Uncovering the immune microenvironmental atlas of breast cancer molecular subtypes based on single-cell transcriptomics

Breast cancer progression is closely linked to immune cells within the tumor microenvironment (TME), but the immune landscape differences across HER2-positive (HER2+), triple-negative (TNBC), and ER-positive (ER+) subtypes have yet to be systematically characterized. In this study, we characterized immune landscape differences across HER2-positive (HER2+), triple-negative (TNBC), and ER-positive (ER+) breast cancers using single-cell RNA sequencing data, focusing on T cells, macrophages, and B cells. Our analysis revealed that cytotoxic CD8 + T cells were more abundant in TNBC but showed signs of dysfunction. Macrophage subsets, including an NDUFB8 + population, exhibited divergent functional orientations across subtypes. B cells in TNBC exhibited functional alterations, characterized by a decreased proportion of plasmablasts and an increased proportion of memory B cells. Single-cell regulatory network inference and clustering (SCENIC) analysis predicted a set of subtype-specific candidate transcription factors (TFs), including E2F8 across all subtypes and ATF7 in HER2 + tumors, whose activity correlated with clinical outcomes. Finally, mapping multicellular communication networks revealed both conserved and subtype-specific signaling pathways. Together, these results present a detailed transcriptional landscape of immune heterogeneity in breast cancer and contribute novel insights that may inform the design of subtype-specific immunotherapies.