Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis

Jing An, Ting Yang, Jiajia Dong, Zenglin Liao, Chun Wan, Yongchun Shen, Lei Chen Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of...

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Autores principales:	An J, Yang T, Dong J, Liao Z, Wan C, Shen Y, Chen L
Formato:	article
Lenguaje:	EN
Publicado:	Dove Medical Press 2021
Materias:	chronic obstructive pulmonary disease weighted gene co-expression network analysis microrna Diseases of the respiratory system RC705-779
Acceso en línea:	https://doaj.org/article/e885bc84cdc3401caf3f1df497d7aa67
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spelling	oai:doaj.org-article:e885bc84cdc3401caf3f1df497d7aa672021-11-16T18:47:50ZIdentifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis1178-2005https://doaj.org/article/e885bc84cdc3401caf3f1df497d7aa672021-11-01T00:00:00Zhttps://www.dovepress.com/identifying-mirna-modules-and-related-pathways-of-chronic-obstructive--peer-reviewed-fulltext-article-COPDhttps://doaj.org/toc/1178-2005Jing An, Ting Yang, Jiajia Dong, Zenglin Liao, Chun Wan, Yongchun Shen, Lei Chen Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of ChinaCorrespondence: Yongchun Shen; Lei Chen Email Shenshen_yongchun@126.com; lchens@126.comBackground: Chronic obstructive pulmonary disease (COPD) is a heterogeneous chronic inflammatory disease characterized by progressive airflow limitation that causes high morbidity and mortality. MicroRNA, a short-chain noncoding RNA, regulates gene expression at the transcriptional level. microRNA modules with a role in the pathogenesis of COPD may serve as COPD biomarkers.Methods: We downloaded the GSE33336 microarray data set from the Gene Expression Omnibus (GEO) database, the data are derived from 29 lung samples of patients with emphysema undergoing curative resection for lung cancer. We used weighted gene co-expression network analysis (WGCNA) to construct co-expression modules and detect trait-related microRNA modules. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to predict the biological function of the interest modules, and we screened out candidate hub microRNAs based on their module membership (MM) value and top proteins on the results of the protein–protein interaction (PPI) network.Results: Three microRNA modules (royal blue, light yellow and grey60) were highly associated with COPD. Axon guidance, proteoglycans in cancer and mitogen-activated protein kinases (MAPK) signaling pathway were common pathways in these three modules. Keratin18 (KRT18) was the top protein in our study. miR-452, miR-149, miR-133a, miR-181a and miR-421 in hub microRNAs may play a role in COPD.Conclusion: These findings provide evidence for the role of miRNAs in COPD and identify biomarker candidates.Keywords: chronic obstructive pulmonary disease, weighted gene co-expression network analysis, microRNAAn JYang TDong JLiao ZWan CShen YChen LDove Medical Pressarticlechronic obstructive pulmonary diseaseweighted gene co-expression network analysismicrornaDiseases of the respiratory systemRC705-779ENInternational Journal of COPD, Vol Volume 16, Pp 3119-3130 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	chronic obstructive pulmonary disease weighted gene co-expression network analysis microrna Diseases of the respiratory system RC705-779
spellingShingle	chronic obstructive pulmonary disease weighted gene co-expression network analysis microrna Diseases of the respiratory system RC705-779 An J Yang T Dong J Liao Z Wan C Shen Y Chen L Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
description	Jing An, Ting Yang, Jiajia Dong, Zenglin Liao, Chun Wan, Yongchun Shen, Lei Chen Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of ChinaCorrespondence: Yongchun Shen; Lei Chen Email Shenshen_yongchun@126.com; lchens@126.comBackground: Chronic obstructive pulmonary disease (COPD) is a heterogeneous chronic inflammatory disease characterized by progressive airflow limitation that causes high morbidity and mortality. MicroRNA, a short-chain noncoding RNA, regulates gene expression at the transcriptional level. microRNA modules with a role in the pathogenesis of COPD may serve as COPD biomarkers.Methods: We downloaded the GSE33336 microarray data set from the Gene Expression Omnibus (GEO) database, the data are derived from 29 lung samples of patients with emphysema undergoing curative resection for lung cancer. We used weighted gene co-expression network analysis (WGCNA) to construct co-expression modules and detect trait-related microRNA modules. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to predict the biological function of the interest modules, and we screened out candidate hub microRNAs based on their module membership (MM) value and top proteins on the results of the protein–protein interaction (PPI) network.Results: Three microRNA modules (royal blue, light yellow and grey60) were highly associated with COPD. Axon guidance, proteoglycans in cancer and mitogen-activated protein kinases (MAPK) signaling pathway were common pathways in these three modules. Keratin18 (KRT18) was the top protein in our study. miR-452, miR-149, miR-133a, miR-181a and miR-421 in hub microRNAs may play a role in COPD.Conclusion: These findings provide evidence for the role of miRNAs in COPD and identify biomarker candidates.Keywords: chronic obstructive pulmonary disease, weighted gene co-expression network analysis, microRNA
format	article
author	An J Yang T Dong J Liao Z Wan C Shen Y Chen L
author_facet	An J Yang T Dong J Liao Z Wan C Shen Y Chen L
author_sort	An J
title	Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
title_short	Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
title_full	Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
title_fullStr	Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
title_full_unstemmed	Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis
title_sort	identifying mirna modules and related pathways of chronic obstructive pulmonary disease associated emphysema by weighted gene co-expression network analysis
publisher	Dove Medical Press
publishDate	2021
url	https://doaj.org/article/e885bc84cdc3401caf3f1df497d7aa67
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Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis

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