Integrated single-cell and bulk RNA sequencing analysis identifies the predictive signature for prognosis and neoadjuvant chemotherapy responses in breast cancer

Abstract

Abstract Neoadjuvant chemotherapy (NAC) is a well-established treatment modality for locally advanced breast cancer (BC). However, it can also result in severe toxicities while controlling tumors. Therefore, reliable predictive biomarkers are urgently needed to objectively and accurately predict NAC response. This study aims to integrate single-cell and bulk RNA-seq data to identify key regulatory factors that contribute to NAC response in BC patients. In specific, we construct an NAC prognostic risk model based on the nine identified prognostic NAC response-related genes and demonstrate its clinical independence and generalizability. Additionally, we explore the underlying cancer hallmarks and microenvironment features of this NAC response-related risk score, and further assess the potential impact of risk score on drug response. In summary, our study involved the development of prognostic biomarkers for NAC in BC, which was accomplished through the integration of single-cell and bulk RNA data. The results of our study are of crucial significance in the prediction of the efficacy of NAC in BC, and may have implications for the clinical management of this disease.