58.8 vs. 26.7%, p = 0.01). SLE flares according to the SELENA-SLEDAI flare index were significantly more frequent in GA (rs13277113) (70 vs. 37%) and CT (rs2736340) genotypes (66.7 vs. 35.2%) than those in other genotypes (p values <0.01). The relative expression of Blk gene was significantly decreased in the SLE group as compared to that in controls (0.52 times, 95%CI 0.19-0.85). The gene expressions of Blk and ZAP70 were significantly lower in SLE patients who had flares according to the SELENA-SLEDAI flare index when compared to those in others (p values 0.01 and 0.017). We observed more frequent heterozygous GA genotypic pattern (rs13277113) in our SLE patients compared to that in controls; and it was associated with disease flares. Blk gene expression in SLE was lower, especially in relapsing patients.
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Affiliation(s)
- Omer Nuri Pamuk
- Department of Rheumatology, Trakya University Medical Faculty, Edirne, Turkey.
- , Eski Yildiz Cad. Park Apt. No:22 Daire:18 Besiktas, 34349, Istanbul, Turkey.
| | - Hakan Gurkan
- Department of Medical Genetics, Trakya University Medical Faculty, Edirne, Turkey
| | - Gulsum Emel Pamuk
- Department of Hematology, Trakya University Medical Faculty, Edirne, Turkey
| | - Hilmi Tozkır
- Department of Medical Genetics, Trakya University Medical Faculty, Edirne, Turkey
| | - Julide Duymaz
- Trakya University Health Services Vocational College, Edirne, Turkey
| | - Metin Yazar
- Department of Medical Genetics, Trakya University Medical Faculty, Edirne, Turkey
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Genetic polymorphisms of cell adhesion molecules in Behcet's disease in a Chinese Han population. Sci Rep 2016; 6:24974. [PMID: 27108704 PMCID: PMC4842956 DOI: 10.1038/srep24974] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/08/2016] [Indexed: 12/20/2022] Open
Abstract
Cell adhesion molecules (CAMs) are involved in various immune-mediated diseases. This study was conducted to investigate the association of single nucleotide polymorphisms (SNPs) of CAMs with Behçet’s disease (BD) in a Chinese Han population. A two-stage association study was carried out in 1149 BD patients and 2107 normal controls. Genotyping of 43 SNPs was performed using MassARRAY System (Sequenom), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan SNP assays. The expression of CD6 and CD11c was examined by real-time PCR and cytokine production was measured by ELISA. A significantly higher frequency of the CT genotype, and a lower frequency of the CC genotype and C allele of CD6 rs11230563 were observed in BD as compared with controls. Analysis of CD11c rs2929 showed that patients with BD had a significantly higher frequency of the GG genotype and G allele, and a lower frequency of the AG genotype as compared with controls. Functional experiments showed an increased CD11c expression and increased production of TNF-α and IL-1beta by LPS stimulated PBMCs in GG carriers of CD11c rs2929 compared to AA/AG carriers. Our study provides evidence that CD6 and CD11c are involved in the susceptibility to BD in a Chinese Han population.
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AlFadhli S, Ghanem AAM, Nizam R. Genome-wide differential expression reveals candidate genes involved in the pathogenesis of lupus and lupus nephritis. Int J Rheum Dis 2015; 19:55-64. [DOI: 10.1111/1756-185x.12745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Suad AlFadhli
- Department of Medical Laboratory Sciences; Faculty of Allied Health Sciences; Kuwait University; Kuwait
| | - Aqeel A. M. Ghanem
- Department of Rheumatology; Mubarak Al-Kabeer Hospital; Ministry of Health; Kuwait
| | - Rasheeba Nizam
- Department of Medical Laboratory Sciences; Faculty of Allied Health Sciences; Kuwait University; Kuwait
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