The urinary bladder-specific proteome

The main function of the urinary bladder is to store and excrete urine made by the kidneys. The urinary bladder consists of three distinct layers; urothelium, adventitia and muscularis propria. The urothelial layer can be further subdivided into three different cell types; umbrella cells, intermediate cells and basal layer cells. Transcriptome analysis shows that 71% (n=14221) of all human proteins (n=20090) are expressed in the urinary bladder and 188 of these genes show an elevated expression in the urinary bladder compared to other tissue types.

  • 188 elevated genes
  • 5 enriched genes
  • 33 group enriched genes
  • Urinary bladder has most group enriched gene expression in common with lymphoid tissue

The urinary bladder transcriptome

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

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

As shown in Figure 1, 188 genes show some level of elevated expression in urinary bladder compared to other tissues. The three categories of genes with elevated expression in urinary bladder compared to other organs are shown in Table 1. In Table 2, the 5 enriched gene is defined.

Table 1. The number of genes in the subdivided categories of elevated expression in urinary bladder.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Tissue enriched 0320 5
Group enriched 07260 33
Tissue enhanced 42710514 150
Total 43713314 188

Table 2. The 5 genes with enriched expression in urinary bladder. "Tissue distribution" describes the transcript detection (nTPM≥1) in urinary bladder as well as in all other tissues. "mRNA (tissue)" shows the transcript level in urinary bladder as nTPM values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in urinary bladder and the tissue with second-highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
UPK2 uroplakin 2 Detected in some 70.1 28
MMP13 matrix metallopeptidase 13 Detected in some 12.9 12
TNFAIP6 TNF alpha induced protein 6 Detected in many 196.0 7
IL23A interleukin 23 subunit alpha Detected in some 44.5 5
IGHV1-58 immunoglobulin heavy variable 1-58 Detected in many 204.7 4

Protein expression of genes elevated in urinary bladder

In-depth analysis of the elevated genes in the urinary bladder using antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different functional compartments including proteins specifically expressed in the urothelium.

Proteins expressed in umbrella cells

Out of the 188 urinary bladder elevated genes, four are specifically expressed in the umbrella cells. These four genes belong to the UPK family (uroplakins), which are transmembrane proteins forming so-called urothelial plaques. Urothelial plaques both prevent the umbrella cells from dissociating from the cell-cell conjunctions and bacterial disturbance.



Proteins expressed in intermediate/basal layer cells

The intermediate cells are the progenitors of the umbrella cells, while the basal layer cells likely originate from a distinct population. Out of the 188 urinary bladder elevated genes, two are specifically expressed in the intermediate/basal layer cells. KRT17 may be a marker of basal cell differentiation in complex epithelia and regulate epithelial cell growth. It has been shown to be upregulated in several cancer types, including urothelial carcinoma.


Gene expression shared between urinary bladder and other tissues

There are 33 group enriched genes expressed in urinary bladder. 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 urinary bladder, compared to all other tissues.

To illustrate the relation of urinary bladder 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 urinary bladder enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of urinary bladder 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 5 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Urinary bladder shares group enriched gene expression with kidney and liver, among others. One example of a protein with group enriched expression in the urinary bladder, kidney and liver is UGT1A6, an enzyme belonging to the UGT family which has been shown to convert carcinogenic compounds to safe metabolites. In fact, reduced expression of all the UGT1A isotopes has been observed in urothelial carcinoma, which further suggests a protective role.

UGT1A6 - urinary bladder

UGT1A6 - kidney

UGT1A6 - liver

Urinary bladder function

The urinary bladder, together with the urethra, forms the lower urinary tract. There are two important functions of the urinary bladder; storage and emptying of the urine. This process is orchestrated by a complex interaction between the urinary tract and the nervous system. During the filling phase, the smooth muscle relaxes, while emptying is preceded by a contraction of the bladder and relaxation of the urethra. Furthermore, the umbrella cells change their morphology and become cuboidal when the bladder is empty, while they stretch and become squamous when the bladder is filled. The smooth muscle is innervated by mainly cholinergic, and a few noradrenergic nerve fibers.

Urinary bladder histology

The urothelium consists of three to seven layers of flat cells which prevents leakage of urinary substances into the blood. The superficial layer is made up of a single row of large, elliptical cells with eosinophilic cytoplasm that store small amounts of mucin and are called umbrella cells. The intermediate cells have a cuboidal to low columnar shape, oval nuclei with stippled chromatin, moderate amounts of cytoplasm and well-defined cell membranes. The basal layer is made up of cuboidal cells that rest on the basal lamina.

The lamina propria is composed of loose connective tissue containing a vascular and lymphatic network.

While the urethra is made up of both smooth and striated muscle, allowing for voluntarily emptying of urine, the muscle layer in the bladder is solely made up of smooth muscle. The smooth muscle of the urinary bladder has three layers; the inner and outer layer with a longitudinal orientation, and the middle layer with a circular orientation.

The histology of human urinary bladder including detailed images and information can be viewed in the Protein Atlas Histology Dictionary.


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

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 54 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

Sundararaghavan VL et al., Glucuronidation and UGT isozymes in bladder: new targets for the treatment of uroepithelial carcinomas? Oncotarget. (2017)
PubMed: 27690298 DOI: 10.18632/oncotarget.12277

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

Habuka M et al., The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling. PLoS One. (2015)
PubMed: 26694548 DOI: 10.1371/journal.pone.0145301

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 urinary bladder