The muscle 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. Muscle cells are found in cardiac muscle, skeletal muscle and smooth muscle tissues. Cardiac muscle ensures the heart can pump blood and maintain blood pressure at all times, skeletal muscle provide stability and movement of the body contraction, and smooth muscle line blood vessels and hollow organs enabling them to contract to perform their specific functions. Vascular smooth muscle cells (vSMC) are specialized smooth muscle cells surrounding blood vessels on either side of the blood circuitry, artery/arteriole and vein/venule sides. The middle part of the blood circuitry, the vast network of capillaries, are instead ensheathed by pericytes. The overlap in gene expression between smooth muscle cells and pericytes is present, due to partly overlapping functions.

  • 890 elevated genes
  • 64 enriched genes
  • 275 group enriched genes
  • Main function: Contraction

Although, pericytes are not muscle cells, they are here grouped with vascular smooth muscle cells, since they both are sometimes referred to as mural cells.

Transcriptome analysis shows that 71% (n=14355) of all human proteins (n=20162) are detected in muscle cells and 890 of these genes show an elevated expression in any muscle cells compared to other brain cell types.

The muscle cell transcriptome

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

Cell type
Tissue origin
Cell type enriched
Group enriched
Cell type enhanced
Total elevated
Pericyte Amygdala, Basal ganglia, Cerebellum, Cerebral cortex, Hippocampus, Hypothalamus, Medulla oblongata, Midbrain, Pons, Spinal cord, Thalamus 25 208 328 561
Vascular associated smooth muscle cell Amygdala, Basal ganglia, Cerebellum, Cerebral cortex, Hippocampus, Hypothalamus, Medulla oblongata, Midbrain, Pons, Spinal cord, Thalamus 39 224 337 600
Any muscle cells 64 275 551 890

Pericytes and vascular smooth muscle cells (vSMC) share several molecular markers, due to shared functions. PDGFRB is a well known marker highly expressed by pericytes, as well a vSMC.


PDGFRB - cerebral cortex
05001,0001,5002,000nTPM
PDGFRB - Cerebral cortex

PDGFRB - cerebral cortex

By exploring the genes classified as group enriched, shared between pericytes and vSMC (157), several examples of shared expression can be found. Histidine rich calcium binding protein (HRC) and Caldesmon 1 (CALD1) are two examples, and by examining the immunohistochemical images of the Tissue Atlas, we can verify the location of CALD1 in both pericyte covered capillaries as well as smooth muscle cells in larger blood vessels, here shown in the cerebellum.


CALD1 - cerebellum
05001,0001,5002,0002,500nTPM
CALD1 - Cerebellum

CALD1 - cerebellum

CALD1 - cerebellum

Among the group enriched genes, there are also several genes shared with endothelial cells, such as CFH, FOXC1, VSIG2 and PGR.


Pericytes

As shown in Table 1, 561 genes are elevated in pericytes compared to other brain cell types. Pericytes play an important part of the blood brain barrier, so it is no surprise that there are several transporters among the gene with pericytes enriched expression profiles, such as SLC12A7, SLC6A12 and SLC30A10. Among the pericyte enriched genes, CD13, (also called ANPEP) is found.


ANPEP - cerebral cortex
020406080100nTPM
ANPEP - Cerebral cortex

ANPEP - cerebral cortex

As mentioned, pericytes and vSMC share many genes, for example UPB1, PTH1R, and ANPEP are highly expressed in pericytes, but also show some expression in vSMC.


Vascular associated smooth muscle cells

As shown in Table 1, 600 genes are elevated in smooth muscle cells compared to other cell types in the brain. Smooth muscle fibers are found throughout the body in blood vessels and hollow organs. Through their ability to apply pressure by involuntary muscle contraction, they can regulate essential bodily functions, such as blood pressure and bowel movement. During contraction, dense bodies are used by smooth muscle cells as anchoring points for the actin and intermediate filaments to exert force upon. Smooth muscle fibers are built up of smooth muscle cells attached by gap junctions to synchronize their response to stimuli. The smooth muscle cells in the brain are associated with the vasculature and found mainly on the artery/arteriolar side of the vascular circuitry.

Examples found in the list of genes classified as vSMC enriched are ITIH3, ACTA2, and the muscle specific protein PLN


ACTA2 - cerebral cortex
05001,0001,5002,000nTPM
ACTA2 - Cerebral cortex

ACTA2 - cerebral cortex


PLN - cerebral cortex
020406080100120nTPM
PLN - Cerebral cortex

PLN - cerebral cortex

Exploring the vascular 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 vascular cluster can be explored to further investigate subtypes of vascular cells across the different brain regions. Since this cluster includes all the vasculature cells, looking at the expression pattern of markers such as, CD34 for endothelial cells, CSPG4 for pericytes and PLN for smooth muscle cells you can clearly see the clustering of the vascular cell types. Or switch on and off the cell type selection in the selection panel to the left.

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