The Muscle cell-specific proteome
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 through contraction, and smooth muscle line blood vessels and hollow organs enabling them to contract to perform their specific functions.
Transcriptome analysis shows that 74% (n=14946) of all human proteins (n=20162) are detected in muscle cells and 1394 of these genes show an elevated expression in any muscle cells compared to other cell type groups. 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 the following types of muscle cells: cardiomyocytes, skeletal myocytes, smooth muscle cells.
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:
As shown in Table 1, 731 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, including the primary structural proteins myosin and actin filaments, which form 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), which is an enzyme catalyzing the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen.
As shown in Table 1, 509 genes are elevated in skeletal myocytes compared to other cell types. Skeletal myocytes form bundles joined together in fibers in the skeletal muscle. The muscle fibers are composed of myofibrils, repeated filaments of actin and myosin called sarcomeres. 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), which has elevated expression specifically in skeletal myocytes.
Smooth muscle cells
As shown in Table 1, 375 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 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. 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 non-muscle cells.
Muscle cell function
Muscle cells are found in several different organs throughout the body in three different subgroups: cardiomyocytes, skeletal muscle cells and smooth muscle cells. Their task is to provide stability and contractile capability which gives us the ability to move. All muscle cells form together fibers, giving them the combined strength of the whole unit rather than just the one cell.
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.
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.
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 long 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 29 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 557 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 29 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)