Differentiation and specification of resident tissue macrophages [ID3-KO RNA-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 ID3+/- and ID3-/- Kupffer cells组织驻留巨噬细胞（tissue resident macrophages）是一类功能多样的细胞，拥有共同的胚胎中胚层起源。然而，调控其特化的分子机制仍未明确。本研究针对小鼠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。我们发现，红系髓系祖细胞（Erythro-Myeloid Progenitors）可生成前巨噬细胞（pre-macrophages，简称pMacs）；此类前巨噬细胞可通过趋化因子受体依赖的方式，于胚胎发育第9.5天（E9.5）同时定植于头部与尾部胚胎，随后进一步分化为F4/80阳性（F4/80+）组织驻留巨噬细胞。在早期巨噬细胞中，于前巨噬细胞内启动的核心巨噬细胞转录程序会快速发生分化，此时转录调控因子的表达呈现组织特异性特征。例如，在早期胎肝巨噬细胞中启动的转录调控因子Id3的偏好性表达，对库普弗细胞（Kupffer cell）的分化至关重要：Id3功能失活会引发选择性的库普弗细胞缺失，且该缺陷会持续至成年个体阶段。我们提出，分化中的巨噬细胞定植于发育中的组织后，会在建立驻留状态的同时立即启动特化过程，由此形成产后组织中观察到的巨噬细胞多样性。本研究对ID3杂合（ID3+/-）与ID3敲除（ID3-/-）库普弗细胞开展了RNA测序（RNA-sequencing）。