The construction and analysis of competitive endogenous RNA (ceRNA) networks in metastatic renal cell carcinoma: a study based on The Cancer Genome Atlas.
Competing endogenous RNA network (ceRNA network)
The Cancer Genome Atlas (TCGA)
biomarkers
metastatic renal cell carcinoma (mRCC)
overall survival (OS)
Journal
Translational andrology and urology
ISSN: 2223-4691
Titre abrégé: Transl Androl Urol
Pays: China
ID NLM: 101581119
Informations de publication
Date de publication:
Apr 2020
Apr 2020
Historique:
entrez:
19
5
2020
pubmed:
19
5
2020
medline:
19
5
2020
Statut:
ppublish
Résumé
The pathogenesis of metastatic renal cell carcinoma (mRCC), one of the most common malignant neoplasms, remains unknown. Studies on competitive endogenous RNAs (ceRNAs) have uncovered new interactions between RNAs, which suggest their roles in cancer pathogenesis. However, the role of ceRNA networks in mRCC has not yet been studied. Thus, this study aims to explore the role of ceRNA networks in mRCC development and identify potential prognostic indicators. We analyzed RNA sequencing data of mRCC patients, which had been obtained from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed long-noncoding RNAs (DElncRNAs), differentially expressed micro RNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in mRCC and clear cell RCC (ccRCC) samples were identified using the edgeR package that is available in R software. Moreover, based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID), enrichment analyses for biological processes and pathways functional were performed. As such, we built a ceRNA network and performed a survival analysis using the survival package in R. A total of 369 DElncRNAs, 12 DEmiRNAs, and 728 DEmRNAs were identified for further analysis. Of these, 11 lncRNAs, 20 mRNAs, and 2 miRNAs were included in the ceRNA network. Moreover, 7 of the 11 lncRNAs and 3 of the 20 mRNAs were associated with the overall survival of mRCC patients (P<0.05). Collectively, our findings allow a deepened understanding of the molecular mechanism of the ceRNA network and its role in mRCC development, which can guide both mRCC therapy and related future research.
Sections du résumé
BACKGROUND
BACKGROUND
The pathogenesis of metastatic renal cell carcinoma (mRCC), one of the most common malignant neoplasms, remains unknown. Studies on competitive endogenous RNAs (ceRNAs) have uncovered new interactions between RNAs, which suggest their roles in cancer pathogenesis. However, the role of ceRNA networks in mRCC has not yet been studied. Thus, this study aims to explore the role of ceRNA networks in mRCC development and identify potential prognostic indicators.
METHODS
METHODS
We analyzed RNA sequencing data of mRCC patients, which had been obtained from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed long-noncoding RNAs (DElncRNAs), differentially expressed micro RNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in mRCC and clear cell RCC (ccRCC) samples were identified using the edgeR package that is available in R software. Moreover, based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID), enrichment analyses for biological processes and pathways functional were performed. As such, we built a ceRNA network and performed a survival analysis using the survival package in R.
RESULTS
RESULTS
A total of 369 DElncRNAs, 12 DEmiRNAs, and 728 DEmRNAs were identified for further analysis. Of these, 11 lncRNAs, 20 mRNAs, and 2 miRNAs were included in the ceRNA network. Moreover, 7 of the 11 lncRNAs and 3 of the 20 mRNAs were associated with the overall survival of mRCC patients (P<0.05).
CONCLUSIONS
CONCLUSIONS
Collectively, our findings allow a deepened understanding of the molecular mechanism of the ceRNA network and its role in mRCC development, which can guide both mRCC therapy and related future research.
Identifiants
pubmed: 32420136
doi: 10.21037/tau.2020.02.17
pii: tau-09-02-303
pmc: PMC7215020
doi:
Types de publication
Journal Article
Langues
eng
Pagination
303-311Informations de copyright
2020 Translational Andrology and Urology. All rights reserved.
Déclaration de conflit d'intérêts
Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tau.2020.02.17). The authors have no conflicts of interest to declare.
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