Kidney and urinary bladder

The kidney and urinary bladder are both part of the urinary system that is responsible for removing waste from the body, control the level of electrolytes and metabolites as well as regulate blood pH, pressure and volume. Kidneys filter the blood and form the urine, which is transported to the urinary bladder via ureters. From the bladder the urine exits the body via the urethra.

In the pig transcriptomic analysis, urinary bladder as well as kidney cortex and kidney medulla are included tissue samples used for quantitative RNA measurements. The gene classification strategy highlights genes with an elevated level of expression in one or a group of tissues compared to all other tissues.

673 genes are classified as kidney elevated out of which 78 genes are highlighted as kidney enriched. Based on the expression in urinary bladder 101 genes are classified as elevated compared to other tissue types, out of which 4 genes are highlighted as tissue enriched.

The function and structure of both kidney and urinary bladder are similar between sexes, only the length of urethra is different between male and female. Based on histological comparison, the pig and human kidney looks similar while the urinary bladder show a slight difference. The pig surface is folded while the human urinary bladder surface is more flat, the stratification and details of the urothelium looks similar, this can be observed in the pig tissue dictionary.

Kidney

The kidney was dissected into cortex and medulla respectively, and the highest expression value was used for gene classification of kidney expression compared to other tissue types.

Figure 1, Schematic drawing of the main compartments of the kidney.

The functional units of the kidneys are so called nephrons and consist of several different specialized structures (figure 1). The first filtrating component, renal glomeruli, is surrounded by the Bowman´s capsule and is found in the cortex. The secondary filtering stage with reabsorption and continuous filtering consists of different types of tubule; proximal tubule (mainly located in the cortex), loop of Henle (located in the medulla), distal tubule (both cortex and medulla) and collecting tubule (mainly located in the medulla).

Gene expression in kidney 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, 16272 genes are detected above cut of (1NX) in pig kidney. The tissue distribution category highlights 26 genes to be only detected in kidney and 673 genes are classified as kidney elevated compared to other tissues. Table 1 shows the overlap for the kidney elevated genes and tissue distribution category.

Figure 2, (A) The distribution of all genes across the five categories based on transcript specificity in kidney as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in kidney 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 kidney

Kidney enriched expression

Genes classified as kidney enriched are well in line with the filtering fluid transport-related function of the kidney and it is very similar to the expression profile of the human kidney. For example, SLC22A11, KCNJ1{/hpa} and SLC22A12 are all reabsorption proteins, located in renal tubule binding to specific small molecules. Both the distal tubule and the collecting duct are responsible for the regulation of potassium, sodium, calcium and PH. The distal tubule includes the expression of the tissue enriched uromodulin, encoded by UMOD gene, which may act as a constitutive inhibitor of calcium crystallization in renal fluids. Some proteins related to electrolyte homeostasis are also associated to the distal tubule, such as SLC12A1.

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

Expression variation between cortex and medulla

Since kidney was dissected into cortex and medulla respectively for the analysis, we were able to further describe the expression profile of the pig kidney based on the comparison of cortex and medulla. In total, 916 genes are highlighted as variable between kidney cortex and kidney medulla. 309 out of those are also classified as kidney elevated when compared to other tissue types and 535 genes show much higher expression in other tissue type than kidney (classified as elevated in a tissue type that is not kidney on the whole body level).

SLC14A2 is classified as kidney elevated and show higher expression in medulla compared to cortex. NPHS2 is an example of glomeruli specific protein, which is only expressed in the kidney cortex and not the medulla. Most renal tubule markers show some variation between cortex and medulla, but a few are highlighted as significantly variable with a higher expression level in cortex compared to medulla, for example BHMT2 and DMGDH, both identified as proximal tubule proteins and interestingly classified as group enriched in kidney and liver.

Immunohistochemical labelling of pig kidney targeting 4 different proteins detected in different structures of the renal nephron. From the top to bottom NPHS2 is detected in glomeruli using HPA049486, DMGDH is detected in proximal tubule using HPA036441, SLC12A1 is detected in distal tubule using HPA014967 and AQP3 is detected in collecting ducts using HPA014924

Urinary bladder

The urinary bladder holds the urine produced by the kidneys, which is transported into the urinary bladder via the ureters into the bladder. The urinary bladder is lined by urothelium, a stratified transitional epithelium that resembles squamous epithelium with cuboidal basal cells. Urothelium also includes umbrella cells, polarized superficial cells with a distinct apical and basolateral membrane.

Gene expression in urinary bladder is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 3 summarizes the number of genes in respective category. In total, 15086 genes are detected above cut of (1NX) in pig urinary bladder. The tissue distribution category highlights 0 genes to be only detected in urinary bladder and 101 genes are classified as urinary bladder elevated compared to other tissues. Table 3 shows the overlap for the urinary bladder elevated genes and tissue distribution category.

Figure 3, (A) The distribution of all genes across the five categories based on transcript specificity in urinary bladder as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in urinary bladder 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 urinary bladder

Urinary bladder enriched expression

Only 4 genes are classified as urinary bladder enriched, one of those is the UPK1A responsible for regulating membrane permeability of superficial umbrella cells and stabilizing the apical membrane through AUM/cytoskeletal interactions.

The majority of genes classified as group enriched or enhanced in urinary bladder are shared with other tissue types rich on smooth muscle or tissues with squamous epithelia. Since the unique features of urinary bladder compared to other tissue types are limited, the low number of tissue enriched is no surprise.

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

Gene expression in kidney and urinary gladder compared to other tissues

In order to illustrate the relation of kidney and urinary bladder 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 4. An interactive network plot of the kidney and urinary bladder enriched and group enriched genes connected to their respective enriched tissues (grey circles). Black circles shows kidney and urinary bladder. 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.