Integration of single-cell and spatial transcriptomics reveals stromal cell features in breast cancer

Stromal cells are key components of the breast cancer tumor microenvironment, yet their heterogeneity, spatial organization, and interactions with tumor and immune cells remain incompletely defined. We integrated single-cell RNA sequencing data from 233,518 non-immune stromal cells across 349 patients with spatial transcriptomic data from 51 patients. This analysis identified 36 fibroblast, endothelial, and mural cell subsets with distinct transcriptional programs, spatial distributions, and functional associations. ABCA8 + lipid-associated fibroblasts were observed at tumor margins, showed predicted interactions with malignant cells, and were associated with exhaustion-associated T-cell phenotypes. CCL19 + inflammatory fibroblasts showed spatial patterns associated with tertiary lymphoid structure formation, whereas tumor-associated pericytes showed predicted interactions with PGF + tip endothelial cells that may be involved in extracellular matrix deposition and vascular remodeling. Together, these findings provide a high-resolution stromal atlas of breast cancer, resolving stromal subtypes, spatial context, and potential intercellular communication. This resource provides a framework for investigating stromal contributions to tumor progression and immune regulation, although further experimental validation is required.