Identification of Key Genes Affecting the Tumor Microenvironment and Prognosis of Triple-Negative Breast Cancer

Jiarong Yi; Wenjing Zhong; Haoming Wu; Jikun Feng; Xiazi Zouxu; Xinjian Huang; Siqi Li; Zeyu Shuang

doi:10.3389/fonc.2021.746058

Identification of Key Genes Affecting the Tumor Microenvironment and Prognosis of Triple-Negative Breast Cancer

Front Oncol. 2021 Oct 21:11:746058. doi: 10.3389/fonc.2021.746058. eCollection 2021.

Authors

Jiarong Yi¹, Wenjing Zhong¹, Haoming Wu¹, Jikun Feng¹, Xiazi Zouxu¹, Xinjian Huang¹, Siqi Li¹, Zeyu Shuang¹

Affiliation

¹ Department of Breast Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.

Abstract

Although the tumor microenvironment (TME) plays an important role in the development of many cancers, its roles in breast cancer, especially triple-negative breast cancer (TNBC), are not well studied. This study aimed to identify genes related to the TME and prognosis of TNBC. Firstly, we identified differentially expressed genes (DEG) in the TME of TNBC, using Expression data (ESTIMATE) datasets obtained from the Cancer Genome Atlas (TCGA) and Estimation of Stromal and Immune cells in Malignant Tumor tissues. Next, survival analysis was performed to analyze the relationship between TME and prognosis of TNBC, as well as determine DEGs. Genes showing significant differences were scored as alternative genes. A protein-protein interaction (PPI) network was constructed and functional enrichment analysis conducted using the DEG. Proteins with a degree greater than 5 and 10 in the PPI network correspond with hub genes and key genes, respectively. Finally, CCR2 and CCR5 were identified as key genes in TME and prognosis of TNBC. Finally, these results were verified using Gene Expression Omnibus (GEO) datasets and immunohistochemistry of TNBC patients. In conclusion, CCR2 and CCR5 are key genes in the TME and prognosis of TNBC with the potential of prognostic biomarkers in TNBC.

Keywords: GEO; TCGA; TNBC; estimate; tumor microenvironment.