Simone Brioschi, Julia A Belk, Vincent Peng, Martina Molgora, Patrick Fernandes Rodrigues, Khai M Nguyen, Shoutang Wang, Siling Du, Wei-Le Wang, Gary E Grajales-Reyes, Jennifer M Ponce, Carla M Yuede, Qingyun Li, John M Baer, David G DeNardo, Susan Gilfillan, Marina Cella, Ansuman T Satpathy, Marco Colonna
Immunity, 14 February 2023

Genetic tools to target microglia specifically and efficiently from the early stages of embryonic development are lacking. We generated a constitutive Cre line controlled by the microglia signature gene Crybb1 that produced nearly complete recombination in embryonic brain macrophages (microglia and border-associated macrophages [BAMs]) by the perinatal period, with limited recombination in peripheral myeloid cells. Using this tool in combination with Flt3-Cre lineage tracer, single-cell RNA-sequencing analysis, and confocal imaging, we resolved embryonic-derived versus monocyte-derived BAMs in the mouse cortex. Deletion of the transcription factor SMAD4 in microglia and embryonic-derived BAMs using Crybb1-Cre caused a developmental arrest of microglia, which instead acquired a BAM specification signature. By contrast, the development of genuine BAMs remained unaffected. Our results reveal that SMAD4 drives a transcriptional and epigenetic program that is indispensable for the commitment of brain macrophages to the microglia fate and highlight Crybb1-Cre as a tool for targeting embryonic brain macrophages.