The smooth muscle-specific proteome

The smooth muscle transcriptome

Transcriptome analysis of the smooth muscle can be visualized with regard to specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the smooth muscle compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

• Tissue enriched: At least four-fold higher mRNA level in smooth muscle compared to any other tissues.
• Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue.
• Tissue enhanced: At least four-fold higher mRNA level in smooth muscle compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the smooth muscle compared to other tissues. As evident in Table 1, all genes elevated in smooth muscle are categorized as:

• Detected in single: Detected in a single tissue
• Detected in some: Detected in more than one but less than one third of tissues
• Detected in many: Detected in at least a third but not all tissues
• Detected in all: Detected in all tissues

Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in smooth muscle as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in smooth muscle as well as in all other tissues.

As shown in Figure 1, 112 genes show some level of elevated expression in smooth muscle compared to other tissues. The three categories of genes with elevated expression in smooth muscle compared to other organs are shown in Table 1.

Table 1. Number of genes in the subdivided categories of elevated expression in smooth muscle.

Protein expression of genes elevated in smooth muscle

In-depth analysis of the elevated genes in smooth muscle using antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different functional compartments including genes involved in contraction and calcium homeostasis.

Proteins related to contraction

The primary structural proteins related to the contraction in smooth muscle cells are myosin and actin filament proteins. Another protein family related to muscular contraction is the filamin family, regulating the binding of actin to membranous glycoproteins. The typical smooth muscle actin (ACTG2) and myosin (MYH11) are shown below as well as Filamin A (FLNA).

ACTG2
MYH11
FLNA

Proteins related to calcium homeostasis

Smooth muscle contraction is dependent on the level of intracellular calcium. Smooth muscle cells, like skeletal myocytes, store calcium in the sarcoplasmic reticulum until a neuronal impulse triggers calcium influx along the smooth muscle cells. Two genes involved in the regulation of muscle contraction via calcium interaction are Caldesmon 1 (CALD1) and Caponin 1 (CNN1).

CALD1
CNN1

Gene expression shared between smooth muscle and other tissues

There are 14 group enriched genes expressed in smooth muscle. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including smooth muscle, compared to all other tissues.

In order to illustrate the relation of smooth muscle tissue to other tissue types, a network plot was generated, displaying the number of genes with shared expression between different tissue types.

Figure 2. An interactive network plot of the smooth muscle enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of smooth muscle enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 4 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

As shown in figure 2, few genes elevated in smooth muscle fit the criteria for group enrichment. This is mainly attributed to the fact that smooth muscle is found in exceptionally many tissues, resulting in most of these genes being categorized as low tissue specificity genes. Smooth muscle shares the most elevated gene expression with heart and skeletal muscle. Examples of elevated gene expression shared between smooth, heart and skeletal muscle are TPM1 and DES.

TPM1 - Smooth muscle
TPM1 - Heart muscle
TPM1 - Skeletal muscle

DES - Smooth muscle
DES - Heart muscle
DES - Skeletal muscle

Another tissue that smooth muscle shares gene expression with is the breast where the contractile myoepithelial cells express genes otherwise specific for smooth muscle cells. Two genes elevated in smooth muscle and breast are CNN1 and MYLK which are both associated with contraction.

MYLK - Smooth muscle
MYLK - Breast

CNN1 - Smooth muscle
CNN1 - Breast

Smooth muscle function

Smooth muscle fibers can be found throughout the body in, among other places; blood vessels, eyes and hollow organs like the bladder, uterus, intestine and stomach. The fibers can exert force on the tissue they are in or around, enabling blood vessel constriction and movement of food through the intestine. Unlike skeletal and heart muscle, smooth muscle fibers do not contain Z-discs, but instead contain dense bodies which are used as the anchoring point for the actin and intermediate filaments.

Smooth muscle histology

Smooth muscle tissue can be either of the single- or multi-unit type. The single-unit smooth muscle tissue is composed of non-striated myocytes that form parallel muscle fibers. The smooth muscle cells are non-striated since the actin and myosin are more randomly organized inside the cell. Multiple smooth muscle cells organize themselves in fibers using gap junctions. Longitudinal as well as transverse fibers can be observed in stained sections. Multi-unit smooth muscle cells can often be found surrounding ducts and small blood vessels and have typically no gap junctions.

The typical smooth muscle cells are small spindle-shaped cells of approximately 30-200 μm long with a single central nucleus.

The activity of smooth muscle is regulated via the autonomous nervous system. Axons around the smooth muscle stimulate smooth muscle activity by secreting neurotransmitters through their boutons, also called varicosities. In single-unit smooth muscle tissue, the smooth muscle cells get stimulated as a group because they are linked via their gap junctions. This way, the nerve does not need to penetrate the muscle tissue, as is the case in the intestine. In contrast, in the multi-unit smooth muscle, the nerve axons go in between all the muscle cells and stimulate all cells separately. This is for example seen in the lens of the eye.

The histology of human smooth muscle including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.

Background

Here, the protein-coding genes expressed in smooth muscle are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in smooth muscle.

Transcript profiling was based on a combination of three transcriptomics datasets (HPA, GTEx and FANTOM5), corresponding to a total of 9332 samples from 113 different human normal tissue types. The final consensus normalized expression (NX) value for each tissue type was used for classification of all genes according to the tissue specific expression into two different categories, based on specificity or distribution.

Relevant links and publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Yu NY et al., Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. (2015)
PubMed: 26117540 DOI: 10.1093/nar/gkv608

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

Histology dictionary - the smooth muscle