The vagina-specific proteome

The vagina is the most exterior part of the female reproductive tract. It consists of an elastic muscular tube lined with a lumenal mucosa that extends from the vulva to the uterine cervix and functions as a receiver of male gametes (sperm) and an exit channel for menstrual flows and the infant during childbirth. The mucosa of the vaginal canal consists of a folded non-keratinized and glycogenated squamous epithelium. The mucosa and other parts of the vagina undergo continuous transformation according to female sex hormone levels. Transcriptome analysis shows that 73% (n=14401) of all human proteins (n=19670) are expressed in the vagina and 91 of these genes show an elevated expression in the vagina compared to other tissue types.

  • 91 elevated genes
  • 3 enriched genes
  • 17 group enriched genes
  • Vagina has most group enriched gene expression in common with esophagus


The vagina transcriptome

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

  • Tissue enriched: At least four-fold higher mRNA level in vagina 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 vagina 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 vagina compared to other tissues. As evident in Table 1, all genes elevated in vagina 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

A. Specificity

B. Distribution

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


As shown in Figure 1, 91 genes show some level of elevated expression in the vagina compared to other tissues. The three categories of genes with elevated expression in vagina compared to other organs are shown in Table 1. In Table 2, the 3 enriched genes are defined.

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

Distribution in the 37 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Tissue enriched 0012 3
Group enriched 01151 17
Tissue enhanced 0232325 71
Total 0342928 91

Table 2. The 3 genes with enriched expression in vagina. "Tissue distribution" describes the transcript detection (NX≥1) in vagina as well as in all other tissues. "mRNA (tissue)" shows the transcript level in vagina as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in vagina and the tissue with second highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
HSPH1 heat shock protein family H (Hsp110) member 1 Detected in all 286.1 5
FKBP4 FK506 binding protein 4 Detected in all 209.6 4
FAM167B family with sequence similarity 167 member B Detected in many 91.1 4


Protein expression of genes elevated in vagina

In-depth analysis of the elevated genes in vagina using antibody-based protein profiling allowed us to visualize where these proteins are expressed within the vagina, including epithelial cells and stromal cells.

Proteins related to expression in vaginal stratified squamous epithelium

Non-keratinized stratified squamous epithelium, like the one found in the vagina, consists of multiple layers of cells, with superficial layers of squamous (flat) cells and underlying replenishing cells. The innermost layer of epithelial cells, in contact with the underlying stroma, consist of cuboidal multipotent stem cells, called basal cells. Basal cells divide to renew the entire epithelial lining which is under repeated stress and abrasion from the environment causing the superficial layers to slough off. The daughter cells of basal cells slowly transition into squamous cornified (rigid) dead cells with a high content of glycogen as they become increasingly superficially located. Examples of proteins with elevated expression in the basal cell layer of the vaginal epithelial lining include keratin 15, KRT15, a member of the fibrous structural keratin proteins which makes the epithelium resistant to mechanical stress and damage, and heat shock protein family A (Hsp70) member 1B, HSPA1B, which is a member of a group of protein-stabilizing heat shock proteins and plays an important role in hormonal regulation of the vaginal mucosa.


KRT15

HSPA1B

Examples of proteins with elevated expression in the intermediate and superficial cell layer of the vaginal epithelial lining include SERPINB3, which may be involved in epithelial proliferation, and cornifelin, CNFN, a part of the insoluble cornified cell envelope of stratified squamous epithelia.


SERPINB3

CNFN

Proteins related to expression in vaginal stroma

The vaginal stroma (lamina propria) consists of a loose fibrovascular tissue which lacks glands and is rich in elastic fibers, nerves and blood vessels. Examples of genes with elevated expression in vaginal stromal cells include FBLN1 and AEBP1. Fibulin 1 (FBLN1) is a secreted glycoprotein that becomes incorporated into the fibrillar extracellular matrix through binding with laminin and nidogen. It also plays a role in coagulation via fibrinogen binding. Adipocyte enhancer-binding protein 1 (AEBP1) is believed to be a positive regulator of collagen fibrillogenesis and involved in the organization and remodeling of the extracellular matrix.


FBLN1

AEBP1


Gene expression shared between vagina and other tissues

There are 17 group enriched genes expressed in vagina. 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 vagina, compared to all other tissues.

In order to illustrate the relation of vagina 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 vagina enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of vagina 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.


Vagina shares most group enriched gene expression with other squamous epithelial tissues, characterized by having luminal epithelium layers, such as the esophagus, tongue and cervix. Such genes are exemplified above in the analysis of elevated genes in vaginal epithelium and stroma. An example of shared group enriched gene expression between vagina and esophagus is keratin 6a (KRT6A), another member of the fibrous structural keratin proteins. Even though vaginal and esophageal epithelia is categorized as non-keratinized, both still utilize keratin proteins to create rigidity and structural integrity. It is however significantly less keratin than produced in the water-resistant stratum corneum layers of the skin.


KRT6A - Vagina

KRT6A - Esophagus

Claudin 17, CLDN17, is a member of the claudin family and is group enriched in vagina and esophagus. Claudins are integral membrane proteins and components of tight junction strands that serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial cell sheets.


CLDN17 - Vagina

CLDN17 - Esophagus


Vagina function

The vagina is the most exterior part of the female reproductive tract. It consists of an elastic muscular tube that extends from the vulva to the uterine cervix and functions as a receiver of male gametes (sperm) and an exit channel for menstrual flows and the infant during childbirth. The vaginal mucosa is maintained at a low pH together with the vaginal symbiotic microflora to protect both the vagina and the upper female reproductive tract from invasive microbes. Low pH is achieved through a symbiotic relationship with lactobacillus type bacteria. Availability of glycogen, produced in high concentration in the epithelial cells under the control of estrogen levels, creates a suitable environment for glycogen-metabolizing lactobacillus, that in turn produce the acidic environment.

During sexual intercourse the folded vaginal mucosa stimulates the male penis to ejaculation, facilitating discharge and migration of the male zygote (sperm) from the male testis, out through the penile urethral opening, into the vagina and on through the cervical opening and further towards the area of fertilization in the fallopian tubes. The vaginal mucosa is lubricated by secretions produced during sexual arousal, pregnancy and menstruation to protect the mucosa from damage. The production and composition of vaginal secretions are different compared to cervical glandular secretions. The vaginal mucosa lacks mucus glands. Secretions are instead produced by the squamous epithelium through plasma seepage facilitated by vasocongestion (increased vaginal fluid pressure).

At childbirth, the cervix is effaced (thinned and dilated), allowing for the infant to pass on through to the vagina, which through its elasticity can increase its width according to the size of the infant to facilitate passage and birth.


Vagina histology

The vagina is a tubular canal that extends from the vestibule (entrance) of the vulva to the uterine cervix. The vagina is posterior to the urinary bladder and anterior to the rectum with an angle of more than 90 degrees between the axis of the vagina and that of the uterus. In the adult, the vagina measures about 9 cm in length. In the upper part of the vagina, there are small recesses between the vaginal walls and the vaginal portion of the cervix (portio vaginalis) termed fornices.

The vaginal wall consists of three layers: mucosa, muscularis and adventitia. The mucosa is folded and, the thickness of the folds varies according to location and hormonal stimulation. The mucosal lining is a stratified squamous epithelium that is normally glycogenated and nonkeratinizing. The basal cell layer consists of a single layer of columnar cells. The nuclei are uniform and hyperchromatic and surrounded by a scant cytoplasm. The parabasal layer consists of two to five layers of cuboidal squamous cells with central, hyperchromatic nuclei. The intermediate and superficial layers are of variable thickness and cells contain moderate to large amounts of cytoplasm. The nuclei of cells in the intermediate layer have a dispersed chromatin structure, whilst those from the superficial layer have pyknotic nuclei. Variable amounts of glycogen may be present in the intermediate and superficial cell layers. The glycogen first appears in the perinuclear region. The lamina propria lies beneath the squamous epithelium and is built up by a loose fibrovascular stroma, containing elastic fibers, nerves and blood vessels. Large, stellate or spindle shaped stromal cells with occasional cells exhibiting multinucleation and/or multilobation may be seen.

The muscularis consists of poorly delineated, inner circular and outer longitudinal bundles of smooth muscle. The adventitia comprises a thin coat of dense connective tissue and contains the lymphatic and venous plexuses and nerve bundles.

The histology of human vagina 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 vagina are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in vagina.


Transcript profiling was based on a combination of three transcriptomics datasets (HPA, GTEx and FANTOM5, corresponding to a total of 483 samples from 37 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 - vagina