Differentiation and specification of resident tissue macrophages [MARS-seq]

Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report that Erythro-Myeloid Progenitors generate pre-macrophages (pMacs) that simultaneously colonize the head and caudal embryo from embryonic day (E)9.5 in a chemokine-receptor dependent manner, to further differentiate into tissue F4/80+ macrophages. The core macrophage transcriptional program initiated in pMacs, is rapidly diversified in early macrophages as expression of transcriptional regulators becomes tissue-specific. For example, the preferential expression of the transcriptional regulator Id3 initiated in early fetal liver macrophages appears critical for Kupffer cell differentiation, as inactivation of Id3 causes a selective Kupffer cell deficiency that persists in adults. We propose that colonization of developing tissues by differentiating macrophages is immediately followed by their specification as they establish residence, hereby generating the macrophage diversity observed in post-natal tissues. RNA-sequencing of sorted macrophage cell populations (Mac) and progenitors (EMP, pMac) from various tissues and collected at different time points, including technical and biological replicates组织驻留巨噬细胞（tissue resident macrophages）是一类功能多样的细胞，其共同起源于胚胎中胚层。然而，调控其细胞特化的具体机制目前仍未阐明。本研究针对小鼠体内巨噬细胞的发育过程，开展了转录组学、分子生物学及原位时空分析。研究发现，红系髓系祖细胞（Erythro-Myeloid Progenitors, EMP）可分化产生前巨噬细胞（pre-macrophages, pMacs）；这类前巨噬细胞于胚胎第9.5天（E9.5）以趋化因子受体依赖的方式，同时定植于头部与尾部胚胎，并进一步分化为组织特异性F4/80阳性巨噬细胞。在前期巨噬细胞中启动的核心巨噬细胞转录程序，会在早期巨噬细胞阶段快速发生分化，此时转录调控因子的表达呈现显著的组织特异性。例如，转录调控因子Id3在早期胎肝巨噬细胞中优先表达，这一过程对库普弗细胞（Kupffer cell）的分化至关重要：敲除Id3会导致选择性库普弗细胞缺失，且该缺陷会持续至成年个体阶段。本研究提出，分化中的巨噬细胞定植发育中的组织后，会在定居的同时立即启动细胞特化程序，由此产生产后组织中观察到的巨噬细胞多样性。本研究对分选获得的不同组织、不同时间点的巨噬细胞群（Mac）以及祖细胞（红系髓系祖细胞EMP、前巨噬细胞pMac）开展了RNA测序，实验包含技术重复与生物学重复。