Identification of early diagnostic biomarkers via WGCNA in gastric cancer.
Alcohol Oxidoreductases
/ analysis
Biomarkers, Tumor
/ analysis
Chemokines, CC
/ analysis
Computational Biology
/ methods
Early Detection of Cancer
/ methods
Gene Expression Profiling
/ methods
Gene Expression Regulation, Neoplastic
/ genetics
Gene Regulatory Networks
Homeodomain Proteins
/ analysis
Humans
Mitochondrial Proteins
/ analysis
Prognosis
Stomach Neoplasms
/ diagnosis
ADHFE1
And HOXB13
CCL14
Gastric Cancer
ITGAX
Transcriptome analysis
WGCNA
Journal
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
ISSN: 1950-6007
Titre abrégé: Biomed Pharmacother
Pays: France
ID NLM: 8213295
Informations de publication
Date de publication:
Jan 2022
Jan 2022
Historique:
received:
10
10
2021
revised:
14
11
2021
accepted:
23
11
2021
pubmed:
6
12
2021
medline:
11
3
2022
entrez:
5
12
2021
Statut:
ppublish
Résumé
Gastric cancer (GC) is the world's second-leading cause of cancer-related mortality, continuing to make it a serious healthcare concern. Even though the prevalence of GC reduces, the prognosis for GC patients remains poor in terms of a lack of reliable biomarkers to diagnose early GC and predict chemosensitivity and recurrence. We integrated the gene expression patterns of gastric cancers from four RNAseq datasets (GSE113255, GSE142000, GSE118897, and GSE130823) from Gene Expression Omnibus (GEO) database to recognize differentially expressed genes (DEGs) between normal and GC samples. A gene co-expression network was built using weighted co-expression network analysis (WGCNA). Furthermore, RT-qPCR was performed to validate the in silico results. The red modules in GSE113255, Turquoise in GSE142000, Brown in GSE118897, and the green-yellow module in GSE130823 datasets were found to be highly correlated with the anatomical site of GC. ITGAX, CCL14, ADHFE1, and HOXB13) as the hub gene are differentially expressed in tumor and non-tumor gastric tissues in this study. RT-qPCR demonstrated a high level of the expression of this gene. The expression levels of ITGAX, CCL14, ADHFE1, and HOXB13 in GC tumor tissues are considerably greater than in adjacent normal tissues. Systems biology approaches identified that these genes could be possible GC marker genes, providing ideas for other experimental studies in the future.
Sections du résumé
BACKGROUND
BACKGROUND
Gastric cancer (GC) is the world's second-leading cause of cancer-related mortality, continuing to make it a serious healthcare concern. Even though the prevalence of GC reduces, the prognosis for GC patients remains poor in terms of a lack of reliable biomarkers to diagnose early GC and predict chemosensitivity and recurrence.
METHODS AND MATERIAL
METHODS
We integrated the gene expression patterns of gastric cancers from four RNAseq datasets (GSE113255, GSE142000, GSE118897, and GSE130823) from Gene Expression Omnibus (GEO) database to recognize differentially expressed genes (DEGs) between normal and GC samples. A gene co-expression network was built using weighted co-expression network analysis (WGCNA). Furthermore, RT-qPCR was performed to validate the in silico results.
RESULTS
RESULTS
The red modules in GSE113255, Turquoise in GSE142000, Brown in GSE118897, and the green-yellow module in GSE130823 datasets were found to be highly correlated with the anatomical site of GC. ITGAX, CCL14, ADHFE1, and HOXB13) as the hub gene are differentially expressed in tumor and non-tumor gastric tissues in this study. RT-qPCR demonstrated a high level of the expression of this gene.
CONCLUSION
CONCLUSIONS
The expression levels of ITGAX, CCL14, ADHFE1, and HOXB13 in GC tumor tissues are considerably greater than in adjacent normal tissues. Systems biology approaches identified that these genes could be possible GC marker genes, providing ideas for other experimental studies in the future.
Identifiants
pubmed: 34864309
pii: S0753-3322(21)01263-4
doi: 10.1016/j.biopha.2021.112477
pii:
doi:
Substances chimiques
Biomarkers, Tumor
0
CCL14 protein, human
0
Chemokines, CC
0
HOXB13 protein, human
0
Homeodomain Proteins
0
Mitochondrial Proteins
0
Alcohol Oxidoreductases
EC 1.1.-
hydroxyacid-oxoacid transhydrogenase
EC 1.1.99.24
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
112477Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Masson SAS.. All rights reserved.