Liver and Gallbladder

The main function of liver is to dissolve various metabolites, synthesize proteins, decompose red blood cell and produce biochemical substances necessary for digestion and growth. The gallbladder is a thin hollow organ where bile is stored and concentrated before it is transferred to the small intestine. Unlike the human liver, swine liver is clover leaf-shaped and has five lobes: right lateral, right central, left central, left lateral, and caudate. The porcine liver is thinner and generally has smaller volume than the human liver. However, like a human liver, the pig liver is divided into 8 segments, with each segment having its own arterial supply and venous and biliary drainage.

940 genes are classified as liver elevated out of which 239 genes are highlighted as liver enriched. Based on the expression in gallbladder 147 genes are classified as elevated compared to other tissue types, out of which 7 genes are highlighted as tissue enriched in gallbladder.

The function of the liver and gallbladder are similar between pig and human. Histological image of the pig tissues used in the analysis can be found in the pig tissue dictionary.

Liver

The main function of liver is to dissolve various metabolites, synthesize proteins, decompose red blood cell and produce biochemical substances necessary for digestion and growth. The liver is composed of parenchymal cells (hepatocyte and bile ducts cell) and non-parenchymal cells (sinusoidal endothelial cells, Kupffer cells and hepatic stellate cells).

Gene expression in liver is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 1 summarizes the number of genes in respective category. In total, 14921 genes are detected above cut of (1NX) in pig liver The tissue distribution category highlights 39 genes only detected in liver while 940 genes are classified as liver elevated compared to other tissues. Table 1 shows the overlap for the liver elevated genes and tissue distribution category.

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 (NX≥1) in liver as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 1, Number of genes in the subdivided categories of elevated expression and tissue distribution in liver

Liver enriched expression

The liver is thought to be responsible for many separate functions, and one of them is to synthesize proteins secreted into the blood. Plasma proteins produced by liver includes albumin and fibrinogens. ALB with enriched expression in liver, belongs to the albumin family, whose main function is to regulate the colloidal osmotic pressure of blood by acting as a plasma carrier for a wide range of small molecules such as water, Ca(2+), Na(+), K(+), fatty acids, hormones, bilirubin. Typical examples of fibrinogens include FGB and FGG, which can be cleaved by thrombin to form fibrin abundant in blood clots.

Other liver specific proteins are liver enzymes that are involved in retinol, drug, xenobiotic, androgen and estrogen metabolism. Typical example of metabolic enzymes predominantly expressed in liver is NNMT that catalyzes the N-methylation of nicotinamide and other pyridines to form pyridinium ions, important for biotransformation of many drugs and xenobiotic compounds. SLC27A5 encodes an isozyme of very long-chain acyl-CoA synthetase (VLCS), which plays a role in fatty acid elongation or complex lipid synthesis.

Transporters are involved in moving ions, chemical molecules or drugs to the cells. For instance, AFM with enriched expression in liver, belongs to the albumin family, functioning as a carrier for hydrophobic molecules in body fluids. Another transporter elevated in liver is ABCB11, it is a member of the superfamily of ATP-binding cassette (ABC) transporters which transports various molecules across extra- and intra-cellular membranes. ASGR1, encoding a transmembrane protein, acts as a target for liver-specific drug delivery.

Table 2, The 10 genes with the highest level of enriched expression in liver. "mRNA (tissue)" shows the transcript level in liver as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in liver and the tissue with second highest expression level.

Immunohistochemical labelling of enriched proteins in pig liver, SLC27A5 is detected in hepatocytes using HPA007292 and ASGR1 is detected in cytoplasm and membrane of hepatocytes using HPA012852.

Gallbladder

The gallbladder is a small hollow organ sitting below the right median lobe of the pig liver. It is responsible for storing and concentrating bile produced by the liver. Through the bile duct, the concentrated bile is released into the small intestine, which helps with digestion of fats in food.

Gene expression in gallbladder is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 2 summarizes the number of genes in respective category. In total, 15526 genes are detected above cut of (1NX) in pig gallbladder The tissue distribution category highlights 2 genes only detected in gallbladder while 147 genes are classified as gallbladder elevated compared to other tissues. Table 3 shows the overlap for the gallbladder elevated genes and tissue distribution category.

Figure 2, (A) The distribution of all genes across the five categories based on transcript specificity in gallbladder as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in gallbladder as well as in all other tissues. The combination of the two categories is shown in table 3.

Table 3, Number of genes in the subdivided categories of elevated expression and tissue distribution in gallbladder

Gallbladder enriched expression

MMP7 is involved in the breakdown of extracellular matrix in normal physiological processes, it degrades casein, gelatins of types I, III, IV, and V, and fibronectin and activates procollagenase. GPBAR1, belonged to the G protein-coupled receptor (GPCR) superfamily, is elevated in gallbladder and also has a high expression in lung and liver. This enzyme acts as a cell surface receptor for bile acids. Bile acid binding induces its internalization, activation of extracellular signal-regulated kinases, and production of cAMP in cells. CA4 belongs to the zinc metalloenzymes family, which catalyzes the reversible hydration of carbon dioxide. In addition to being elevated in the gallbladder, it is also expressed in the kidneys and lungs. ANXA4 belongs to the annexin family of calcium-dependent phospholipid binding proteins. It is also has a ubiquitous expression in lung and kidney.

Table 4, The 7 genes classified as enriched in gallbladder. "mRNA (tissue)" shows the transcript level in gallbladder as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in gallbladder and the tissue with second highest expression level.

Gene expression in liver and gallbladder compared to other tissues

The shared expression between liver and gallbladder is sparse, only 6 genes are classified as group enriched in liver and gallbladder, which includes ONECUT1 and TMEM86B. We observed a relationship between kidney and liver based on the overlap and number of group enriched genes shared, including several transporter proteins, such as SLC11A1 and SLC17A1 and also several enzymes like BHMT2, CYP4A24 and AGXT.

Immunohistochemically labeled BHMT2 in pig kidney and liver using HPA044573.

In order to illustrate the relation of eye tissue to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, compared to all other tissues.

Figure 3. An interactive network plot of the liver and gallbladder enriched and group enriched genes connected to their respective enriched tissues (grey circles). Black circles shows the liver and gallbladder. Red nodes represent the number of tissue 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.