Retrospective Study
Copyright ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Clin Cases. Jul 26, 2023; 11(21): 5023-5034
Published online Jul 26, 2023. doi: 10.12998/wjcc.v11.i21.5023
Identification of functional genes regulating gastric cancer progression using integrated bioinformatics analysis
Kun Yu, Dong Zhang, Qiang Yao, Xing Pan, Gang Wang, Hai-Yang Qian, Yao Xiao, Qiong Chen, Ke Mei
Kun Yu, Qiang Yao, Xing Pan, Gang Wang, Hai-Yang Qian, Qiong Chen, Ke Mei, Department of Radiology, Shanghai Xuhui Dahua Hospital, Shanghai 200090, China
Dong Zhang, Department of Spinal Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200090, China
Yao Xiao, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 200090, China
Author contributions: Yu K, Xiao Y, and Mei K contributed to study concept and design, data mining and bioinformatic analysis, preparation of the manuscript, and obtained funding; Qian HY and Pan X carried out experiments, data analysis, and preparation of figures; Wang G and Pan X carried out analysis; Mei K and Zhang D contributed to study design and obtained funding.
Institutional review board statement: The study was reviewed and approved by the Shanghai Yueyang Hospital Institutional Review Board (Approval No. 20210316).
Informed consent statement: All study participants, or their legal guardian, provided informed written consent prior to study enrollment.
Conflict-of-interest statement: The authors have no conflicts of interest to disclose.
Data sharing statement: No additional data are available.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Qiong Chen, MD, Doctor, Department of Radiology, Shanghai Xuhui Dahua Hospital, No. 901 Lao’ humin Road, Xuhui District, Shanghai 200090, China. cq1444@sina.com
Received: March 3, 2023
Peer-review started: March 3, 2023
First decision: May 19, 2023
Revised: June 1, 2023
Accepted: June 26, 2023
Article in press: June 26, 2023
Published online: July 26, 2023
Processing time: 145 Days and 11.7 Hours
ARTICLE HIGHLIGHTS
Research background

Gastric cancer (GC) is one of the most common cancers and has a poor prognosis. Treatment of GC has remained unchanged over the past few years. Genetic factors have been revealed to play an important role in susceptibility to GC. Significantly upregulated genes associated with poor prognosis were detected in GC using integrated bioinformatics methods.

Research motivation

In order to identify core prognostic biomarkers in GC, several databases were searched for GC-related genes as tumor markers, and cellular tests were performed to confirm the results.

Research objectives

Bioinformatics analysis of the molecular mechanism involved in GC revealed that three differentially expressed genes (DEGs) (BIRC5, TRIP13, or UBE2C) play critical roles in the progression of GC. Bioinformatics were used to identify hub genes and important pathways in GC, resulting in a biological relationship between the pathways and gene expression likely involved in GC.

Research methods

In the theoretical analysis, microarray data information, data processing of DEGs, Gene Ontology and pathway enrichment analysis, PPI network and module analysis, and survival analysis were used. In the cellular experiments, RNA sequencing expression of core genes, patient samples and RT-PCR detection, cells and transfection, CCK-8 assay, apoptosis assay, colony formation assay, and statistical analysis were used.

Research results

Three hundred and forty-eight GC tissues and 141 normal tissues were analyzed; 251 DEGs were identified including 187 down-regulated genes and 64 up-regulated genes. We found that knockdown of BIRC5, TRIP13, or UBE2C significantly inhibited cell proliferation and induced cell apoptosis. Knockdown of BIRC5, TRIP13, or UBE2C increased cellular sensitivity to cisplatin.

Research conclusions

The molecular mechanism of GC, via bioinformatics analysis, showed that three DEGs (BIRC5, TRIP13, or UBE2C) played key roles in the progression of GC. These findings will help to elucidate GC pathogenesis and identify novel biomarkers or drug targets for improved diagnostics and therapeutics for GC.

Research perspectives

Bioinformatics was used to identify hub genes and important pathways in GC, resulting in a biological relationship between the pathways and gene expression likely involved in the progression of GC. Bioinformatics analysis revealed the relevant genes and cellular pathways involved in the genesis and development of GC.