UCSF

Macrophage (MØ) identities are coupled to specialized functions and local niches of residence. The diverse roles of macrophages in the breast, including epithelial development and remodeling, immune surveillance, and angiogenesis, imply a spatial organization of distinct transcriptional states. Yet, how this heterogeneity is spatially arranged in the normal human breast at microanatomical resolution remains largely uncharacterized. Here, we leveraged Xenium in situ to delineate two discrete macrophage populations. We identify a TREM2+ population intercalated between basal-myoepithelial cells and analogous to previously identified ductal niche macrophages in the mouse mammary gland. FOLR2+ macrophages broadly distribute across the interlobular stroma, and unbiased niche analyses further resolved a periepithelial subpopulation that localized to the intralobular stroma. Spatially weighted communication inference highlights differentially enriched signaling patterns between TREM2+ and FOLR2+ macrophage subsets with their surrounding microenvironment. Orthogonal spatial co-expression analyses of ligand-receptor pairs converged on CX3CL1-CX3CR1, in which TREM2+ macrophages interact with the neighboring epithelia. Collectively, these findings show that macrophage heterogeneity in the normal human breast is organized across transcriptional and microanatomical axes, thereby providing a spatially resolved framework for the resident mammary immune microenvironment.