The choroid plexus (ChP), located in each brain ventricle, produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier, but is under-characterized. Here, we combine single cell RNA-Seq and spatial mapping of RNA and proteins to construct an atlas of each ChP in the developing and adult mouse brain. Each ChP comprises of epithelial, endothelial, mesenchymal, immune, neuronal, and glial cells, with distinct subtypes, differentiation states and anatomical locations.Epithelial, fibroblast, and macrophage populations had ventricle-specific, regionalized gene expression programs across the developing brain. Key cell types are retained in adult, with loss of developmental signatures and maturation of ventricle-specific regionalization in the epithelial cells. Expression of cognate ligand-receptor pairs across cell subtypes suggests substantial cellcell interactions within the ChP. Our atlas sheds new light on the development and function of the ChP brain barrier system, and will facilitate future studies on its role in brain development, homeostasis and disease. of mice and profiled them by droplet-based single cell RNA-seq (scRNA-Seq, Methods, Fig. 1B, S1A). We partitioned the cells into clusters (Methods) followed by post hoc annotation by expression of canonical cell markers, which identified epithelial, mesenchymal (mural and fibroblast), endothelial, immune, neuron and glia-like cell types in each ChP from all ventricles ( Fig. 1C,D, S1B), and associated each cell type with marker genes (Fig. 1D). We used canonical markers to determine the spatial positions of each major cell type within the ChP tissue from each ventricle ( Fig. 1E, S1C). Notably, actively cycling cell subsets were present within each of the six major cell classes (Fig. S1D), and positionally enriched along the base of the ChP proximal to the brain based on staining for the proliferation marker Ki67 (Fig. S1E).
Neurogenic and gliogenic cell populations are found within all developing ChPsIn agreement with previous studies documenting the presence of neuronal cell bodies and neural innervation of the ChP 23 , we captured both neuronal (Tubb3 expressing) and glial-like (Slc1a3/EAAT1 expressing) populations in each developing ChP (Fig. S1F,G) in all developing ChPs (Fig. S1B). Subsets of glial-like cells expressed markers of glia-neuron progenitors/stemlike cells (Rspo2/3, Nes, Sox2, Fabp7, Hes1, Pax6) as well as oligodendrocyte precursor cells (OPCs, Olig1, Olig2) 24 (Fig. 1F, S1H). Subsets of neurons expressed markers of immediate progenitor (Eomes/Tbr2) and immature neurons (Neurod1/2, Dlx1/2, Fig. 1F, S1H), which also expressed a range of neuropeptides ( Fig. S1H). We confirmed the presence of differentiated neurons using whole LV ChP explants (Methods, Fig. 1G), leveraging the relatively simpler three-dimensional structure of LV ChP (Fig. 1A) to facilitate whole tissue imaging, reconstruction and cell identification. Moreover, some of the neuronal cell bodies with processes within the LV ChP stained positive for the neurotransmitter s...