The endothelial cell-specific proteome

Transcriptome analysis shows that 68% (n=13636) of all human proteins (n=20090) are detected in endothelial cells and 331 of these genes show an elevated expression in any endothelial cells compared to other cell type groups. In-depth analysis of the elevated genes in endothelial cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in endothelial cells.

The endothelial cell transcriptome

The scRNA-seq-based endothelial cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in endothelial cells 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.

Endothelial cells

As shown in Table 1, 331 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 is 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) 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 endothelial cells, including interactive images, is described in the Protein Atlas Histology Dictionary.

Background

Here, the protein-coding genes expressed in endothelial 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 endothelial cell types.

The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 25 tissues and peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering, resulting in a total of 444 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 mean normalized protein-coding transcripts per million (nTPM) 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 25 tissues and PBMC 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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