Highlights d Flow cytometry, RNA-seq, and protein and image analyses reveal brain TME complexity d Glioma IDH mutation status and brain metastasis primary tumors shape the brain TME d Microglia and monocyte-derived macrophages exhibit multifaceted activation d TME immune cells show disease-and cell-type-specific expression patterns

SUMMARY Extensive transcriptional and ontogenetic diversity exists among normal tissue-resident macrophages, with unique transcriptional profiles endowing the cells with tissue-specific functions. However, it is unknown whether the origins of different macrophage populations affect their roles in malignancy. Given potential artifacts associated with irradiation-based lineage tracing, it remains unclear if bone marrow-derived macrophages (BMDM) are present in tumors of the brain, a tissue with no homeostatic involvement of BMDM. Here, we employed multiple models of murine brain malignancy and genetic lineage tracing to demonstrate that BMDM are abundant in primary and metastatic brain tumors. Our data indicate that distinct transcriptional networks in brain-resident microglia and recruited BMDM are associated with tumor-mediated education, yet are also influenced by chromatin landscapes established before tumor initiation. Furthermore, we demonstrate that microglia specifically repress Itga4 (CD49D), enabling its utility as a discriminatory marker between microglia and BMDM in primary and metastatic disease in mouse and human.