Transcriptomic signature of triple-negative breast cancer as chemotherapy sensitivity predictor.

Neoadjuvant chemotherapy is the foundation treatment for triple-negative breast cancer (TNBC) and frequently results in temporary pathological complete response (pCR). However, there are large differences in clinical response and survival after neoadjuvant chemotherapy of TNBC patients.Transcriptomes of 46 Formalin-Fixed Paraffin-Embedded (FFPE) tumor samples from TNBC patients were analyzed by RNA-seq by comparing 26 TNBCs with pCR versus 20 TNBCs with pathological partial remission (pPR). Subsequently, we narrowed down list of genes to those that strongly correlated with drug sensitivity 63 breast cancer cell lines based on Dependency Map Consortium data re-analysis. Furthermore, list of genes was limited to those displaying specific expression in breast tumor cells as revealed in three large published single cell RNA-seq breast cancer datasets. Finally, we analyzed which of selected genes were significantly associated with overall survival (OS) in TNBC TCGA dataset.