Urinary proteome analysis identifies infants but not older children requiring pyeloplasty

Current status and future directions of application of urine proteomics in neonatology

With continuous advancements in mass spectrometry technology, researchers increasingly utilize this method to investigate the molecular mechanisms underlying various diseases, and to identify novel diagnostic and therapeutic strategies. Among proteomics applications, urinary proteomics stands out for its non-invasive nature, making it particularly suitable for vulnerable populations like neonates. This review provides a comprehensive overview of recent research on urinary proteomics in the field of neonatology. It summarizes findings from numerous studies, illustrating how urinary proteomic profiles provide critical insights into neonatal health and disease. By identifying specific protein biomarkers in urine, researchers can gain insights into the early detection and monitoring of neonatal diseases, potentially leading to more timely and effective interventions. As technology evolves, the sensitivity and accuracy of proteomic analyses are expected to improve, opening new avenues for research and clinical applications.

Fetal biomarkers for lower urinary tract obstruction secondary to posterior urethral valves

Today, prenatal diagnosis of congenital urogenital malformations is mostly dependent on anatomical variations found on imaging. However, these findings can mislead us in telling us when to intervene, and about post-natal prognosis. Since many findings are dependent on multiple assessments, delayed diagnosis can occur, leading to less optimal outcomes compared to early intervention. Analyses of fetal urinary biomarkers have been proposed as a method of finding biological changes that are predictive for diagnosis and prognosis in fetuses at risk of kidney disease. We interviewed a group of researchers that have demonstrated that by combining multiple omics traits extracted from fetal urine, the biological variability found in single omics data can be circumvented. By analyzing multiple fetal urine peptides and metabolites at single time point, the prognostic power of postnatal renal outcome in fetuses with lower urinary tract obstruction is significantly increased. In this interview, we inquired about the technical aspects of the tests, challenges, and limitations the research group have come across, and how they envision the future for multi-omics fetal analysis in the clinic.

Comparison of clean catch and bag urine using LC-MS/MS proteomics in infants

BACKGROUND

Urinary proteomics identifies the totality of urinary proteins and can therefore help in getting an early and precise diagnosis of various pathological processes in the kidneys. In infants, non-invasive urine collection is most commonly accomplished with a urine bag or clean catch. The influence of those two collection methods on urinary proteomics was assessed in this study.

METHODS

Thirty-two urine samples were collected in infants using urine bag and clean catch within 24 h. Nine boys and seven girls with a mean age of 4.3 ± 2.9 months were included (5 × post-pyelonephritis, 10 × non-kidney disease, 1 × chronic kidney disease (CKD)). Liquid chromatography-mass spectrometry (LC-MS/MS) was performed in data-independent acquisition (DIA) mode. Protein identification and quantification were achieved using Spectronaut.

RESULTS

A total of 1454 urinary proteins were detected. Albumin and α-1-microglobulin were detected the most. The 18 top-abundant proteins accounted for 50% of total abundance. The number of proteins was slightly, but insignificantly higher in clean catch (957 ± 245) than in bag urine (876 ± 255). The median intensity was 1.2 × higher in the clean catch. Overall, differential detection of proteins was 29% between the collection methods; however, it diminished to 3% in the 96 top-abundant proteins. Pearson's correlation coefficient was 0.81 ± 0.11, demonstrating a high intraindividual correlation. A principal component analysis and a heat map showed clustering according to diagnoses and patients rather than to the collection method.

CONCLUSION

Urinary proteomics shows a high correlation with minor variation in low-abundant proteins between the two urine collection methods. The biological characteristics overrule this variation. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information.

A novel urinary biomarker protein panel to identify children with ureteropelvic junction obstruction - A pilot study

INTRODUCTION AND OBJECTIVE

Reliable urinary biomarker proteins would be invaluable in identifying children with ureteropelvic junction obstruction (UPJO) as the existing biomarker proteins are inconsistent in their predictive ability. Therefore, the aim of this study was to identify consistent and reliable urinary biomarker proteins in children with UPJO.

METHODS

To identify candidate biomarker proteins, total protein from age-restricted (<2 years) and sex-matched (males) control (n = 22) and UPJO (n = 21) urine samples was analyzed by mass spectrometry. Proteins that were preferentially identified in UPJO samples were selected (2-step process) and ranked according to their diagnostic odds ratio value. The top ten proteins with highest odds ratio values were selected and tested individually by ELISA. The total amount of each protein was normalized to urine creatinine and the median with interquartile ranges for control and UPJO samples was determined. Additionally, fold change (UPJO/Control) of medians of the final panel of 5 proteins was also determined. Finally, we calculated the average + 3(SD) and average + 4(SD) values of each of the 5 proteins in the control samples and used it as an arbitrary cutoff to classify individual control and UPJO samples.

RESULTS

In the first step of our selection process, we identified 171 proteins in UPJO samples that were not detected in the majority of the control samples (16/22 samples, or 72.7%). Of the 171 proteins, only 50 proteins were detected in at least 11/21 (52.4%) of the UPJO samples and hence were selected in the second step. Subsequently, these 50 proteins were ranked according to the odds ratio value and the top 10 ranked proteins were validated by ELISA. Five of the 10 proteins - prostaglandin-reductase-1, ficolin-2, nicotinate-nucleotide pyrophosphorylase [carboxylating], immunoglobulin superfamily-containing leucine-rich-repeat-protein and vascular cell adhesion molecule-1 were present at higher levels in the UPJO samples (fold-change of the median protein concentrations ranging from 2.9 to 9.4) and emerged as a panel of biomarkers to identify obstructive uropathy. Finally, the order of prevalence of the 5 proteins in UPJO samples is PTGR1>FCN2>QPRT>ISLR>VCAM1.

CONCLUSION

In summary, this unique screening strategy led to the identification of previously unknown biomarker proteins that when screened collectively, may reliably distinguish between obstructed vs. non-obstructed infants and may prove useful in identifying informative biomarker panels for biological samples from many diseases.

A single-center study to evaluate the efficacy of a fetal urine peptide signature predicting postnatal renal outcome in fetuses with posterior urethral valves

BACKGROUND

Posterior urethral valves (PUVs) account for 17% of pediatric renal failure. The management of pregnancies involving fetuses with PUV is hampered by the fact that current clinical parameters obtained from fetal ultrasound and/or fetal urine biochemistry are insufficient to predict postnatal renal function. We previously have developed a fetal urine peptide signature (12PUV) that predicted with high precision postnatal renal failure at 2 years of age in fetuses with PUV. Here, we evaluated the accuracy of this signature to predict postnatal renal outcome in fetuses with PUV in an independent single-center study.

METHODS

Thirty-three women carrying fetuses with suspected PUV were included. Twenty-five fetuses received vesicoamniotic shunts during pregnancy. PUV was confirmed postnatally in 23 patients. Of those 23 fetuses, 2 were lost in follow-up. Four and 3 patients died in the pre- and perinatal periods, respectively. Follow-up renal function at 6 months of age was obtained for the remaining 14 patients. The primary outcome was early renal failure, defined by an eGFR < 60 mL/min/1.73 m² before 6 months of age or pre- or perinatal death.

RESULTS

The peptide signature predicted postnatal renal outcome in postnatally confirmed PUV fetuses with an AUC of 0.94 (95%CI 0.74-1.0) and an accuracy of 90% (95%CI 78-100). The signature predicted postnatal renal outcome for the suspected PUV cases with an AUC of 0.89 (95%CI 0.72-0.97) and an accuracy of 84% (95%CI 71-97).

CONCLUSIONS

This single-center study confirms the predictive power of the previously identified 12PUV fetal urinary peptide signature.

Implementation of Proteomics Biomarkers in Nephrology: From Animal Models to Human Application?

Preclinical animal models are extensively used in nephrology. In this review, the utility of performing proteome analysis of kidney tissue or urine in such models and transfer of the results to human application has been assessed. Analysis of the literature identified 68 relevant publications. Pathway analysis of the reported proteins clearly indicated links with known biological processes in kidney disease providing validation of the observed changes in the preclinical models. However, although most studies focused on the identification of early markers of kidney disease or prediction of its progression, none of the identified makers has made it to substantial validation in the clinic or at least in human samples. Especially in renal disease where urine is an abundant source of biomarkers of diseases of the kidney and the urinary tract, it therefore appears that the focus should be on human material based discovery studies. In contrast, the most valid information of proteome analysis of preclinical models in nephrology for translation in human disease resides in studies focusing on drug evaluation, both efficacy for translation to the clinic and for mechanistic insight.

Urinary proteomics using capillary electrophoresis coupled to mass spectrometry for diagnosis and prognosis in kidney diseases

PURPOSE OF REVIEW

Urine is the most useful of body fluids for biomarker research. Therefore, we have focused on urinary proteomics, using capillary electrophoresis coupled to mass spectrometry, to investigate kidney diseases in recent years.

RECENT FINDINGS

Several urinary proteomics studies for the detection of various kidney diseases have indicated the potential of this approach aimed at diagnostic and prognostic assessment. Urinary protein biomarkers such as collagen fragments, serum albumin, α-1-antitrypsin, and uromodulin can help to explain the processes involved during disease progression.

SUMMARY

Urinary proteomics has been used in several studies in order to identify and validate biomarkers associated with different kidney diseases. These biomarkers, with improved sensitivity and specificity when compared with the current gold standards, provide a significant alternative for diagnosis and prognosis, as well as improving clinical decision-making.

The molecular biology of pelvi-ureteric junction obstruction

Over recent years routine ultrasound scanning has identified increasing numbers of neonates as having hydronephrosis and pelvi-ureteric junction obstruction (PUJO). This patient group presents a diagnostic and management challenge for paediatric nephrologists and urologists. In this review we consider the known molecular mechanisms underpinning PUJO and review the potential of utilising this information to develop novel therapeutics and diagnostic biomarkers to improve the care of children with this disorder.

Urinary biomarkers for renal tract malformations

INTRODUCTION

Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications. Areas covered: In this review, we summarized relevant studies identified in "Pubmed" using the keywords "urinary biomarkers" and "proteomics" and "renal tract malformations" or "hydronephrosis" or "ureteropelvic junction obstruction" or "posterior urethral valves" or "vesicoureteral reflux". These publications represent studies on potential protein-based biomarkers, either individually or combined in panels, of RTMs in human and animal models. Expert commentary: Successful use in the clinic of these protein-based biomarkers will need to involve larger scale studies to reach sufficient power. Improved performance will potentially come from combining immunoassay- and MS-based markers.

Prognostic factors and biomarkers of congenital obstructive nephropathy

Congenital obstructive nephropathy (CON) is the leading cause of chronic kidney disease (CKD) in children. Anomalies of the urinary tract are often associated with abnormal nephrogenesis, which is compounded by obstructive injury and by maternal risk factors associated with low birth weight. Currently available fetal and postnatal imaging and analytes of amniotic fluid, urine, or blood lack predictive value. For ureteropelvic junction obstruction, biomarkers are needed for optimal timing of pyeloplasty; for posterior urethral valves, biomarkers of long-term prognosis and CKD are needed. The initial nephron number may be a major determinant of progression of CKD, and most patients with CON who progress to renal failure reach this point in adulthood, presumably compounded by episodes of acute kidney injury. Biomarkers of tubular injury may be of particular value in predicting the need for surgical intervention or in tracking progression of CKD, and must be adjusted for patient age. Discovery of new biomarkers may depend on "unbiased" proteomics, whereby patterns of urinary peptide fragments from patients with CON are analyzed in comparison to controls. Most promising are the analysis of urinary exosomes (restricting biomarkers to relevant tubular cells) and quantitative magnetic resonance imaging techniques allowing precise determination of nephron number and tubular mass. The greatest need is for large prospective multicenter studies with centralized biomarker sample repositories to follow patients with CON from fetal life through adulthood.

Urine exoglycosidases are potential markers of renal tubular injury in children with ureteropelvic junction obstruction

AIM

Hydronephrosis caused by ureteropelvic junction obstruction (UPJO) is an important problem in children and young adults. The aim of this pilot study was to determine the urine profiles of a number of lysosomal exoglycosidases to see whether they indicated tubular renal damage in children with UPJO.

METHODS

We measured lysosomal exoglycosidases urine activities in 32 patients with UPJO, dividing them into three groups. The surgical group comprised 16 children with severe hydronephrosis who required surgery, the nonsurgical group comprised 16 patients with mild hydronephrosis, and the reference group comprised 42 healthy children. The following indicators were measured: N-acetyl-β-hexosaminidase and its A and B isoenzymes, α-fucosidase, β-galactosidase, α-mannosidase and β-glucuronidase.

RESULTS

The urine activities of all exoglycosidases were significantly higher in children with UPJO than children in the reference group (p < 0.01). A strong positive correlation was also found between most of the urine exoglycosidases and the urine albumin/creatinine ratio (p < 0.01).

CONCLUSION

Our findings demonstrated that children with UPJO showed increased renal activities of assessed exoglycosidases, which correlated positively with the urine albumin/creatinine ratio. A larger multicentre study is required to confirm the clinical applications of these observations.

Congenital urinary tract obstruction: the long view

Maldevelopment of the collecting system resulting in urinary tract obstruction (UTO) is the leading identifiable cause of CKD in children. Specific etiologies are unknown; most cases are suspected by discovering hydronephrosis on prenatal ultrasonography. Congenital UTO can reduce nephron number and cause bladder dysfunction, which contribute to ongoing injury. Severe UTO can impair kidney growth in utero, and animal models of unilateral ureteral obstruction show that ischemia and oxidative stress cause proximal tubular cell death, with later development of interstitial fibrosis. Congenital obstructive nephropathy, therefore, results from combined developmental and obstructive kidney injury. Because of inadequacy of available biomarkers, criteria for surgical correction of upper tract obstruction are poorly established. Lower tract obstruction requires fetal or immediate postnatal intervention, and the rate of progression of CKD is highly variable. New biomarkers based on proteomics and determination of glomerular number by magnetic resonance imaging should improve future care. Angiotensin inhibitors have not been effective in slowing progression, although avoidance of nephrotoxins and timely treatment of hypertension are important. Because congenital UTO begins in fetal life, smooth transfer of care from perinatologist to pediatric and adult urology and nephrology teams should optimize quality of life and ultimate outcomes for these patients.

Proteomic urinary biomarker approach in renal disease: from discovery to implementation

Biomarkers hold the promise of significantly improving health care by enabling prognosis and diagnosis with improved accuracy, and at earlier points in time. Previous results have indicated that single biomarkers are not suitable to describe complex diseases such as kidney disease. Here we provide an update on the progress of urinary proteomics-based studies and strategies to develop biomarker-based classifiers that tolerate instability and inconsistency of individual biomarkers. The examples focus on two major fields in nephrology: chronic kidney disease in the adult population and obstructive nephropathies in the pediatric population. When employed adequately, urinary proteomics demonstrates a clear value in kidney disease, indicating that the current status quo ruling for decades now could be changed by applying modern "omics" approaches. However, while research is able to deliver these useful tools for patient management, the issues associated with implementation are not yet solved. Active engagement of the relevant clinical professional societies, as well as patient's organizations, might help to implement these omics approaches that have shown a clear benefit for the patient.

Label-free quantitative urinary proteomics identifies the arginase pathway as a new player in congenital obstructive nephropathy

Obstructive nephropathy is a frequently encountered situation in newborns. In previous studies, the urinary peptidome has been analyzed for the identification of clinically useful biomarkers of obstructive nephropathy. However, the urinary proteome has not been explored yet and should allow additional insight into the pathophysiology of the disease. We have analyzed the urinary proteome of newborns (n = 5/group) with obstructive nephropathy using label free quantitative nanoLC-MS/MS allowing the identification and quantification of 970 urinary proteins. We next focused on proteins exclusively regulated in severe obstructive nephropathy and identified Arginase 1 as a potential candidate molecule involved in the development of obstructive nephropathy, located at the crossroad of pro- and antifibrotic pathways. The reduced urinary abundance of Arginase 1 in obstructive nephropathy was verified in independent clinical samples using both Western blot and MRM analysis. These data were confirmed in situ in kidneys obtained from a mouse obstructive nephropathy model. In addition, we also observed increased expression of Arginase 2 and increased total arginase activity in obstructed mouse kidneys. mRNA expression analysis of the related arginase pathways indicated that the pro-fibrotic arginase-related pathway is activated during obstructive nephropathy. Taken together we have identified a new actor in the development of obstructive nephropathy in newborns using quantitative urinary proteomics and shown its involvement in an in vivo model of disease. The present study demonstrates the relevance of such a quantitative urinary proteomics approach with clinical samples for a better understanding of the pathophysiology and for the discovery of potential therapeutic targets.

Clinical proteomics in obstetrics and neonatology

Clinical proteomics has been applied to the identification of biomarkers of obstetric and neonatal disease. We will discuss a number of encouraging studies that have led to potentially valid biomarkers in the context of Down's syndrome, preterm birth, amniotic infections, preeclampsia, intrauterine growth restriction and obstructive uropathies. Obtaining noninvasive biomarkers (e.g., from the maternal circulation, urine or cervicovaginal fluid) may be more feasible for obstetric diseases than for diseases of the fetus, for which invasive methods are required (e.g., amniotic fluid, fetal urine). However, studies providing validated proteomics-identified biomarkers are limited. Efforts should be made to save well-characterized samples of these invasive body fluids so that many valid biomarkers of pregnancy-related diseases will be identified in the coming years using proteomics based analysis upon adoption of 'clinical proteomics guidelines'.

Evaluation of TGF-β1, CCL5/RANTES and sFas/Apo-1 urine concentration in children with ureteropelvic junction obstruction

INTRODUCTION

The aim of this study was to evaluate changes in expression of soluble biomarkers tumor factor growth-β1 (TGF-β1), CCL5/RANTES, and sFas/Apo-1 in the urine of patients undergoing ureteropyeloplasty for ureteropelvic junction (UPJ) obstruction. These factors are connected with different processes ongoing in the obstructive uropathy. If their urine concentrations correlate with AP diameter of the renal pelvis and differential function of the affected kidney, they can be helpful in making a decision on corrective surgery.

MATERIAL AND METHODS

Creatinine, TGF-β1, CCL5/RANTES, and sFas/Apo-1 levels were measured in the urine from the bladder and renal pelvis of 45 patients undergoing ureteropyeloplasty and from bladders of 25 patients undergoing inguinal herniorrhaphy.

RESULTS

LEVELS OF EXAMINED BIOMARKERS WERE HIGHER IN THE RENAL PELVIS AND BLADDER OF CHILDREN WITH UPJ OBSTRUCTION AS COMPARED TO CONTROLS: TGF-β1 in older children and adolescents (p < 0.05), CCL5/RANTES in the youngest and older children (p < 0.05), and sFas/Apo-1 in all patients (p < 0.05). Twelve months after surgery their levels in the bladder decreased: TGF-β1 in younger and older children (p < 0.05), CCL5/RANTES in the youngest patients and adolescents (p < 0.05), and sFas/Apo-1 in the youngest and older children (p < 0.05). A significant decrease in the AP diameter of the renal pelvis post-operatively (32.09 mm vs. 18.72 mm) (p < 0.01) and significant improvement in renal function (36.94% vs. 42.76%) (p < 0.05) were observed in the examined group.

CONCLUSIONS

Mean TGF-β1, CCL5/RANTES, and sFas/Apo-1 urine levels are significantly increased in patients with UPJ and decreased 1 year after ureteropyeloplasty. Bladder concentrations of examined factors may be clinically useful markers of obstruction.

Glomerular filtration rate and urine osmolality in unilateral ureteropelvic junction obstruction

Background:

Renal maldevelopment, interstitial fibrosis, ischemic atrophy, decreased glomerular filtration rate (GFR), and renal blood flow (RBF) are inevitable consequences of chronic kidney obstruction that only partially improve after early intervention. There are only few studies that evaluated urine osmolality in affected kidney and its correlation with short-term outcome.

Materials and Methods:

Thirty patients (age<1 year) with unilateral ureteropelvic junction obstruction (UUPJO) were enrolled in this study. UUPJO was confirmed using Technetium 99 isotope scans and the patients were indicated to be operated afterward. Urine and blood samples were obtained before, 24, 48, and 72 h after the surgery. The serum level of blood urea nitrogen, creatinine, and glucose were measured. GFR, urine osmolality (measured and calculated), and urine specific gravity were determined too.

Results:

Cortical thickness of hydronephrotic kidney was significantly increased 6 months after the surgery. GFR was significantly increased 72-h postsurgery compared to before operation.

Neither means of calculated nor of measured urine osmolalities were significantly different in various stages. The last calculated urine osmolality (72 h) had significant correlation with the last measured osmolality (72 h); r=0.962, P=0.0001. The last GFR (72 h) had positive significant correlation with GFR before the surgery and GFRs at 24 and 48 h postsurgery.

Using regression tests, only the before surgery GFR was the predictor of the last GFR(72 h).

Conclusion:

In UUPJO the measured and calculated urine osmolality of the affected kidney did not differ. In addition, GFR before surgery should be considered as the predictor of the GFR shortly after repair.

Urinary NGAL levels correlate with differential renal function in patients with ureteropelvic junction obstruction undergoing pyeloplasty

PURPOSE

Recent investigations described the use of NGAL, a sensitive biomarker for kidney injury, in the setting of ureteropelvic junction obstruction. We prospectively evaluated urinary NGAL levels in the affected renal pelvis and bladder of children with ureteropelvic junction obstruction undergoing unilateral dismembered pyeloplasty. Our hypothesis was that higher NGAL in the kidney and bladder would correlate with decreased ipsilateral differential function.

MATERIALS AND METHODS

We performed a prospective cohort study in patients treated with unilateral dismembered pyeloplasty from 2010 to 2012. Urine was obtained intraoperatively from the bladder and obstructed renal pelvis. A control population of unaffected children was recruited to provide a voided bladder specimen. Bladder NGAL levels were compared between the study and control populations. We tested our study hypothesis by correlating bladder and renal pelvic NGAL levels with the differential renal function of the affected kidney.

RESULTS

A total of 61 patients with a median age at surgery of 1.62 years (range 0.12 to 18.7) were enrolled in the study. Median bladder NGAL was 18.6 ng/mg (range 1.4-1,650.8) and median renal pelvic NGAL was 26.2 ng/mg (range 1.2-18,034.5, p = 0.004). Median bladder NGAL was significantly higher than in controls (p = 0.004). The correlation of bladder and renal pelvic NGAL with differential renal function was r = -0.359 (p = 0.004) and r = -0.383 (p = 0.002), respectively.

CONCLUSIONS

Bladder NGAL is increased in children with ureteropelvic junction obstruction. Renal pelvic and bladder normalized urinary NGAL levels correlate inversely with the relative function of the affected kidney in cases of unilateral ureteropelvic junction obstruction.

Metabolomics in adult and pediatric nephrology

Metabolomics, the latest of the “omics” sciences, has a non-selective approach and can thus lead to the identification of all the metabolites (molecules < 1 kDa) in a biological system. The metabolomic profile can be considered the most predictive phenotype capable of evaluating epigenetic modifications determined by external factors. It is so close to the phenotype as to be considered the phenotype itself in its unique individuality (fingerprinting), both in health (phenome), and disease (diseasome). Urine, compared to other biological liquids, has the advantage of being a complex fluid with many components, including intermediate metabolites. Metabolomics may thus play a role in the study of different kidney diseases and overcome diagnostic difficulties. We shall present the studies that to our knowledge have been published on Nephrology and Pediatric Nephrology. Some are experimental while others are clinical. We have not considered carcinomas and transplantations. Although scarce, the data on adults and the very few ones in pediatrics are quite interesting. Further studies on kidneys are needed to determine the practical clinical impact of metabolomics in kidney renal pathologies. The “multiplatform” “omic” study of urine and namely metabolomics can contribute to improving early diagnosis and the outcome of kidney diseases.

Recent advances in capillary electrophoresis-based proteomic techniques for biomarker discovery

Due to the inherent disadvantage of biomarker dilution in complex biological fluids such as serum/plasma, urine, and saliva, investigative studies directed at tissues obtained from the primary site of pathology probably afford the best opportunity for the discovery of disease biomarkers. Still, the large variation of protein relative abundances with clinical specimens often exceeds the dynamic range of currently available proteomic techniques. Furthermore, since the sizes of human tissue biopsies are becoming significantly smaller due to the advent of minimally invasive methods and early detection and treatment of lesions, a more effective discovery-based proteomic technology is critically needed to enable comprehensive and comparative studies of protein profiles that will have diagnostic and therapeutic relevance.This review therefore focuses on the most recent advances in capillary electrophoresis-based single and multidimensional separations coupled with mass spectrometry for performing comprehensive proteomic analysis of clinical specimens. In addition to protein identification, monitoring quantitative changes in protein expression is essential for the discovery of disease-associated biomarkers. Comparative proteomics involving measurements in changes of biological pathways or functional processes are further expected to provide relevant markers and networks, molecular relationships among different stages of disease, and molecular mechanisms that drive the progression of disease.

Urinary cytokine profiles in unilateral congenital hydronephrosis

BACKGROUND

We aimed to evaluate possible clinical application of urinary monocyte chemotactic protein-1 (MCP-1), osteopontin (OPN), and regulated upon activation, normal T-cell expressed and secreted (RANTES) chemokine as useful noninvasive markers in children with congenital hydronephrosis (HN) caused by ureteropelvic junction obstruction (UPJO).

METHODS

The study cohort consisted of surgical cases (study group 1), comprising 15 children with severe HN who required surgery (median age 1.03 years), conservative cases (study group 2), comprising 21 patients with mild, nonobstructive HN, and control group, comprising 19 healthy children. All children had normal renal function. Urinary (u) concentrations of MCP-1, OPN, and RANTES were measured using immunoenzymatic enzyme-linked immunosorbent assay (ELISA) commercial kits and were expressed in nanograms per milligram creatinine. Increased levels of MCP-1 and OPN were found in children with HN in comparison with study group 2 and controls (p < 0.05). UMCP-1/Cr correlated with half-time (T(1/2)) of the elimination phase of tracer excretion of technetium-99m-mercaptoacetyltriglycine ((99m)Tc-MAG-3) (p < 0.05).

RESULTS

Receiver operator characteristic (ROC) analyses revealed good diagnostic profile for uMCP-1 only in identifying children (<40 %) with abnormal differential renal function (DRF) [area under the curve (AUC) 0.862], and in detecting kidney injury in all examined children (AUC 0.704).

CONCLUSIONS

Additional studies with larger number of patients are required to confirm a potential application of uMCP-1 as a promising parameter for early identification of kidney obstruction.

How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS

Clinical proteomics is defined as application of proteome analysis aiming at improving the current clinical situation. As such, the success of clinical proteomics should be assessed based on the clinical impact following implementation of the findings. While we have experienced significant technological advancements in mass spectrometry in the last years, based on the above measure, this has not at all resulted in similar advancements in clinical proteomics. Although a large number of proteomic biomarkers have been described, most of them were not subsequently validated, and certainly have had no impact in clinical decision making as yet. Under the current conditions, it appears likely that the situation will not change significantly: we will be flooded by reports on biomarkers, but not see any implementation. In this article, some key issues in proteomic biomarker research are pinpointed, based on the experience with CE-MS, likely also holding true for biomarkers resulting from other analysis domains.

Urinary proteome analysis in congenital bilateral hydronephrosis

OBJECTIVE

A proteomics strategy was applied to map protein changes in urine after relief of congenital bilateral hydronephrosis to identify proteins correlated with the pathophysiological processes in congenital obstructive nephropathy as potential urinary biomarkers.

MATERIAL AND METHODS

Urine samples from 10 infants with bilateral abnormal drainage from the kidneys were collected at the time of relief from obstruction, and after 2 and 4 weeks. Proteomics techniques were used on samples from three patients for identification of protein changes between the three time-points, and enzyme-linked immunosorbent assay (ELISA) was used on samples from all 10 patients for validation of five selected proteins.

RESULTS

Mass spectrometry quantified 315 protein hits, out of which 33 proteins showed significantly changed urinary excretion between the time-points. Validation by ELISA showed high urinary excretion of fibrinogen, plasminogen, transthyretin and transferrin at the time of relief from obstruction, followed by a significant reduction. In contrast, Tamm-Horsfall protein exhibited the reverse pattern.

CONCLUSION

Using a mass spectrometry-based proteomics approach, this study identified 33 proteins related to congenital bilateral hydronephrosis, and pinpointed a panel of five proteins consistently linked to this congenital kidney disorder as potential urinary biomarkers.

Urinary proteomics in the assessment of chronic kidney disease

PURPOSE OF REVIEW

Urinary proteomics has emerged as an approach that could deliver relevant clinical information. In this review, we aim at highlighting the recent developments, especially with respect to clinical implementation. We review several of the recent publications reporting on larger cohorts, focusing on those that aim at qualification and/or validation of urinary proteomics biomarkers.

RECENT FINDINGS

Several components of the urinary proteome, especially its low molecular weight fraction (sometimes referred to as the 'peptidome'), have been significantly associated with chronic kidney disease (CKD). Independent studies, encompassing sometimes close to 1000 independent samples, indicate that specific peptides from extracellular matrix (ECM) proteins encompass a major component of the urinary proteome. Highly significant changes in the abundance of some of these peptides are associated with CKD indicating that alterations in ECM, reflected via the urinary proteome, may represent an early stage in CKD pathology. These peptides may serve as specific early biomarkers, and interference with pathological ECM accumulation may be a valuable new therapeutic approach in CKD.

SUMMARY

Urinary proteomic biomarkers have emerged as clinically relevant variables. First studies involving several hundred individuals indicate a potential added benefit of urinary proteomic biomarkers. First large clinical trials are being initiated to employ urinary proteomics in clinical decision making.

Urinary proteome analysis to exclude severe vesicoureteral reflux

OBJECTIVES

High-grade vesicoureteral reflux (VUR, grade IV or V) is a risk factor for renal scarring, impaired renal function, and arterial hypertension. Voiding cystourethrography is the gold standard for detecting the severity of VUR. High-grade VUR is present in the minority of children with urinary tract infection (UTI), thus exposing the majority to invasive diagnostics that have no surgical consequence. We therefore aimed at establishing a noninvasive test to identify children with high-grade VUR.

METHODS

In a case-control study, a specific urinary proteome pattern was established by capillary electrophoresis coupled to mass spectrometry in 18 patients with primary VUR grade IV or V, distinguishing these from 19 patients without VUR after UTI. This proteome pattern was independently validated in a blinded cohort of 17 patients with VUR grade IV or V and 19 patients without VUR.

RESULTS

Sensitivity in detecting VUR grade IV or V in the blinded study was 88%, specificity was 79%. The test's accuracy was independent of age, gender, and grade of VUR in the contralateral kidney. The odds ratio of suffering from VUR grade IV or V when tested positive was 28 (95% confidence interval: 4.5 to 176.0).

CONCLUSIONS

This noninvasive test is ready for prospective validation in large cohorts with the aim of identifying those children with UTI and hydronephrosis in need of further invasive diagnostics, such as voiding cystourethrography, thus sparing most children without pathologic urinary proteome patterns from additional diagnostics.

Urinary proteome analysis at 5-year followup of patients with nonoperated ureteropelvic junction obstruction suggests ongoing kidney remodeling

PURPOSE

Severe ureteropelvic junction obstruction is treated surgically. However, for milder cases most clinical teams adopt a watchful waiting approach and only operate in the presence of significant decline of renal function combined with severe hydronephrosis. Little is known about the long-term consequences of ureteropelvic junction obstruction.

MATERIALS AND METHODS

Using capillary electrophoresis coupled with mass spectrometry, we analyzed the urinary proteome of 42 patients with ureteropelvic junction obstruction 5 years postoperatively or 5 years following spontaneous resolution.

RESULTS

At 5-year followup urinary proteomes were similar between patients with early surgical correction of ureteropelvic junction obstruction and age matched controls. In contrast, urinary proteomes differed significantly between conservatively followed patients and controls. Analyses of the proteomic differences suggested ongoing renal or ureteral remodeling in the conservatively followed patients that was not visible clinically.

CONCLUSIONS

Long-term followup studies are warranted in patients with ureteropelvic junction obstruction, especially those followed conservatively, to determine whether the observed changes in the urinary proteomes become clinically relevant at a later stage.

Urinary metabolomics in newborns and infants

Metabolomics is a new approach based on the systematic study of the full complement of metabolites in a biological sample. This technology consists of two sequential steps: (1) an experimental technique, based on nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry, designed to profile low-molecular-weight compounds, and (2) multivariate data analysis. The metabolomic analysis of biofluids or tissues has been successfully used in the fields of physiology, diagnostics, functional genomics, pharmacology, toxicology, and nutrition. Recent studies have evaluated how physiological variables or pathological conditions can affect metabolomic profiles of different biofluids in pediatric populations. The overall metabolic status of the neonate is little known. If more information on perinatal/neonatal maturational processes and their metabolic background were available, the management of sick or preterm newborns might be improved. Currently, the use of metabolomics in neonatology is still in the pioneering phase. Meaningful diagnostic information and simple, noninvasive collection techniques make urine a particularly suitable biofluid for metabolomic approach in neonatal medicine, although blood has also been investigated. Different fields of neonatology such as postnatal maturation, asphyxia/hypoxia, inborn errors of metabolism, nutrition, nephrouropathies, nephrotoxicity, cardiovascular diseases, and other conditions have been investigated using a metabolomic approach. Together with genomics and proteomics, metabolomics appears to be a promising tool in neonatology for the monitoring of postnatal metabolic maturation, the identification of biomarkers as early predictors of outcome, the diagnosis and monitoring of various diseases, and the "tailored" management of neonatal disorders.

Urinary levels of TGF β-1 and of cytokines in patients with prenatally detected nephrouropathies

This study aimed to identify noninvasive biomarkers of clinically significant nephrouropathies in patients with antenatal renal and/or urinary tract alterations. Spot-urine levels of interleukin-6 (IL-6), transforming growth factor-β1 (TGF-β1) and tumor necrosis factor-α (TNF-α) were measured in 100 patients with antenatal detected nephrouropathies. Patients were divided in idiopathic hydronephrosis (n = 47), urinary tract malformations (n  = 35), and dysplastic kidneys (n = 18). Urinary concentrations of TGF-β1, IL-6, and TNF-α were compared between groups according to clinical and image findings. Receiver-operating characteristic (ROC) curves were analyzed for the overall diagnostic accuracy of TGF-β1, IL-6, and TNF-α levels in discriminating infants with nephrouropathies. No significant differences in urinary TGF- β1, IL-6, and TNF-α levels were found in the comparison between the groups. TGF-β1 levels tended to be higher in patients with renal hypodysplasia compared to idiopathic hydronephrosis (p = 0.07). Twenty-nine patients had reduced DMSA uptake. In these cases, absolute urinary concentration of TGF-β1 and levels standardized for creatinine were significantly higher than in patients with normal DMSA uptake, while IL6 and TNF-α did not differ between groups. Urinary cytokine measurements were not useful as a screening test for clinically significant nephrouropathies. Conversely, increased concentrations of TGF-β1 pointed out to renal damage as indicated by reduced DMSA uptake.

Urinary biomarkers in prenatally diagnosed unilateral hydronephrosis

The introduction of prenatal ultrasonography as a screening method entails an increasing number of infants diagnosed with prenatal hydronephrosis. Ureteropelvic junction obstruction accounts for 35% of prenatal hydronephrotic cases. Urinary tract obstruction that occurs during early kidney development affects renal morphogenesis, maturation and growth, and in the most severe cases this will ultimately cause renal insufficiency. A major challenge in the clinical management of these patients is to preserve renal function by selection of the 15%-20% who require early surgical intervention, leaving those for whom watchful waiting may be appropriate because of spontaneous resolution/stabilization without significant loss of renal function. Today, this requires medical surveillance, including repetitive invasive diuretic renograms relying on arbitrary threshold values, and therefore there is a need for non-arbitrary, non-invasive urinary biomarkers that may be used as predictors for renal structural changes and/or decreasing renal function, and thereby provide the surgeon with more clear indications for surgical intervention. In this review, we summarize the currently well-known facts about urinary biomarkers in ureteropelvic junction obstruction concerning renal function, and we also suggest potential novel urinary biomarkers.

Capillary electrophoresis-mass spectrometry for the analysis of intact proteins 2007-2010

CE coupled to MS has proven to be a powerful analytical tool for the characterization of intact proteins, as it combines the high separation efficiency of CE with the selectivity of MS. This review provides an overview of the development and application of CE-MS methods within the field of intact protein analysis as published between January 2007 and June 2010. Ongoing technological developments with respect to CE-MS interfacing, capillary coatings for CE-MS, coupling of CIEF with MS and chip-based CE-MS are treated. Furthermore, CE-MS of intact proteins involving ESI, MALDI and ICP ionization is outlined and overviews of the use of the various CE-MS methods are provided by tables. Representative examples illustrate the applicability of CE-MS for the characterization of proteins, including glycoproteins, biopharmaceuticals, protein-ligand complexes, biomarkers and dietary proteins. It is concluded that CE-MS is a valuable technique with high potential for intact protein analysis, providing useful information on protein identity and purity, including modifications and degradation products.

Urinary proteomics based on capillary electrophoresis-coupled mass spectrometry in kidney disease: discovery and validation of biomarkers, and clinical application

Use of capillary electrophoresis coupled to mass spectrometry (CE-MS) technology in proteome analysis has increased, with a focus on the identification of biomarker peptides in clinical proteomics. Among the reported applications, the main focus is on the urinary biomarkers for kidney disease. In this review, we discuss the principal, theoretical, and practical obstacles that are encountered when using CE-MS for the analysis of body fluids for biomarker discovery. We present several examples of a successful application of CE-MS for biomarker discovery in kidney disease, implications for disease diagnosis, prognosis, and therapy evaluation, and will also discuss current challenges and possible future improvements.

Urinary proteome analysis and the management of ureteropelvic junction obstruction

Ureteropelvic junction obstruction (UPJO) detected prenatally may over time deteriorate and require surgery, improve, or remain stable, and it may take upwards of 3 years for its natural history to unfold. Clinical decisions for or against operative corrections are usually based on scintigraphy follow-up studies. A non-invasive method for facilitating clinical decisions has recently been presented: urinary proteome analysis utilizing capillary electrophoresis mass spectrometry (CE-MS) has been shown to predict the outcome of UPJO in newborns. The group that developed this assay has now validated their seminal findings and extended the investigations to older age groups (this issue). The results of the blinded analysis correctly identified patients with UPJO who underwent surgery with a sensitivity of 83% (5 of 6 patients) and a specificity of 92% (12 of 13 patients) in infants up to 1 year of age. The validity of the analysis was poor in children >1 year of age with unilateral UPJO. A large number of patients will be needed to answer the question of to what extent the normal variability of urinary proteomes overlap with the variability of the pattern in UPJO beyond early infancy.