Single-cell RNA sequencing reveals the heterogeneity of tumor-associated macrophages in three subtypes of breast cancer

Abstract

Abstract Breast cancer (BC) is a disease characterized by molecular heterogeneity and has been classified into different subtypes. The heterogeneity of breast cancer is influenced by both the mutations of cancer cells and the significant heterogeneity in the tumor microenvironment. Tumor-associated macrophages (TAMs) play a significant role in the progression and heterogeneity of different subtypes of BC, as they are the most abundant tumor-infiltrating immune cells. Nevertheless, there remains a dearth of investigation to reveal the heterogeneity and potential functions of TAMs in different subtypes of BC. This work elucidated the variations in marker genes, drug sensitivity, functions and cellular communication among the TAMs in the three subtypes of BC (TNBC, luminal, HER2) using published single-cell RNA sequencing data from 24 BC patients, and identification of specific marker genes of each TAMs were experimentally verified by co-culturing M0 macrophages with three subtypes of BC cells. In detail, we found that TNBC-TAMs exhibited elevated expression levels of CCL3L3, luminal-TAMs expressed high levels of SPP1, and HER2-TAMs highly expressed CXCL8. The expression of these marker genes was linked to differences in the sensitivity of TAMs to anticancer drugs, and identifying the marker genes expressed by diverse TAMs in different BC subtypes could potentially optimize the guidance of personalized treatment. Furthermore, the ligand-receptor pair analysis highlighted that the heterogeneous TAMs can activate different pathways via VEGFA/FLT1, SPP1/CD44 and SPP1/ITGB1 ligand-receptor pairs in three subtypes of BC, respectively. In conclusion, we demonstrated for the first time that the expression patterns and unique role of heterogeneous TAMs in regulating the biological functions of different tumor microenvironments, and by targeting heterogeneous TAMs in different BC subtypes may provide a novel insight into more precise and individualised treatment strategies for patients with different subtypes of BC.