The ductus deferens-specific proteome

The ductus deferens transcriptome

Transcriptome analysis of the ductus deferens 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 ductus deferens compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

• Tissue enriched: At least four-fold higher mRNA level in ductus deferens 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 ductus deferens 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 ductus deferens compared to other tissues. As evident in Table 1, all genes elevated in ductus deferens 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 ductus deferens as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in ductus deferens as well as in all other tissues.

As shown in Figure 1, 115 genes show some level of elevated expression in smooth muscle compared to other tissues. The three categories of genes with elevated expression in ductus deferens compared to other organs are shown in Table1.

Table 1. Number of genes in the subdivided categories of elevated expression in ductus deferens.

Gene expression shared between ductus deferens and other tissues

There are 34 group enriched genes expressed in ductus deferens. 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 ductus deferens, compared to all other tissues.

In order to illustrate the relation of ductus deferens 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 ductus deferens enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of ductus deferens 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 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Ductus deferens share most group enriched gene expression with the seminal vesicle and epididymis. Two genes that are group enriched in both ductus deferens and seminal vesicle are SEMG1 and SEMG2 The proteins that are encoded by the genes SEMG1 and SEMG2 are the predominant proteins in semen. These secreted proteins are involved in the formation of a gel matrix that encases ejaculated spermatozoa. The preproproteins of SEMG1 and SEMG2 are proteolytically processed by the prostate-specific antigen (PSA) protease to generate multiple peptide products that exhibit distinct functions. One of these peptides is an antimicrobial peptide with antibacterial activity. This proteolysis process also breaks down the gel matrix and allows the spermatozoa to move more freely.

SEMG1 - seminal vesicle
SEMG2 - seminal vesicle

The first line of defense against invading pathogens is the antimicrobial proteins. A vast majority of these proteins are produced and secreted by immune cells, phagocytic, dendritic cells and by all cavity-lining epithelial cells in the body. The beta defensin gene family are diverse, antimicrobial and antiviral peptides that have evolved through repeated gene duplication, and are found in most vertebrates. One of the defensins in the epididymis, which also is group enriched in ductus deferens, is DEFB132.

Another gene that is group enriched in ductus deferens and epididymis is EDDM3A. The protein product of this gene is synthesized and secreted by epididymal epithelial cells and is a part of the microenvironment that is taking care of the sperm maturation processes.

DEFB132 - epididymis
EDDM3A - epididymis

The ductus deferens anatomy and function

The ductus deferens primary function is to transport sperm cells from the epididymis to the ampulla close to the seminal vesicles and out to the urethra. The ductus deferens also store sperm before ejaculation. The tubes are approximately 30 centimeters long and begin at the end of epididymis posterior to the scrotum and ascend to the urinary bladder where it passes and descend towards the prostate and seminal vesicles. The end of the ducts is called the ampulla, which is a region where the tubes get wider in diameter. The walls within the ductus deferens consist of smooth muscle with ciliated pseudostratified columnar epithelium and elastin fibers bundles. These muscles contract with peristaltic movements when ejaculation is anticipated and is forcing the sperm cells forward. Before the sperm enters the urethra it collects fluids from the prostate and the seminal vesicle to complete the ejaculate. The sperm can be stored in the ducts awaiting ejaculation and old, unused sperm cells will be broken down and absorbed in the ducts.

Background

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

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