Integration of single-cell and bulk transcriptome analyses unravels a macrophage-based gene signature for prognostication and treatment in triple-negative breast cancer

Abstract

Objective As a dominant component within the tumor microenvironment, macrophages exert an essential role in almost all aspects of triple-negative breast cancer (TNBC). This work explored macrophage-associated signature genes for prognostication and treatment for TNBC. Methods Single-cell (GSE180286) and bulk transcriptome profiles (TCGA-TNBC, GSE96058 and GSE45255) were analyzed by executing multiple computational approaches. The expression of signature genes was verified in breast cancer cells (MDA-MB-231, and MCF-7) and mammary epithelial cells (MCF10A) through RT-qPCR and western blot. After RNA interference or overexpression, wound scratch assay was implemented. Results A single-cell map of the microenvironment of non-TNBC and TNBC was depicted. Both at the single-cell and bulk levels, macrophages exhibited the higher abundance in TNBC versus non-TNBC. A macrophage-based gene signature was built, containing CTSD, CTSL, ELK4, HSPA8, and XRCC4. High risk score was predictive of worse prognostic outcomes. Based upon external validation, the signature could reliably predict patient prognosis, notably one-year survival. High-risk patients were more responsive to immunotherapy. The aberrant expression of CTSD, CTSL, ELK4, HSPA8, and XRCC4 was proven in breast cancer cells and mammary epithelial cells. Knockdown of XRCC4 attenuated migrative abilities of MDA-MB-231, MCF-7, and MCF10A cells, with opposite findings for overexpressed CTSD, CTSL, and HSPA8. Conclusions Altogether, a novel macrophage-based gene signature was proposed for estimating survival outcomes and treatment response in TNBC. The aberrant expression of the signature genes contributed to tumor aggressiveness. Our findings exert a positive impact on future clinical research involving macrophages in TNBC.