1
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Fang F, Sun Y. Prediction of systemic lupus erythematosus-related genes based on graph attention network and deep neural network. Comput Biol Med 2024; 175:108371. [PMID: 38691916 DOI: 10.1016/j.compbiomed.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 05/03/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder intricately linked to genetic factors, with numerous approaches having identified genes linked to its development, diagnosis and prognosis. Despite genome-wide association analysis and gene knockout experiments confirming some genes associated with SLE, there are still numerous potential genes yet to be discovered. The search for relevant genes through biological experiments entails significant financial and human resources. With the advancement of computational technologies like deep learning, we aim to identify SLE-related genes through deep learning methods, thereby narrowing down the scope for biological experimentation. This study introduces SLEDL, a deep learning-based approach that leverages DNN and graph neural networks to effectively identify SLE-related genes by capturing relevant features in the gene interaction network. The above steps transform the identification of SLE related genes into a binary classification problem, ultimately solved through a fully connected layer. The results demonstrate the superiority of SLEDL, achieving higher AUC (0.7274) and AUPR (0.7599), further validated through case studies.
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Affiliation(s)
- Fang Fang
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yizhou Sun
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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2
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Hu W, Liu Y, Lian C, Lu H. Genetic insight into putative causes of xanthelasma palpebrarum: a Mendelian randomization study. Front Immunol 2024; 15:1347112. [PMID: 38601164 PMCID: PMC11004296 DOI: 10.3389/fimmu.2024.1347112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Xanthelasma palpebrarum (XP) is the most common form of cutaneous xanthoma, with a prevalence of 1.1%~4.4% in the population. However, the cause of XP remains largely unknown. In the present study, we used Mendelian randomization to assess the genetic association between plasma lipids, metabolic traits, and circulating protein with XP, leveraging summary statistics from large genome-wide association studies (GWAS). Genetically predicted plasma cholesterol and LDL-C, but not HDL-C or triglyceride, were significantly associated with XP. Metabolic traits, including BMI, fasting glucose, type 2 diabetes, systolic and diastolic blood pressure, were not significantly associated with XP. Furthermore, we found genetically predicted 12 circulating proteins were associated with XP, including FN1, NTM, FCN2, GOLM1, ICAM5, PDE5A, C5, CLEC11A, CXCL1, CCL2, CCL11, CCL13. In conclusion, this study identified plasma cholesterol, LDL-C, and 12 circulating proteins to be putative causal factors for XP, highlighting the role of plasma cholesterol and inflammatory response in XP development.
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Affiliation(s)
- Wenting Hu
- Department of Dermatology, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, China
| | - Yaozhong Liu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Cuihong Lian
- Department of Dermatology, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, China
| | - Haocheng Lu
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
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3
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Liu S, Liu ZC, Zhang MY, Wang SJ, Pan M, Ji P, Zhu C, Lin P, Wang Y. ICAM-1 mediated cell-cell adhesion exerts dual roles on human B cell differentiation and IgG production. iScience 2023; 26:108505. [PMID: 38162034 PMCID: PMC10755720 DOI: 10.1016/j.isci.2023.108505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 01/28/2023] [Accepted: 11/17/2023] [Indexed: 01/03/2024] Open
Abstract
Intercellular adhesion molecule 1 (ICAM-1) plays prominent roles in mediating cell-cell adhesion which also facilitates B cell activation and differentiation with the help from CD4+ T cells. Here, we have reported a unique phenomenon that increased ICAM-1 on purified human CD4+ T cells upon anti-CD3/CD28 stimulation enhanced CD4+ T-B cell adhesion whereas induced less B cell differentiation and IgG production. This was largely due to increased PD-1 expression on CD19hi B cells after coculturing with hyperactivated CD4+ T cells. Consequently, ICAM-1 blockade during CD4+ T cell-B cell coculture promoted IgG production with the activation of ERK1/2 and Blimp-1/IRF4 upregulation. Consistently, CD4+ T cells from moderate-to-severe SLE patients with high ICAM-1 expression mediated less IgG production after T-B coculture. Therefore, ICAM-1-mediated human CD4+ T-B cell adhesion provides dual roles on B cell differentiation and IgG production partially depending on expression levels of PD-1 on B cells, supporting cell adhesion and subsequent PD-1 induction as an alternative intrinsic checkpoint for B cell differentiation.
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Affiliation(s)
- Shuai Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Diagnostic Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Zhi-cui Liu
- Department of Dermatology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Mei-yu Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shu-jun Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Meng Pan
- Department of Dermatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ping Ji
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ping Lin
- Department of Diagnostic Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Ying Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Institute of Virology, Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
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4
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Sestan M, Kifer N, Arsov T, Cook M, Ellyard J, Vinuesa CG, Jelusic M. The Role of Genetic Risk Factors in Pathogenesis of Childhood-Onset Systemic Lupus Erythematosus. Curr Issues Mol Biol 2023; 45:5981-6002. [PMID: 37504294 PMCID: PMC10378459 DOI: 10.3390/cimb45070378] [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: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
The pathogenesis of childhood-onset systemic lupus erythematosus (cSLE) is complex and not fully understood. It involves three key factors: genetic risk factors, epigenetic mechanisms, and environmental triggers. Genetic factors play a significant role in the development of the disease, particularly in younger individuals. While cSLE has traditionally been considered a polygenic disease, it is now recognized that in rare cases, a single gene mutation can lead to the disease. Although these cases are uncommon, they provide valuable insights into the disease mechanism, enhance our understanding of pathogenesis and immune tolerance, and facilitate the development of targeted treatment strategies. This review aims to provide a comprehensive overview of both monogenic and polygenic SLE, emphasizing the implications of specific genes in disease pathogenesis. By conducting a thorough analysis of the genetic factors involved in SLE, we can improve our understanding of the underlying mechanisms of the disease. Furthermore, this knowledge may contribute to the identification of effective biomarkers and the selection of appropriate therapies for individuals with SLE.
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Affiliation(s)
- Mario Sestan
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Nastasia Kifer
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Todor Arsov
- Faculty of Medical Sciences, University Goce Delchev, 2000 Shtip, North Macedonia
- The Francis Crick Institute, London NW1 1AT, UK
| | - Matthew Cook
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
- Department of Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Julia Ellyard
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | | | - Marija Jelusic
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
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5
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Lichtnekert J, Anders HJ, Lech M. Lupus Nephritis: Current Perspectives and Moving Forward. J Inflamm Res 2022; 15:6533-6552. [PMID: 36483271 PMCID: PMC9726217 DOI: 10.2147/jir.s363722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/22/2022] [Indexed: 08/07/2023] Open
Abstract
Lupus nephritis is a severe organ manifestation of systemic lupus erythematosus, and its pathogenesis involves complex etiology and mechanisms. Despite significant knowledge gains and extensive efforts put into understanding the development and relapsing disease activity, lupus nephritis remains a substantial cause of morbidity and mortality in lupus patients. Current therapies retain a significant unmet medical need regarding rates of complete response, preventing relapse of lupus nephritis, progression of chronic kidney disease to kidney failure, drug toxicity, and pill burden-related drug non-adherence. Connected to progression of chronic kidney disease are the associated risks for disabling or even lethal cardiovascular events, as well as chronic kidney disease-related secondary immunodeficiency and serious infections. In this regard, biomarkers are needed that can predict treatment response to specific drugs to enable personalized precision medicine. A series of clinical trials with innovative immunomodulatory drugs are ongoing and raise expectations for improvements in the management of lupus nephritis. Here, we review how new developments in pathogenesis connect with current and future perspectives for the management of lupus nephritis.
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Affiliation(s)
- Julia Lichtnekert
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Hans-Joachim Anders
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Maciej Lech
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
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6
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Ding S, Liu J, Han X, Ding W, Liu Z, Zhu Y, Zhan W, Wan Y, Gai S, Hou J, Wang X, Wu Y, Wu A, Li CY, Zheng Z, Tian XL, Cao H. ICAM-1-related noncoding RNA accelerates atherosclerosis by amplifying NF-κB signaling. J Mol Cell Cardiol 2022; 170:75-86. [PMID: 35714558 DOI: 10.1016/j.yjmcc.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/20/2022] [Accepted: 06/04/2022] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) are critical regulators of inflammation with great potential as new therapeutic targets. However, the role of lncRNAs in early atherosclerosis remains poorly characterized. This study aimed to identify the key lncRNA players in activated endothelial cells (ECs). The lncRNAs in response to pro-inflammatory factors in ECs were screened through RNA sequencing. ICAM-1-related non-coding RNA (ICR) was identified as the most potential candidate for early atherosclerosis. ICR is essential for intercellular adhesion molecule-1 (ICAM1) expression, EC adhesion and migration. In a high fat diet-induced atherosclerosis model in mice, ICR is upregulated in the development of atherosclerosis. After intravenous injection of adenovirus carrying shRNA for mouse ICR, the atherosclerotic plaque area was markedly reduced with the declined expression of ICR and ICAM1. Mechanistically, ICR stabilized the mRNA of ICAM1 in quiescent ECs; while under inflammatory stress, ICR upregulated ICAM1 in a nuclear factor kappa B (NF-κB) dependent manner. RNA-seq analysis showed pro-inflammatory targets of NF-κB were regulated by ICR. Furthermore, the chromatin immunoprecipitation assays showed that p65 binds to ICR promoter and facilitates its transcription. Interestingly, ICR, in turn, promotes p65 accumulation and activity, forming a positive feedback loop to amplify NF-κB signaling. Preventing the degradation of p65 using proteasome inhibitors rescued the expression of NF-κB targets suppressed by ICR. Taken together, ICR acts as an accelerator to amplify NF-κB signaling in activated ECs and suppressing ICR is a promising early intervention for atherosclerosis through ICR/p65 loop blockade.
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Affiliation(s)
- Shuangjin Ding
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China; Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jiankun Liu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - XiaoRui Han
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zhirui Liu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - Ying Zhu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - Wenxing Zhan
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - Yiqi Wan
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - Shujie Gai
- National Clinical Research Center of Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junjie Hou
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiaoxia Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yixia Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Andong Wu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
| | - Chuan-Yun Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zhe Zheng
- National Clinical Research Center of Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao-Li Tian
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China.
| | - Huiqing Cao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
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7
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Ferreté-Bonastre AG, Cortés-Hernández J, Ballestar E. What can we learn from DNA methylation studies in lupus? Clin Immunol 2022; 234:108920. [PMID: 34973429 DOI: 10.1016/j.clim.2021.108920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 11/17/2022]
Abstract
During the past twenty years, a wide range of studies have established the existence of epigenetic alterations, particularly DNA methylation changes, in lupus. Epigenetic changes might have different contributions in children-onset versus adult-onset lupus. DNA methylation alterations have been identified and characterized in relation to disease activity and damage, different lupus subtypes and responses to drugs. However, to date there has been no practical application of these findings in the clinical milieu. In this article, we provide a review of key studies showing the relationship between DNA methylation and the many clinical aspects related to lupus. We also propose several options, in relation to the range of methodological developments and experimental design, that could optimize these findings and make them amenable for use in clinical practice.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241, China.
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8
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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Goulielmos GN, Zervou MI. Comment on: Association of systemic lupus erythematosus with peripheral arterial disease: a meta-analysis of literature studies. Rheumatology (Oxford) 2021; 60:e187-e188. [PMID: 33367892 DOI: 10.1093/rheumatology/keaa869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete.,Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete
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10
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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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11
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Autoimmunity and organ damage in systemic lupus erythematosus. Nat Immunol 2020; 21:605-614. [PMID: 32367037 DOI: 10.1038/s41590-020-0677-6] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/31/2020] [Indexed: 01/07/2023]
Abstract
Impressive progress has been made over the last several years toward understanding how almost every aspect of the immune system contributes to the expression of systemic autoimmunity. In parallel, studies have shed light on the mechanisms that contribute to organ inflammation and damage. New approaches that address the complicated interaction between genetic variants, epigenetic processes, sex and the environment promise to enlighten the multitude of pathways that lead to what is clinically defined as systemic lupus erythematosus. It is expected that each patient owns a unique 'interactome', which will dictate specific treatment.
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12
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Kim T, Bae SC, Kang C. Synergistic activation of NF-κB by TNFAIP3 (A20) reduction and UBE2L3 (UBCH7) augment that synergistically elevate lupus risk. Arthritis Res Ther 2020; 22:93. [PMID: 32334614 PMCID: PMC7183688 DOI: 10.1186/s13075-020-02181-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/02/2020] [Indexed: 02/03/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is an autoimmune inflammatory rheumatic disease. SLE susceptibility is affected by multiple genetic elements, environmental factors, and their interactions. We aimed in this study to statistically and functionally characterize a gene-gene interaction (epistasis) recently documented to affect SLE risk. Methods Two single-nucleotide polymorphisms, rs2230926 in TNFAIP3 (A20) gene and rs131654 in UBE2L3 (UBCH7) gene, were genotyped in all 3525 Korean participants, and their SLE risk association and epistasis were statistically analyzed by calculating odds ratio (OR), 95% confidence interval (CI), and P values in genotype comparisons between 1318 SLE patients and 2207 healthy controls. Furthermore, their effects on gene functions were assessed by comparatively examining separate and combined effects of TNFAIP3 and UBE2L3 knockdowns on NF-κB transcription factor activity in human cells. Results SLE susceptibility is associated with TNFAIP3 rs2230926 (OR = 1.9, 95% CI 1.6–2.4, P = 8.6 × 10−11) and UBE2L3 rs131654 (OR = 1.2, 95% CI 1.1–1.4, P = 1.1 × 10−4) in a Korean population of this study. Their risk-associated alleles synergistically elevate SLE susceptibility in both multivariate logistic regression analysis (ORinteraction = 1.6, P = 0.0028) and genotype-stratified analysis (ORinteraction = 2.4), confirming the synergistic TNFAIP3-UBE2L3 interaction in SLE risk. Additionally, the SLE-susceptible alleles confer decreased TNFAIP3 expression (P = 1.1 × 10−6, n = 610) and increased UBE2L3 expression (P = 9.5 × 10−11, n = 475), respectively, in B cell analysis of the International HapMap Project individuals with adjustment for ethnicity. Furthermore, when compared with TNFAIP3 non-knockdown and UBE2L3 knockdown in human HeLa cells, TNFAIP3 knockdown and UBE2L3 non-knockdown synergistically increase three cytokines, CCL2, CXCL8 (IL8), and IL6, all regulated by NF-κB in the human TNFR signaling pathway. Conclusions A synergistic interaction between TNFAIP3 and UBE2L3 genes is observed in SLE risk, as being evident in comparison of genotype distributions between SLE patients and controls. Additionally, the synergistic gene-gene interaction is functionally validated, as TNFAIP3 reduction and UBE2L3 augment exert synergism in activation of NF-κB and subsequent induction of inflammatory cytokines. Accordingly, SLE inflammation and risk could be synergistically alleviated by TNFAIP3 upregulation and UBE2L3 downregulation.
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Affiliation(s)
- Taehyeung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222-1 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Changwon Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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13
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Zorro MM, Aguirre-Gamboa R, Mayassi T, Ciszewski C, Barisani D, Hu S, Weersma RK, Withoff S, Li Y, Wijmenga C, Jabri B, Jonkers IH. Tissue alarmins and adaptive cytokine induce dynamic and distinct transcriptional responses in tissue-resident intraepithelial cytotoxic T lymphocytes. J Autoimmun 2020; 108:102422. [PMID: 32033836 PMCID: PMC7049906 DOI: 10.1016/j.jaut.2020.102422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
The respective effects of tissue alarmins interleukin (IL)-15 and interferon beta (IFNβ), and IL-21 produced by T cells on the reprogramming of cytotoxic T lymphocytes (CTLs) that cause tissue destruction in celiac disease is poorly understood. Transcriptomic and epigenetic profiling of primary intestinal CTLs showed massive and distinct temporal transcriptional changes in response to tissue alarmins, while the impact of IL-21 was limited. Only anti-viral pathways were induced in response to all the three stimuli, albeit with differences in dynamics and strength. Moreover, changes in gene expression were primarily independent of changes in H3K27ac, suggesting that other regulatory mechanisms drive the robust transcriptional response. Finally, we found that IL-15/IFNβ/IL-21 transcriptional signatures could be linked to transcriptional alterations in risk loci for complex immune diseases. Together these results provide new insights into molecular mechanisms that fuel the activation of CTLs under conditions that emulate the inflammatory environment in patients with autoimmune diseases.
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Affiliation(s)
- Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Raul Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Toufic Mayassi
- Department of Medicine, University of Chicago, Chicago, USA; Committee on Immunology, University of Chicago, Chicago, USA
| | | | | | - Shixian Hu
- Department of Gastroenterology and Hepatology, University Medical Center, Groningen, University of Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center, Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School. Hannover, Germany
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Bana Jabri
- Department of Medicine, University of Chicago, Chicago, USA; Committee on Immunology, University of Chicago, Chicago, USA.
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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14
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Guo Y, Gu R, Yu J, Lei B, Gan D, Xu G. Synthetic Glucocorticoid-Induced Leucine Zipper Peptide Inhibits Lipopolysaccharide-Induced Ocular Inflammation in Rats. Ophthalmic Res 2019; 63:434-442. [PMID: 31770752 DOI: 10.1159/000505003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/26/2019] [Indexed: 11/19/2022]
Abstract
PURPOSE To demonstrate the anti-inflammatory action of a synthetic glucocorticoid-induced leucine zipper (GILZ98-134) peptide (GILZ-p) in a model of endotoxin-induced uveitis (EIU) in rats. METHODS The EIU model was induced in Sprague Dawley rats with an intravitreal injection of lipopolysaccharide (LPS). Synthetic GILZ-p was injected intravitreally 6 h after the LPS injection. To evaluate the anti-inflammatory effects of GILZ-p, the inflammatory response in the anterior chamber and iris of the rat eyes was evaluated with a slitlamp microscope on days 0, 1, 2, 3, and 4 after GILZ-p injection. The retinal expression of inflammatory cytokines was measured on days 0, 1, 2, 3, and 4 after GILZ-p injection. Müller cell gliosis was also detected at planned time points after GILZ-p injection. RESULTS Anterior segment inflammation peaked at 24 h after LPS injection in the EIU model. Compared with the controls, intravitreal GILZ-p significantly suppressed LPS-induced anterior segment inflammation in the EIU rats. The levels of retinal inflammatory factors IL-1β, TNF-α, MCP-1, and ICAM-1 were simultaneously reduced by the intravitreal GILZ-p injection. The expression of vimentin in the EIU retina was significantly reduced by GILZ-p, and the downregulated aquaporin 4 in the EIU retina was significantly restored by GILZ-p. CONCLUSION The synthetic GILZ-p inhibited the inflammatory reaction in the EIU model and may have utility in the treatment of inflammatory ocular disease.
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Affiliation(s)
- Yue Guo
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Ruiping Gu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Jian Yu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Boya Lei
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Dekang Gan
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Gezhi Xu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China, .,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China, .,Key Laboratory of Myopia of State Health Ministry, Shanghai, China,
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Kwon YC, Chun S, Kim K, Mak A. Update on the Genetics of Systemic Lupus Erythematosus: Genome-Wide Association Studies and Beyond. Cells 2019; 8:cells8101180. [PMID: 31575058 PMCID: PMC6829439 DOI: 10.3390/cells8101180] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of complex etiology that primarily affects women of childbearing age. The development of SLE is attributed to the breach of immunological tolerance and the interaction between SLE-susceptibility genes and various environmental factors, resulting in the production of pathogenic autoantibodies. Working in concert with the innate and adaptive arms of the immune system, lupus-related autoantibodies mediate immune-complex deposition in various tissues and organs, leading to acute and chronic inflammation and consequent end-organ damage. Over the past two decades or so, the impact of genetic susceptibility on the development of SLE has been well demonstrated in a number of large-scale genetic association studies which have uncovered a large fraction of genetic heritability of SLE by recognizing about a hundred SLE-susceptibility loci. Integration of genetic variant data with various omics data such as transcriptomic and epigenomic data potentially provides a unique opportunity to further understand the roles of SLE risk variants in regulating the molecular phenotypes by various disease-relevant cell types and in shaping the immune systems with high inter-individual variances in disease susceptibility. In this review, the catalogue of SLE susceptibility loci will be updated, and biological signatures implicated by the SLE-risk variants will be critically discussed. It is optimistically hoped that identification of SLE risk variants will enable the prognostic and therapeutic biomarker armamentarium of SLE to be strengthened, a major leap towards precision medicine in the management of the condition.
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Affiliation(s)
- Young-Chang Kwon
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222–1 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea;
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| | - Anselm Mak
- Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
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A. Hegazy G, Shaker O, Sayed S, Elzaher AA, Fathy K, Wahby I, Elsamanoudy A, Mustafa HN. Biomarkers of Systemic Lupus Erythematosus and Systemic Sclerosis diseases activity in a sample of Egyptian patients :Soluble Intercellular Adhesion Molecule-1 and Soluble Interleukin-2 Receptor, Case Control Study. BIOMEDICAL & PHARMACOLOGY JOURNAL 2019; 12:1207-1216. [DOI: 10.13005/bpj/1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Systemic Lupus Erythematosus (SLE) and systemic sclerosis (SSc) are systemic inflammatory autoimmune disorders characterized by a large spectrum of clinical and laboratory features. The aim of the present study was to investigate the possible use of serum level of soluble intercellular adhesion molecule-1(sICAM-1) and soluble interleukin-2 receptor (sIL-2Ra) as biomarkers for monitoring of SLE and SSc disease activity. Moreover, it aimed to compare the specificity and sensitivity as well as cut-off value of both biomarkers in a sample of Egyptian patients. 50 SLE patients, 30 SSc patients and 60 age and sex matched healthy controls were enrolled in our study. sICAM-1and sIL-2Ra were measured in serum samples obtained from all participants. In addition to Erythosedimentation rate (ESR), complete blood count (CBC), Antineuclearantibodies (ANA) estimation, disease activity of both diseases were also assessed. sICAM-1and sIL-2Ra levels were higher in SLE and SSc patients versus control. Both parameters are correlated with each other as well as the activity parameters. A cut-off levels of 455.59 (ng/ml) &2525935 (pg/ml) in both SLE & SSs respectively was observed with the highest specificity and sensitivity. It could be concluded that sICAM-1 and sIL-2Ra are noninvasive biomarkers for SLE and SSc that could play a pathophysiologic role in development and progression of both diseases. Moreover, sICAM-1 and sIL-2Ra are correlated with the disease activity at cut-off values of 455.59 (ng/ml) & 2525935(pg/ml) respectively.
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Affiliation(s)
- Gehan A. Hegazy
- Clinical Biochemistry Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia. 2Medical Biochemistry Department, National Research Centre, Cairo, Egypt
| | - Olfat Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Egypt
| | - Safaa Sayed
- Rheumatology and Rehabilitation Department, Cairo University, Cairo, Egypt
| | - Amr Abd Elzaher
- Internal Medicine Department, Ain Shams University, Cairo, Egypt
| | - Khaled Fathy
- Internal Medicine Department, Ain Shams University, Cairo, Egypt
| | - Iman Wahby
- Family and Community Medicine Department, Rabigh, King Abdul Aziz University, Saudi Arabia. 7Community and Occupational Health Department, Al Azhar University, Faculty of Medicine, Egypt
| | - Ayman Elsamanoudy
- Clinical Biochemistry Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia. Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Hesham N. Mustafa
- Anatomy Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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17
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The genetics and molecular pathogenesis of systemic lupus erythematosus (SLE) in populations of different ancestry. Gene 2018; 668:59-72. [DOI: 10.1016/j.gene.2018.05.041] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/13/2018] [Indexed: 01/21/2023]
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18
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Nowatzky J, Manches O, Khan SA, Godefroy E, Bhardwaj N. Modulation of human Th17 cell responses through complement receptor 3 (CD11 b/CD18) ligation on monocyte-derived dendritic cells. J Autoimmun 2018; 92:57-66. [PMID: 29908907 DOI: 10.1016/j.jaut.2018.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/30/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Apoptotic cell receptors contribute to the induction of tolerance by modulating dendritic cell function following the uptake of apoptotic cells or microparticles. Dendritic cells that have bound or ingested apoptotic cells produce only low amounts of pro-inflammatory cytokines and fail to prime effector T cell responses. Specifically, ligation of the apoptotic cell receptor CR3 (CD11 b/CD18) on human monocyte-derived dendritic cells (moDC) down-modates proinflammatory cytokine secretion, but the consequences for human Th17 cell homeostasis and effector responses remain unknown. Here, we aimed to establish whether CD11b-ligated moDC modulate Th17 cell effector reponses to assess their potential for future use in moDC-based suppressive immunotherapy. METHODS We generated a bead-based surrogate system to target CD11b on monocyte-derived human dendritic cells and examined the effects of CD11b ligation on Th17-skewing cytokine secretion, priming, expansion and functional plasticity in DC/T cell co-culture systems at the poly- and monoclonal level. RESULTS We show that Th17 cell expansion within the human memory CD4+ T cell compartment was efficiently constricted by targeting the CD11b receptor on moDC. This tolerogenic capacity was primarily dependent on cytokine skewing. Furthermore, ligation of CD11b on healthy homozygous carriers of the rs11143679 (ITGAM) variant - a strong genetic susceptibility marker for human systemic lupus erythematosus - also down-modulated the secretion of Th17-skewing cytokines. CONCLUSION Overall, our findings underline the potential of targeted CD11b ligation on human dendritic cells for the engineering of suppressive immunotherapy for Th17-related autoimmune disorders.
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Affiliation(s)
| | | | | | | | - Nina Bhardwaj
- New York University School of Medicine, New York, NY, USA.
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19
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Lumsden AL, Ma Y, Ashander LM, Stempel AJ, Keating DJ, Smith JR, Appukuttan B. ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells. BMC Res Notes 2018; 11:285. [PMID: 29743093 PMCID: PMC5944171 DOI: 10.1186/s13104-018-3384-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/30/2018] [Indexed: 11/22/2022] Open
Abstract
Objective Regulation of intercellular adhesion molecule (ICAM)-1 in retinal endothelial cells is a promising druggable target for retinal vascular diseases. The ICAM-1-related (ICR) long non-coding RNA stabilizes ICAM-1 transcript, increasing protein expression. However, studies of ICR involvement in disease have been limited as the promoter is uncharacterized. To address this issue, we undertook a comprehensive in silico analysis of the human ICR gene promoter region. Results We used genomic evolutionary rate profiling to identify a 115 base pair (bp) sequence within 500 bp upstream of the transcription start site of the annotated human ICR gene that was conserved across 25 eutherian genomes. A second constrained sequence upstream of the orthologous mouse gene (68 bp; conserved across 27 Eutherian genomes including human) was also discovered. Searching these elements identified 33 matrices predictive of binding sites for transcription factors known to be responsive to a broad range of pathological stimuli, including hypoxia, and metabolic and inflammatory proteins. Five phenotype-associated single nucleotide polymorphisms (SNPs) in the immediate vicinity of these elements included four SNPs (i.e. rs2569693, rs281439, rs281440 and rs11575074) predicted to impact binding motifs of transcription factors, and thus the expression of ICR and ICAM-1 genes, with potential to influence disease susceptibility. We verified that human retinal endothelial cells expressed ICR, and observed induction of expression by tumor necrosis factor-α. Electronic supplementary material The online version of this article (10.1186/s13104-018-3384-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanda L Lumsden
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Yuefang Ma
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Liam M Ashander
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Andrew J Stempel
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Damien J Keating
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Justine R Smith
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia.
| | - Binoy Appukuttan
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
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20
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Zhao M, Li MY, Gao XF, Jia SJ, Gao KQ, Zhou Y, Zhang HH, Huang Y, Wang J, Wu HJ, Lu QJ. Downregulation of BDH2 modulates iron homeostasis and promotes DNA demethylation in CD4 + T cells of systemic lupus erythematosus. Clin Immunol 2017; 187:113-121. [PMID: 29113828 DOI: 10.1016/j.clim.2017.11.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/31/2022]
Abstract
DNA hypomethylation plays an important role in the pathogenesis of systemic lupus erythematosus (SLE). Here we investigated whether 3-hydroxy butyrate dehydrogenase 2 (BDH2), a modulator of intracellular iron homeostasis, was involved in regulating DNA hypomethylation and hyper-hydroxymethylation in lupus CD4+ T cells. Our results showed that BDH2 expression was decreased, intracellular iron was increased, global DNA hydroxymethylation level was elevated, while methylation level was reduced in lupus CD4+ T cells compared with healthy controls. The decreased BDH2 contributed to DNA hyper-hydroxymethylation and hypomethylation via increasing intracellular iron in CD4+ T cells, which led to overexpression of immune related genes. Moreover, we showed that BDH2 was the target gene of miR-21. miR-21 promoted DNA demethylation in CD4+ T cells through inhibiting BDH2 expression. Our data demonstrated that the dysregulation of iron homeostasis in CD4+ T cells induced by BDH2 deficiency contributes to DNA demethylation and self-reactive T cells in SLE.
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Affiliation(s)
- Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
| | - Meng-Ying Li
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Xiao-Fei Gao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Su-Jie Jia
- Department of Pharmaceutics, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Ke-Qin Gao
- Department of Pharmaceutics, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Yin Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hui-Hui Zhang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yi Huang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jing Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hai-Jing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Qian-Jin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
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Abstract
PURPOSE OF REVIEW Our understanding on genetic basis of SLE has been advanced through genome-wide association studies. We review recent progress in lupus genetics with a focus on SLE-associated loci that have been functionally characterized, and discuss the potential for clinical translation of genetics data. RECENT FINDINGS Over 100 loci have been confirmed to show robust association with SLE and many share with other immune-mediated diseases. Although causative variants captured at these established loci are limited, they guide biological studies of gene targets for functional characterization which highlight the importance of aberrant recognition of self-nucleic acid, type I interferon overproduction, and defective immune cell signaling underlying the pathogenesis of SLE. Increasing examples illustrate a predictive value of genetic findings in susceptibility/prognosis prediction, clinical classification, and pharmacological implication. Genetic findings provide a foundation for better understanding of disease pathogenic mechanisms and opportunities for target selection in lupus drug development.
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Abstract
PURPOSE OF REVIEW To describe the recent studies on the genetics of systemic lupus erythematosus (SLE) and Sjögren's syndrome. RECENT FINDINGS We overview the most recent findings on the genetic susceptibility of the diseases and provide information on their genetic similarities and differences. SUMMARY SLE and Sjögren's syndrome are two closely related systemic autoimmune diseases that share multiple clinical and molecular aspects, including a significant number of susceptibility genes. Several genome-wide association studies were recently published in different populations that provide a better picture of their molecular mechanisms. It is becoming clear that their genetic architecture is quite well established, but more information is required on expression quantitative trait loci, epigenetic genome-wide analyses, gene × gene interactions and the role of rare variants.
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Kwon KS, Cho HY, Chung YJ. Recapitulation of Candidate Systemic Lupus Erythematosus-Associated Variants in Koreans. Genomics Inform 2016; 14:85-89. [PMID: 27729837 PMCID: PMC5056901 DOI: 10.5808/gi.2016.14.3.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 08/26/2016] [Accepted: 08/28/2016] [Indexed: 11/29/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association. For this, we selected five SNPs (rs1801274 in FCGR2A and rs2286672 in PLD2, rs887369 in CXorf21, rs9782955 in LYST, and rs3794060 in NADSYN1). Through the replication study with 656 cases and 622 controls, rs1801274 in FCGR2A was found to be significantly associated with SLE in Koreans (odds ratio, 1.26, 95% confidence interval, 1.06 to 1.50; p = 0.01 in allelic model). This association was also significant in two other models (dominant and recessive). The other four SNPs did not show a significant association. Our data support that FCGR polymorphisms play important roles in the susceptibility to SLE in diverse populations, including Koreans.
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Affiliation(s)
- Ki-Sung Kwon
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye-Young Cho
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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Teruel M, Alarcón-Riquelme ME. The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned. J Autoimmun 2016; 74:161-175. [PMID: 27522116 DOI: 10.1016/j.jaut.2016.08.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Abstract
The genome-wide association study is a free-hypothesis approach based on screening of thousands or even millions of genetic variants distributed throughout the whole human genome in relation to a phenotype. The relevant role of the genome-wide association studies in the last decade is undisputed because it has permitted to elucidate multiple risk genetic factors associated with the susceptibility to several human complex diseases. Regarding systemic lupus erythematosus (SLE) this approach has allowed to identify more than 60 risk loci for SLE susceptibility across populations to date, increasing our understanding on the pathogenesis of this disease. We present the latest findings in the genetic of SLE across populations using genome-wide approaches. These studies revealed that most of the genetic risk is shared across borders and ethnicities. Finally, we focus on describing the most important risk loci for SLE attempting to cover the genetic findings in relation to functional polymorphisms, such as missense single nucleotide polymorphisms (SNPs) or regulatory variants involved in the development of the disease. The functional studies try to identify the causality of some GWAS-associated variants, many of which fall in non-coding regions of the genome, suggesting a regulatory role. Many loci show an environmental interaction, another aspect revealed by the studies of epigenetic modifications and those associated with genetic variants. Finally, new-generation sequencing technologies can open other paths in the research on SLE genetics, the role of rare variants and the detailed identification of causal regulatory variation. The clinical relevance of the genetic factors will be shown when we are able to use them or in combination with other molecular measurements to re-classify a heterogeneous disease such as SLE.
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Affiliation(s)
- Maria Teruel
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain.
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain; Institute of Environmental Medicine, Karolinska Institute, Stockholm, 171 67, Sweden.
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25
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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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Genetic association study of systemic lupus erythematosus and disease subphenotypes in European populations. Clin Rheumatol 2016; 35:1161-8. [DOI: 10.1007/s10067-016-3235-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 01/10/2023]
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27
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Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK. Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. eLife 2016; 5:e12089. [PMID: 26880555 PMCID: PMC4811771 DOI: 10.7554/elife.12089] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/13/2016] [Indexed: 12/15/2022] Open
Abstract
Targeted sequencing of sixteen SLE risk loci among 1349 Caucasian cases and controls produced a comprehensive dataset of the variations causing susceptibility to systemic lupus erythematosus (SLE). Two independent disease association signals in the HLA-D region identified two regulatory regions containing 3562 polymorphisms that modified thirty-seven transcription factor binding sites. These extensive functional variations are a new and potent facet of HLA polymorphism. Variations modifying the consensus binding motifs of IRF4 and CTCF in the XL9 regulatory complex modified the transcription of HLA-DRB1, HLA-DQA1 and HLA-DQB1 in a chromosome-specific manner, resulting in a 2.5-fold increase in the surface expression of HLA-DR and DQ molecules on dendritic cells with SLE risk genotypes, which increases to over 4-fold after stimulation. Similar analyses of fifteen other SLE risk loci identified 1206 functional variants tightly linked with disease-associated SNPs and demonstrated that common disease alleles contain multiple causal variants modulating multiple immune system genes.
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Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ekta Rai
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shaheen Khan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kasthuribai Viswanathan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ferdicia Carr-Johnson
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Graham B Wiley
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Bernard R Lauwerys
- Pole de pathologies rhumatismales, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Bruxelles, Belgium
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, Hershey, United States
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Christine K Garcia
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carol A Wise
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, United States
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, United States
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - John B Harley
- Cincinnati VA Medical Center, Cincinnati, United States
- Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, United States
| | - Betty P Tsao
- Department of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - David R Karp
- Rheumatic Diseases Division, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Quan Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
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Single-Nucleotide Polymorphisms and Haplotypes of Intercellular Adhesion Molecule-1 in Uterine Cervical Carcinogenesis in Taiwanese Women. Reprod Sci 2015; 23:401-8. [DOI: 10.1177/1933719115604731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abstract
PURPOSE OF REVIEW Genome-wide association studies have identified more than 50 robust loci associated with systemic lupus erythematosus (SLE) susceptibility, and follow-up studies help reveal candidate causative genetic variants and their biological relevance contributing to the development of SLE. Epigenetic modulation is emerging as an important mechanism for understanding how the implicated genes interact with environmental factors. We review recent progress toward identifying causative variants of SLE-associated loci and epigenetic impact on lupus, especially genetic-epigenetic interactions that modulate expression levels of SLE susceptibility genes. RECENT FINDINGS A few SLE-risk loci have been refined to localize likely causative variants responsible for the observed genome-wide association study signals. Few of such variants disrupt coding sequences resulting in gain or loss of function for the encoded protein, whereas most fall in noncoding regions with potential to regulate gene expression through alterations in transcriptional activity, splicing, mRNA stability and epigenetic modifications. Multiple key pathways related to the SLE pathogenesis have been indicated by the identified genetic risk factors, including type I interferon signaling pathway that can also be regulated by epigenetic changes occurred in SLE. SUMMARY These findings provide novel insights into the disease pathogenesis and promise better diagnostic accuracy and new therapeutic targets for patient management.
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Affiliation(s)
- Yun Deng
- Division of Rheumatology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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Kirino Y, Remmers EF. Genetic architectures of seropositive and seronegative rheumatic diseases. Nat Rev Rheumatol 2015; 11:401-14. [PMID: 25907699 DOI: 10.1038/nrrheum.2015.41] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis and some other rheumatic diseases are genetically complex, with evidence of familial clustering, but not of Mendelian inheritance. These diseases are thought to result from contributions and interactions of multiple genetic and nongenetic risk factors, which have small effects individually. Genome-wide association studies (GWAS) of large collections of data from cases and controls have revealed many genetic factors that contribute to non-Mendelian rheumatic diseases, thus providing insights into associated molecular mechanisms. This Review summarizes methods for the identification of gene variants that influence genetically complex diseases and focuses on what we have learned about the rheumatic diseases for which GWAS have been reported. Our review of the disease-associated loci identified to date reveals greater sharing of risk loci among the groups of seropositive (diseases in which specific autoantibodies are often present) or seronegative diseases than between these two groups. The nature of the shared and discordant loci suggests important similarities and differences among these diseases.
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Affiliation(s)
- Yohei Kirino
- Yokohama City University Graduate School of Medicine, Department of Internal Medicine and Clinical Immunology, 3-9 Fukuura, Kanazawa-Ku, Yokohama 236-0004, Japan
| | - Elaine F Remmers
- National Institutes of Health, National Human Genome Research Institute, Inflammatory Disease Section, 10 Center Drive, MSC 1849, Bethesda, MD 20892, USA
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31
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Cai TT, Muhali FS, Song RH, Qin Q, Wang X, Shi LF, Jiang WJ, Xiao L, Li DF, Zhang JA. Genome-wide DNA methylation analysis in Graves' disease. Genomics 2015; 105:204-10. [DOI: 10.1016/j.ygeno.2015.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 11/25/2014] [Accepted: 01/15/2015] [Indexed: 12/23/2022]
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32
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Chou CH, Ueng KC, Liu YF, Wu CH, Yang SF, Wang PH. Impact of Intercellular Adhesion Molecule-1 Genetic Polymorphisms on Coronary Artery Disease Susceptibility in Taiwanese Subjects. Int J Med Sci 2015; 12:510-6. [PMID: 26078712 PMCID: PMC4466516 DOI: 10.7150/ijms.12097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/25/2015] [Indexed: 11/23/2022] Open
Abstract
The principal pathogenesis of coronary artery disease (CAD) is coronary artery atherosclerosis, a chronic inflammatory disease of the vessel walls of the coronary artery. Intercellular adhesion molecule-1 (ICAM-1) displays an important role in the development of the inflammation reaction and atherosclerosis. Few studies report the association of ICAM-1 genetic polymorphisms with CAD in Taiwanese subjects. Therefore, we conducted a study to associate the single nucleotide polymorphisms (SNPs) of ICAM-1, rs5491, rs5498, rs281432 and rs3093030 with CAD. Five hundred and twenty-five male and female subjects, who received elective coronary angiography in Taiwan Chung Shan Medical University Hospital, were recruited to determine four ICAM-1 SNPs by real time-polymerase chain reaction and genotyping. The relationships among ICAM-1 SNPs, haplotypes, demographic and characteristics and CAD were analyzed. This study showed that rs281432 (C8823G) was the only ICAM-1 SNP which affect the development of CAD. Multivariate analysis revealed that ICAM-1 SNP rs281432 CC/CG [p=0.016; odds ratio (OR): 2.56, 95% confidence interval (CI): 1.19-5.56], male gender (p=0.018; OR: 1.66, 95% CI: 1.09-2.51), aspirin use in the past 7 days (p=0.001; OR: 2.05, 95% CI: 1.33-3.14), hypertension (p<0.001; OR: 2.15, 95% CI: 1.42-3.25), serum cardiac troponin I elevation (p<0.001; OR: 2.14, 95% CI: 1.47-3.24) and severe angina in recent 24 hours (p=0.001; OR: 1.97, 95% CI: 1.31- 2.95) increase the risk of CAD. In conclusion, ICAM-1 SNP rs281432 is an independent factor to predict the development of CAD. ICAM-1 SNP rs281432 homozygotic mutant GG can reduce the susceptibility to the CAD in Taiwanese subjects.
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Affiliation(s)
- Chi-Hung Chou
- 1. Institute of Medicine, Chung Shan Medical University,110, Section 1, Chien-Kuo North Road, Taichung, 40201, Taiwan ; 2. Division of Cardiology, Department of Internal Medicine, Yuan-Sheng Hospital and Changhua Christian Hospital, Yuanlin Branch, Yuanlin, Taiwan
| | - Kwo-Chang Ueng
- 3. Department of Internal Medicine, Chung Shan Medical University Hospital, 110, Section 1, Chien-Kuo North Road, Taichung, 40201, Taiwan ; 4. School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Fan Liu
- 5. Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsien Wu
- 1. Institute of Medicine, Chung Shan Medical University,110, Section 1, Chien-Kuo North Road, Taichung, 40201, Taiwan
| | - Shun-Fa Yang
- 1. Institute of Medicine, Chung Shan Medical University,110, Section 1, Chien-Kuo North Road, Taichung, 40201, Taiwan ; 6. Department of Medical Research, Chung Shan Medical University Hospital, Taichung, 40201, Taiwan
| | - Po-Hui Wang
- 1. Institute of Medicine, Chung Shan Medical University,110, Section 1, Chien-Kuo North Road, Taichung, 40201, Taiwan ; 4. School of Medicine, Chung Shan Medical University, Taichung, Taiwan ; 7. Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
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33
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Kottyan L, Kelly JA, Harley JB. Genetics of lupus. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Lee HS, Bae SC. Recent advances in systemic lupus erythematosus genetics in an Asian population. Int J Rheum Dis 2014; 18:192-9. [DOI: 10.1111/1756-185x.12498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hye-Soon Lee
- Hanyang University Hospital for Rheumatic Diseases; Seoul Korea
| | - Sang Cheol Bae
- Hanyang University Hospital for Rheumatic Diseases; Seoul Korea
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35
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Kariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, Kimberly RP, Alarcón-Riquelme ME, Jacob CO, Criswell LA, Sivils KL, Langefeld CD, Harley JB, Skol AD, Niewold TB. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun 2014; 16:15-23. [PMID: 25338677 PMCID: PMC4305028 DOI: 10.1038/gene.2014.57] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. 40–50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs. low IFN-α in over 1550 SLE cases, including GWAS and replication cohorts. In meta-analysis, the top associations in European ancestry were PRKG1 rs7897633 (PMeta=2.75 × 10−8) and PNP rs1049564 (PMeta=1.24 × 10−7). We also found evidence for cross-ancestral background associations with the ANKRD44 and PLEKHF2 loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic subphenotypes becomes an attractive strategy for genetic discovery in complex disease.
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Affiliation(s)
- S N Kariuki
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Y Ghodke-Puranik
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - J M Dorschner
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - B S Chrabot
- Gwen Knapp Center for Lupus Research, University of Chicago, Chicago, IL, USA
| | - J A Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - B P Tsao
- Department of Medicine, University of California, Los Angeles, CA, USA
| | - R P Kimberly
- Department of Medicine, University of Alabama, Birmingham, AL, USA
| | - M E Alarcón-Riquelme
- 1] Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA [2] GENYO Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - C O Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - L A Criswell
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - K L Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - C D Langefeld
- Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - J B Harley
- Cincinnati Children's Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - A D Skol
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - T B Niewold
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
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36
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Lee YH, Bae SC. Association between the functional ITGAM rs1143679 G/A polymorphism and systemic lupus erythematosus/lupus nephritis or rheumatoid arthritis: an update meta-analysis. Rheumatol Int 2014; 35:815-23. [PMID: 25315704 DOI: 10.1007/s00296-014-3156-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
The aim of this study was to determine whether the functional integrin-α-M (ITGAM) rs1143679 polymorphism is associated with susceptibility to systemic lupus erythematosus (SLE), lupus nephritis (LN), and rheumatoid arthritis (RA). A series of meta-analyses were conducted to test for associations between the ITGAM rs1143679 polymorphism and SLE, LN, or RA. A total of 24 comparisons involving 7,738 patients and 8,309 controls for SLE, and 2,663 patients and 2,694 controls in RA were considered. Meta-analysis showed a significant association between the ITGAM rs1143679 A allele and SLE in all subjects (OR 1.773, 95 % CI 1.656, 1.901, p < 1.0 × 10(-9)). After stratification by ethnicity, the A allele was found to be significantly associated with SLE in European, Latin American, and Asian. A significant association was also found between the ITGAM A allele and lupus nephritis in Europeans (OR 2.131, 95 % CI 1.565, 2.903, p = 1.6 × 10(-7)). However, no association was found between RA and the ITGAM rs1143679 polymorphism. Our meta-analyses confirm that the ITGAM rs1143679 polymorphism is associated with SLE susceptibility in different ethnic groups and demonstrate that the polymorphism is associated with LN in European.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-705, Korea,
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37
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He Q, Lin X, Wang F, Xu J, Ren Z, Chen W, Xing X. Associations of a polymorphism in the intercellular adhesion molecule-1 (ICAM1) gene and ICAM1 serum levels with migraine in a Chinese Han population. J Neurol Sci 2014; 345:148-53. [DOI: 10.1016/j.jns.2014.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/09/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
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38
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Abstract
Neutrophil firm adhesion to endothelial cells plays a critical role in inflammation in both health and disease. The process of neutrophil firm adhesion involves many different adhesion molecules including members of the β2 integrin family and their counter-receptors of the ICAM family. Recently, naturally occurring genetic variants in both β2 integrins and ICAMs are reported to be associated with autoimmune disease. Thus, the quantitative adhesive capacity of neutrophils from individuals with varying allelic forms of these adhesion molecules is important to study in relation to mechanisms underlying development of autoimmunity. Adhesion studies in flow chamber systems can create an environment with fluid shear stress similar to that observed in the blood vessel environment in vivo. Here, we present a method using a flow chamber assay system to study the quantitative adhesive properties of human peripheral blood neutrophils to human umbilical vein endothelial cell (HUVEC) and to purified ligand substrates. With this method, the neutrophil adhesive capacities from donors with different allelic variants in adhesion receptors can be assessed and compared. This method can also be modified to assess adhesion of other primary cell types or cell lines.
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Affiliation(s)
- Yebin Zhou
- Genetics and Genomic Sciences Graduate Program, University of Alabama at Birmingham
| | - Dennis F Kucik
- Birmingham Veterans Affairs Medical Center; Department of Pathology, University of Alabama at Birmingham; Department of Biomedical Engineering, University of Alabama at Birmingham
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39
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Wang SS, Hsieh MJ, Ou YC, Chen CS, Li JR, Hsiao PC, Yang SF. Impacts of ICAM-1 gene polymorphisms on urothelial cell carcinoma susceptibility and clinicopathologic characteristics in Taiwan. Tumour Biol 2014; 35:7483-90. [PMID: 24789429 DOI: 10.1007/s13277-014-1934-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/03/2014] [Indexed: 01/13/2023] Open
Abstract
Intercellular adhesion molecule (ICAM)-1, a cell adhesion molecule, is reportedly overexpressed in several cancers and may contribute to tumorgenesis and metastasis. The current study explored the effect of ICAM-1 gene polymorphisms on the susceptibility of developing urothelial cell carcinoma (UCC) and the clinicopathological status. A total of 558 participants, including 279 healthy people and 279 patients with UCC, were recruited for this study. Four single-nucleotide polymorphisms of the ICAM-1 gene were assessed by a real-time polymerase chain reaction with the TaqMan assay. After adjusting for other covariants, the individuals carrying at least one G allele at ICAM-1 rs5498 had a 1.603-fold risk of developing UCC than did wild-type (AA) carriers. Furthermore, UCC patients who carried at least one G allele at rs5498 had a higher invasive stage risk (p < 0.05) than did patients carrying the wild-type allele. In conclusion, the rs5498 polymorphic genotypes of ICAM-1 might contribute to the prediction of susceptibility to and pathological development of UCC. This is the first study to provide insight into risk factors associated with ICAM-1 variants in carcinogenesis of UCC in Taiwan.
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Affiliation(s)
- Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan
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40
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Maiti AK, Kim-Howard X, Motghare P, Pradhan V, Chua KH, Sun C, Arango-Guerrero MT, Ghosh K, Niewold TB, Harley JB, Anaya JM, Looger LL, Nath SK. Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant within ITGAM. Hum Mol Genet 2014; 23:4161-76. [PMID: 24608226 DOI: 10.1093/hmg/ddu106] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integrin alpha M (ITGAM; CD11b) is a component of the macrophage-1 antigen complex, which mediates leukocyte adhesion, migration and phagocytosis as part of the immune system. We previously identified a missense polymorphism, rs1143679 (R77H), strongly associated with systemic lupus erythematosus (SLE). However, the molecular mechanisms of this variant are incompletely understood. A meta-analysis of published and novel data on 28 439 individuals with European, African, Hispanic and Asian ancestries reinforces genetic association between rs1143679 and SLE [Pmeta = 3.60 × 10(-90), odds ratio (OR) = 1.76]. Since rs1143679 is in the most active region of chromatin regulation and transcription factor binding in ITGAM, we quantitated ITGAM RNA and surface protein levels in monocytes from patients with each rs1143679 genotype. We observed that transcript levels significantly decreased for the risk allele ('A') relative to the non-risk allele ('G'), in a dose-dependent fashion: ('AA' < 'AG' < 'GG'). CD11b protein levels in patients' monocytes were directly correlated with RNA levels. Strikingly, heterozygous individuals express much lower (average 10- to 15-fold reduction) amounts of the 'A' transcript than 'G' transcript. We found that the non-risk sequence surrounding rs1143679 exhibits transcriptional enhancer activity in vivo and binds to Ku70/80, NFKB1 and EBF1 in vitro, functions that are significantly reduced with the risk allele. Mutant CD11b protein shows significantly reduced binding to fibrinogen and vitronectin, relative to non-risk, both in purified protein and in cellular models. This two-pronged contribution (nucleic acid- and protein-level) of the rs1143679 risk allele to decreasing ITGAM activity provides insight into the molecular mechanisms of its potent association with SLE.
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Affiliation(s)
- Amit K Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Prasenjeet Motghare
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Kek Heng Chua
- Department of Biomedical Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - María Teresa Arango-Guerrero
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Juan-Manual Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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41
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Fagerholm SC, MacPherson M, James MJ, Sevier-Guy C, Lau CS. The CD11b-integrin (ITGAM) and systemic lupus erythematosus. Lupus 2014; 22:657-63. [PMID: 23753600 DOI: 10.1177/0961203313491851] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Variations at the ITGAM gene, which encodes for the CD11b chain of the Mac-1 (alphaMbeta2; CD11b/CD18; complement receptor-3) integrin, is one of the strongest genetic risk factors for systemic lupus erythematosus (SLE). More specifically, a genetic variant (rs1143679) which results in an arginine to histidine substitution at position 77 in the extracellular portion of the integrin is associated with disease. It has recently been shown that this amino acid substitution results in a dysfunctional integrin, which is deficient in mediating cell adhesion to integrin ligands, phagocytosis and in addition cannot restrict inflammatory cytokine production in macrophages. In this review, we discuss immunological functions of the Mac-1 integrin and how defects in the genetic variant of Mac-1 may relate to SLE development.
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Affiliation(s)
- S C Fagerholm
- Medical Research Institute, Ninewells Hospital and Medical School, Institute of Biotechnology, University of Helsinki, Finland.
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42
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Ramos PS, Shaftman SR, Ward RC, Langefeld CD. Genes associated with SLE are targets of recent positive selection. Autoimmune Dis 2014; 2014:203435. [PMID: 24587899 PMCID: PMC3920976 DOI: 10.1155/2014/203435] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/12/2013] [Indexed: 01/03/2023] Open
Abstract
The reasons for the ethnic disparities in the prevalence of systemic lupus erythematosus (SLE) and the relative high frequency of SLE risk alleles in the population are not fully understood. Population genetic factors such as natural selection alter allele frequencies over generations and may help explain the persistence of such common risk variants in the population and the differential risk of SLE. In order to better understand the genetic basis of SLE that might be due to natural selection, a total of 74 genomic regions with compelling evidence for association with SLE were tested for evidence of recent positive selection in the HapMap and HGDP populations, using population differentiation, allele frequency, and haplotype-based tests. Consistent signs of positive selection across different studies and statistical methods were observed at several SLE-associated loci, including PTPN22, TNFSF4, TET3-DGUOK, TNIP1, UHRF1BP1, BLK, and ITGAM genes. This study is the first to evaluate and report that several SLE-associated regions show signs of positive natural selection. These results provide corroborating evidence in support of recent positive selection as one mechanism underlying the elevated population frequency of SLE risk loci and supports future research that integrates signals of natural selection to help identify functional SLE risk alleles.
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Affiliation(s)
- Paula S. Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stephanie R. Shaftman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ralph C. Ward
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carl D. Langefeld
- Department of Public Health Sciences, Wake Forest School of Medicine and Center for Public Health Genomics, Winston-Salem, NC 27157, USA
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43
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Arriens C, Mohan C. Systemic lupus erythematosus diagnostics in the 'omics' era. ACTA ACUST UNITED AC 2013; 8:671-687. [PMID: 24860621 DOI: 10.2217/ijr.13.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Systemic lupus erythematosus is a complex autoimmune disease affecting multiple organ systems. Currently, diagnosis relies upon meeting at least four out of eleven criteria outlined by the ACR. The scientific community actively pursues discovery of novel diagnostics in the hope of better identifying susceptible individuals in early stages of disease. Comprehensive studies have been conducted at multiple biological levels including: DNA (or genomics), mRNA (or transcriptomics), protein (or proteomics) and metabolites (or metabolomics). The 'omics' platforms allow us to re-examine systemic lupus erythematosus at a greater degree of molecular resolution. More importantly, one is hopeful that these 'omics' platforms may yield newer biomarkers for systemic lupus erythematosus that can help clinicians track the disease course with greater sensitivity and specificity.
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Affiliation(s)
- Cristina Arriens
- Rheumatic Diseases Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8884, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Blvd, Room 2018, Houston, TX 77204, USA
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Zuo XB, Sheng YJ, Hu SJ, Gao JP, Li Y, Tang HY, Tang XF, Cheng H, Yin XY, Wen LL, Sun LD, Yang S, Cui Y, Zhang XJ. Variants in TNFSF4, TNFAIP3, TNIP1, BLK, SLC15A4 and UBE2L3 interact to confer risk of systemic lupus erythematosus in Chinese population. Rheumatol Int 2013; 34:459-64. [PMID: 24091983 DOI: 10.1007/s00296-013-2864-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/02/2013] [Indexed: 12/12/2022]
Abstract
Our previous genome-wide association studies on SLE have identified several susceptibility genes involved in NF-κB signaling pathway, including TNFSF4, TNFAIP3, TNIP1, BLK, SLC15A4 and UBE2L3. The aim of this study is to investigate the association model (additive, dominant, recessive) of these genes and search for possible gene-gene interactions between them. In this study, we explored the association model of these six genes and search for possible gene-gene interactions based on identified single-nucleotide polymorphisms (SNPs) among them by using logistic regression analysis in the combined sample of 4,199 cases and 8,255 controls. The most significant association evidence was observed under recessive model for all of these SNPs. Besides, significant interactions between these SNPs were observed in this study: the TNFSF4 and TNIP1 SNPs (P adjusted = 1.68E-10), the TNFSF4 and SLC15A4 SNPs (P adjusted = 3.55E-08), the TNFSF4 and UBE2L3 SNPs (P adjusted = 8.74E-13), the TNIP1 and BLK SNPs (P adjusted = 9.45E-10), the TNIP1 and UBE2L3 SNPs (P adjusted = 8.25E-11), the TNFAIP3 and UBE2L3 SNPs (P adjusted = 3.06E-14) and the BLK and SLC15A4 SNPs (P adjusted = 4.51E-12). These results may contribute to our understanding of SLE genetic interactions and account for the additional risk of certain patients to develop SLE.
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Affiliation(s)
- Xian-Bo Zuo
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
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Petit A, Dadzie O. Multisystemic diseases and ethnicity: a focus on lupus erythematosus, systemic sclerosis, sarcoidosis and Behçet disease. Br J Dermatol 2013; 169 Suppl 3:1-10. [PMID: 24098896 DOI: 10.1111/bjd.12533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2013] [Indexed: 01/15/2023]
Affiliation(s)
- A. Petit
- Service de Dermatologie; APHP Hôpital Saint-Louis; 1 avenue Claude Vellefaux 75010 Paris France
| | - O.E. Dadzie
- Department of Dermatology and Histopathology; The North West London Hospitals NHS Trust; Northwick Park Hospital; Watford Road Harrow HA1 3UJ U.K
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Lin CW, Chuang CY, Tang CH, Chang JL, Lee LM, Lee WJ, Chow JM, Yang SF, Chien MH. Combined effects of icam-1 single-nucleotide polymorphisms and environmental carcinogens on oral cancer susceptibility and clinicopathologic development. PLoS One 2013; 8:e72940. [PMID: 24069166 PMCID: PMC3771971 DOI: 10.1371/journal.pone.0072940] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/14/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In Taiwan, oral cancer has causally been associated with environmental carcinogens. Intercellular adhesion molecule (ICAM)-1, a cell adhesion molecule with a key role in inflammation and immunosurveillance, was implicated in carcinogenesis by facilitating instability in the tumor environment. The current study explored the combined effect of ICAM-1 gene polymorphisms and exposure to environmental carcinogens on the susceptibility of developing oral squamous cell carcinoma (OSCC) and the clinicopathological characteristics of the tumors. METHODOLOGY AND PRINCIPAL FINDINGS Four single-nucleotide polymorphisms (SNPs) of the ICAM-1 gene from 595 patients with oral cancer and 561 non-cancer controls were analyzed by a real-time PCR. We found that the ICAM-1 rs5498 polymorphism and the TAGG or TACG haplotype of 4 ICAM-1 SNPs (rs3093030, rs5491, rs281432, and rs5498) combined were associated with oral-cancer susceptibility. Among 727 smokers, ICAM-1 polymorphisms carriers with the betel-nut chewing habit had a 27.49-36.23-fold greater risk of having oral cancer compared to ICAM-1 wild-type (WT) carriers without the betel-nut chewing habit. Among 549 betel-nut chewers, ICAM-1 polymorphisms carriers who smoked had a 9.93-14.27-fold greater risk of having oral cancer compared to those who carried the WT but did not smoke. Finally, patients with oral cancer who had at least 1 T allele of ICAM-1 rs5491 or 1 G allele of rs281432 were at lower risk of developing an advanced clinical stage (III/IV) (p<0.05), compared to those patients with AA or CC homozygotes. CONCLUSIONS Our results suggest that the ICAM-1 rs5498 SNP and either of 2 haplotypes of 4 SNPs combined have potential predictive significance in oral carcinogenesis. Gene-environment interactions of ICAM-1 polymorphisms, smoking, and betel-nut chewing might alter oral-cancer susceptibility. ICAM-1 rs5491 and rs281432 may be applied as factors to predict the clinical stage in OSCC patients.
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Affiliation(s)
- Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chun-Yi Chuang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan
| | - Junn-Liang Chang
- Department of Medical Management, Taoyuan Armed Forces General Hospital, Taoyuan County, Taiwan
- School of Medicine, Pathology Department, National Defense Medical Center, Taipei, Taiwan
| | - Liang-Ming Lee
- Department of Urology, Wan Fan Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Jiunn Lee
- Department of Urology, Wan Fan Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jyh-Ming Chow
- Section of Hematology-Oncology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
- * E-mail: (MHC); (SFY)
| | - Ming-Hsien Chien
- Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- * E-mail: (MHC); (SFY)
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Namjou B, Kim-Howard X, Sun C, Adler A, Chung SA, Kaufman KM, Kelly JA, Glenn SB, Guthridge JM, Scofield RH, Kimberly RP, Brown EE, Alarcón GS, Edberg JC, Kim JH, Choi J, Ramsey-Goldman R, Petri MA, Reveille JD, Vilá LM, Boackle SA, Freedman BI, Tsao BP, Langefeld CD, Vyse TJ, Jacob CO, Pons-Estel B, Niewold TB, Moser Sivils KL, Merrill JT, Anaya JM, Gilkeson GS, Gaffney PM, Bae SC, Alarcón-Riquelme ME, Harley JB, Criswell LA, James JA, Nath SK. PTPN22 association in systemic lupus erythematosus (SLE) with respect to individual ancestry and clinical sub-phenotypes. PLoS One 2013; 8:e69404. [PMID: 23950893 PMCID: PMC3737240 DOI: 10.1371/journal.pone.0069404] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/09/2013] [Indexed: 12/20/2022] Open
Abstract
Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is a negative regulator of T-cell activation associated with several autoimmune diseases, including systemic lupus erythematosus (SLE). Missense rs2476601 is associated with SLE in individuals with European ancestry. Since the rs2476601 risk allele frequency differs dramatically across ethnicities, we assessed robustness of PTPN22 association with SLE and its clinical sub-phenotypes across four ethnically diverse populations. Ten SNPs were genotyped in 8220 SLE cases and 7369 controls from in European-Americans (EA), African-Americans (AA), Asians (AS), and Hispanics (HS). We performed imputation-based association followed by conditional analysis to identify independent associations. Significantly associated SNPs were tested for association with SLE clinical sub-phenotypes, including autoantibody profiles. Multiple testing was accounted for by using false discovery rate. We successfully imputed and tested allelic association for 107 SNPs within the PTPN22 region and detected evidence of ethnic-specific associations from EA and HS. In EA, the strongest association was at rs2476601 (P = 4.7 × 10(-9), OR = 1.40 (95% CI = 1.25-1.56)). Independent association with rs1217414 was also observed in EA, and both SNPs are correlated with increased European ancestry. For HS imputed intronic SNP, rs3765598, predicted to be a cis-eQTL, was associated (P = 0.007, OR = 0.79 and 95% CI = 0.67-0.94). No significant associations were observed in AA or AS. Case-only analysis using lupus-related clinical criteria revealed differences between EA SLE patients positive for moderate to high titers of IgG anti-cardiolipin (aCL IgG >20) versus negative aCL IgG at rs2476601 (P = 0.012, OR = 1.65). Association was reinforced when these cases were compared to controls (P = 2.7 × 10(-5), OR = 2.11). Our results validate that rs2476601 is the most significantly associated SNP in individuals with European ancestry. Additionally, rs1217414 and rs3765598 may be associated with SLE. Further studies are required to confirm the involvement of rs2476601 with aCL IgG.
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Affiliation(s)
- Bahram Namjou
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Sharon A. Chung
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Kenneth M. Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Stuart B. Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Robert H. Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth E. Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Graciela S. Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jae-Hoon Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Jiyoung Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michelle A. Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John D. Reveille
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Luis M. Vilá
- Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Susan A. Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Barry I. Freedman
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Betty P. Tsao
- Division of Rheumatology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Timothy J. Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, King's College London, London, United Kingdom
| | - Chaim O. Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | | | | | - Timothy B. Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kathy L. Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Joan T. Merrill
- Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research, Universidad del Rosario, Bogota, Colombia
| | - Gary S. Gilkeson
- Department of Medicine, Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Centro de Genómica e Investigación Oncológica (GENYO) Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | | | - John B. Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Lindsey A. Criswell
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
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Su X, Chen X, Liu L, Chang X, Yu X, Sun K. Intracellular adhesion molecule-1 K469E gene polymorphism and risk of diabetic microvascular complications: a meta-analysis. PLoS One 2013; 8:e69940. [PMID: 23922864 PMCID: PMC3724680 DOI: 10.1371/journal.pone.0069940] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/13/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND A number of studies evaluated the association of intracellular adhesion molecule-1 (ICAM-1) K469E (rs5498, A/G) gene polymorphism with diabetic microvascular complications (DMI) including diabetic nephropathy (DN) and diabetic retinopathy (DR) in different populations. However, the results of individual studies remain conflicting. METHODS A comprehensive search was conducted to identify all eligible studies of the above-mentioned associations. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were assessed using the fixed or random effect model. RESULTS Seven studies involving 3411 subjects were included. Overall, the meta-analysis showed a significant association of the A allele with increased risk of DMI susceptibility in a recessive model (OR = 1.37, 95% CI 1.04-1.80, P = 0.02). In the subgroup analysis stratified by ethnicity, significant association was found in Asians but not in Caucasians (OR = 1.78, 95% CI 1.13-2.81, P = 0.01; OR = 1.10, 95% CI 0.79-1.54, P = 0.58, respectively). Moreover, it showed a significant association between the A allele and risk of DN in a recessive model (OR = 1.25, 95% CI 1.02-1.55, P = 0.04). CONCLUSIONS This meta-analysis suggested that the K469E polymorphism in ICAM-1 gene might affect individual susceptibility to DMI and showed a discrepancy in different ethnicities. Further investigations are needed to validate the association.
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Affiliation(s)
- Xianghui Su
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
| | - Xi Chen
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Lei Liu
- Department of Internal Medicine,Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Xiangyun Chang
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
| | - Xuefeng Yu
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Kan Sun
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
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Xiao X, Mruk DD, Cheng CY. Intercellular adhesion molecules (ICAMs) and spermatogenesis. Hum Reprod Update 2013; 19:167-86. [PMID: 23287428 DOI: 10.1093/humupd/dms049] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND During the seminiferous epithelial cycle, restructuring takes places at the Sertoli-Sertoli and Sertoli-germ cell interface to accommodate spermatogonia/spermatogonial stem cell renewal via mitosis, cell cycle progression and meiosis, spermiogenesis and spermiation since developing germ cells, in particular spermatids, move 'up and down' the seminiferous epithelium. Furthermore, preleptotene spermatocytes differentiated from type B spermatogonia residing at the basal compartment must traverse the blood-testis barrier (BTB) to enter the adluminal compartment to prepare for meiosis at Stage VIII of the epithelial cycle, a process also accompanied by the release of sperm at spermiation. These cellular events that take place at the opposite ends of the epithelium are co-ordinated by a functional axis designated the apical ectoplasmic specialization (ES)-BTB-basement membrane. However, the regulatory molecules that co-ordinate cellular events in this axis are not known. METHODS Literature was searched at http://www.pubmed.org and http://scholar.google.com to identify published findings regarding intercellular adhesion molecules (ICAMs) and the regulation of this axis. RESULTS Members of the ICAM family, namely ICAM-1 and ICAM-2, and the biologically active soluble ICAM-1 (sICAM-1) are the likely regulatory molecules that co-ordinate these events. sICAM-1 and ICAM-1 have antagonistic effects on the Sertoli cell tight junction-permeability barrier, involved in Sertoli cell BTB restructuring, whereas ICAM-2 is restricted to the apical ES, regulating spermatid adhesion during the epithelial cycle. Studies in other epithelia/endothelia on the role of the ICAM family in regulating cell movement are discussed and this information has been evaluated and integrated into studies of these proteins in the testis to create a hypothetical model, depicting how ICAMs regulate junction restructuring events during spermatogenesis. CONCLUSIONS ICAMs are crucial regulatory molecules of spermatogenesis. The proposed hypothetical model serves as a framework in designing functional experiments for future studies.
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Affiliation(s)
- Xiang Xiao
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, 1230 York Avenue, New York, NY 10065, USA
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