Microglia Display Heterogeneous Initial Responses to Disseminated Tumor Cells

Brain metastases are frequent and often lethal complications of advanced cancers. Microglia, resident immune cells of the brain, are known to exert both anti- and protumor functions in late-stage metastases; however, their response during the initial outgrowth of metastatic lesions is not well characterized. Understanding how heterogeneous microglial subgroups are regulated in the developing tumor microenvironment could pave the way for therapeutic strategies to eliminate metastatic tumors at an early stage. In this study, we used a combination of in vivo fate map imaging, single-cell RNA sequencing, and a holographic photoconversion-based technique (opto-omics) to track tumor fate and early microglial responses over time in the same animals during the colonization of disseminated tumor cells. The microglial population was transcriptionally and morphologically heterogeneous, comprising both pro- and antitumor subsets. Genetic and pharmacologic perturbations revealed that microglial phenotypes could be shifted by inhibiting TGFβ signaling or by deleting the tumor cell surface antigens CD24 and CD47. These findings reveal targetable plasticity in early-stage microglial responses to brain metastasis and suggest that harnessing prophagocytic microglial states may offer a therapeutic window before systemic immunosuppression becomes dominant. SIGNIFICANCE: In vivo imaging with optical labeling and transcriptomics reveals heterogeneous microglia and identifies that CD24/CD47 loss or TGFβ modulation alters subpopulation fate, exposing a therapeutic window and actionable targets for brain metastases. See related commentary by Vallebuona and Smalley, p. 1345. ©2025 The Authors; Published by the American Association for Cancer Research.