The salivary gland-specific proteome

The salivary gland is an exocrine gland with the main function to produce saliva. The salivary gland also produces digestive enzymes that break down different nutrients. The main salivary gland is the parotid gland in addition to the sublingual, submandibular gland and numerous smaller salivary glands that debouch into the mouth. The salivary glands contain both serous and mucous glands as well as ductal cells. Transcriptome analysis shows that 71% (n=14348) of all human proteins (n=20162) are expressed in the salivary gland and 300 of these genes show an elevated expression in the salivary gland compared to other tissue types.

  • 300 elevated genes
  • 43 enriched genes
  • 80 group enriched genes
  • Salivary gland has most group enriched gene expression in common with intestine

The salivary gland transcriptome

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

  • Tissue enriched: At least four-fold higher mRNA level in salivary gland 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 salivary gland compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the salivary gland compared to other tissues. As evident in Table 1, all genes elevated in salivary gland 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 salivary gland as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in salivary gland as well as in all other tissues.

As shown in Figure 1, 300 genes show some level of elevated expression in the salivary gland compared to other tissues. The three categories of genes with elevated expression in salivary gland compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in salivary gland are defined.

Table 1. The number of genes in the subdivided categories of elevated expression in salivary gland.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Tissue enriched 62791 43
Group enriched 039392 80
Tissue enhanced 24010629 177
Total 810615432 300

Table 2. The 12 genes with the highest level of enriched expression in salivary gland. "Tissue distribution" describes the transcript detection (nTPM≥1) in salivary gland as well as in all other tissues. "mRNA (tissue)" shows the transcript level in salivary gland as nTPM values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in salivary gland and the tissue with the second-highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
PRB2 proline rich protein BstNI subfamily 2 Detected in some 11778.1 3818
HTN1 histatin 1 Detected in some 47123.7 2616
PRB3 proline rich protein BstNI subfamily 3 Detected in some 13472.2 1882
BPIFA2 BPI fold containing family A member 2 Detected in some 6665.1 1611
HTN3 histatin 3 Detected in some 131918.2 1103
PRB1 proline rich protein BstNI subfamily 1 Detected in some 6182.2 992
CST5 cystatin D Detected in some 2090.3 961
PRR27 proline rich 27 Detected in some 1071.7 959
SMR3B submaxillary gland androgen regulated protein 3B Detected in many 210537.1 948
STATH statherin Detected in some 8851.0 925
PRH2 proline rich protein HaeIII subfamily 2 Detected in some 22313.4 909
MUC7 mucin 7, secreted Detected in many 25265.8 877

Protein expression of genes elevated in salivary gland

In-depth analysis of the elevated genes in the salivary gland using antibody-based protein profiling allowed us to create a map of where these proteins are expressed within the salivary gland with respect to serous or mucous cells secretion and expression in ductal epithelial cells.

Proteins specifically expressed in serous salivary glands

Serous salivary glands are found mainly in the parotid gland and secrete granules that are rich in proteins that have high amylase activity. Four examples of proteins expressed in serous salivary glands are CA6, CST2, PIP and AMY1B.





Proteins specifically expressed in mucous salivary glands

Mucous salivary glands are found mainly in the sublingual gland and are rich in glycoproteins. A group of proteins specific for mucous salivary glands are the mucins like for example MUC5B, MUC7 and MUC16. These mucins have a protective property by promoting clearance of bacteria in the oral cavity, as well as aiding in mastication, speech and swallowing.




Proteins specifically expressed in salivary ducts

The ducts of the salivary gland are essential for passage of the saliva from the glands to the oral cavity. They also have ion-pumping activity, modifying the composition of the secretion from the acinar cells. Two examples of proteins expressed in salivary ducts are SLC5A5 and SLC26A9. SLC5A5 is important for iodine uptake in the thyroid but its function in the salivary gland is unknown. SLC26A9 is a chloride ion channel regulated by WNK kinases.



Gene expression shared between salivary gland and other tissues

There are 80 group enriched genes expressed in salivary gland. 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 salivary gland, compared to all other tissues.

To illustrate the relation of salivary gland tissue to other tissue types, a network plot was generated, displaying the number of genes with a shared expression between different tissue types.

Figure 2. An interactive network plot of the salivary gland enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of salivary gland 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.

The salivary gland shares many group enriched gene expression with the intestine and pancreas. One of the genes enriched in the salivary gland and intestine is FAM3D, a protein involved in regulating metabolism.

FAM3D - salivary gland

FAM3D - duodenum

The pancreas is an organ with an exocrine function, with high similarity to salivary gland function. An example of group enriched gene expression shared between the pancreas and salivary gland is BHLHA15, a transcription factor regulating acinar cell function.

BHLHA15 - salivary gland

BHLHA15 - pancreas

Salivary gland function

The main function of the salivary glands is to wet and lubricate the oral cavity and its contents, in order to initiate the digestion of carbohydrates using the enzyme amylase. Saliva also has an important buffer function and plays a role in taste. Moreover, salivary glands are involved in the defense against microorganisms, secreting various protective substances. There are three pairs of major salivary glands: parotid glands, submandibular (submaxillary) glands and sublingual glands. In addition to the main salivary glands, 600-1,000 minor mucous secreting glands are present in the palate, nasal and oral cavity.

Salivary gland histology

The major salivary glands include paired parotid, submandibular and sublingual glands. They produce saliva, a mixture of serous and mucous secretions containing water, proteins, glycoproteins and electrolytes, secreted into the oral cavity. Saliva is rich in enzymes that initiate the breakdown of the food we eat and lubricates ingested food to facilitate swallowing.

The salivary glands are surrounded by connective tissue capsules, which also divide the gland into lobes and lobules and contain larger arteries and veins. The salivary glands are tubuloacinar glands, with branched ducts ending in a sac like dilations (acini) where the excretory cells are located. The secretory units of the salivary gland are the acini, consisting of an acinus, connected to a merging tubular network of intercalated ducts, striated ducts and finally the excretory duct.

The acini can be of serous, mucous or mixed type. The serous acini secrete a fluid that is rich in proteins, with triangular shaped cells that appear darkly stained with hematoxylin-eosin (HE) and have basally located nucleus. The basal portion of the glands appear darker stained due to the presence of rough endoplasmic reticulum, while the apical portion stains lighter due to the presence of secretory granules. Mucous acini can easily be distinguished from serous acini, as the cells of the mucous acini are paler and contain flattened nuclei located towards the base of these cells.

Intercalated ducts, with low cuboidal epithelium, lead away from the acini. In serous secreting glands these small ducts are more evident and secrete bicarbonate and absorb chloride ion from the acinar secretions.

Striated ducts connect the intercalated ducts with the larger excretory ducts. They are lined with simple cuboidal or simple columnar epithelium, depending on the size of the duct. They are termed striated ducts because the basal plasma membrane folds into the lower portion of the cell, resulting in a striated appearance. The nuclei are spherical and located in the center of the cell.

Excretory ducts are located in the interlobular and interlobar connective tissue. As the diameter of the ducts increase, the epithelium changes from simple cuboidal to pseudostratified columnar or stratified cuboidal. Excretory ducts eventually open into the oral cavity.

Within the salivary glands there are also aggregations of adipocytes. Fat is stored in adipocytes as a single large lipid droplet. In routine embedding of histological specimens, the lipid is dissolved, leaving a large unstained and empty appearing space within each adipocyte. The nucleus is flattened and displaced by the lipid droplet to the periphery of the cell.

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


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

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 50 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the 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

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 salivary gland