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Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
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Predicting functional circular RNA-based competitive endogenous RNA network in gastric carcinoma using novel
Zirui Zhu1, Rui Huang2, Baojun Huang1
1Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, 159407The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China.
Experimental Biology and Medicine (Maywood, N.J.)
|October 7, 2021
Summary
This study identifies a key circular RNA-microRNA-messenger RNA network in gastric cancer (GC) pathogenesis. The findings reveal crucial regulatory pathways and potential biomarkers for this lethal malignancy.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Gastric cancer (GC) is a leading cause of cancer-related deaths globally.
- Circular RNAs (circRNAs) play a role in GC, but their regulatory mechanisms are unclear.
Purpose of the Study:
- To uncover the critical circRNA-microRNA (miRNA)-messenger RNA (mRNA) regulatory network in gastric cancer.
- To identify potential diagnostic and prognostic biomarkers for GC.
Main Methods:
- Analysis of public microarray datasets (Gene Expression Omnibus) for circRNA, miRNA, and mRNA expression profiles.
- Utilized robust rank aggregation for differential circRNA expression analysis.
- Constructed circRNA-based competitive endogenous RNA (ceRNA) networks using Cytoscape and bioinformatics tools.
- Performed functional enrichment and protein-protein interaction network analysis to identify hub genes.
- Validated hub gene expression and clinical relevance using GEPIA and Kaplan-Meier Plotter databases.
Main Results:
- Identified differentially expressed circRNAs and constructed a circRNA-based ceRNA network.
- Discovered a significant protein-protein interaction network involving 51 mRNAs, with several hub genes identified.
- Found associations between specific hub genes, GC survival rates, and clinical stages.
- Elucidated a detailed circRNA-related ceRNA regulatory subnetwork comprising four circRNAs, six miRNAs, and eight key hub genes.
Conclusions:
- A comprehensive circRNA-miRNA-mRNA regulatory network in gastric cancer has been elucidated.
- The identified hub genes and regulatory network offer potential therapeutic targets and prognostic biomarkers for GC.
- This research provides novel insights into the molecular mechanisms underlying GC progression.
