A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. [bulk RNA-Seq]

While the roles of parenchymal microglia in brain homeostasis and disease are fairly clear, other brain-resident myeloid cells remain less understood. By dissecting border regions and combining single-cell RNA sequencing with high-dimensional cytometry, bulk RNA-sequencing, fate-mapping and microscopy, we reveal the diversity of non-parenchymal brain macrophages. Border-associated macrophages (BAMs) residing in the dura mater, subdural meninges and choroid plexus consisted of distinct subsets with tissue-specific transcriptional signatures, and their cellular composition changed during postnatal development. BAMs exhibited a mixed ontogeny and subsets displayed distinct self-renewal capacities upon depletion and repopulation. Single-cell and fate-mapping analysis both suggested there is a unique microglial subset residing on the apical surface of the choroid plexus epithelium. Finally, gene network analysis and conditional deletion revealed IRF8 as a master regulator that drives the maturation and diversity of brain macrophages. Our results provide a framework for understanding host-macrophage interactions in the healthy and diseased brain. 4 replicates of ME-MHCII-high, 4 replicates of ME-MHCII-int, 4 replicates of PM, 4 replicates of NCPM and 4 replicates of NMG. We compared these samples with the AMF Cre- and KC Cre- samples of GSE117081尽管实质内小胶质细胞在脑稳态与疾病进程中的作用已较为明晰，但其他脑驻留髓系细胞的相关功能与机制仍有待深入阐释。本研究通过剖析脑边界区域，并将单细胞RNA测序（single-cell RNA sequencing）与高维流式细胞术、批量RNA测序（bulk RNA-sequencing）、命运图谱（fate-mapping）技术及显微镜成像相结合，系统揭示了非实质脑巨噬细胞的多样性。定位于硬脑膜、硬脑膜下脑膜及脉络丛的边界相关巨噬细胞（border-associated macrophages, BAMs）可划分为多个具有组织特异性转录特征的独特亚群，其细胞组成在出生后发育过程中发生动态改变。BAMs呈现出混合的个体发生起源，且各亚群在细胞清除与再增殖过程中表现出截然不同的自我更新能力。单细胞测序与命运图谱分析均证实，存在一类独特的小胶质细胞亚群定植于脉络丛上皮的顶侧表面。最后，通过基因网络分析与条件性基因敲除实验，本研究确认IRF8是驱动脑巨噬细胞成熟与多样性形成的核心调控因子。本研究结果为解析健康与疾病状态下宿主-巨噬细胞互作机制提供了系统性的研究框架。本研究包含ME-MHCII-high、ME-MHCII-int、PM、NCPM及NMG各4次生物学重复。我们将上述样本与GSE117081数据集的AMF Cre-及KC Cre-样本进行了对比分析。