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. Transcriptome analysis shows that 67% (n=13563) of all human proteins (n=20162) are expressed in the liver and 978 of these genes show an elevated expression in the liver compared to other tissue types.
The liver transcriptome
Transcriptome analysis of the liver 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 liver compared to other tissues. Elevated expression includes three subcategory types of elevated expression:
Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the liver compared to other tissues. As evident in Table 1, all genes elevated in liver are categorized as:
Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in liver as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in liver as well as in all other tissues.
As shown in Figure 1, 978 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. In Table 2, the 12 genes with the highest enrichment in liver are defined.
Table 1. The number of genes in the subdivided categories of elevated expression 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 visualize the expression patterns of these proteins in different functional compartments including plasma proteins, enzymes, bile proteins and transporters.
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.
The liver, the most metabolically active tissue in humans, plays a major role in the overall human metabolism. Several enzymes are elevated in the liver and include proteins involved in retinol, drug, xenobiotic, androgen and estrogen metabolism as well as a 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 P450 enzymes and transferases. Examples of metabolic enzymes include HAO1, RDH16, and ALDOB.
Another important feature of the liver is primary bile acid biosynthesis. Bile is a dark green to yellow brown fluid involved in the digestion of lipids. Examples of proteins involved in bile acid synthesis include AKR1C4, SLC27A5 and BAAT.
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.
Gene expression shared between liver and other tissues
There are 178 group enriched genes expressed in liver. 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 liver, compared to all other tissues.
To illustrate the relation of liver 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 liver enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of liver 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.
The liver shares most group enriched gene expression with kidney and intestine. Examples of group enriched gene expression shared between liver and kidney as well as liver and intestine are BHMT and OTC, respectively.
The liver is both the largest internal organ and the largest gland in the human body. It has several 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 hepatocyte is a polygonal cell that usually contains a single, central nucleus and rare brownish pigment representing intracellular bile. The classical hexagonal liver lobule is surrounded on an average by six portal tracts and drained by a terminal branch of the hepatic vein called 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.
Using light sheet microscopy and immunostaining we are able to study and visualize the complexity of the liver in detail. The video below visualizes one of the portal veins that run in parallel with the hepatic artery and bile duct. Other videos can be found here.
Here, the protein-coding genes expressed in liver are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in liver.
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)