THE HUMAN TISSUE PROTEOMES

The liver-specific proteome


The liver is both the largest internal organ and the largest gland in the human body. The human liver has a number of physiological functions including production of bile, hormones and vitamins, storage of glycogen, removal of toxic substances, decomposition of red blood cells, synthesis of plasma proteins and homeostatic regulation of the plasma constituents. The liver is formed by parenchymal cells (hepatocytes and bile ducts cells) and non-parenchymal cells (sinusoidal endothelial cells, Kupffer cells, and hepatic stellate cells) that together synchronize the vital functions in liver homeostasis. The transcriptome analysis shows that 59% of all human proteins (n=19628) are expressed in the liver and 422 of these genes show an elevated expression in liver compared to other tissue types. An analysis of the genes with elevated expression in the liver with regard to biological functions shows genes associated with immune system processes, response to stimulus, growth and metabolic processes.

  • 156 liver enriched genes
  • Most of the enriched genes encode secreted proteins
  • 422 genes defined as elevated in the liver
  • Most group enriched genes share expression with the kidney

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


422 genes show some level of elevated expression in the liver compared to other tissues. The three categories of genes with elevated expression in liver compared to other organs are shown in Table 1. The list of tissue enriched genes (n=156) are well in-line with the function of the liver.

Table 1. The genes with elevated expression in liver

Category

Number of genes

Description

Tissue enriched 156 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 121 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 145 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 422 Total number of elevated genes in liver


Table 2. The 12 genes with the highest level of enriched expression in liver. "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

CFHR2 complement factor H-related 2 Secreted 465.5 4655
F9 coagulation factor IX Secreted 364.7 2286
SPP2 secreted phosphoprotein 2, 24kDa Intracellular,Secreted 264.2 2165
AHSG alpha-2-HS-glycoprotein Secreted 2819.2 1899
F2 coagulation factor II (thrombin) Intracellular,Secreted 627.1 1471
MBL2 mannose-binding lectin (protein C) 2, soluble Secreted 141.3 1413
APOA2 apolipoprotein A-II Intracellular,Secreted 18141.3 1053
SERPINC1 serpin peptidase inhibitor, clade C (antithrombin), member 1 Secreted 2511.4 675
FGB fibrinogen beta chain Intracellular,Secreted 9991.3 558
RP4-608O15.3 Complement factor H-related protein 2 Secreted 201.9 530
HPX hemopexin Secreted 2610.6 508
CFHR5 complement factor H-related 5 Secreted 88.0 495

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 liver 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 52% of the mRNA molecules in the liver correspond to housekeeping genes and interestingly 45% of the mRNA pool corresponds to genes categorized to be either liver enriched, group enriched, or enhanced. Thus, a big part of the transcriptional activity in the liver relates to proteins with presumed liver specific functions as they are elevated in liver.



Protein expression of genes elevated in liver


In-depth analysis of the elevated genes in liver using antibody-based protein profiling allowed us to identify plasma proteins, enzymes, bile proteins and transporters.



Plasma proteins


One of the main functions of the liver is to produce proteins secreted into the blood. Plasma proteins consist of many known proteins including albumin, fibrinogens and apolipoproteins. Factors involved in hemostasis and fibrinolysis including coagulation factors, anti-trypsin and plasminogen are secreted into the blood as well as carrier proteins such as transferrin and retinol binding protein. Examples of plasma proteins include APOB, APOA1, FGG, C2, KNG1, and FGA.

Liver

Plasma

APOB - gallbladder
APOA1 - gallbladder
FGG - gallbladder


C2 - colon
KNG1 - duodenum
FGA - stomach


Enzymes


The liver, the most metabolically active tissue in human, plays a major role in the overall human metabolism. Several enzymes are elevated in liver and include proteins involved in retinol, drug, xenobiotic, androgen and estrogen metabolism as well as steroid hormone and primary bile acid biosynthesis, functions that are known as liver tissue-specific pathways. Throughout these pathways, xenobiotic metabolism that covers the detoxification and removal of toxic substances is an important feature for the liver. Enzymes involved in this process include cytochrome 450 enzymes and transferases. Examples of metabolic enzymes include HAO1, RDH16, and ALDOB.



Bile proteins


Another important feature of the liver tissue is primary bile acid biosynthesis. Bile is a dark green to yellow brown fluid involved in digestion of lipids. Examples of proteins involved in bile acid synthesis include BAAT, AKR1C4 and SLC27A5.



Transporters


Transporter proteins allow natural chemicals or drugs to enter cells or, in some cases, acts to keep them out and may account for discrepancies in the way drugs such as antidepressants, anticonvulsants, and chemotherapy agents work in different people. Examples of transporters include ABCB11, SLC2A2 and SLCO1B3.



Genes shared between liver and other tissues


There are 121 group enriched genes expressed in the liver. 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 liver, compared to all other tissues.

In order to illustrate the relation of liver tissue 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 theáliveráenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofáliver 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 toá5átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.



The liver shows a specific pattern of shared group enriched genes with the kidney (53 genes). A Gene Ontology-based analysis of these genes shows that a majority are associated with metabolic process. Examples of group enriched genes shared between liver and kidney are BHMT and HPD.

BHMT - liver
BHMT - kidney

HPD - liver
HPD - kidney


Liver function


The liver is both the largest internal organ and the largest gland in the human body. The human liver has a number of physiological functions including production of bile, hormones and vitamins, storage of glycogen, removal of toxic substances, decomposition of red blood cells, synthesis of plasma proteins and homeostatic regulation of the plasma constituents. The liver is formed by parenchymal cells (hepatocytes and bile ducts cells) and non-parenchymal cells (sinusoidal endothelial cells, Kupffer cells, and hepatic stellate cells) that together synchronize the vital functions in liver homeostasis.



Liver histology


The hepatocyte is a polygonal cell that usually contains a single, central nucleus and occasional brownish pigment representing intracellular bile. The classical hexagonal liver lobule is surrounded on an average by six portal tracts and centered on a terminal twig of the hepatic vein: the centrilobular or central vein. The portal vein ramifications in the portal tracts give off a series of branches in the plane between adjacent portal tracts; these give rise to the sinusoids that drain the blood towards the center of the lobule. The lobule may be viewed to comprise a periportal zone, midzonal area and centrilobular area.

The hepatocytes are usually arranged in one-cell thick plates called muralia with a sinusoid on either side thus exposing the hepatocyte to portal blood on two surfaces. Within the muralium each hepatocyte adjoins the adjacent cell with its intercellular surface. The intercellular domain of the cell membrane carries a groove termed the hemicanaliculus. The hemicanaliculus of two adjacent hepatocytes comprises the intercellular bile canaliculus.

The space of Disse is formed between the sinusoidal lining cells and the sinusoidal domain of the hepatocyte surface. Several different cell types including sinusoidal endothelial cells, Kupffer cells, hepatic stellate cells (Ito cells) line the hepatic sinusoids, each having its own special function.

The portal tracts at the lobular periphery are composed of connective tissue ensheathing branches of the hepatic artery, portal vein, bile duct (together termed the portal triad) and lymphatics. The caliber of the portal tracts decreases from the hilum of the liver towards its periphery.

The histology of human liver 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 liver 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 liver.

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 10 fresh frozen tissues representing normal liver was compared to 162 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in liver. A tissue-specific score, defined as the ratio between mRNA levels in liver 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 liver, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in liver, and genes not expressed in any tissue. Genes with elevated expression in liver were further sub-categorized as i) genes with enriched expression in liver, ii) genes with group enriched expression including liver and iii) genes with enhanced expression in liver.

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. The human liver-specific proteome defined by transcriptomics and antibody-based profiling. FASEB J.
PubMed: 24648543 DOI: 10.1096/fj.14-250555

The virtual liver

The database of Liver Proteome Expression Profile

Histology dictionary - the liver