The mesenchymal cell-specific proteome
Mesenchymal cells are a diverse group of cells that originate from mesenchymal stem cells. The differentiated forms of mesenchymal cells have important roles in various types of connective tissues in which they perform a variety of functions, including; extracellular matrix organization, immune response, wound healing and formation of bone and cartilage.
Transcriptome analysis shows that 77% (n=15429) of all human proteins (n=20090) are detected in mesenchymal cells and 1202 of these genes show an elevated expression in any mesenchymal cells compared to other cell type groups. 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 the following types of mesenchymal cells: fibroblasts, hepatic stellate cells, peritubular cells and endometrial stromal cells.
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:
As shown in Table 1, 461 genes are elevated in fibroblasts compared to other cell types. Fibroblasts are found ubiquitously throughout the body except for the brain. They 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. An example of a protein with elevated expression in fibroblasts is platelet derived growth factor receptor alpha (PDGFRA), which is a receptor located on the surface of a wide range of cell types including fibroblasts. Another example is vimentin (VIM), which is a type III intermediate filament, a principal component of the cytoskeleton that is ubiquitously expressed in many cell types, including fibroblasts.
Hepatic stellate cells
As shown in Table 1, 352 genes are elevated in hepatic stellate (HSCs) cells compared to other cell types. HSCs are located in the liver between hepatocytes and sinusoids. HSCs are important for hepatic development, immune response, the liver’s response to injuries and can store vitamin A. An example of a protein elevated in hepatic stellate cells is c-type lectin domain family 4 member M (CLEC4M), which 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. Another example is c-type Lectin Domain Family 4 Member G (CLEC4G), which is a type II integral membrane protein expressed mainly by sinusoidal endothelial cells in the liver. CLEC4G has demonstrated to recognize activated T-cells and negatively regulate its immune response in the liver.
As shown in Table 1, 365 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. 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. Another example is fibulin-5 (FBLN5), which is a secreted protein that forms elastic fibers found in the extracellular matrix with various functions such as providing strength and flexibility of the connective tissue.
Endometrial stromal cells
As shown in Table 1, 338 genes are elevated in endometrial stromal cells compared to other cell types. The endometrial stromal layer is the largest compartment of the endometrium, which comprises uterine fibroblasts and a mix of immune cells. Through hormones and immune cells it controls the proliferation, remodeling and breakdown of the tissue during the menstrual or estrous cycle. The endometrial stromal cells can also quickly evolve into decidualized cells when activated by an implanting blastocyst. An example of a protein with elevated expression in endometrial stromal cells is homeobox A11 (HOXA11), which is is suggested to play an important role in proliferation, differentiation and receptivity of the tissue. Another example is matrix metallopeptidase 11 (MMP11), a secreted protein that belongs to the matrix metalloproteinase family, which is involved in the breakdown of extracellular matrix in both normal physiological processes and disease processes.
Other mesenchymal cells
There are additional mesenchymal cells in the body that currently lack scRNA-seq data at Human Protein Atlas.
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.
The Mesenchymal cell function
Fibroblasts, hepatic stellate cells, peritubular cells and endometrial stromal cells all originate from mesenchymal stem cells and can therefore show morphologically similar fusiform structure, but they can also demonstrate similar functions since they all reside in connective tissue. The primary function of fibroblasts is to maintain the structural integrity within the connective tissue through the synthesis of collagen fibers, glycosaminoglycans and elastic fibers. In addition to extracellular matrix organization they also take part in the response to tissue injury.
Endometrial stromal cells are specialized in the sense that they can proliferate, remodel or break down the tissue depending on the menstrual or estrous cycle. Furthermore, endometrial stromal cells are also able to become decidualized, which is essential during pregnancy for the survival and development of the embryo.
Hepatic stellate cells reside in the liver in a quiescent state, where they can be activated to respond to hepatic injury. Apart from producing extracellular matrices they are a storage place for vitamin A.
Peritubular cells surround the seminiferous tubules and are accepted to have a contractile function to help the move of spermatozoa and fluid. However, further studies are required to fully understand their function.
Other differentiated types of mesenchymal cells such as chondroblasts, osteoblasts and adipocytes have important specialized functions, including bone formation and energy storage.
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 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.
Relevant links and publications
Uhlén M et al., Tissue-based map of the human proteome. Science (2015)