Background:
Breast cancer is one of the deadly
tumors in women, and its incidence continues to increase. This study aimed to identify novel therapeutic molecules using
RNA sequencing (
RNA-seq) data of
breast cancer from our hospital. Methods: 30 pairs of human
breast cancer tissue and matched normal tissue were collected and
RNA sequenced in our hospital. Differentially expressed genes (DEGs) were calculated with raw data by the R package "edgeR", and functionally annotated using R package "clusterProfiler".
Tumor-infiltrating immune cells (TIICs) were estimated using a website tool TIMER 2.0. Effects of key genes on therapeutic efficacy were analyzed using
RNA-seq data and drug sensitivity data from two databases: the
Cancer Cell Line Encyclopedia (CCLE) and the
Cancer Therapeutics Response Portal (CTRP). Results: There were 2,953 DEGs between cancerous and matched normal tissue, as well as 975 DEGs between primary
breast cancer and metastatic
breast cancer. These genes were primarily enriched in PI3K-Akt signaling pathway, calcium signaling pathway, cAMP signaling pathway, and cell cycle. Notably, CD8+ T cell, M0 macrophage, M1 macrophage, regulatory T cell and follicular helper T cell were significantly elevated in cancerous tissue as compared with matched normal tissue. Eventually, we found five genes (GALNTL5, MLIP, HMCN2, LRRN4CL, and
DUOX2) were markedly corelated with CD8+ T cell infiltration and cytotoxicity, and associated with therapeutic response. Conclusion: We found five key genes associated with
tumor progression, CD8+ T cell and therapeutic efficacy. The findings would provide potential molecular targets for the treatment of
breast cancer.