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Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis

Increasing evidence indicated that aberrant expression of long noncoding RNAs (lncRNAs) are involved in tumorigenesis of nasopharyngeal carcinoma (NPC). The purpose of this study was to construct a lncRNA-mediated ceRNA network based on weighted correlation network analysis (WGCNA). First, modules w...

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Autores principales: Zou, Zhenning, Liu, Shuguang, Ha, Yanping, Huang, Bowan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569441/
https://www.ncbi.nlm.nih.gov/pubmed/33102573
http://dx.doi.org/10.1155/2020/1468980
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author Zou, Zhenning
Liu, Shuguang
Ha, Yanping
Huang, Bowan
author_facet Zou, Zhenning
Liu, Shuguang
Ha, Yanping
Huang, Bowan
author_sort Zou, Zhenning
collection PubMed
description Increasing evidence indicated that aberrant expression of long noncoding RNAs (lncRNAs) are involved in tumorigenesis of nasopharyngeal carcinoma (NPC). The purpose of this study was to construct a lncRNA-mediated ceRNA network based on weighted correlation network analysis (WGCNA). First, modules with highly correlated genes were identified from GSE102349 via WGCNA, and the preservation of the modules was evaluated by GSE68799. Then, the differentially expressed lncRNAs and mRNAs identified from GSE12452 which belonged to the same WGCNA modules and the differentially expressed miRNAs identified from GSE32960 were used to construct a ceRNA network. The prognostic value of the network was evaluated by survival analysis. Furthermore, a risk score model for predicting progression-free survival (PFS) of NPC patients was established via LASSO-penalized Cox regression, and the differences in the expression of the lncRNAs between high- and low-risk groups were investigated. Finally, 14 stable modules were identified, and a ceRNA network composed of 11 lncRNAs, 15 miRNAs, and 40 mRNAs was established. The lncRNAs and mRNAs in the network belonged to the turquoise and salmon modules. Survival analysis indicated that ZNF667-AS1, LDHA, LMNB2, TPI1, UNG, and hsa-miR-142-3p were significantly correlated with the prognosis of NPC. Gene set enrichment analysis indicated that the upregulation of ZNF667-AS1 was associated with some immune-related pathways. Besides, a risk score model consisting of 12 genes was constructed and showed a good performance in predicting PFS for NPC patients. Among the 11 lncRNAs in the ceRNA network, SNHG16, SNHG17, and THAP9-AS1 were upregulated in the high-risk group of NPC, while ZNF667-AS1 was downregulated in the high-risk group of NPC. These results will promote our understanding of the crosstalk among lncRNAs, miRNAs, and mRNAs in the tumorigenesis and progression of NPC.
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spelling pubmed-75694412020-10-22 Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis Zou, Zhenning Liu, Shuguang Ha, Yanping Huang, Bowan Biomed Res Int Research Article Increasing evidence indicated that aberrant expression of long noncoding RNAs (lncRNAs) are involved in tumorigenesis of nasopharyngeal carcinoma (NPC). The purpose of this study was to construct a lncRNA-mediated ceRNA network based on weighted correlation network analysis (WGCNA). First, modules with highly correlated genes were identified from GSE102349 via WGCNA, and the preservation of the modules was evaluated by GSE68799. Then, the differentially expressed lncRNAs and mRNAs identified from GSE12452 which belonged to the same WGCNA modules and the differentially expressed miRNAs identified from GSE32960 were used to construct a ceRNA network. The prognostic value of the network was evaluated by survival analysis. Furthermore, a risk score model for predicting progression-free survival (PFS) of NPC patients was established via LASSO-penalized Cox regression, and the differences in the expression of the lncRNAs between high- and low-risk groups were investigated. Finally, 14 stable modules were identified, and a ceRNA network composed of 11 lncRNAs, 15 miRNAs, and 40 mRNAs was established. The lncRNAs and mRNAs in the network belonged to the turquoise and salmon modules. Survival analysis indicated that ZNF667-AS1, LDHA, LMNB2, TPI1, UNG, and hsa-miR-142-3p were significantly correlated with the prognosis of NPC. Gene set enrichment analysis indicated that the upregulation of ZNF667-AS1 was associated with some immune-related pathways. Besides, a risk score model consisting of 12 genes was constructed and showed a good performance in predicting PFS for NPC patients. Among the 11 lncRNAs in the ceRNA network, SNHG16, SNHG17, and THAP9-AS1 were upregulated in the high-risk group of NPC, while ZNF667-AS1 was downregulated in the high-risk group of NPC. These results will promote our understanding of the crosstalk among lncRNAs, miRNAs, and mRNAs in the tumorigenesis and progression of NPC. Hindawi 2020-10-10 /pmc/articles/PMC7569441/ /pubmed/33102573 http://dx.doi.org/10.1155/2020/1468980 Text en Copyright © 2020 Zhenning Zou et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zou, Zhenning
Liu, Shuguang
Ha, Yanping
Huang, Bowan
Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title_full Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title_fullStr Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title_full_unstemmed Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title_short Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
title_sort construction and analysis of lncrna-mediated cerna network in nasopharyngeal carcinoma based on weighted correlation network analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569441/
https://www.ncbi.nlm.nih.gov/pubmed/33102573
http://dx.doi.org/10.1155/2020/1468980
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