Single-cell RNA sequencing and bulk sequencing reveal the immunosuppressive role of malignant cells in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and the limiting efficacy is achieved for TNBC patients with immunotherapy. The role of malignant cells in the tumor microenvironment (TME) is still complicated. Here, we firstly identified and characterized the malignant cells in the TME of TNBC based on single-cell and bulk RNA sequencing. Then a high score of gene copy number variation (CNV) was found in the malignant cells. And 2507 up-regulated genes and 830 down-regulated genes were obtained based on a difference analysis between the malignant cells and other epithelial cells. Furthermore, KLF3-targeted genes were identified as being associated with the development of breast cancer. Finally, an immunosuppressive role of the malignant cells was identified in the TME of TNBC as the strong interactions between tumor cells and CD8-positive exhausted T cells. Together, these findings provide new insights into the malignant cells of TME and a new idea to develop therapeutic strategy for immunotherapy of TNBC.