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Key Genes And Functional Coexpression Modules Involved In The Pathogenesis Of Systemic Lupus Erythematosus

S. Yan, W. Wang, Guohong Gao, M. Cheng, X. Wang, Zengyan Wang, Xiufen Ma, Chunxiang Chai, Donghua Xu
Published 2018 · Medicine, Biology

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We performed a systematic review of genome‐wide gene expression datasets to identify key genes and functional modules involved in the pathogenesis of systemic lupus erythematosus (SLE) at a systems level. Genome‐wide gene expression datasets involving SLE patients were searched in Gene Expression Omnibus and ArrayExpress databases. Robust rank aggregation (RRA) analysis was used to integrate those public datasets and identify key genes associated with SLE. The weighted gene coexpression network analysis (WGCNA) was adapted to identify functional modules involved in SLE pathogenesis, and the gene ontology enrichment analysis was utilized to explore their functions. The aberrant expressions of several randomly selected key genes were further validated in SLE patients through quantitative real‐time polymerase chain reaction. Fifteen genome‐wide gene expression datasets were finally included, which involved a total of 1,778 SLE patients and 408 healthy controls. A large number of significantly upregulated or downregulated genes were identified through RRA analysis, and some of those genes were novel SLE gene signatures and their molecular roles in etiology of SLE remained vague. WGCNA further successfully identified six main functional modules involved in the pathogenesis of SLE. The most important functional module involved in SLE included 182 genes and mainly enriched in biological processes, including defense response to virus, interferon signaling pathway, and cytokine‐mediated signaling pathway. This study identifies a number of key genes and functional coexpression modules involved in SLE, which provides deepening insights into the molecular mechanism of SLE at a systems level and also provides some promising therapeutic targets.
This paper references
Exposure to Epstein-Barr virus infection is associated with mild systemic lupus erythematosus disease.
G. Zandman-Goddard (2009)
pathways in type 1 diabetes
P. e0156006. Roda‐Navarro (2000)
Key genes and functional coexpression modules involved in the pathogenesis of systemic lupus erythematosus
S Yan (2018)
From mechanism to therapies in systemic lupus erythematosus
Michael A Paley (2017)
Supporting Information section at the end of the article. How to cite
S Yan (2018)
KLRG1 signaling induces defective Akt (ser473) phosphorylation and proliferative dysfunction of highly differentiated CD8+ T cells.
S. Henson (2009)
In vitro type-1 and type-2 cytokine production in systemic lupus erythematosus: lack of relationship with clinical disease activity
W. Barcellini (1996)
Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus
D. Haddon (2015)
KLRG 1 signaling induces defective Akt ( ser 473 ) phosphorylation and proliferative dysfunction of highly differentiated CD 8 + T cells
S. M. Henson (2009)
Computational Systems Biology
X. Zhao (2013)
Systematic review and meta-analysis of the sero-epidemiological association between Epstein-Barr virus and systemic lupus erythematosus
P. Hanlon (2014)
Acceleration of SLE-like syndrome development in NZBxNZW F1 mice by beta-glucan
P. Fagone (2014)
Enhancing Biological Relevance of a Weighted Gene Co-Expression Network for Functional Module Identification
S. Prom-on (2011)
Cardiovascular disease in systemic lupus erythematosus: A comprehensive update.
Mayra Giannelou (2017)
Pathogenesis of Human Systemic Lupus Erythematosus: A Cellular Perspective.
Vaishali R. Moulton (2017)
Pathways leading to an immunological disease: systemic lupus erythematosus
O. Zharkova (2017)
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
C. A. Odhams (2017)
Human KLRF1, a novel member of the killer cell lectin-like receptor gene family: molecular characterization, genomic structure, physical mapping to the NK gene complex and expression analysis.
P. Roda-Navarro (2000)
Meta ‐ analysis of genome ‐ wide gene expression differences in onset and maintenance phases of genetic
F. Z. Marques (2010)
A diverse range of gene products
P. Bieniasz (2011)
Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach.
Urmo Võsa (2014)
Cytokine production, serum levels and disease activity in systemic lupus erythematosus.
G. Gröndal (2000)
Expanding the Immunology Toolbox: Embracing Public-Data Reuse and Crowdsourcing.
R. Sparks (2016)
Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers?
Tuba Sevimoğlu (2015)
Identification of potential genomic biomarkers for Sjögren’s syndrome using data pooling of gene expression microarrays
S. Khuder (2014)
H. G. Raterman (2012)
Survival in adults and children with systemic lupus erythematosus: a systematic review and Bayesian meta-analysis of studies from 1950 to 2016
M. Tektonidou (2017)
Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease
G. Wiley (2014)
Prevalence of interferon type I signature in CD14 monocytes of patients with Sjögren's syndrome and association with disease activity and BAFF gene expression
Z. Brkić (2013)
Blockade of interferon‐gamma normalizes interferon‐regulated gene expression and serum CXCL10 levels in patients with systemic lupus erythematosus
A. A. Welcher (2015)
Human KLRF 1 , a novel member of the killer cell lectin ‐ like receptor gene family : Molecular characterization , genomic structure , physical mapping to the NK gene complex and expression analysis
P. Roda ‐ Navarro (2000)
Immunization with hepatitis B vaccine accelerates SLE-like disease in a murine model.
N. Agmon-Levin (2014)
New insights into the immunopathogenesis of systemic lupus erythematosus
G. Tsokos (2016)
Chronic hepatitis E virus infection is specifically associated with an interferon-related transcriptional program.
V. Moal (2013)
VGX‐1027 modulates genes involved in lipopolysaccharide‐induced Toll‐like receptor 4 activation and in a murine model of systemic lupus erythematosus
P. Fagone (2014)
Bioinformatics Analysis of the Factors Controlling Type I IFN Gene Expression in Autoimmune Disease and Virus-Induced Immunity
D. Feng (2013)
Role of the adaptor proteins
A. Allam (2005)
Systematic review of genome-wide gene expression studies of bipolar disorder
F. Seifuddin (2013)
Vaccinations and risk of systemic lupus erythematosus and rheumatoid arthritis: A systematic review and meta-analysis.
Bin Wang (2017)
Research and therapeutics-traditional and emerging therapies in systemic lupus erythematosus.
L. Davis (2017)
Reactive oxygen species induce virus-independent MAVS oligomerization in systemic lupus erythematosus
Iwona A. Buskiewicz (2016)
Systemic lupus erythematosus biomarkers: the challenging quest
Cristina Arriens (2017)
Increased Expression of B Cell Activation Factor Supports the Abnormal Expansion of Transitional B Cells in Systemic Lupus Erythematosus
C. Landolt-Marticorena (2011)
Treatment of lupus-prone mice with a dual inhibitor of TLR7 and TLR9 leads to reduction of autoantibody production and amelioration of disease symptoms.
F. Barrat (2007)
The interferon type I signature towards prediction of non-response to rituximab in rheumatoid arthritis patients
H. Raterman (2012)
Systemic Lupus,
Blockade of Interferon‐γ Normalizes Interferon‐Regulated Gene Expression and Serum CXCL10 Levels in Patients With Systemic Lupus Erythematosus
Andrew A. Welcher (2015)
Association of increased interferon-inducible gene expression with disease activity and lupus nephritis in patients with systemic lupus erythematosus.
X. Feng (2006)
International and multidisciplinary expert recommendations for the use of biologics in systemic lupus erythematosus.
Jean-François Kleinmann (2017)
Role of the adaptor proteins Bam32, TAPP1 and TAPP2 in lymphocyte activation.
Atef K. Allam (2005)
Brief Report: Pharmacodynamics, Safety, and Clinical Efficacy of AMG 811, a Human Anti–Interferon‐γ Antibody, in Patients With Discoid Lupus Erythematosus
V. Werth (2017)
Structural insights into a human anti-IFN antibody exerting therapeutic potential for systemic lupus erythematosus
S. Ouyang (2012)
Type I Interferon in the Pathogenesis of Lupus
M. Crow (2014)
Weighted gene co‐expression
S. 1191–1204. Sundarrajan (2016)
Corrigendum: A diverse range of gene products are effectors of the type I interferon antiviral response
J. Schoggins (2015)
Influenza A (H1N1) virus infection triggers severe pulmonary inflammation in lupus-prone mice following viral clearance.
Samantha R Slight-Webb (2015)
Senescence marker killer cell lectin-like receptor G1 (KLRG1) contributes to TNF-α production by interaction with its soluble E-cadherin ligand in chronically inflamed joints
L. Melis (2014)
Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus.
A. Nzeusseu Toukap (2007)
Reuse of public genome-wide gene expression data
Johan P. Rung (2013)
Robust rank aggregation for gene list integration and meta-analysis
Raivo Kolde (2012)
Systemic Lupus Erythematosus--A Disease with A Dysregulated Type I Interferon System.
N. Hagberg (2015)
Autologous hematopoietic stem cell transplantation in Systemic Lupus Erythematosus and antiphospholipid syndrome: A systematic review.
Alessia Leone (2017)
The role of bioinformatics
M. Sirota (2011)
Targeted therapeutics in SLE: emerging strategies to modulate the interferon pathway
S. Oon (2016)
Quadrivalent human papillomavirus vaccine and autoimmune adverse events: a case–control assessment of the vaccine adverse event reporting system (VAERS) database
D. Geier (2017)
Meta-Analysis of Genome-Wide Gene Expression Differences in Onset and Maintenance Phases of Genetic Hypertension
F. Marques (2010)
Weighted gene co-expression based biomarker discovery for psoriasis detection.
Sudharsana Sundarrajan (2016)
The genetic basis
M. 2009–2016. Teruel (2016)
Systemic lupus erythematosus
J. Manson (2006)
The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned.
M. Teruel (2016)
TAPP1 and TAPP2 Are Targets of Phosphatidylinositol 3-Kinase Signaling in B Cells: Sustained Plasma Membrane Recruitment Triggered by the B-Cell Antigen Receptor
A. Marshall (2002)
WGCNA: an R package for weighted correlation network analysis
P. Langfelder (2008)
The role of bioinformatics in studying rheumatic and autoimmune disorders
M. Sirota (2011)
Lack of proliferative capacity of human effector and memory T cells expressing killer cell lectinlike receptor G1 (KLRG1).
D. Voehringer (2002)
Humoral markers of active Epstein–Barr virus infection associate with anti-extractable nuclear antigen autoantibodies and plasma galectin-3 binding protein in systemic lupus erythematosus
N. Rasmussen (2016)
Identification of differential co-expressed gene networks in early rheumatoid arthritis achieving sustained drug-free remission after treatment with a tocilizumab-based or methotrexate-based strategy
X. M. Teitsma (2017)
Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes
Ignacio Riquelme Medina (2016)
IFI44L promoter methylation as a blood biomarker for systemic lupus erythematosus
M. Zhao (2016)

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