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CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis

Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), which often progresses to end-stage renal disease (ESRD) and ultimately leads to death. At present, there are no definitive therapies towards LN, so that illuminating the molecular mechanism behind the disease has...

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Autores principales: Yang, Huiying, Li, Hua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777479/
https://www.ncbi.nlm.nih.gov/pubmed/31592160
http://dx.doi.org/10.7717/peerj.7722
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author Yang, Huiying
Li, Hua
author_facet Yang, Huiying
Li, Hua
author_sort Yang, Huiying
collection PubMed
description Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), which often progresses to end-stage renal disease (ESRD) and ultimately leads to death. At present, there are no definitive therapies towards LN, so that illuminating the molecular mechanism behind the disease has become an urgent task for researchers. Bioinformatics has become a widely utilized method for exploring genes related to disease. This study set out to conduct weighted gene co-expression network analysis (WGCNA) and screen the hub gene of LN. We performed WGCNA on the microarray expression profile dataset of GSE104948 from the Gene Expression Omnibus (GEO) database with 18 normal and 21 LN samples of glomerulus. A total of 5,942 genes were divided into 5 co-expression modules, one of which was significantly correlated to LN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on the LN-related module, and the module was proved to be associated mainly with the activation of inflammation, immune response, cytokines, and immune cells. Genes in the most significant GO terms were extracted for sub-networks of WGNCA. We evaluated the centrality of genes in the sub-networks by Maximal Clique Centrality (MCC) method and CD36 was ultimately screened out as a hub candidate gene of the pathogenesis of LN. The result was verified by its differentially expressed level between normal and LN in GSE104948 and the other three multi-microarray datasets of GEO. Moreover, we further demonstrated that the expression level of CD36 is related to the WHO Lupus Nephritis Class of LN patients with the help of Nephroseq database. The current study proposed CD36 as a vital candidate gene in LN for the first time and CD36 may perform as a brand-new biomarker or therapeutic target of LN in the future.
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spelling pubmed-67774792019-10-07 CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis Yang, Huiying Li, Hua PeerJ Bioinformatics Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), which often progresses to end-stage renal disease (ESRD) and ultimately leads to death. At present, there are no definitive therapies towards LN, so that illuminating the molecular mechanism behind the disease has become an urgent task for researchers. Bioinformatics has become a widely utilized method for exploring genes related to disease. This study set out to conduct weighted gene co-expression network analysis (WGCNA) and screen the hub gene of LN. We performed WGCNA on the microarray expression profile dataset of GSE104948 from the Gene Expression Omnibus (GEO) database with 18 normal and 21 LN samples of glomerulus. A total of 5,942 genes were divided into 5 co-expression modules, one of which was significantly correlated to LN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on the LN-related module, and the module was proved to be associated mainly with the activation of inflammation, immune response, cytokines, and immune cells. Genes in the most significant GO terms were extracted for sub-networks of WGNCA. We evaluated the centrality of genes in the sub-networks by Maximal Clique Centrality (MCC) method and CD36 was ultimately screened out as a hub candidate gene of the pathogenesis of LN. The result was verified by its differentially expressed level between normal and LN in GSE104948 and the other three multi-microarray datasets of GEO. Moreover, we further demonstrated that the expression level of CD36 is related to the WHO Lupus Nephritis Class of LN patients with the help of Nephroseq database. The current study proposed CD36 as a vital candidate gene in LN for the first time and CD36 may perform as a brand-new biomarker or therapeutic target of LN in the future. PeerJ Inc. 2019-10-01 /pmc/articles/PMC6777479/ /pubmed/31592160 http://dx.doi.org/10.7717/peerj.7722 Text en ©2019 Yang and Li https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Yang, Huiying
Li, Hua
CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title_full CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title_fullStr CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title_full_unstemmed CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title_short CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
title_sort cd36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777479/
https://www.ncbi.nlm.nih.gov/pubmed/31592160
http://dx.doi.org/10.7717/peerj.7722
work_keys_str_mv AT yanghuiying cd36identifiedbyweightedgenecoexpressionnetworkanalysisasahubcandidategeneinlupusnephritis
AT lihua cd36identifiedbyweightedgenecoexpressionnetworkanalysisasahubcandidategeneinlupusnephritis