RNA sequencing data of CNS-associated macrophages (CAMs) isolated from brains of Mrc1-CreERT2 mice

All tissue resident macrophages of the central nervous system (CNS), including parenchymal microglia as well as CNS-associated macrophages (CAMs) such as meningeal (mMF) and perivascular macrophages (pvMF) are part of the CNS endogenous innate immune system that acts as the first line of defense during infections or trauma. It has been suggested that microglia and all CAM subsets are derived from prenatal cellular sources in the yolk sac that were defined as early erythromyeloid progenitors. However, the precise ontogenetic relationships, the underlying transcriptional programs and the molecular signals that drive the development of distinct CAMs subsets in situ are poorly understood. Using novel fate mapping systems, single-cell profiling and cell-specific mutants, we show that only mMF and microglia share a common prenatal progenitor. In contrast, pvMF originate from perinatal mMF only after birth in an integrin-dependent manner. Furthermore, the establishment of pvMF critically requires the presence of vascular smooth muscle cells. In summary, our data reveal a novel precisely timed process in distinct anatomical niches for the establishment of CNS macrophage subsets. Overall design: Bulk transcriptomics data of FACS sorted CAMs isolated from brain tissue of 3-4 individual mice per genotype (from wild type and Mrc1-CreERT2 lines) and RNA expression levels between genotypes were compared.

中枢神经系统（Central Nervous System, CNS）的所有组织驻留巨噬细胞，包括脑实质小胶质细胞，以及脑膜巨噬细胞（meningeal macrophage, mMF）、血管周围巨噬细胞（perivascular macrophage, pvMF）这类中枢神经系统相关巨噬细胞（CNS-associated macrophages, CAMs），均属于中枢神经系统内源性先天免疫系统的组成部分，可在感染或创伤时充当机体第一道防线发挥防御作用。
已有研究表明，小胶质细胞与所有CAM亚群均起源于卵黄囊中的产前细胞类群，即早期红髓系祖细胞。然而，驱动不同CAM亚群在原位发育的确切个体发育关系、潜在转录程序及分子信号通路，目前尚未完全明晰。
本研究采用新型命运图谱系统、单细胞谱分析及细胞特异性突变体模型，证实仅mMF与小胶质细胞共享同一产前祖细胞。与之相反，pvMF仅在出生后由围产期的mMF分化而来，且该过程依赖整合素信号通路。此外，pvMF的建立严格依赖血管平滑肌细胞的存在。
综上，本研究数据揭示了在不同解剖微环境中，中枢神经系统巨噬细胞亚群建立的新型精准时序调控过程。
实验设计概述：对不同基因型（野生型及Mrc1-CreERT2品系）小鼠脑组织中经荧光激活细胞分选（Fluorescence-Activated Cell Sorting, FACS）纯化的CAMs进行批量转录组测序，每个基因型使用3-4只个体小鼠，随后比较不同基因型间的RNA表达水平差异。