Identification of differentially expressed genes between triple and non-triple-negative breast cancer using bioinformatics analysis
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Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), is characterized by early recurrence of disease and poor survival.
Here, we sought to identify genes associated with TNBC that could provide new insight into gene dysregulation in TNBC and, at the same time, provide additional potential therapeutic targets for breast cancer treatment.
Gene expression profiles from accession series GSE76275 were downloaded from the Gene Expression Omnibus database (GEO). The Cancer Genome Atlas (TCGA) was used to validate potential hub genes in the TCGA database. Protein–protein interaction (PPI) networks were identified using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins). Finally, overall survival (OS) and relapse-free survival (RFS) analysis of hub genes was performed using a Kaplan–Meier plotter online tool.
A total of 750 genes were identified after analysis of GSE76275. After validation with the TCGA database, a total of 155 differentially expressed genes (DEGs) were consistent with those identified by GSE76275. Based on the STRING database, we constructed a PPI network using the DEGs obtained from GSE76275 datasets. Furthermore, in the prognostic analysis of the 155 DEGs, we found that there were 10 genes associated with OS and 33 genes associated with RFS. Combined with the degree scores from the PPI network, a total of ten genes with the highest degree scores were selected as hub genes pertaining to TNBC.
Our research provides new insight into the subnetwork of biomarkers connected with TNBC, which could be useful for prognostication and risk stratification of TNBC patients.
KeywordsTriple-negative breast cancer Differentially expressed genes Protein–protein Interaction Kaplan–Meier plotter
Triple-negative breast cancer
Human epidermal growth factor receptor 2
Differentially expressed genes
Gene expression omnibus
The Cancer genome atlas
Log fold control
Epidermal growth factor receptor
Sex-determining region Y-box 1
PDZ domain-containing 1
X-box binding protein 1
Trefoil factor 3
Prostaglandin E receptor 3
NME/NM23 family member 5
Interleukin 6 signal transducer
Conceived and designed the experiments and revised the manuscript: XMW, YY. Performed the experiments: QXZ, LPS, HL. Analyzed the data: QXZ, HL. Responsible for bioinformatics and bio-statistics analysis: QXZ, HL. Wrote the paper: QXZ.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- 12.Nakai K, Hung MC, Yamaguchi H. A perspective on anti-EGFR therapies targeting triple-negative breast cancer. Am J Cancer Res. 2016;6:1609–23.Google Scholar
- 18.Joosse Simon A, Hannemann Juliane, Spotter Julia, Bauche Andreas, Andreas Antje, Muller Volkmar, et al. Changes in keratin expression during metastatic progression of breast cancer: impact on the detection of circulating tumor cells. Hum Cancer Biol. 2012;18(4):993–1003.Google Scholar
- 29.Kocher O, Comella N, Tognazzi K, Brown LF. Identification and partial characterization of PDZK1: a novel protein containing PDZ interaction domains. Lab Invest. 1998;78:117–25.Google Scholar
- 31.Vic P, Vignon F, Derocq D, Rochefort H. Effect of estradiol on the ultrastructure of the MCF7 human breast cancer cells in culture. Cancer Res. 1982;42:667–73.Google Scholar
- 38.Cheuk IW, Shin VY, Siu MT, Tsang JY, Ho JC, Chen J, et al. Association of EP2 receptor and SLC19A3 in regulating breast cancer metastasis. Am J Cancer Res. 2015;5(11):3389–99.Google Scholar
- 41.Wu X, Tao P, Zhou Q, Li J, Yu Z, Wang X, et al. IL-6 secreted by cancer-associated fibroblasts promotes epithelial-mesenchymal transition and metastasis of gastric cancer via JAK2/STAT3 signaling pathway. Oncotarget. 2017;8(13):20741–50.Google Scholar