The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells

High-Density Lipoproteins and Acute Kidney Injury

High-density lipoprotein (HDL) particles, best known for their anti-atherosclerotic effects, also may play a beneficial role during acute renal stress. HDL from healthy human beings also shows anti-inflammatory and anti-oxidant capacities, promotes endothelial function and repair, and serves as a systemic signaling mechanism facilitating rapid interorgan communication during times of physiologic stress. Higher concentrations of HDL are associated with less acute kidney injury after sepsis, cardiac and vascular surgery, and contrast-exposure during percutaneous coronary interventions. A better understanding of the interplay between HDL and the kidney both under homeostatic conditions and under acute physiologic stress could lead to the identification of novel risk factors and therapeutic targets for acute kidney injury prevention and treatment in the future.

Ferritin in Kidney and Vascular Related Diseases: Novel Roles for an Old Player

Iron is at the forefront of a number of pivotal biological processes due to its ability to readily accept and donate electrons. However, this property may also catalyze the generation of free radicals with ensuing cellular and tissue toxicity. Accordingly, throughout evolution numerous pathways and proteins have evolved to minimize the potential hazardous effects of iron cations and yet allow for readily available iron cations in a wide variety of fundamental metabolic processes. One of the extensively studied proteins in the context of systemic and cellular iron metabolisms is ferritin. While clinicians utilize serum ferritin to monitor body iron stores and inflammation, it is important to note that the vast majority of ferritin is located intracellularly. Intracellular ferritin is made of two different subunits (heavy and light chain) and plays an imperative role as a safe iron depot. In the past couple of decades our understanding of ferritin biology has remarkably improved. Additionally, a significant body of evidence has emerged describing the significance of the kidney in iron trafficking and homeostasis. Here, we briefly discuss some of the most important findings that relate to the role of iron and ferritin heavy chain in the context of kidney-related diseases and, in particular, vascular calcification, which is a frequent complication of chronic kidney disease.

Effects of arginine vasopressin on the urine proteome in rats

Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats’ urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett’s T3 test. Three differential proteins were described in prior studies as related to AVP physiological processes, and nine differential proteins are known disease biomarkers. Sixteen of the 17 differential proteins have human orthologs. These results suggest that we should consider the effects of AVP on urinary proteins in future urinary disease biomarker researches. The study data provide clues regarding underlying mechanisms associated with AVP for future physiological researches on AVP. This study provide a sensitive changes associated with AVP. However, the limitation of this result is that the candidate biomarkers should be further verified and filtered. Large clinical samples must be examined to verify the differential proteins identified in this study before these proteins are used as biomarkers for pathological AVP increased diseases, such as syndrome of inappropriate antidiuretic hormone secretion (SIADH).

Hephaestin and ceruloplasmin facilitate iron metabolism in the mouse kidney

Multicopper ferroxidases (MCFs) play an important role in cellular iron homeostasis. However, the role of MCFs in renal metabolism remains unclear. We used Hephaestin (Heph) and Ceruloplasmin (Cp) single or double (Heph/Cp) knockout (KO) mice to study the roles of MCFs in the kidney. Renal iron levels and the expression of iron metabolism genes were examined. The non-heme iron content both in the renal cortex and medulla of Heph/Cp KO mice was significantly increased. Perls' Prussian blue staining showed iron accumulation on the apical side of renal tubular cells in Heph/Cp KO mice. A significant increase in ferritin protein expression was also observed in the renal medulla and cortex of Heph/Cp KO mice. Both DMT1 and TfR1 protein expression were significantly decreased in the renal medulla of Heph/Cp KO mice, while the expression of DMT1 protein was significantly increased in the renal cortex of these animals. Significant increase in proteinuria and total urinary iron was observed in the double knockout mice, and this was associated with compromised structural integrity. These results suggest that KO of both the HEPH and CP genes leads to kidney iron deposition and toxicity, MCFs could protect kidney against a damage from iron excess.

Proteomics as a Tool for Clinically Relevant Biomarker Discovery and Validation

The excitement associated with clinical applications of proteomics was initially focused on its potential to serve as a vehicle for both biomarker discovery and drug discovery and routine clinical sample analysis. Some approaches were thought to be able to “identify” mass spectral characteristics that distinguished between control and disease samples, and thereafter it was believed that the same tool could be employed to screen samples in a high-throughput clinical setting. However, this has been difficult to achieve, and the early promise is yet to be fully realized. While we see an important place for mass spectrometry in drug and biomarker discovery, we believe that alternative strategies will prove more fruitful for routine analysis. Here we discuss the power and versatility of 2D gels and mass spectrometry in the discovery phase of biomarker work but argue that it is better to rely on immunochemical methods for high-throughput validation and routine assay applications.

The Specific α1-Adrenergic Receptor Antagonist Prazosin Influences the Urine Proteome

Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible impact of α1-adrenergic receptor on urine proteome, this study investigated effects of the specific inhibitor prazosin on the urine proteome in a rat model by using tandem mass tagging and two-dimensional liquid chromatography-tandem mass spectrometry. A total of 775 proteins were identified, approximately half of which were influenced by prazosin treatment, indicating that the sympathetic nervous system exerts a significant impact on urine proteome. Eight significantly changed proteins were previously annotated as urinary candidate biomarkers. Angiotensinogen, haptoglobin, and beta-2 microglobulin, which were reported to be associated with blood pressure, were validated via Western blot. Prazosin is widely used in clinical practice; thus, these protein changes should be considered when studying corresponding diseases such as hypertension, post-traumatic stress disorder and benign prostatic hyperplasia. The related physiological activities of α1-receptors, controlling blood pressure and fear response might significantly affect the urine proteome and warrant further biomarker studies.

Iron transport in the kidney: implications for physiology and cadmium nephrotoxicity

The kidney has recently emerged as an organ with a significant role in systemic iron (Fe) homeostasis. Substantial amounts of Fe are filtered by the kidney, which have to be reabsorbed to prevent Fe deficiency. Accordingly Fe transporters and receptors for protein-bound Fe are expressed in the nephron that may also function as entry pathways for toxic metals, such as cadmium (Cd), by way of "ionic and molecular mimicry". Similarities, but also differences in handling of Cd by these transport routes offer rationales for the propensity of the kidney to develop Cd toxicity. This critical review provides a comprehensive update on Fe transport by the kidney and its relevance for physiology and Cd nephrotoxicity. Based on quantitative considerations, we have also estimated the in vivo relevance of the described transport pathways for physiology and toxicology. Under physiological conditions all segments of the kidney tubules are likely to utilize Fe for cellular Fe requiring processes for metabolic purposes and also to contribute to reabsorption of free and bound forms of Fe into the circulation. But Cd entering tubule cells disrupts metabolic pathways and is unable to exit. Furthermore, our quantitative analyses contest established models linking chronic Cd nephrotoxicity to proximal tubular uptake of metallothionein-bound Cd. Hence, Fe transport by the kidney may be beneficial by preventing losses from the body. But increased uptake of Fe or Cd that cannot exit tubule cells may lead to kidney injury, and Fe deficiency may facilitate renal Cd uptake.

Application of Proteomics in Cancer Biomarker Discovery: GeLC-MS/MS

Proteomic approaches are being increasingly applied to study multiple facets of healthy and diseased processes. In particular, the application of global proteome profiling in the field of oncology is already starting to shape the diagnostic, prognostic, monitoring, and therapeutic approaches. At the heart of such approaches lies a quest for clinically relevant biomarkers, particularly arising from global analyses of body fluids, as, in major part, they represent easily accessible and noninvasive matrices. A detailed protocol of one of the popular approaches for global proteome profiling, SDS-PAGE-liquid chromatography-tandem mass spectrometry or GeLC-MS/MS, and its application for biomarker discovery in urine is provided here.

Urine proteome analysis in Dent's disease shows high selective changes potentially involved in chronic renal damage

Definition of the urinary protein composition would represent a potential tool for diagnosis in many clinical conditions. The use of new proteomic technologies allows detection of genetic and post-trasductional variants that increase sensitivity of the approach but complicates comparison within a heterogeneous patient population. Overall, this limits research of urinary biomarkers. Studying monogenic diseases are useful models to address this issue since genetic variability is reduced among first- and second-degree relatives of the same family. We applied this concept to Dent's disease, a monogenic condition characterised by low-molecular-weight proteinuria that is inherited following an X-linked trait. Results are presented here on a combined proteomic approach (LC-mass spectrometry, Western blot and zymograms for proteases and inhibitors) to characterise urine proteins in a large family (18 members, 6 hemizygous patients, 6 carrier females, and 6 normals) with Dent's diseases due to the 1070G>T mutation of the CLCN5. Gene ontology analysis on more than 1000 proteins showed that several clusters of proteins characterised urine of affected patients compared to carrier females and normal subjects: proteins involved in extracellular matrix remodelling were the major group. Specific analysis on metalloproteases and their inhibitors underscored unexpected mechanisms potentially involved in renal fibrosis.

BIOLOGICAL SIGNIFICANCE

Studying with new-generation techniques for proteomic analysis of the members of a large family with Dent's disease sharing the same molecular defect allowed highly repetitive results that justify conclusions. Identification in urine of proteins actively involved in interstitial matrix remodelling poses the question of active anti-fibrotic drugs in Dent's patients.

Effects of anesthetics pentobarbital sodium and chloral hydrate on urine proteome

Urine can be a better source than blood for biomarker discovery since it accumulates many changes. The urine proteome is susceptible to many factors, including anesthesia. Pentobarbital sodium and chloral hydrate are commonly used anesthetics in animal experiments. This study demonstrated the effects of these two anesthetics on the rat urine proteome using liquid chromatography–tandem mass spectrometry (LC-MS/MS). With anesthesia, the urinary protein-to-creatinine ratio of all rats increased twofold. The relative abundance of 22 and 23 urinary proteins were changed with pentobarbital sodium or chloral hydrate anesthesia, respectively, as determined by label-free quantification. Among these changed proteins, fifteen had been considered as candidate biomarkers such as uromodulin, and sixteen had been considered stable in healthy human urine, which are more likely to be considered as potential biomarkers when changed, such as transferrin. The pattern of changed urinary proteins provides clues to the discovery of urinary proteins regulatory mechanisms. When determining a candidate biomarker, anesthetic-related effects can be excluded from future biomarker discovery studies. Since anesthetics take effects via nervous system, this study is the first to provide clues that the protein handling function of the kidney may possibly be regulated by the nervous system.

Dynamic changes of urinary proteins in focal segmental glomerulosclerosis model

Compare to blood, which has mechanisms to maintain homeostasis, urine is more likely to reflect changes in the body. As urine accumulates all types of changes, identifying the precise cause of changes in the urine proteome is challenging and crucial in biomarker discovery. To reduce the confounding factors to minimal, some studies used animal model resembling human diseases. This chapter highlights the importance of animal models and introduces a strategic research which focused on adriamycin-induced nephropathy. In this study, urine samples were collected at before adriamycin administration and days 3, 7, 11, 15, and 23 after, urinary proteins were profiled by LC-MS/MS. Of 23 changed proteins with disease development, 13 proteins were identified as stable in normal human urine, meaning that changes in these proteins are more likely to reflect disease. We think this stage-dependent dynamic changes of urine proteome in animal models will help to support the role of urine as key source in biomarker discovery especially in kidney diseases and help to identify corresponding biomarkers for clinical validation.

Effects of diuretics on urinary proteins

Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. The human orthologs of most of these 14 proteins affected are stable in the healthy human urinary proteome, and 10 of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.

Dynamic changes of urinary proteins in a focal segmental glomerulosclerosis rat model

Background

In contrast to blood, which has mechanisms to maintain a homeostatic internal environment, urine is more likely to reflect changes in the body. As urine accumulates all types of changes, identifying the precise cause of changes in the urine proteome is challenging and crucial in biomarker discovery. To reduce the effects of both genetic and environmental factors on the urinary proteome, this study used a rat model of adriamycin-induced nephropathy resembling human focal segmental glomerulosclerosis (FSGS) development.

Results

Urine samples were collected at before adriamycin administration and day3, 7, 11, 15 and 23 after. Urinary proteins were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Of 23 changed proteins with disease development, 20 have human orthologs, and 13 proteins were identified as stable in normal human urine, meaning that changes in these proteins are more likely to reflect disease. Fifteen of the identified proteins have not been established to function in FSGS development. Seven proteins were selected for verification in ten more rats as markers closely associated with disease severity by western blot.

Conclusion

We identified proteins changed in different stages of FSGS in rat models, which may aid in biomarker development and the understanding of FSGS pathogenesis.

Urine retinol-binding protein 4: a functional biomarker of the proximal renal tubule

Measurement of retinol-binding protein 4 in urine (uRBP4) is arguably the most sensitive biomarker for loss of function of the human proximal renal tubule. Megalin- and cubilin-receptor-mediated endocytosis normally absorbs > 99% of the approximately 1.5 g/24 h of protein filtered by the renal glomerulus. When this fails there is "tubular proteinuria," comprising uRBP4, albumin, and many other proteins and peptides. This tubular proteinuria is a consistent feature of the renal Fanconi syndrome (FS) and measurement of uRBP4 appears to be an excellent screening test for FS. FS occurs in rare inherited renal diseases including cystinosis, Dent disease, Lowe syndrome, and autosomal dominant FS. Acquired FS occurs in paraproteinemias, tubulointerstitial renal disease, oncogenic osteomalacia, Chinese herbs nephropathy, and Balkan endemic nephropathy. Though poorly understood, FS may be associated with HIV disease and antiretroviral treatment; cadmium poisoning may cause FS. In addition to FS, uRBP4 measurement has a different role: the early detection of acute kidney injury. Urine RBP4 comprises several isoforms, including intact plasma RBP4, MW 21.07 kDa, and C-terminal truncated forms, des-L- and des-LL-RBP4, also probably plasma derived. In FS, uRBP4 levels are about 104-fold above the upper limit of normal and small increments are frequently seen in carriers of some inherited forms of FS and in acquired disease. The very high levels in disease, frequent assay nonlinearity, lack of defined calibrants, and multiple uRBP4 isoforms make accurate assay challenging; top-down mass spectrometry has brought advances. Assays for uRBP4 with defined molecular targets allowing good interlaboratory comparisons are needed.

Unveiling the rat urinary proteome with three complementary proteomics approaches

Urine is a suitable biological fluid to look for markers of physiological and pathological processes, including renal and nonrenal diseases. In addition, it is an optimal body sample for diagnosis, because it is easily obtained without invasive procedures and can be sampled in large quantities at almost any time. Rats are frequently used as a model to study human diseases, and rat urine has been analyzed to search for disease biomarkers. The normal human urinary proteome has been studied extensively, but the normal rat urinary proteome has not been studied in such depth. In light of this, we were prompted to analyze the normal rat urinary proteome using three complementary proteomics platforms: SDS-PAGE separation, followed by LC-ESI-MS/MS; 2DE, followed by MALDI-TOF-TOF and 2D-liquid chromatography-chromatofocusing, followed by LC-ESI-Q-TOF. A total of 366 unique proteins were identified, of which only 5.2% of unique proteins were identified jointly by the three proteomics platforms used. This suggests that simultaneous proteomics techniques provide complementary and nonredundant information. Our analysis affords the most extensive rat urinary protein database currently available and this may be useful in the study of renal physiology and in the search for biomarkers related to renal and nonrenal diseases.

Effects of three commonly-used diuretics on the urinary proteome

Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S) on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the criteria of P≤0.05, a fold change ≥2, a spectral count ≥5, and false positive rate (FDR) ≤1%, 14 proteins (seven for F, five for H, and two for S) were identified by Progenesis LC-MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.

Proteomic analysis of renal diseases: unraveling the pathophysiology and biomarker discovery

Current biomedical applications of proteomics have been conducted with four main objectives: to better understand the normal biology and physiology of cells, microorganisms, tissues and organs; to explore the pathogenic mechanisms and better understand the pathophysiology of medical diseases; to identify novel biomarkers for early disease detection, prediction and prognosis; and to define new therapeutic targets, drugs and vaccines. This review focuses predominantly on proteomic applications to unravel the pathophysiology and to define novel biomarkers for various renal diseases (i.e., glomerular diseases, tubulointerstitial diseases, renal vascular disorders and renal cancers). In addition, proteomic evaluations of renal transplantation and renal replacement therapy (for acute renal failure and end-stage renal disease) are summarized. Personal opinion, future perspectives and information resources for the field of renal and urinary proteomics are provided.

Stage-specific quantitative changes in renal and urinary proteome during the progression and development of streptozotocin-induced diabetic nephropathy in rats

Diabetic nephropathy (DN) is a microvascular complication associated with diabetes causing slow deterioration of kidneys leading to end-stage renal disease. Timely intervention and diagnosis are crucial in order to ameliorate and halt the progression of DN. Current diagnosis of DN consists of urine assays for detection of microalbuminuria, which have inadequate specificity and sensitivity. Hence, there arises a need to discover stage-specific biomarkers which can aid in the early detection of DN and also in identifying the mechanisms underlying pathogenesis of DN. Therefore the present study was undertaken to identify the differentially expressed proteins in the urine and to examine the pattern of proteomic changes occurring in the rat kidneys during the course of progression of streptozotocin-induced model of DN in rats. Two-dimensional gel electrophoresis coupled to MALDI-TOF mass spectrometry was employed to identify the differentially expressed proteins under diabetic conditions. Among the identified proteins Calgranulin A and Calgranulin B appeared in the urinary proteome at the fourth week of induction of diabetes while we recorded a time-dependent decrease in the expression of major urinary protein (alpha 2u globulin) in the urine as well as kidneys of diabetic rats. Parallel monitoring of targeted proteomic changes in the renal proteome revealed an increase in histone H2B phosphorylation at serine14 along with a gradual decrease in Bcl-2 and MMP-13 expression during the course of progression and development of streptozotocin-induced DN.

Urine protein concentration estimation for biomarker discovery

Recent advances have been made in the study of urinary proteomics as a diagnostic tool for renal disease and pre-eclampsia which requires accurate measurement of urinary protein. We compared different protein assays (Bicinchoninic acid (BCA), Lowry and Bradford) against the 'gold standard' amino-acid assay in urine from 43 women (8 non-pregnant, 34 pregnant, including 8 with pre-eclampsia). BCA assay was superior to both Lowry and Bradford assays (Bland Altman bias: 0.08) compared to amino-acid assay, which performed particularly poorly at higher protein concentrations. These data highlight the need to use amino-acid or BCA assays for unprocessed urine protein estimation.

Evaluation of the Zucker diabetic fatty (ZDF) rat as a model for human disease based on urinary peptidomic profiles

Representative animal models for diabetes-associated vascular complications are extremely relevant in assessing potential therapeutic drugs. While several rodent models for type 2 diabetes (T2D) are available, their relevance in recapitulating renal and cardiovascular features of diabetes in man is not entirely clear. Here we evaluate at the molecular level the similarity between Zucker diabetic fatty (ZDF) rats, as a model of T2D-associated vascular complications, and human disease by urinary proteome analysis. Urine analysis of ZDF rats at early and late stages of disease compared to age- matched LEAN rats identified 180 peptides as potentially associated with diabetes complications. Overlaps with human chronic kidney disease (CKD) and cardiovascular disease (CVD) biomarkers were observed, corresponding to proteins marking kidney damage (eg albumin, alpha-1 antitrypsin) or related to disease development (collagen). Concordance in regulation of these peptides in rats versus humans was more pronounced in the CVD compared to the CKD panels. In addition, disease-associated predicted protease activities in ZDF rats showed higher similarities to the predicted activities in human CVD. Based on urinary peptidomic analysis, the ZDF rat model displays similarity to human CVD but might not be the most appropriate model to display human CKD on a molecular level.

Urine proteomics and biomarkers in renal disease

The application of urine proteomics is a useful approach to the study of the proteins involved in healthy and diseased kidneys and may provide a noninvasive approach to assess disease activity and to monitor clinical response in patients with renal diseases. This technique may provide an additional tool in clinical trials and for the assessment of prognosis for patients. Both soluble proteins and membrane-bound (exosomal) proteins may be studied, and multiple approaches are available. Discovery proteomics is an unbiased approach to detect novel proteins in urine samples. Mass spectrometry (MS) is often needed to identify specific protein fragments. Targeted proteomics often involves specific immunoassays or modified MS, which enables a hypothesis-based design. These approaches may be integrated. For example, specific proteins may be identified by the discovery approach or laboratory study of disease mechanisms. These proteins will then be studied further by targeted proteomics. In order to translate to clinical practice, the specific assays need vigorous validation by means of sufficiently statistically powered clinical trials.

Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy

To identify biomarker candidates associated with early IgA nephropathy (IgAN) and thin basement membrane nephropathy (TBMN), the most common causes presenting isolated hematuria in childhood, a proteomic approach of urinary exosomes from early IgAN and TBMN patients was introduced. The proteomic results from the patients were compared with a normal group to understand the pathophysiological processes associated with these diseases at the protein level. The urinary exosomes, which reflect pathophysiological processes, collected from three groups of young adults (early IgAN, TBMN, and normal) were trypsin-digested using a gel-assisted protocol, and quantified by label-free LC-MS/MS, using an MS(E) mode. A total of 1877 urinary exosome proteins, including cytoplasmic, membrane, and vesicle trafficking proteins, were identified. Among the differentially expressed proteins, four proteins (aminopeptidase N, vasorin precursor, α-1-antitrypsin, and ceruloplasmin) were selected as biomarker candidates to differentiate early IgAN from TBMN. We confirmed the protein levels of the four biomarker candidates by semi-quantitative immunoblot analysis in urinary exosomes independently prepared from other patients, including older adult groups. Further clinical studies are needed to investigate the diagnostic and prognostic value of these urinary markers for early IgAN and TBMN. Taken together, this study showed the possibility of identifying biomarker candidates for human urinary diseases using urinary exosomes and might help to understand the pathophysiology of early IgAN and TBMN at the protein level.

Study of urinary proteomes in Anderson-Fabry disease

BACKGROUND

Anderson-Fabry disease (AFD) is an X-linked genetic disorder with deficient α-galactosidase A activity. The main aim of this work was to investigate possible differences in urine proteins between healthy controls and AFD patients and to identify abnormal proteins as potential biomarkers of disease.

MATERIAL AND METHODS

We studied 2D electrophoresis images of urine samples collected from AFD patients and healthy subjects. The proteins were separated using isoelectric focusing method followed by SDS-PAGE. The proteins were then visualized by silver staining and characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

RESULTS

We found out that the urinary spectra of all the Fabry disease samples included identical proteins with molecular weight around 20-40 kDa. The concentration of some proteins was more than three times higher in the AFD samples, compared to the controls. The abundant proteins were identified by MALDI-TOF MS and included the following: alpha-1-antitrypsin, alpha-1-microglobulin, prostaglandin H2 d-isomerase, complement-c1q tumor necrosis factor-related protein, and Ig kappa chain V-III. Possible glycosylation at Asn51 and Asn78 sites of the prostaglandin H2 d-isomerase was detected.

CONCLUSIONS

AFD urinary proteomics revealed increased secretion of several proteins. We postulate that the observed difference in the amount of prostaglandin H2 d-isomerase and its position on two-dimensional gels might be related to different glycosylation in AFD subjects.

Analysis of peptides in biological fluids by LC-MS/MS

Urine contains large amounts of small peptides, which may represent a rich, yet largely unexplored, source of novel biomarkers for disease monitoring. This chapter describes detailed procedures for the analysis of urinary polypeptides by LC-MS/MS. Hundreds to thousands of small peptides (∼700 to ∼7000 Da) can be detected in urine with the described techniques. Extraction procedures, based on commercially available reagents, effectively remove interfering urinary organic and inorganic salts and neutral compounds, making this a robust and simple assay with the power to detect hundreds to thousands of polypeptides in urine. Analysis time is relatively short, making this protocol a valuable alternative to conventional proteomic techniques based on multidimensional separations. The methodology is therefore particularly useful when the aim is to analyse samples with sufficient depth and throughput so as to make it useful to compare large numbers of specimens. Procedures for enhancing quantitative and qualitative analysis of LC-MS/MS data are also detailed.

Advances in urinary proteome analysis and biomarker discovery in pediatric renal disease

Recent progress in proteomic analysis and strategies for the identification of clinically useful biomarkers in biofluids has led to the identification of urine as an excellent non-invasive reservoir for biomarkers of disease. Urinary biomarkers have been identified and validated on independent cohorts in different high-incidence adult renal diseases, including diabetic nephropathy, chronic kidney disease and immunoglobulin A-nephropathy, but also in extrarenal disease, such as coronary artery disease. Unfortunately, this type of research is underrepresented in the pediatric population. Here, we present the rare studies in the pediatric population that identified potential clinically useful urinary biomarkers in ureteropelvic junction (UPJ) obstruction and renal Fanconi syndrome. These studies, although limited in number, clearly show the potential of urinary proteomics, especially in the pediatric population. It is anticipated that the advances made in the adult population, the lessons learned on the use of appropriate statistics and the inclusion of independent blinded validation cohorts in these types of studies will rapidly lead to clinical useful urinary biomarkers for other pediatric (renal) disease in a population where non-invasive analysis is particularly appreciated.

Urine proteomic analysis: use of two-dimensional gel electrophoresis, isotope coded affinity tags, and capillary electrophoresis

The identities and abundance levels of proteins excreted in urine are not only key indicators of diseases associated with renal function but are also indicators of the overall health of individuals. Urine specimens are readily available and provide a noninvasive means to assess and diagnose many disease states. Proteins in urine originate from two sources: the ultrafiltrate of plasma, and those that are shed from the urinary tract. The protein concentration in urine excreted from a normal adult is approximately 150 mg/day, and is typically not greater than 10 mg/100 mL in any single specimen. Following precipitation, concentration, and fractionation methods, proteins of interest from urine samples can be separated, identified, and quantified. One of the most commonly used techniques in the field of urine proteomics is gel electrophoresis followed by identification with mass spectrometry and protein database search algorithms. In this chapter, two-dimensional gel electrophoresis (2-DE) will be discussed, along with less frequently applied techniques, such as isotope coded affinity tags (ICAT) and capillary electrophoresis (CE). Publications discussing the application of these techniques to urine proteomic analyses of healthy individuals and urinary disease biomarker discovery will also be summarized.

Hereditary renal tubular disorders

The multiple and complex functions of the renal tubule in regulating water, electrolyte, and mineral homeostasis make it prone to numerous genetic abnormalities resulting in malfunction. The phenotypic expression depends on the mode of interference with the normal physiology of the segment affected, and whether the abnormality is caused by loss of function or, less commonly, gain of function. In this review we address the current knowledge about the association between the genetics and clinical manifestations and treatment of representative disorders affecting the length of the nephron.

Should urine pH be adjusted prior to gel-based proteome analysis?

The urine has become one of the most widely used clinical samples for biomarker discovery. The pH of human urine may vary largely from 4.5 to 8.0. Previously, it was questionable whether the urine pH would affect proteome analysis and whether the urine pH needed to be adjusted prior to proteome analysis remained unclear. We therefore performed a systematic analysis of the effect of urine pH on proteome profile. Midstream second morning and random afternoon urine samples were collected from 5 males and 5 females who were healthy and had no recent medication. After removal of cells and debris by low-speed centrifugation, pH levels of individual samples were measured and urinary proteins were isolated by 75% ethanol precipitation. Equally loaded 100 microg of proteins from individual samples were resolved in 2-DE (linear pH 3-10) and visualized with SYPRO Ruby fluorescence stain. There was no significant correlation between difference in the morning versus afternoon urine pH (DeltapH) and %match of protein spots derived from morning versus afternoon urine samples in individual samples (Pearson's r = 0.074; p = 0.839). In parallel, all individual samples with equal volume were pooled. The pH of the pooled urine was adjusted to 4-10 and urinary proteome profiles were analyzed as for individual samples. ANOVA with Tukey's posthoc multiple comparisons showed no significant differences in total number of detected spots and %match among various pH levels. Our data suggest that the urine pH has no significant effects on urinary proteome profile and thus needs no adjustment prior to gel-based proteome analysis.

The non-invasive biopsy--will urinary proteomics make the renal tissue biopsy redundant?

Proteomics is a rapidly advancing technique which gives functional insight into gene expression in living organisms. Urine is an ideal medium for study as it is readily available, easily obtained and less complex than other bodily fluids. Considerable progress has been made over the last 5 years in the study of urinary proteomics as a diagnostic tool for renal disease. Advantages over the traditional renal biopsy include accessibility, safety, the possibility of serial sampling and the potential for non-invasive prognostic and diagnostic monitoring of disease and an individual's response to treatment. Urinary proteomics is now moving from a discovery phase in small studies to a validation phase in much larger numbers of patients with renal disease. Whilst there are still some limitations in methodology, which are assessed in this review, the possibility of urinary proteomics replacing the invasive tissue biopsy for diagnosis of renal disease is becoming an increasingly realistic option.

Proteomic analysis of peritoneal dialysate fluid in patients with dialysis-related peritonitis

The prognosis of uremia patients on continuous ambulatory peritoneal dialysis (CAPD) is related to frequent peritonitis rate. Frequent peritonitis will lead to peritoneum failure, making CAPD unfeasible. We have performed proteomic profiling of peritoneal dialysis effluent samples from a cross-section of CAPD patients with and without peritonitis in order to identify biomarkers of peritonitis. We performed 2D gel electrophoresis and surface-enhanced laser esorption/ionization time of flight mass spectrometry (SELDI-TOF MS) on peritoneal dialysis effluent from 16 subjects with peritonitis. A genetic algorithm search of principal component space revealed a group of a peak distinguishing peritonitis-positive subjects, with mass/charge (m/z) values of 11,117.4. Our analyses identified the peak at m/z 11,117.4 with an accuracy of 95% for classifying peritonitis. Mass spectrometric analysis of peritonitis PDE samples identified the 11,117.4 protein as beta2-microglobulin (B2M). Using an unbiased protein profiling approach, we have validated previously reported findings of B2M as a biomarker associated with CAPD peritonitis. Prospective studies are warranted to establish additional biomarkers that would be predictive of peritoneal dialysis peritonitis. Besides, extending the study to a larger number of patients with subgroup analyses may yield additional information of the peritoneal dialysate proteins in association with dialysis adequacy, residual renal function, nutritional status, and risk of peritoneal infection.

Urinary proteome pattern in children with renal Fanconi syndrome

BACKGROUND

The renal Fanconi syndrome (FS) is characterized by renal glucosuria, loss of electrolytes, bicarbonate and lactate, generalized hyperaminoaciduria and low-molecular-weight proteinuria. We studied the urinary low-molecular-weight proteome to identify excreted peptides indicative of a pathogenetic mechanism leading to tubular dysfunction.

METHODS

We established a urinary proteome pattern using capillary electrophoresis mass spectrometry (CE-MS) of 7 paediatric patients with cystinosis and 6 patients with ifosfamide-induced FS as the study group, and 54 healthy volunteers and 45 patients suffering from other renal diseases such as lupus nephritis (n = 8), focal segmental glomerulosclerosis (n = 27), minimal change disease (n = 7) and membranous glomerulonephritis (n = 3) as controls. Consequently, we conducted a blinded study consisting of 11 FS patients and 9 patients with renal disease other than FS. Additionally, we applied this pattern to 294 previously measured samples of patients with different renal diseases. Amino acid sequences of some marker proteins were obtained.

RESULTS

Specificity for detecting FS was 89% and sensitivity was 82%. The marker peptides constituting the proteome pattern are fragments derived from osteopontin, uromodulin and collagen alpha-1.

CONCLUSIONS

CE-MS can be used to diagnose FS in paediatric patients and might be a future tool for the non-invasive diagnosis of FS. The reduced amount of the marker proteins osteopontin and uromodulin indicates loss of function of tubular excretion in all patients suffering from FS regardless of the underlying cause. In addition, the six different fragments of the collagen alpha-1 (I) chain were either elevated or reduced in the urine. This indicates a change of proteases in collagen degradation as observed in interstitial fibrosis. These changes were prominent irrespectively of the stages of FS. This indicates fibrosis as an early starting pathogenetic reason for the development of renal insufficiency in FS patients.

Urine proteomic profiling of uranium nephrotoxicity

Uranium is used in many chemical forms in civilian and military industries and is a known nephrotoxicant. A key issue in monitoring occupational exposure is to be able to evaluate the potential damage to the body, particularly the kidney. In this study we used innovative proteomic techniques to analyse urinary protein modulation associated with acute uranium exposure in rats. Given that the rat urinary proteome has rarely been studied, we first identified 102 different proteins in normal urine, expanding the current proteome data set for this central animal in toxicology. Rats were exposed intravenously to uranyl nitrate at 2.5 and 5 mg/kg and samples were collected 24 h later. Using two complementary proteomic methods, a classic 2-DE approach and semi-quantitative SDS-PAGE-LC-MS/MS, 14 modulated proteins (7 with increased levels and 7 with decreased levels) were identified in urine after uranium exposure. Modulation of three of them was confirmed by western blot. Some of the modulated proteins corresponded to proteins already described in case of nephrotoxicity, and indicated a loss of glomerular permeability (albumin, alpha-1-antiproteinase, serotransferrin). Others revealed tubular damage, such as EGF and vitamin D-binding protein. A third category included proteins never described in urine as being associated with metal stress, such as ceruloplasmin. Urinary proteomics is thus a valuable tool to profile uranium toxicity non-invasively and could be very useful in follow-up in case of accidental exposure to uranium.

Current issues in measurement and reporting of urinary albumin excretion

BACKGROUND

Urinary excretion of albumin indicates kidney damage and is recognized as a risk factor for progression of kidney disease and cardiovascular disease. The role of urinary albumin measurements has focused attention on the clinical need for accurate and clearly reported results. The National Kidney Disease Education Program and the IFCC convened a conference to assess the current state of preanalytical, analytical, and postanalytical issues affecting urine albumin measurements and to identify areas needing improvement.

CONTENT

The chemistry of albumin in urine is incompletely understood. Current guidelines recommend the use of the albumin/creatinine ratio (ACR) as a surrogate for the error-prone collection of timed urine samples. Although ACR results are affected by patient preparation and time of day of sample collection, neither is standardized. Considerable intermethod differences have been reported for both albumin and creatinine measurement, but trueness is unknown because there are no reference measurement procedures for albumin and no reference materials for either analyte in urine. The recommended reference intervals for the ACR do not take into account the large intergroup differences in creatinine excretion (e.g., related to differences in age, sex, and ethnicity) nor the continuous increase in risk related to albumin excretion.

DISCUSSION

Clinical needs have been identified for standardization of (a) urine collection methods, (b) urine albumin and creatinine measurements based on a complete reference system, (c) reporting of test results, and (d) reference intervals for the ACR.

Iron transport and the kidney

Over the last decade there has been an explosion in our understanding of the proteins that modulate iron homeostasis. Much research has focused on the tissues classically associated with iron absorption and metabolism, namely the duodenum, the liver and the reticulo-endothelial system. Expression profiling has highlighted that many of the components associated with iron homeostasis, are also expressed in tissues which hitherto have received relatively little attention in terms of iron research. These include, testis, lung and, the subject of this review, the kidney. The latter is of great interest because other than a source of erythropoietin, a function that is of course of utmost importance for iron homeostasis, the kidney is regarded as more or less irrelevant in terms of iron handling. However, the fact that the kidneys of our favourite subjects, namely rats, mice and humans, contain many if not all of the proteins that are central to iron balance, that in some cases are expressed in considerable amounts, implies that the kidney handles iron in some way that has demanded evolutionary conservation and therefore is likely to be of importance. This review will document the evidence of iron transporter expression in the kidney, detail data showing the expression of other proteins associated with iron homeostasis and discuss the relevance of renal iron transport to pathophysiological states. Based on these data, a hypothetical model of renal iron handling will be presented.

Quantitative assessment of serum and urinary polyclonal free light chains in patients with type II diabetes: an early marker of diabetic kidney disease?

OBJECTIVE

Free light chains (FLCs) are bi-products of normal immunoglobulin synthesis and are predominately removed from the circulation by the kidneys. This study assessed polyclonal FLCs as a novel biomarker of early diabetic kidney disease.

RESEARCH DESIGN/METHODS

Serum and urinary FLCs were assessed by the immunoassay Freelite, in white and South-Asian patients with type II diabetes recruited from the United Kingdom Asian Diabetes Study.

RESULTS

The incidence of monoclonal proteins in this diabetic population was 1.9%. Type II diabetic patients had significantly raised concentrations of serum polyclonal FLCs before overt renal impairment developed (p < 0.001). Both kappa and lambda FLCs correlated with all tested markers of renal function; in particular cystatin-C: Spearman's coefficient (R) = 0.55 (p < 0.01) and R = 0.56 (p < 0.01), respectively. The South-Asian diabetic patients had higher serum polyclonal FLCs than Caucasian diabetic patients and this was independent of renal function. Urinary FLCs concentrations were raised in diabetic patients (p < 0.001). The majority (68%) of diabetic patients with normal urinary albumin:creatinine ratios (ACRs) had abnormal urinary FLC:creatinine ratios. Both kappa and lambda FLC concentrations correlated with urinary ACR: R = 0.32, p < 0.01 and R = 0.25, p < 0.01 respectively.

CONCLUSIONS

Type II diabetic patients can have significantly raised concentrations of serum and urinary polyclonal FLCs before overt renal disease occurs. These novel findings provide the basis for future studies to assess whether polyclonal FLCs could provide a useful tool for early diagnosis of diabetic kidney disease.

Characterisation of tumoral markers correlated with ErbB2 (HER2/Neu) overexpression and metastasis in breast cancer

The receptor tyrosine kinase ErbB2 (HER2/neu) is overexpressed in ˜30% of breast cancers and is associated with poor prognosis and an increased likelihood of metastasis. Clinical treatments such as trastuzumab are effective in less than 35% of women diagnosed as ErbB2-positive, highlighting the necessity of searching for novel targets and alternative therapies. Herein, a proteomic screening strategy combining quantitative-based gel electrophoresis and MS was used to compare the protein expression of 48 normal human breast and tumour tissues differing in ErbB2 expression and lymph node status. The aim was to identify proteins associated with the aggressive phenotype of ErbB2-positive breast cancer which could be potential biomarkers of the disease as well as therapy targets. In total, 177 protein isoforms (107 gene products) differentially expressed between tissue groups were identified. Immunohistochemical staining of a tissue-microarray was used for validation of selected protein candidates. We found that expression of HSP90α, laminin and GSTP1 significantly correlated with ErbB2 expression, while others such as AGR2, NM23H1 and Annexin 2 were overexpressed in greater than 40% of tumours. Finally, knocking-down the expression by RNA interference of three candidates, AGR2, Transgelin2 and NM23H1 resulted in an enhanced invasive capacity of MDA-MB435 cells. These data support the involvement of these targets in tumour progression and identify them as novel biomarkers of the disease.