Published online Aug 24, 2022. doi: 10.5306/wjco.v13.i8.675
Peer-review started: August 2, 2021
First decision: November 6, 2021
Revised: December 23, 2021
Accepted: July 26, 2022
Article in press: July 26, 2022
Published online: August 24, 2022
Processing time: 386 Days and 8.1 Hours
Breast cancer (BC) is the most common malignant tumor in women.
To investigate BC-associated hub genes to obtain a better understanding of BC tumorigenesis.
In total, 1203 BC samples were downloaded from The Cancer Genome Atlas database, which included 113 normal samples and 1090 tumor samples. The limma package of R software was used to analyze the differentially expressed genes (DEGs) in tumor tissues compared with normal tissues. The cluster Profiler package was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of upregulated and downregulated genes. Univariate Cox regression was conducted to explore the DEGs with statistical significance. Protein-protein interaction (PPI) network analysis was employed to investigate the hub genes using the CytoHubba plug-in of Cytoscape software. Survival analyses of the hub genes were carried out using the Kaplan-Meier method. The expression level of these hub genes was validated in the Gene Expression Profiling Interactive Analysis database and Human Protein Atlas database.
A total of 1317 DEGs (fold change > 2; P < 0.01) were confirmed through bioinformatics analysis, which included 744 upregulated and 573 downregulated genes in BC samples. KEGG enrichment analysis indicated that the upregulated genes were mainly enriched in the cytokine-cytokine receptor interaction, cell cycle, and the p53 signaling pathway (P < 0.01); and the downregulated genes were mainly enriched in the cytokine-cytokine receptor interaction, peroxisome proliferator-activated receptor signaling pathway, and AMP-activated protein kinase signaling pathway (P < 0.01).
In view of the results of PPI analysis, which were verified by survival and expression analyses, we conclude that MAD2L1, PLK1, SAA1, CCNB1, SHCBP1, KIF4A, ANLN, and ERCC6L may act as biomarkers for the diagnosis and prognosis in BC patients.
Core Tip: This study identified 1317 DEGs related to the occurrence and development of breast cancer (BC), 165 DEGs related to prognosis, and 8 hub genes (MAD2L1, PLK1, SAA1, CCNB1, SHCBP1, KIF4A, ANLN, and ERCC6L). Each of these eight hub genes has different expression levels in BC and is significantly related to prognosis. The results of this study indicate that studying these DEGs may help provide a full understanding of the molecular mechanisms underlying BC pathogenesis and progression. Moreover, these hub genes may serve as potential prognostic markers and therapeutic targets, which provide a reference for more in-depth and extensive prospective clinical research.