The kidney-specific proteome

The kidney transcriptome

Transcriptome analysis of the kidney can be visualized with regard to specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the kidney compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

• Tissue enriched: At least four-fold higher mRNA level in kidney 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 kidney compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the kidney compared to other tissues. As evident in Table 1, all genes elevated in kidney 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 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.

As shown in Figure 1, 413 genes show some level of elevated expression in the kidney compared to other tissues. The three categories of genes with elevated expression in kidney compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in kidney are defined.

Table 1. Number of genes in the subdivided categories of elevated expression in kidney.

Table 2. The 12 genes with the highest level of enriched expression in kidney. "Tissue distribution" describes the transcript detection (NX≥1) in kidney as well as in all other tissues. "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.

Protein expression of genes elevated in the kidney

In-depth analysis of the elevated genes in the kidney using antibody-based protein profiling clearly shows that the main locations of the kidney elevated proteins are in glomeruli, proximal tubules, distal tubules and collecting ducts.

Proteins specifically expressed in glomerulus

The process of urine formation begins in the glomerulus, where an ultrafiltrate of plasma is formed, and the filtered fluid enters the renal tubules. The filter consists of three layers; the fenestrated endothelium, the basement membrane, and the podocyte slit diaphragm. The analysis of the glomerulus elevated proteins is well in line with the function of the glomerulus as a filtration apparatus assembling a slit diaphragm. The list of kidney elevated proteins includes several well-known glomeruli associated genes, such as podocin (NPHS2) and nephrin (NPHS1), well established as proteins creating the filtration diaphragm making up a filter for large molecules. In addition, KIRREL1 is present in the glomerulus as described before. This latter protein is not identified as elevated in the kidney, instead the placenta shows higher mRNA levels than the kidney for this gene. The placenta also acts as a filtration machinery for large and small molecules is therefore interesting. Another kidney elevated gene expressed in the glomerulus is FGF1.

NPHS2
NPHS1

Proteins specifically expressed in proximal tubule

Approximately 60% of the filtered Na+, Cl-, K+, Ca2+, H2O and more than 90% of the filtered HCO3- are absorbed along the proximal tubule. This is also the segment that normally reabsorbs virtually all the filtered glucose and amino acids. An additional function is the secretion of numerous organic anions and cations. Most of the proteins elevated in the kidney are localized to the proximal tubule, which is in line with the function of the proximal tubule as a compartment for reabsorption of small molecules back to the blood. This includes many genes coding for transport proteins responsible for specific adsorption of various small molecules. In particular, there are numerous members of the solute carrier family proteins (SLC) each binding specific small molecules. It is also reassuring to find several enzymes involved in the digestion of proteins, such as peptidases, to allow adsorption of amino acids and peptides originating from proteins transported into the proximal tubule. Examples of genes expressed in the proximal tubule are SLC22A8, localized in the basolateral surface (blood), and SLC22A13, localized in the luminal surface (urine). AGMAT, BHMT, DPYS, GGT1, RIDA, LRP2, PKLR and XPNPEP2 are all kidney elevated genes expressed in the proximal tubule.

SLC22A8
SLC22A13

Proteins specifically expressed in the distal tubule

Both the distal tubule and collecting duct are the sites where critical regulatory hormones such as aldosterone and vasopressin regulate acid and potassium excretion and determine the final urinary concentration of K+, Na+, and Cl-. The distal tubule contains the most abundant and most tissue-specific protein in the kidney; (UMOD), although the specific function of this protein is yet somewhat unclear. Similarly, the well-known calbindin (CALB1) is also elevated in the distal tubules. In addition, the list of kidney elevated genes contains several receptors for electrolyte transport, including potassium, sodium, and calcium transporters, such as SLC12A1. Again this is in line with the function of the distal tubule being responsible for reabsorption of electrolyte to the blood and excretion of potassium to the urine. Another example of a gene expressed in the distal tubule is SLC12A3.

UMOD
SLC12A1

Proteins specifically expressed in collecting duct

There are two different cell types in the collecting duct: principal cells and intercalated cells. Principal cells are the main site of salt and water transport, and intercalated cells are the key site for acid-base regulation. Examples of the genes expressed in the collecting duct are the aquaporin 2 (AQP2), localized in the luminal surface, and ATP6V0D2 localized only in the intercalated cells. TMEM213 is also a kidney elevated gene expressed in the collecting ducts.

AQP2
ATP6V0D2

Gene expression shared between kidney and other tissues

There are 131 group enriched genes expressed in kidney. 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 kidney, compared to all other tissues.

In order to illustrate the relation of kidney tissue to other tissue types, a network plot was generated, displaying the number of genes with shared expression between different tissue types.

Figure 2. An interactive network plot of the kidney enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of kidney 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 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

The network plot shows that the kidney shares most group enriched gene expression with the liver. One example of a protein expressed in both kidney and liver is BHMT2, an amino acid that plays a crucial role in methylation reactions. BHMT2 is expressed in hepatocytes in the liver and proximal tubules in the kidney.

BHMT2 - kidney
BHMT2 - liver

Kidney function

The kidney is a specialized tissue that plays a vital role in maintaining body homeostasis. The main functions can be categorized as follows:

1. Maintenance of body composition: The kidney regulates the volume of fluid in the body; its osmolarity, electrolyte content, electrolyte concentration and acidity by varying the amounts of water and ions excreted in the urine.
2. Excretion of metabolic end products and foreign substances: The kidney excretes several products of metabolism, most notably urea, and many toxins and drugs.
3. Production and secretion of enzymes and hormones: The kidney is a source for several important hormones such as renin, which catalyzes the formation of angiotensin, the key peptide for blood pressure regulation, erythropoietin, which regulates the production of red blood cells, and activated vitamin D3, which regulates body calcium and phosphate balance.

Kidney histology

The kidneys form the first part of the urinary system and their principal function is to maintain homeostasis by the regulation of electrolytes and the acid-base balance. Kidney function is vital for regulating blood pressure and the kidneys are also a source for several important hormones such as erythropoietin, which regulates the production of red blood cells. Histologically, the renal parenchyma consists of four parts: glomeruli, tubules, interstitium and blood vessels. Glomeruli are complex vascular structures composed of specialized endothelial, epithelial and mesangial cells arranged around a basement membrane. The glomerulus arises from the afferent arteriole to form lobules then rejoin the vascular pole to drain into the efferent arteriole. Normally the lobules are poorly defined but highlighted in some disease processes. The capillaries lie within the lumen of the expanded proximal end of the nephron, or Bowman's space, which is lined on its parietal aspect by a layer of attenuated epithelial cells overlying a thick basement membrane. Together the epithelial cells and basement membrane comprise the Bowman's capsule. The function of the glomerulus is the filtration of the blood that leads to the formation of urine.

A complex tubular system begins at the urinary pole (where urine is first formed in the Bowman's space) that extends to the renal papilla. The system comprises the proximal tubule, the loop of Henle, distal tubule and collecting duct. The proximal tubule consists of convoluted and straight portions, lined by tall columnar cells with abundant, acidophilic cytoplasm rich in structures for active fluid transport. The loop of Henle has thin descending and thick ascending portions lined by cuboidal and columnar cells. The distal tubule is narrower and shorter than the proximal tubule and lined by low cuboidal cells that do not display the deeply acidophilic, granular cytoplasm characteristic of the proximal tubule. Cuboidal cells with pale acidophilic cytoplasm and central nuclei line the collecting ducts.

The interstitium is more easily conceptualized as space rather than a structure; it is visualized only when abnormal. The interstitium contains specialized interstitial cells and connective tissue elements. The larger renal blood vessels are structurally similar to those in other body sites.

The histology of human kidney 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 kidney are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in kidney.

Transcript profiling was based on a combination of three transcriptomics datasets (HPA, GTEx and FANTOM5), corresponding to a total of 9332 samples from 113 different human normal tissue types. The final consensus normalized expression (NX) value for each tissue type was used for 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

Habuka M et al., The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling. PLoS One. (2014)
PubMed: 25551756 DOI: 10.1371/journal.pone.0116125

Histology dictionary - the kidney