The vascular cell-specific proteome

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.

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.

Background

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.

Relevant links and publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Vieira Braga FA et al., A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. (2019)
PubMed: 31209336 DOI: 10.1038/s41591-019-0468-5

Chen J et al., PBMC fixation and processing for Chromium single-cell RNA sequencing. J Transl Med. (2018)
PubMed: 30016977 DOI: 10.1186/s12967-018-1578-4

Guo J et al., The adult human testis transcriptional cell atlas. Cell Res. (2018)
PubMed: 30315278 DOI: 10.1038/s41422-018-0099-2

Henry GH et al., A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Rep. (2018)
PubMed: 30566875 DOI: 10.1016/j.celrep.2018.11.086

MacParland SA et al., Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. (2018)
PubMed: 30348985 DOI: 10.1038/s41467-018-06318-7

Menon M et al., Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. (2019)
PubMed: 31653841 DOI: 10.1038/s41467-019-12780-8

Qadir MMF et al., Single-cell resolution analysis of the human pancreatic ductal progenitor cell niche. Proc Natl Acad Sci U S A. (2020)
PubMed: 32354994 DOI: 10.1073/pnas.1918314117

Solé-Boldo L et al., Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. (2020)
PubMed: 32327715 DOI: 10.1038/s42003-020-0922-4

Vento-Tormo R et al., Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. (2018)
PubMed: 30429548 DOI: 10.1038/s41586-018-0698-6