The Significance of Tumor Microenvironment Score for Breast Cancer Patients

Abstract

Purpose. This study was designed to clarify the prognostic value of tumor microenvironment score and abnormal genomic alterations in TME for breast cancer patients. Method. The TCGA-BRCA data were downloaded from TCGA and analyzed with R software. The results from analyses were further validated using the dataset from GSE96058, GSE124647, and GSE25066. Results. After analyzing the TCGA data and verifying it with the GEO data, we developed a TMEscore model based on the TME infiltration pattern and validated it in 3273 breast cancer patients. The results suggested that our TMEscore model has high prognostic value. TME features with the TMEscore model can help to predict breast cancer patients’ response to immunotherapy and provide new strategies for breast cancer treatment. Signature 24 was first found in breast cancer. In focal SCNAs, a total of 95 amplified genes and 169 deletion genes in the TMEscore high group were found to be significantly related to the prognosis of breast cancer patients, while 61 amplified genes and 174 deletion genes in the TMEscore low group were identified. LRRC48, CFAP69, and cg25726128 were first discovered and reported to be related to the survival of breast cancer patients. We identified specific mutation signatures that correlate with TMEscore and prognosis. Conclusion. TMEscore model has high predictive value regarding prognosis and patients’ response to immunotherapy. Signature 24 was first found in breast cancer. Specific mutation signatures that correlate with TMEscore and prognosis might be used for providing additional indicators for disease evaluation.