The mesenchymal cell-specific proteome

Mesenchymal stem cells (MSCs) also known as mesenchymal stromal cells or medicinal signaling cells are multilineage cells with the ability of self-renewal that can differentiate into a variety of cell types. MSCs exist in all tissues including the perivascular space, where they are called pericytes. Transcriptome analysis shows that 72% (n=14245) of all human proteins (n=19670) are detected in mesenchymal cells and 1177 of these genes show an elevated expression in any mesenchymal cells compared to other cell type groups.

  • 1177 elevated genes
  • 42 enriched genes
  • 247 group enriched genes
  • Main function: Tissue support

The mesenchymal cell transcriptome

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

Cell type Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Fibroblasts 3 53 186 242
Ito cells 30 113 409 552
Peritubular cells 9 130 424 563
Any mesenchymal cells 42 247 888 1177

Protein expression of genes elevated in mesenchymal cells

In-depth analysis of the elevated genes in mesenchymal cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of mesenchymal cells: in fibroblasts, ito cells and peritubular cells in testis.


As shown in Table 1, 242 genes are elevated in fibroblasts compared to other cell types. Fibroblasts have slim elongated spindle-shaped cell bodies with oval nuclei and are found ubiquitously throughout the body except for the brain. Fibroblasts are the main and prototypic mesenchymal cell type that produces collagen fibers, glycosaminoglycans, reticular and elastic fibers, which constitute the basic structural framework of connective tissue. Besides their structural function in extracellular matrix synthesis, they also play a critical role in the response to a tissue injury such as immune response and wound healing. Platelet derived growth factor receptor alpha (PDGFRA), is a receptor located on the surface of a wide range of cell types including fibroblasts. Vimentin (VIM) is a type III intermediate filament, a principal component of the cytoskeleton that is ubiquitously expressed in many cell types, including fibroblasts.

PDGFRA - skin

PDGFRA - skin

PDGFRA - skin

VIM - skin

VIM - skin

VIM - skin

Ito cells - liver

As shown in Table 1, 552 genes are elevated in ito cells compared to other cell types. Ito cells, also known as hepatic stellate cells (HSCs) have spindle-shaped cell bodies with an elongated nucleus and are located in the liver between hepatocytes and sinusoids. Ito cells are important for hepatic development, immune response, the liver’s response to injuries and can store vitamin A. In a normal healthy liver, the ito cells are in a quiescent state, waiting for activation, and when an injury occurs these cells can differentiate into myofibroblasts that contribute to responses such as inflammation, angiogenesis, contraction, and production of extracellular matrix, which can lead to an increasing level of fibrosis in the liver. The ito cells can also act as antigen-presenting cells. Genes elevated in Ito cells include C-type lectin domain family 4 member M (CLEC4M), which encodes a protein that is highly expressed on the liver sinusoidal endothelium and is involved in the innate immune system by recognizing numerous evolutionarily divergent pathogens ranging from parasites to viruses.

CLEC4M - liver

CLEC4M - liver

CLEC4M - liver

Peritubular cells - testis

As shown in Table 1, 563 genes are elevated in peritubular cells compared to other cell types. The spermatogenesis takes place in the seminiferous tubules, a compartment that is surrounded by a wall made of peritubular cells and extracellular matrix. This structure is approximately 5-7 layers of thin spindle-shaped cells, where the innermost layer and outermost layers differ. The innermost layers are made up of smooth-muscle-like cells that express the protein desmin, while the outermost layers consist of connective tissue types of cells with elevated expression of vimentin. The peritubular cells are involved in the contraction of the seminiferous tubules to help move the spermatozoa. Genes elevated in peritubular cells include smooth muscle alpha actin (ACTA2), encoding a protein highly expressed in the peritubular structure.

ACTA2 - testis

ACTA2 - testis

ACTA2 - testis

Other mesenchymal cells

Adipocytes are cells that are derived from MSCs and are specialized in storing energy as fat through adipogenesis. Adipocytes are classified as white or brown, where white fat is the major cell type in adipose tissue and important for systemic metabolic homeostasis, like insulin sensitivity. Adipose tissue is also recognized as an important endocrine organ since adipocytes may secrete a large number of growth factors and hormones. Hormone-sensitive lipase (LIPE) is a hormone-sensitive lipase that in adipose tissue primarily hydrolyzes stored triglycerides to free fatty acids.

LIPE - soft tissue

Osteoblasts are cuboidal mononuclear cells specialized in bone development and homeostasis by synthesizing bone matrix components that are progressively mineralized through regulation of calcium and phosphate in the area. Type 1 collagen (encoded by the genes COL1A1 and COL1A2) is the most abundant ECM protein produced by osteoblasts.

Chondroblasts are cells important in forming chondrocytes and cartilage matrix, and once the chondroblasts are embedded in the cartilage matrix they are called chondrocytes. These cells are localized in the perichondrium, which is a dense irregular layer of connective tissue that surrounds the cartilage. Type II collagen (COL2A1) is the major component of the cartilage matrix. Aggrecan (ACAN) is an integral part of the extracellular matrix in cartilaginous tissue and it withstands compression in cartilage.

ACAN - soft tissue

The Mesenchymal cell function

One of the criteria that must be fulfilled to be called a mesenchymal stem cell, is the ability to differentiate into osteoblasts, adipocytes and chondroblasts in vitro, but several studies have shown that MSCs can differentiate into several other types of cells e.g. myoblasts and fibroblasts. Since MSCs can give rise to fibroblasts, they have a function in the maintenance and reparation of the tissues through depositing extracellular matrix components. They can also respond to different inflammatory factors secreted by activated immune cells and tissue cells and therefore possess immunomodulatory features.

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


Here, the protein-coding genes expressed in mesenchymal 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 mesenchymal 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

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PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Uhlén M et al., The human secretome. Sci Signal. (2019)
PubMed: 31772123 DOI: 10.1126/scisignal.aaz0274

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PubMed: 31209336 DOI: 10.1038/s41591-019-0468-5

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

Solé-Boldo L et al., Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. (2020)
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Vento-Tormo R et al., Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. (2018)
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Wang L et al., Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function. Nat Cell Biol. (2020)
PubMed: 31915373 DOI: 10.1038/s41556-019-0446-7