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Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma

BACKGROUND: Recently, a growing body of evidence has revealed the role of competing endogenous RNA (ceRNA) networks in various human cancers. However, there is still a lack of research on the systemic ceRNA network related to gastric adenocarcinoma. METHODS: The intersection of differentially expres...

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Autores principales: Wu, Chen, Hou, Xinfang, Li, Shuai, Wang, Jufeng, Luo, Suxia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AME Publishing Company 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10186539/
https://www.ncbi.nlm.nih.gov/pubmed/37201096
http://dx.doi.org/10.21037/jgo-22-1201
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author Wu, Chen
Hou, Xinfang
Li, Shuai
Wang, Jufeng
Luo, Suxia
author_facet Wu, Chen
Hou, Xinfang
Li, Shuai
Wang, Jufeng
Luo, Suxia
author_sort Wu, Chen
collection PubMed
description BACKGROUND: Recently, a growing body of evidence has revealed the role of competing endogenous RNA (ceRNA) networks in various human cancers. However, there is still a lack of research on the systemic ceRNA network related to gastric adenocarcinoma. METHODS: The intersection of differentially expressed genes (DEGs) was obtained by mining the GSE54129, GSE13861, and GSE118916 datasets from the Gene Expression Omnibus (GEO) website. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for the enrichment analysis. A protein-protein interaction (PPI) network was established with the STRING online database, and hub genes were identified by Cytoscape software. The prediction of key microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) was conducted by miRNet. The prognostic analysis, expression difference, and correlation analysis of messenger RNAs (mRNAs), lncRNAs, and miRNAs were carried out using the Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, and Encyclopedia of RNA Interactomes (ENCORI). RESULTS: We identified180 significant DEGs. Extracellular matrix (ECM) receptor interaction, focal adhesion, ECM tissue, and collagen catabolic processes were the most significant pathways in the functional enrichment analysis. Nineteen upregulated hub genes and one downregulated hub gene were found to be significantly associated with the prognosis of gastric adenocarcinoma. Of the 18 miRNAs targeting 12 key genes, only six were associated with a promising prognosis in gastric adenocarcinoma. By comprehensive differential expression and survival analysis, 40 key lncRNAs were identified. Finally, we constructed a network of 24 ceRNAs associated with gastric adenocarcinoma. CONCLUSIONS: Potential mRNA-miRNA-lncRNA subnets were constructed, each RNA of which can be used as a prognostic biomarker for gastric adenocarcinoma.
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spelling pubmed-101865392023-05-17 Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma Wu, Chen Hou, Xinfang Li, Shuai Wang, Jufeng Luo, Suxia J Gastrointest Oncol Original Article BACKGROUND: Recently, a growing body of evidence has revealed the role of competing endogenous RNA (ceRNA) networks in various human cancers. However, there is still a lack of research on the systemic ceRNA network related to gastric adenocarcinoma. METHODS: The intersection of differentially expressed genes (DEGs) was obtained by mining the GSE54129, GSE13861, and GSE118916 datasets from the Gene Expression Omnibus (GEO) website. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for the enrichment analysis. A protein-protein interaction (PPI) network was established with the STRING online database, and hub genes were identified by Cytoscape software. The prediction of key microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) was conducted by miRNet. The prognostic analysis, expression difference, and correlation analysis of messenger RNAs (mRNAs), lncRNAs, and miRNAs were carried out using the Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, and Encyclopedia of RNA Interactomes (ENCORI). RESULTS: We identified180 significant DEGs. Extracellular matrix (ECM) receptor interaction, focal adhesion, ECM tissue, and collagen catabolic processes were the most significant pathways in the functional enrichment analysis. Nineteen upregulated hub genes and one downregulated hub gene were found to be significantly associated with the prognosis of gastric adenocarcinoma. Of the 18 miRNAs targeting 12 key genes, only six were associated with a promising prognosis in gastric adenocarcinoma. By comprehensive differential expression and survival analysis, 40 key lncRNAs were identified. Finally, we constructed a network of 24 ceRNAs associated with gastric adenocarcinoma. CONCLUSIONS: Potential mRNA-miRNA-lncRNA subnets were constructed, each RNA of which can be used as a prognostic biomarker for gastric adenocarcinoma. AME Publishing Company 2023-01-05 2023-04-29 /pmc/articles/PMC10186539/ /pubmed/37201096 http://dx.doi.org/10.21037/jgo-22-1201 Text en 2023 Journal of Gastrointestinal Oncology. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Original Article
Wu, Chen
Hou, Xinfang
Li, Shuai
Wang, Jufeng
Luo, Suxia
Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title_full Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title_fullStr Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title_full_unstemmed Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title_short Identification of a potential competing endogenous RNA (ceRNA) network in gastric adenocarcinoma
title_sort identification of a potential competing endogenous rna (cerna) network in gastric adenocarcinoma
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10186539/
https://www.ncbi.nlm.nih.gov/pubmed/37201096
http://dx.doi.org/10.21037/jgo-22-1201
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