Increasing evidence suggests that macrophages critically shape brain homeostasis and disease.However, while the pivotal role of parenchymal microglia has gradually emerged, other brain-resident myeloid cells remain elusive. By dissecting border regions and combining single-cell RNA sequencing with high-dimensional cytometry, bulk RNA-sequencing, fate-mapping and microscopy, we reveal the remarkable diversity of non-parenchymal brain macrophages. Border-associated macrophages or BAMs residing in the dura mater, subdural meninges and choroid plexus consisted of distinct subsets that exhibited tissue-specific transcriptional signatures and underwent strong compositional changes during postnatal development. The gene regulatory networks of BAMs were identified and fundamentally differed from those of microglia. Importantly, we identified a unique non-homeostatic microglia-like population residing on the apical surface of the choroid plexus epithelium. Niche accessibility drove BAM ontogeny and determined whether embryonic macrophages were progressively replaced by bone marrow progenitors. Together, our work provides important insights into the biology of brain macrophages and offers a solid framework for future investigations.

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer‐reviewed by leading experts in the field, making this an essential research companion.

We have identified the first molecular components that control lateral root founder cell identity in the Arabidopsis root. These include an IAA28-dependent auxin signaling module in the basal meristem region that regulates GATA23 expression and thereby lateral root founder cell specification and root branching patterns.

Tissue-resident macrophages can derive from yolk sac macrophages (YS-Macs), fetal liver monocytes (FL-MOs), or adult bone-marrow monocytes (BM-MOs). The relative capacity of these precursors to colonize a niche, self-maintain, and perform tissue-specific functions is unknown. We simultaneously transferred traceable YS-Macs, FL-MOs, and BM-MOs into the empty alveolar macrophage (AM) niche of neonatal Csf2rb(-/-) mice. All subsets produced AMs, but in competition preferential outgrowth of FL-MOs was observed, correlating with their superior granulocyte macrophage-colony stimulating factor (GM-CSF) reactivity and proliferation capacity. When transferred separately, however, all precursors efficiently colonized the alveolar niche and generated AMs that were transcriptionally almost identical, self-maintained, and durably prevented alveolar proteinosis. Mature liver, peritoneal, or colon macrophages could not efficiently colonize the empty AM niche, whereas mature AMs could. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages and the plasticity of the mononuclear phagocyte system is largest at the precursor stage.