The Muscle cell-specific proteome

Muscle cells are found in skeletal muscle, cardiac muscle tissue and smooth muscle. Skeletal muscles provide stability and movement of the body through contraction, cardiac muscle ensures the heart can pump blood and maintain blood pressure at all times and smooth muscle line blood vessels and hollow organs enabling them to contract in order to perform their specific functions. Transcriptome analysis shows that 69% (n=13617) of all human proteins (n=19670) are detected in muscle cells and 1177 of these genes show an elevated expression in any muscle cells compared to other cell type groups.

  • 1177 elevated genes
  • 184 enriched genes
  • 192 group enriched genes
  • Main function: Contraction

The Muscle cell transcriptome

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

Cell type Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Cardiomyocytes 179 139 562 880
Smooth muscle cells 5 66 278 349
Any muscle cells 184 192 801 1177

Protein expression of genes elevated in muscle cells

In-depth analysis of the elevated genes in muscle cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different types of muscle cells: Cells in smooth muscle cells, cardiomyocytes and other muscle cells.


As shown in Table 1, 880 genes are elevated in cardiomyocytes compared to other cell types. To allow for the continuous beating and the long contraction period, the heart muscle is different from skeletal muscle. As a result, several proteins related to contraction are only expressed in the heart. The primary structural proteins in the heart myocytes related to contraction are myosin and actin filaments, forming a striated pattern that can be observed in electron microscopy. Another protein family related to muscular contraction is the troponin family, regulating the binding of myosin to actin via conformational changes dependent on the calcium ion concentration in the cells. Examples of proteins elevated in heart muscle cells include myoglobin (MB), which facilitates the transport of oxygen in muscles and ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 (ATP2A2), an enzyme catalyzing the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen.

MB - heart muscle

MB - heart muscle

MB - heart muscle

ATP2A2 - heart muscle

ATP2A2 - heart muscle

ATP2A2 - heart muscle

Smooth muscle cells

As shown in Table 1, 349 genes are elevated in smooth muscle cells compared to other cell types. 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 are able to 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 to each other using gap junctions to synchronize their response to stimuli. Examples of proteins elevated in smooth muscle cells include calponin 1 (CNN1), which is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity, and caldesmon 1 (CALD1), an actin- and myosin-binding protein implicated in the regulation of actomyosin interactions in smooth muscle and nonmuscle cells.

CNN1 - prostate

CNN1 - prostate

CNN1 - prostate

CALD1 - prostate

CALD1 - prostate

CALD1 - prostate

Other muscle cells

Muscle cell proteins are also found in various other locations in the body, primarily in skeletal muscle. Skeletal muscle refers to bundles of cells joined together in fibers. The muscle fibers are composed of myofibrils, repeated filaments of actin and myosin called sarcomeres. These are what formed the striated pattern recognizable in microscopic imaging. An example of a contraction related protein primarily elevated in skeletal muscle is myosin heavy chain 2 (MYH2), most commonly expressed in fast twitch muscle fibers. Heart and skeletal muscle both initiate contraction based on the levels of intracellular calcium. Unlike the cardiomyocytes, skeletal myocytes store calcium in the sarcoplasmic reticulum awaiting a neuronal impulse that triggers the influx of calcium along the myofilaments. A protein related to this calcium storage in the sarcoplasmic reticulum is calsequestrin 1 (CASQ1) and it has elevated expression specifically in skeletal myocytes.

MYH2 - skeletal muscle

CASQ1 - skeletal muscle

Muscle cell function

Muscle cells are found in several different organs throughout the body in three different subgroups: Skeletal muscle cells, smooth muscle cells and heart muscle cells. Their task is to provide stability and contractile capability which gives us the ability to move. All muscle cells form together in fibers, giving them the combined strength of the whole unit rather than just the one cell.

The skeletal muscle is one of the largest organs in the human body and up to 50% of the total body mass is skeletal muscle. It is a form of striated muscle tissue arranged in sarcomeres connected to bones by tendons. In contrast to heart muscle, another striated muscle similar in structure, the contraction of skeletal muscles is under voluntary control and initiated by impulses from the brain.

Cardiac muscle, found only in the heart, is responsible for pumping blood throughout the body. It cannot be controlled consciously like skeletal muscle. The cardiac muscle stimulates itself to contract and the signals from the brain only stimulate the rate of contraction rather than the action itself as with skeletal muscle. Cardiac muscle is striated, similar to skeletal muscle but connected at branching, irregular angled structures called intercalated discs.

Smooth muscle is located inside other organs like the stomach, intestines and blood vessels. They help them contract to move food through the gastrointestinal tract, blood back to the heart and many more things without any input from the conscious mind. Smooth muscle is different from skeletal and cardiac muscle in terms of structure, function and regulation of contraction. They are non-striated, which means they lack the sarcomeres that cardiomyocytes and skeletal muscles have. They contract slower than their skeletal counterparts but instead have the ability to do so with more power during longer periods of contraction while using less energy.

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


Here, the protein-coding genes expressed in muscle 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 muscle 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

UhlĂ©n 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

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

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

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