THE HUMAN TISSUE PROTEOMES

The gallbladder-specific proteome


The gallbladder is a pear-shaped organ just under the liver connected to the small intestine (duodenum). The main functions of the gallbladder are to store bile and digest fats. Bile is a yellow-brown liquid produced by the hepatocytes in the gallbladder. The innermost layer of the gallbladder (mucosa) is lined with a simple columnar epithelium and concentrates the bile by absorption of water through the gallbladder wall. The transcriptome analysis shows that 73% of all human proteins (n=19628) are expressed in the gallbladder and 151 of these genes show an elevated expression in gallbladder compared to other tissue types. An analysis of the genes with elevated expression in the gallbladder with regard to gallbladder functions shows a close connection to the liver and tissues in the gastrointestinal tract.

  • 4 gallbladder enriched genes
  • 151 genes defined as elevated in the gallbladder
  • Most of the elevated genes encode secreted or membranous proteins
  • Most group enriched genes share expression with liver and tissues in the gastrointestinal tract including duodenum

Figure 1. The distribution of all genes across the five categories based on transcript abundance in gallbladder as well as in all other tissues.


151 genes show some level of elevated expression in the gall bladder compared to other tissues. The three categories of genes with elevated expression in gall bladder compared to other organs are shown in Table 1.

Table 1. The genes with elevated expression in gallbladder

Category

Number of genes

Description

Tissue enriched 4 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 40 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 107 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 151 Total number of elevated genes in gallbladder


Table 2. The 4 genes with the highest level of enriched expression in gallbladder. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. "mRNA (tissue)" shows the transcript level asáTPM values,áTS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.

Gene

Description

Predicted localization

mRNA (tissue)

TS-score

FGF19 fibroblast growth factor 19 Secreted 263.2 27
CHST4 carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4 Secreted 102.9 13
MOGAT1 monoacylglycerol O-acyltransferase 1 Membrane 30.8 11
CAPN12 calpain 12 Intracellular 35.0 7

Some of the proteins predicted to be membrane-spanning are intracellular, e.g. in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer face of the cell membrane by a GPI anchor.

The gallbladder transcriptome


An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 82% of the mRNA molecules in the gallbladder correspond to housekeeping genes and only 4% of the mRNA pool corresponds to genes categorized to be either gallbladder enriched, group enriched, or enhanced. Thus, most of the transcriptional activity in the gallbladder relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.



Protein expression of genes elevated in gallbladder


In-depth analysis of the elevated genes in gallbladder using antibody-based protein profiling allowed us to create a map of where these proteins are expressed within the gallbladder and in tissues connected to the gallbladder including cells in the gastrointestinal tract and various ducts.



Proteins specifically expressed in glandular cells of gallbladder


The gallbladder is part of the biliary system which refers to the liver, gallbladder and bile ducts. The main functions of the gallbladder are to store bile, produced by hepatocytes in the liver, and release it into the duodenum.

Examples of proteins with elevated expression in the gallbladder include CHST4 and MUC5B.

CHST4 - gallbladder
CHST4 - liver
CHST4 - pancreas


MUC5B - gallbladder
MUC5B - liver
MUC5B - salivary gland


Genes shared between gallbladder and other tissues


There are 40 group enriched genes expressed in the gall bladder. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 tissues, including gall bladder, compared to all other tissues.

In order to illustrate the relation of gallbladder to other tissue types, a network plot was generated, displaying the number of commonly expressed genes between different tissue types.

Figure 2. An interactive network plot of theágallbladderáenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofágallbladder enriched genes andáorangeánodes 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 toá6átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.



The gallbladder shows a specific pattern of shared group enriched genes with duodenum (19), small intestine (19), colon (11) and liver (14 genes). A Gene Ontology (GO)-based analysis of these shared genes shows that several of the group-enriched genes were associated with metabolic processes. Examples of proteins with shared expression in the gallbladder and other tissues include FXYD2 and TM4SF4.

FXYD2 - gallbladder
FXYD2 - kidney
FXYD2 - salivary gland

TM4SF4 - gallbladder
TM4SF4 - liver
TM4SF4 - duodenum


TM4SF4 - small intestine


Gallbladder function


The main functions of the gallbladder are to store and release bile into the duodenum. Bile is a yellow-brown liquid produced by the hepatocytes in the liver. The release of bile is stimulated by the presence of dietary fats in the small intestine where it acts as a surfactant to emulsify and digest lipids from the food. The innermost layer of the gallbladder (mucosa) is lined with a simple columnar epithelium and concentrates the bile by absorption of water through the gallbladder wall.



Gallbladder histology


The gallbladder sac is attached to the posterior surface of the right lobe of liver. It is divided into the fundus, body and neck. The portion that joins the neck is referred to as the infundibulum.

The wall of the gallbladder is composed of three layers: mucosa, muscularis, and serosa. There are no muscularis mucosae or submucosa. The mucosa is made up of branching folds lined by a single layer of columnar cells having a pale cytoplasm. The lamina propria encompasses loose connective tissue, blood vessels, nerves, and sparse plasma cells. The muscularis is made up of randomly distributed smooth muscle fibers.

The histology of human gallbladder 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 the gallbladder are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the gallbladder.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 3 fresh frozen tissues representing normal gallbladder was compared to 169 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in gallbladder. A tissue-specific score, defined as the ratio between mRNA levels in gallbladder compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in gallbladder, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in gallbladder, and genes not expressed in any tissue. Genes with elevated expression in gallbladder were further sub-categorized as i) genes with enriched expression in gallbladder, ii) genes with group enriched expression including gallbladder and iii) genes with enhanced expression in gallbladder.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.


Relevant links and publications


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

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

Fagerberg L et al, 2014. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics.
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Kampf C et al, 2014. Defining the human gallbladder proteome by transcriptomics and affinity proteomics. Proteomics.
PubMed: 25175928 DOI: 10.1002/pmic.201400201

Histology dictionary - the gallbladder