Single-cell transcriptomics reveals functionally specialized vascular endothelium in brain
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Germany
- Cells-in-Motion Interfaculty Centre (CiMIC), University of Münster, Germany
Figures
Figure 1 with 2 supplements
Single-cell RNA-seq analysis of non-neuronal cell types in mouse cerebral cortex.
(A) Uniform manifold approximation and projection (UMAP) plot of 29,406 myelin-depleted single cells from murine cerebral cortex. Colors represent endothelial cells (EC), microglia (Micro), …
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Figure 1—source data 1
Source data for Figure 1C.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig1-data1-v2.xlsx
Figure 1—figure supplement 1
Analysis of vascular and perivascular cell types in mouse cerebral cortex using single-cell RNA-seq.
(A) Workflow for the enrichment of blood vessel-associated cell types from cerebral cortex of juvenile (P10), adult (7–11 weeks), aged (18 months), and experimental autoimmune encephalomyelitis (EAE;…
Figure 1—figure supplement 2
Expression of major cell type marker genes.
(A) Violin plots displaying number of genes (nFeature_Gene), number of unique molecular identifiers (UMI; nFeature_UMI), and percentage of mitochondrial genes (percent.mito) in juvenile, adult, and …
Figure 2 with 3 supplements
Endothelial cell (EC) subclustering and identification of intercellular adhesion molecule-1 (ICAM-1+) endothelial population.
(A–B) Uniform manifold approximation and projection (UMAP) plots of 10,741 adult and aged mouse ECs. Colors represent cell subclusters (A) or age groups (B), respectively. Box indicates ICAM-1+ …
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Figure 2—source data 1
Source data for Figure 2E.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Subclustering analysis of endothelial cells (ECs) during postnatal development.
(A–B) Uniform manifold approximation and projection (UMAP) plots of juvenile ECs. Colors represent EC subclusters (A) or cell cycle phases (B). (C) Trajectory analysis of juvenile ECs depicting …
Figure 2—figure supplement 2
Differential gene expression analysis of adult and aged endothelial cells (ECs).
(A) Scatter dot plot of differentially expressed genes (yellow dots, Padj <0.001) between ECs from adult and aged samples (407 genes). The 25 most significant genes for each sample (red dots) are …
Figure 2—figure supplement 3
Subclustering analysis of endothelial cells (ECs) during homeostasis.
(A) Uniform manifold approximation and projection (UMAP) plots depicting the expression of representative marker genes for each subcluster: Alkbh5 (Venous), Tmsb10 (CapV), Alpl (CapA), and Fbln5 …
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Figure 2—figure supplement 3—source data 1
Source data for panel E.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig2-figsupp3-data1-v2.xlsx
Figure 3 with 1 supplement
Localization of perivascular macrophages (PVMs).
(A) Heatmap and expression dot plot for top differentially expressed genes between microglia and PVMs. Dot size represents the percentage of cells expressing each gene, and color keys indicate …
Figure 3—figure supplement 1
Distinct populations of microglia and perivascular macrophages (PVMs).
(A) Uniform manifold approximation and projection (UMAP) plots depicting the expression of the known myeloid cell markers Cd68, Fcgr3, Cx3cr1, and Aif1. Color key represents the scaled expression. (B…
Figure 4 with 1 supplement
Perivascular macrophage (PVM) heterogeneity.
(A) Uniform manifold approximation and projection (UMAP) plot of 1725 PVMs from juvenile, adult, and aged mice distributed into Lyve1+ and MHCII+ subclusters. (B) Split UMAP plots of PVMs from …
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Figure 4—source data 1
Source data for Figure 4H.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
Differentially expressed genes in perivascular macrophage (PVM) subtypes.
(A) MA plot of differentially expressed genes between Lyve1+ and MHCII+ PVM subtypes. Blue dots, p-adjusted value <0.001; Red dots, p-adjusted value <0.001, and Log2 fold change >0.5. (B) Violin …
Figure 5 with 4 supplements
Gene expression changes in endothelial cells (ECs) by experimental autoimmune encephalomyelitis (EAE).
(A) Uniform manifold approximation and projection (UMAP) plots of 11,810 ECs from adult and EAE mice. Colors represent each EC subcluster (left) or condition (right). (B) UMAP plots depict Icam1 and …
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Figure 5—source data 1
Source data for Figure 5D.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig5-data1-v2.xlsx
Figure 5—figure supplement 1
Single-cell RNA-seq analysis of experimental autoimmune encephalomyelitis (EAE) mice.
(A) Uniform manifold approximation and projection (UMAP) plots of 26,106 myelin-depleted cells from adult and EAE cerebral cortex. Colors represent each cell type. (B) Dot plot displaying the top …
Figure 5—figure supplement 2
Subclustering of endothelial cells (ECs) from adult and experimental autoimmune encephalomyelitis (EAE) mice.
(A) Bar plots indicating the frequency of EC subtypes in healthy adult and EAE brain. (B) Dot plot showing the expression of top subcluster-specific genes, with the dot size representing the …
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Figure 5—figure supplement 2—source data 1
Source data for panel A.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig5-figsupp2-data1-v2.xlsx
Figure 5—figure supplement 3
Intercellular adhesion molecule-1 (ICAM-1) expression in brain cortical parenchyma upon experimental autoimmune encephalomyelitis (EAE).
(A) Confocal images showing ICAM-1 immunofluorescence in cortex of control, EAE onset, and peak mice. Arrowheads indicate expansion of ICAM-1 staining from reactive endothelial venules (REVs) into …
Figure 5—figure supplement 4
Differentially expressed genes between adult and experimental autoimmune encephalomyelitis (EAE) endothelial cells (ECs).
(A) Volcano plots depicting differentially expressed genes between adult and EAE EC subtypes. Blue dots, p-adjusted value <0.001; red dots, p-adjusted value <0.001, and Log2 fold change >0.5. (B) …
Figure 6 with 1 supplement
Experimental autoimmune encephalomyelitis (EAE)-induced changes in perivascular macrophages (PVMs).
(A) Representative immunohistochemistry images for CD206+ PVMs and ICAM-1+ vessels in control and EAE brain cortical parenchyma. Scale bars, 100 μm. (B) Frequency of CD206+ PVMs associated to ICAM-1+…
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Figure 6—source data 1
Source data for Figure 6B.
- https://cdn.elifesciences.org/articles/57520/elife-57520-fig6-data1-v2.xlsx
Figure 6—figure supplement 1
Cell cycle phases and localization of perivascular macrophages (PVMs) in experimental autoimmune encephalomyelitis (EAE).
(A) Uniform manifold approximation and projection (UMAP) plot and pie chart of PVMs in adult and EAE brain cortex in the indicated cell cycle phases. (B) CD31 and CD206 immunostaining of brain …
Figure 7 with 2 supplements
Interactions between different endothelial cell (EC) subpopulations and blood-brain barrier (BBB) cell types.
(A) Overview of potential ligand-receptor interactions for CapV, reactive endothelial venule (REV), and venous EC populations in adult and experimental autoimmune encephalomyelitis (EAE) based on …
Figure 7—figure supplement 1
Interactome of blood-brain barrier (BBB) cell types in postcapillary venules.
Overview of differential ligand-receptor interactions between reactive endothelial venule (REV) endothelial cell (EC), perivascular macrophage (PVM), mural cell (Mural), and astroependymal cells …
Figure 7—figure supplement 2
Schematic summary of experimental findings.
Schematic summary of proposed findings. Reactive endothelial venules (REVs) are specialized cellular gateways in the CNS vasculature with associated perivascular macrophages (PVMs) as gatekeepers in …
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