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The endothelial and mural cell-specific proteomeThe endothelial and mural cell transcriptomeVascular endothelial cellsPericytesVascular smooth muscle cellsBackground
Single nuclei brain methods
The endothelial and mural cell-specific proteomeThe human circulatory system consists of blood and lymphatic vessels that transport blood and lymph throughout the body. The vascular system is essential for maintaining tissue homeostasis by delivering oxygen and nutrients, removing metabolic waste products, and supporting immune surveillance. The inner surface of all blood and lymphatic vessels is lined by a single layer of endothelial cells, forming a selective barrier between the circulation and surrounding tissues. These cells regulate the exchange of substances between the blood or lymph and the surrounding environment, while also contributing to vascular integrity and function. Mural cells are specialized cells that surround blood vessels and provide structural support and regulate vascular function. They include vascular smooth muscle cells (vSMCs), which form layers around arteries, arterioles, veins, and venules, and pericytes, which are closely associated with the endothelial cells of capillaries and small vessels. While vascular smooth muscle cells primarily regulate vessel diameter and blood flow through contraction, pericytes contribute to capillary stability, vascular permeability, and local blood flow regulation. These two mural cell populations share several functional characteristics and exhibit partially overlapping gene expression profiles, reflecting their related roles in maintaining vascular structure and function. Transcriptome analysis shows that 68% (n=13658) of all human proteins (n=20162) are detected in endothelial and mural cells and 947 of these genes show an elevated expression in any endothelial and mural cells compared to other brain cell types.
The endothelial and mural cell transcriptomeThe snRNA-seq-based endothelial and mural cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in endothelial and mural cell type compared to other brain cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed endothelial and mural cell types compared to other grouped cell types.
Vascular endothelial cellsAs shown in Table 1, 561 genes are elevated in vascular endothelial cells compared to other cell types of the brain. The endothelial cells of the brain can be compared with the endothelial cells in peripheral tissues, where 179 genes are highlighted for an elevated (enriched and enhanced categories combined) expression in endothelial cells. 106 of those genes are overlapping. LCN6 and SELE being the only two genes classified as endothelial cell enriched in the peripheral cell type data as well as the single nuclei brain data. Below are barplots showing the expression profile in peripheral tissues and a brain regions.
There are several genes with enriched expression in brain endothelial cells, that also show expression in other cell types besides endothelial cells when comparing to the peripheral tissue types. Some examples are Fms related receptor tyrosine kinase 1 (FLT1), CD34 and Nitric oxide synthase 3 (NOS3). These three examples can be confirmed on protein level using immunohistochemistry and antibody labeling.
PericytesAs shown in Table 1, 269 genes show elevated expression in pericytes compared to other brain cell types. Pericytes play an important part of the blood brain barrier, so it is no surprise that there are several transporters among the gene with pericytes enriched expression profiles, such as SLC12A7, SLC6A12 and SLC30A10. Among the pericyte enriched genes, CD13, (also called ANPEP) is found.
Pericytes and vSMC share many genes, for example UPB1, PTH1R, and ANPEP are highly expressed in pericytes, but also show expression in vSMC. Vascular smooth muscle cellsAs shown in Table 1, 296 genes show elevated expression in vascular smooth muscle cells compared to other cell types in the brain. Smooth muscle fibers are found throughout the body in blood vessels and hollow organs. Through their ability to apply pressure by involuntary muscle contraction, they can regulate essential bodily functions, such as blood pressure and bowel movement. During contraction, dense bodies are used by smooth muscle cells as anchoring points for the actin and intermediate filaments to exert force upon. Smooth muscle fibers are built up of smooth muscle cells attached by gap junctions to synchronize their response to stimuli. The smooth muscle cells in the brain are associated with the vasculature and found mainly on the artery/arteriolar side of the vascular circuitry. Examples found in the list of genes classified as vSMC enriched are ITIH3, ACTA2, and the muscle specific protein PLN.
General mural functionPericytes and vascular smooth muscle cells (vSMC) share several molecular markers, due to shared functions. PDGFRB is a well known marker highly expressed by pericytes, as well a vSMC.
By exploring the genes classified as group enriched, shared between pericytes and vSMC (87), several examples of shared expression can be found. Histidine rich calcium binding protein (HRC) and Caldesmon 1 (CALD1) are two examples, and by examining the immunohistochemical images of the Tissue Atlas, we can verify the location of CALD1 in both pericyte covered capillaries as well as smooth muscle cells in larger blood vessels, here shown in the cerebellum.
Among the group enriched genes, there are also several genes shared with endothelial cells, such as CFH, FOXC1, VSIG2 and PGR. Exploring the vascular clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The vascular cluster can be explored to further investigate subtypes of vascular cells across the different brain regions. Since this cluster includes all the vasculature cells, looking at the expression pattern of markers such as, CD34 for endothelial cells, CSPG4 for pericytes and PLN for smooth muscle cells you can clearly see the clustering of the vascular cell types. Or switch on and off the cell type selection in the selection panel to the left. BackgroundSingle nuclei RNAseq dataSiletti K et al. (2023) published single nuclei RNA sequencing result, based on over 3 million cells from multiple brain regions, in Science magazine and created an interactive portal (The Human Brain Cell Atlas v1.0 ) available for single cell exploration across human gene expression in healthy brain cells. The Human Protein Atlas aims to generate a comprehensive resource representing the human body and its complexity, and with a need for better representation of the different cell types of the human brain, we imported the expression profiles re-processed the data by reclustering, naming and grouping cell clusters into main cell types. This way providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). Some of the supercluster names were kept thanks to good correlation and overlap with the new cell cluster annotation. The expression profile of the different clusters is shown for each of the 11 different brain regions. More details, related to number of M reads and number of cells per brain region/UMAP can be found here. The published cerebral cortex data is represented by a larger number of cells, and we only included a random selection of 500 thousand cells. In total, expression data for 2526725 brain cells is displayed in the Brain single nuclei dataset, for browsing the gene expression and provide easy comparison to cell type expression in peripheral tissues.
Relevant publications Uhlén M et al., Tissue-based map of the human proteome. Science (2015) |
The Human Protein Atlas project is funded
