Comprehensive Analysis of a Competing Endogenous RNA Co-Expression Network in Chronic Obstructive Pulmonary Disease

Abstract

Jingwei Wang,1,2,* Bowen Xia,3,* Ruimin Ma,1 Qiao Ye1,2 1Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China; 2Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China; 3Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Qiao Ye, Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Chaoyang Hospital, Capital Medical University, No. 8 Worker’s Stadium, Chaoyang District, Beijing, 100020, People’s Republic of China, Email [email protected]: Chronic obstructive pulmonary disease (COPD) is the main cause of mortality world widely. Non-coding RNAs (lncRNAs) and associated competitive endogenous RNAs (ceRNAs) networks were recently proved to lead to mRNA gene expression downregulation but were still unclear in COPD. This study aims to investigate and elucidate the mechanisms underlying the involvement of ceRNA co-expression networks in COPD pathogenesis.Methods: Obtained expression signature of data from the Gene Expression Omnibus database and compared the differentially expression of mRNAs and miRNAs between COPD patients and healthy smokers. Predicted the miRNA–lncRNA and miRNA–mRNA interaction using online library and employed CIBERSORT to measure the proportions of the 22 immune cells in the COPD and control groups.Results: Established a ceRNA-network comprising 11 lncRNAs, 5 miRNAs, and 16 mRNAs. Using the weighted correlation network analysis method, we identified hub genes and hub miRNAs and obtained one core sub-network, XIST, FGD5-AS1, KCNQ1OT1, HOXA11-AS, LINC00667, H19, PRKCQ-AS1, NUTM2A-AS1/has-mir-454-3p/ZNF678, PRRG4. COPD patients had different proportions of immune cells than controls, and these variations were associated with the magnitude of pulmonary function parameters.Conclusion: The ceRNA-network, particularly the core sub-network, may be a putative goal for COPD, in which specific immune cells were involved.Keywords: chronic obstructive pulmonary disease, competing endogenous RNA network, microRNAs, miRNAs, CIBERSORT algorithm, gene expression omnibus

Keywords

• chronic obstructive pulmonary disease
• copd
• competing endogenous rna network
• micrornas
• mirnas
• cibersort algorithm
• gene expression omnibus;