Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [bulkRNA_isolatedBrainParenchymalMacrophages]

Microglia arise from yolk sac (YS) progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain unsettled. Here, we combine lineage tracing, pharmacological microglia depletion, and multi-omics profiling to define the ontogeny, identity, and function of MDM in the mouse brain. Despite sharing the parenchymal milieu, MDM display unique transcriptional and epigenetic landscapes distinct from YSM. Fate-mapping reveals that newly engrafted MDM transiently express CD206, echoing a developmental stage of embryonic microglial precursors. The engraftment and polarization of MDM are modulated by the CSF1R ligand IL 34 and the chemokine receptor CCR2. Furthermore, parabiosis and skull‑flap transplantation reveal that both blood and skull marrow supply the niche via distinct routes, yielding origin‑biased MDM states. Functionally, engraftment of MDM exacerbates cuprizone-mediated demyelination. Together, our study reveals the cellular dynamics of brain parenchymal macrophages at homeostasis and during turnover. We define the core molecular features and heterogeneous origins of MDM and imply their context-dependent roles in CNS pathology.