Identification of prognostic genes from the breast cancer microenvironment

Abstract Background Prognostic evaluation of breast cancer is crucial in deciding the course of clinical treatment. The levels of immune cells and stromal cells in tumor microenvironment provide a new approach to evaluate the prognosis of breast cancer. Method: We obtained mRNA gene expression profiles of breast cancer patients from The Cancer Genome Atlas (TCGA), evaluated immune and stromal scores in tumor microenvironment (TME) using the ESTIMATE algorithm. We also constructed a protein-protein interaction (PPI) network, and performed function enrichment analysis and prognostic analysis.Results A total of 898 samples were divided into two groups corresponding to high and low score for both stromal as well as immune scores. 247 differentially expressed genes were identified, most of which were associated with T cell activation, lymphocyte differentiation, and cytokine receptor activity. We finally found 10 hub genes. Among them, we were able to confirm the following genes significantly association with prognosis: CCR5, CD2, CD3E, and CD5. Two important modules were isolated from the PPI network and for further analysis.Conclusion This study identified a group of genes significantly associated with the prognosis of breast cancer, and their efficacy still requires further clinical data validation.