The mesenchymal cell-specific proteome

The function of the brain, defined as the central nervous system, is to receive, process and execute the coordinated higher functions of perception, motion and cognition that signify human life. Fibroblasts are sparse in the brain, compared to most other tissue types. Fibroblasts has recently gotten more attention within brain reserach (Duan L et al. (2024) and Lendahl U et al. (2022)) thanks to single cell sequencing results showing the molecular heterogeneity of brain fibroblasts related to meninges, perivascular space, and choroid plexus.

  • 665 elevated genes
  • 64 enriched genes
  • 234 group enriched genes
  • Main function: Tissue support

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. 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.

Transcriptome analysis shows that 70% (n=14123) of all human proteins (n=20162) are detected in mesenchymal cells and 665 of these genes show an elevated expression in any mesenchymal cells compared to other brain cell types.

The mesenchymal cell transcriptome

The snRNA-seq-based mesenchymal cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in mesenchymal cell type compared to other brain 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 within the brain.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type within the brain.
  • 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 within the brain.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed mesenchymal cell types.
Cell type
Tissue origin
Cell type enriched
Group enriched
Cell type enhanced
Total elevated
Fibroblast Amygdala, Basal ganglia, Cerebellum, Cerebral cortex, Hippocampus, Hypothalamus, Medulla oblongata, Midbrain, Pons, Spinal cord, Thalamus 64 234 367 665

Brain fibroblasts

Fibroblasts are found through out all the brain regions, and found surrounding larger blood vessels on both arterial and venule side of the blood circuitry. As show in Table 1, 64 genes are classified as fibroblast enriched when comparing gene expression within the brain cells. In the list of enriched genes, there are several plasma proteins, such as C1S and ITIH2, both with high expression in hepatocytes in peripheral tissue comparison. AKR1C2 is an enzyme with high expression in hepatocytes, and is classified as fibroblast enriched, when comparing brain cell expression. C1S and AKR1C2 are both detected by immunohistochemistry in the perivascular space, surrounding larger blood vessels, in line with the location of fibroblasts in the brain.


C1S - basal ganglia
050100150200250300nTPM
C1S - Basal ganglia

C1S


AKR1C2 - cerebral cortex
050100150200nTPM
AKR1C2 - Cerebral cortex

AKR1C2

GUCY2F is a plasma protein, with high expression in retina, but when comparing gene expression within the brain it is highlighted as fibroblast enriched. Several transporters, such as SLC6A20, SLC22A2, and SLC26A7 are all listed as fibroblast enriched when comparing expression across brain cell types.

Known fibroblasts markers, such as COL1A1 and COL3A1, both show highest expression in the brain fibroblasts, with additional expression in vascular smooth muscle cells. The OPC marker PDGFRA, is also a marker for fibroblasts.

Exploring the fibroblast cluster

In the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The fibroblast cluster can be explored to further investigate subtypes of fibroblasts across the different brain regions.

Background

Single nuclei RNAseq data

Siletti K et al. (2023) published single nuclei RNA sequencing result, based on over 3 million cells from multiple brain regions, in Science magazine and created an interactive portal (The Human Brain Cell Atlas v1.0 ) available for single cell exploration across human gene expression in healthy brain cells. The Human Protein Atlas aims to generate a comprehensive resource representing the human body and its complexity, and with a need for better representation of the different cell types of the human brain, we imported the expression profiles and grouped them based on our cell type- strategy (providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). We based the cell type clusters on the 31 superclusters, as well as the provided assigned cell types, and the data is shown as 34 different "supercluster cell types". The expression profile of the different clusters are shown for each of the 11 different brain regions. More details, related to number of M reads and number of cells per brain region/UMAP can be found here. The published cerebral cortex data is represented by a larger number of cells and we only included a random selection of 500 thousand cells. In total, expression data for 2526725 brain cells is displayed in the Brain single nuclei resource, for browsing the gene expression and profide easy comparison to cell type expression in peripheral tissues.

Relevant 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

Sjöstedt E et al., An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. (2020)
PubMed: 32139519 DOI: 10.1126/science.aay5947

Siletti K et al., Transcriptomic diversity of cell types across the adult human brain. Science. (2023)
PubMed: 37824663 DOI: 10.1126/science.add7046