The kidney-specific proteome

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Figure 1. The distribution of all genes across the five categories based on transcript abundance in kidney as well as in all other tissues.

334 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. The list of tissue enriched genes (n=54) are well in-line with the function of the kidney. In Table 2, the 12 genes with the highest level of expression among 54 enriched genes are defined.

Table 2. The 12 genes with the highest level of enriched expression in kidney. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. "mRNA (tissue)" shows the transcript level as TPM values, TS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.

Some of the proteins predicted to be membrane-spanning are intracellular, e.g. in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer surface of the cell membrane by a GPI anchor.

The kidney transcriptome

An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 87% of the mRNA molecules in the kidney correspond to housekeeping genes and only 7% of the mRNA pool corresponds to genes categorized to be either kidney enriched, group enriched, or enhanced. Thus, most of the transcriptional activity in the kidney relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.

Protein expression of genes elevated in the kidney

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

A Gene Ontology analysis shows that a majority of genes and the corresponding proteins are involved in different metabolic and transport processes. The most common functions of these proteins is transmembrane transport activity.

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 (Blum et al, 2007). In addition, NEPH1, mainly referred to as KIRREL, is present in the glomerulus as described before (Donoviel et al, 2001). Interestingly, this latter protein is not identified as elevated in kidney, since the placenta shows higher mRNA levels than kidney for this gene. The placenta also acts as a filtration machinery for large and small molecules is therefore interesting (Beall et al, 2005). The protein PODXL has been reported to give a negative charge of the apical plasma membrane of the podocytes and also vascular endothelial cells in general (Nielsen and McNagny, 2009). Another kidney elevated gene expressed in the glomerulus is FGF1.

Proteins specifically expressed in proximal tubule

Approximately 60% of the filtered Na+, Cl-, K+, Ca2+, and 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 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 with binding of specific small molecules (He et al, 2009). It is also reassuring to find several enzymes involved in digestion of proteins, such as peptidases, to allow adsorption of amino acids and peptides originating from proteins transported into in 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, HPD, , LRP2, PKLR and XPNPEP2 are all kidney elevated genes expressed in the proximal tubule.

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 final urinary concentration of K+, Na+, and Cl-. The distal tubule contains the most abundant and most tissue specific protein in the kidney; the well-known uromodulin (UMOD), although the specific function of this protein is yet somewhat unclear (Bleyer et al, 2011). 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 as 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.

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.

Genes shared between kidney and other tissues

There are 119 group enriched genes expressed in the kidney. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 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 shared 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 genes with the liver. A Gene Ontology-based analysis of these shared group enriched genes and the corresponding proteins shows an association with metabolic processes. One example of a protein expressed in both kidney and liver is BHMT2, a amino acid that plays a crucial role in methylation reactions. BHMT2 is expressed in hepatocytes in liver and in proximal tubulesi in kidney.

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 a number of products of metabolism, most notably urea, and a number of 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 principle 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 a tuft of capillaries comprised of specialized endothelial, epithelial and mesangial cells arranged around a relatively thick 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 tuft of capillaries lies 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 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 a 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 the kidney are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the kidney.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 9 fresh frozen tissues representing normal kidney was compared to 163 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in kidney. A tissue-specific score, defined as the ratio between mRNA levels in kidney compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in kidney, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in kidney, and genes not expressed in any tissue. Genes with elevated expression in kidney were further sub-categorized as i) genes with enriched expression in kidney, ii) genes with group enriched expression including kidney and iii) genes with enhanced expression in kidney.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.

Relevant links and publications

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PubMed: 25613900 DOI: 10.1126/science.1260419

Yu NY et al, 2015. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res.
PubMed: 26117540 DOI: 10.1093/nar/gkv608

Fagerberg L et al, 2014. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics.
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

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

Blum S et al, 2007. Renal slit diaphragm--the open zipper and the failing heart. Isr Med Assoc J.
PubMed: 17348483 

Donoviel DB et al, 2001. Proteinuria and perinatal lethality in mice lacking NEPH1, a novel protein with homology to NEPHRIN. Mol Cell Biol.
PubMed: 11416156 DOI: 10.1128/MCB.21.14.4829-4836.2001

Beall MH et al, 2005. Placental and fetal membrane Nephrin and Neph1 gene expression: response to inflammation. J Soc Gynecol Investig.
PubMed: 15979540 DOI: 10.1016/j.jsgi.2005.02.009

Nielsen JS et al, 2009. The role of podocalyxin in health and disease. J Am Soc Nephrol.
PubMed: 19578008 DOI: 10.1681/ASN.2008070782

He L et al, 2009. Analysis and update of the human solute carrier (SLC) gene superfamily. Hum Genomics.
PubMed: 19164095 

Bleyer AJ et al, 2011. Uromodulin-associated kidney disease. Nephron Clin Pract.
PubMed: 21071970 DOI: 10.1159/000320889

Histology dictionary - the kidney