The liver-specific proteome

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:

• Tissue enriched: At least four-fold higher mRNA level in liver 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 liver 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 liver compared to other tissues. As evident in Table 1, all genes elevated in liver 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

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, 973 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.

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

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.

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

APOB
APOA1
FGG

C2
KNG1
FGA

Plasma

APOB - gallbladder
APOA1 - gallbladder
FGG - gallbladder

C2 - colon
KNG1 - duodenum
FGA - stomach

Enzymes

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.

HAO1
RDH16
ALDOB

Bile proteins

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.

AKR1C4
SLC27A5
BAAT

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.

ABCB11
SLC2A2
SLCO1B3

Gene expression shared between liver and other tissues

There are 171 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 4 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.

BHMT - liver
BHMT - kidney

OTC - liver
OTC - small intestine

Liver function

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.

Liver histology

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.

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 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 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

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

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

Kampf C et al., The human liver-specific proteome defined by transcriptomics and antibody-based profiling. FASEB J. (2014)
PubMed: 24648543 DOI: 10.1096/fj.14-250555

Histology dictionary - the liver