The vascular cell-specific proteome

The human circulatory system is composed of blood and lymphatic vessels that transport blood and lymph throughout the body. Our bodies rely heavily on our vascular system to function since it is the key as to how our tissues and organs receive and dispose of nutrients, gases, rest products and pathogens. The innermost layer of cells in a vessel is a single layer of squamous endothelial cells. Endothelial cells form the barrier between vessels and tissue in every type of vessel there is, from blood vessels such as arteries, veins and capillaries to lymphatic vessels. This barrier separates the blood or lymph from the rest of the vessel wall, creating an interface between the two, that enables control over the exchange of substances in and out of surrounding tissues. Transcriptome analysis shows that 59% (n=11688) of all human proteins (n=19670) are detected in vascular cells and 256 of these genes show an elevated expression in any vascular cells compared to other cell type groups.

  • 256 elevated genes
  • 2 enriched genes
  • 73 group enriched genes
  • Main function: Support and regulation of the circulatory system

The endothelial cell transcriptome

The scRNA-seq-based vascular cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific vascular cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:

  • Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type.
  • Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in endothelial cells.

Cell type Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Endothelial cells 2 73 181 256

Protein expression of genes elevated in endothelial cells

In-depth analysis using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of the elevated genes in endothelial cells .

Endothelial cells

As shown in Table 1, 256 genes are elevated in vascular endothelial cells compared to other cell types.

The innermost layer of cells in a vessel is a single layer of squamous endothelial cells. These cells have unique functions throughout the circulatory system such as aiding in upholding homeostasis, fluid filtration, blood vessel tone and hormone trafficking.

Proteins with elevated expression in endothelial cells include platelet and endothelial cell adhesion molecule 1 (PECAM1) and CD34 molecule (CD34), which are well-known endothelial markers used for diagnostics in clinical pathology, in particular for examining e.g. angiogenesis. PECAM1, also known as CD31, is a major component of cell junctions located between endothelial cells and also expressed on the surface of several immune cells. It is proposed to be involved in leukocyte migration, angiogenesis, and integrin activation. CD34 is a possible adhesion molecule suggested to mediate the attachment of stem cells to the bone marrow extracellular matrix or directly to stromal cells during early hematopoiesis. Another example is selectin E (SELE), which is thought to be expressed on endothelial cells stimulated by cytokines and bind blood leukocytes to facilitate the aggregation of these cells at sites of inflammation.

PECAM1 - lung

PECAM1 - lung

PECAM1 - lung

CD34 - placenta

CD34 - placenta

CD34 - placenta

SELE - lung

SELE - lung

SELE - lung

Endothelial cell function

The cardiovascular system is considered a closed system due to blood never leaving the vessels. Nutrients and oxygen are regulated via diffusion over the vascular endothelial layer into the interstitial fluid, which transport compounds to target cells and vice versa. In contrast, the lymphatic circulatory system is an open system that collects and transports waste products, damaged cells and bacteria over the endothelial layer from the interstitial fluid via lymphatic capillaries. These capillaries then drain the collected lymph into lymphatic vessels, which transport it through numerous lymphatic organs and ducts where waste products are filtered out. The filtered fluids are then returned to the blood circulation.

The vascular wall consists of three layers, the tunica intima, media and adventitia. The outermost layer (tunica adventitia), is mainly composed of collagen that anchors the vessels to nearby organs, giving them stability. The middle layer (tunica media) consists of smooth muscle cells, while the innermost layer (tunica intima) and consists of a single layer of squamous endothelial cells facing the lumen and a layer of elastic tissue called elastica interna.

Endothelial cells form the barrier between vessels and tissue in every type of vessel there is. Depending on vessel type the endothelial cells are classified as either vascular endothelial cells (in direct contact with blood) or lymphatic endothelial cells (in direct contact with lymph). Both types have unique functions throughout the circulatory system such as aiding in upholding homeostasis, fluid filtration, blood vessel tone and hormone trafficking. Any impaired function can lead to serious health issues.

The histology of organs that contain vascular cells, including interactive images, is described in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in vascular cells are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in different vascular cell types.

The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 13 different normal tissues, as well as analysis of human peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering and the clusters obtained were gathered at the end, resulting in a total of 192 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The scRNA-seq data from each cluster of cells was aggregated to average normalized protein-coding transcripts per million (pTPM) and the normalized expression value (nTPM) across all protein-coding genes. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively.

It should be noted that since the analysis was limited to datasets from 13 organs only, not all human cell types are represented. Furthermore, some cell types are present only in low amounts, or identified only in mixed cell clusters, which may affect the results and bias the cell type specificity.

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