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Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.7K

Construction of a circular RNA-microRNA-messengerRNA regulatory network in stomach adenocarcinoma

Qincheng Liu1,2, Wei Zhang1,2, Zhenqian Wu3

  • 1Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.

Journal of Cellular Biochemistry
|September 6, 2019
PubMed
Abstract

Insights

This study reveals novel circular RNA (circRNA)-microRNA (miRNA)-messenger RNA (mRNA) regulatory networks in stomach adenocarcinoma (STAD). Identified hub genes like COL10A1 are linked to poor survival and advanced tumor stage in STAD patients.

Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Circular RNAs (circRNAs) and microRNAs (miRNAs) are key regulators of gene expression in cancer.
  • The role of competitive endogenous RNA (ceRNA) networks, involving circRNAs, miRNAs, and messenger RNAs (mRNAs), in stomach adenocarcinoma (STAD) is not well understood.
  • This research aims to elucidate novel regulatory networks in STAD.

Purpose of the Study:

  • To explore novel regulatory mechanisms in stomach adenocarcinoma (STAD) using ceRNA networks.
  • To identify key differentially expressed circRNAs (DECs), miRNAs (DEMIs), and mRNAs (DEMs) in STAD.
  • To construct and analyze a circRNA-miRNA-mRNA regulatory network for STAD.

Main Methods:

  • Expression profiles of circRNAs, miRNAs, and mRNAs were obtained from public databases (GEO, TCGA) for STAD.
  • A comprehensive bioinformatics strategy was employed to identify candidate molecules and construct the ceRNA network.
  • Hub genes were identified via protein-protein interaction (PPI) analysis and their expression validated using quantitative reverse transcription (RT) polymerase chain reaction.

Main Results:

  • A total of 51 DECs, 11,448 DEMs, and 458 DEMIs were identified in STAD.
  • A circRNA-miRNA-mRNA regulatory network was constructed involving 6 DECs, 6 DEMIs, and 36 DEMs.
  • Four hub genes (COL10A1, COL5A2, COL4A1, COL3A1) were identified; overexpression of COL10A1, COL5A1, and COL4A1 correlated with poor overall survival and advanced TNM stage in STAD patients.

Conclusions:

  • This study presents a novel perspective on the regulatory mechanisms in STAD through ceRNA networks.
  • The identified circRNA-miRNA-mRNA interactions and hub genes offer potential biomarkers for STAD diagnosis and prognosis.
  • Further investigation into these regulatory networks could lead to new therapeutic strategies for STAD.
Keywords:
bioinformatics analysiscircular RNAcompeting endogenous RNAmicro RNAstomach adenocarcinoma

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