Urinary proteomics: a tool to discover biomarkers of kidney diseases

There is intense interest in applying proteomics to urine analysis in order to promote a better understanding of kidney disease processes, develop new biomarkers for diagnosis and detect early factors that contribute to end–stage renal diseases. This interest creates numerous opportunities as well as challenges. To fulfill this task, proteomics requires, in its different stages of realization, various technological platforms with high sensitivity, high throughput and large automation ability. In this review, we will give an overview of promising proteomic methods that can be used for analyzing urinary proteome and detecting biomarkers for different kidney diseases. Furthermore, we will focus on the current status and future directions in investigating kidney diseases using urinary proteomics.     

Biology and proteomics of extracellular vesicles: harnessing their clinical potential

Extracellular membrane vesicles have recently emerged as versatile mediators of intercellular communication, pathogenesis, drug and gene delivery and as potentially rich reservoirs of clinical biomarkers. Channeling their properties toward patient care is dependent on technological progress in approaches used for their analysis and molecular profiling.     

Leptin and chronic kidney diseases

Chronic kidney diseases (CKD), a common outcome of various kidney diseases, cause a series of refractory complications, which lead to great economic burdens on patients. The clinical outcomes of CKD depend on various factors, including metabolic disorders. Leptin, a peptide hormone, produced in adipose tissues, plays an important role in regulating food consumption and energy expenditure. Leptin also influences the immune system and hematopoiesis. Increased leptin status is observed in CKD, leptin deficiency attenuates the immune response in nephritis. Conversely, leptin inhibits the development of obesity, which is closely associated glomerular disorder. Now, the precise role of leptin in CKD remains elusive. This review will give an integrated understanding of the potential role of leptin and its interactions with other signal molecules in CKD.     

Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers

Exosomes are tiny vesicles (30–150 nm) constantly secreted by all healthy and abnormal cells, and found in abundance in all body fluids. These vesicles, loaded with unique RNA and protein cargo, have a wide range of biological functions, including cell-to-cell communication and signalling. As such, exosomes hold tremendous potential as biomarkers and could lead to the development of minimally invasive diagnostics and next generation therapies within the next few years. Here, we describe the strategies for isolation of exosomes from human blood serum and urine, characterization of their RNA cargo by sequencing, and present the initial data on exosome labelling and uptake tracing in a cell culture model. The value of exosomes for clinical applications is discussed with an emphasis on their potential for diagnosing and treating neurodegenerative diseases and brain cancer.     

Urinary proteomics: a tool to discover biomarkers of kidney diseases

There is intense interest in applying proteomics to urine analysis in order to promote a better understanding of kidney disease processes, develop new biomarkers for diagnosis and detect early factors that contribute to end-stage renal diseases. This interest creates numerous opportunities as well as challenges. To fulfill this task, proteomics requires, in its different stages of realization, various technological platforms with high sensitivity, high throughput and large automation ability. In this review, we will give an overview of promising proteomic methods that can be used for analyzing urinary proteome and detecting biomarkers for different kidney diseases. Furthermore, we will focus on the current status and future directions in investigating kidney diseases using urinary proteomics.     

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’.     

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.     

Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases

Chronic kidney disease (CKD) is the gradual decrease in renal function. Currently available biomarkers are effective only in detecting late stage CKD. Biomarkers of early stage CKD and prognostic biomarkers are required. We review the major findings in urinary proteomics in CKD during the last five years. Significant progress has been made and today urinary proteomics is applied in large randomized trials, and in patient management. Many of the biomarkers indicate altered protease activity. We therefore also review the literature on proteases associated with renal function loss. We anticipate in silico prediction tools of protease activity and additional system biology studies may contribute to biomarker discovery and elucidate the role of proteases in CKD development and progression. These approaches will enable the deciphering of the molecular pathophysiology of CKD, and hence definition of the most appropriate therapeutic targets in the future. Together with stable biomarker panels available today, this will significantly improve patient management.     

Urinary proteomics in chronic kidney disease: diagnosis and risk of progression beyond albuminuria

Background

The contrast between a high prevalence of chronic kidney disease (CKD) and the low incidence of end-stage renal disease highlights the need for new biomarkers of progression beyond albuminuria testing. Urinary proteomics is a promising method, but more studies focusing on progression rate and patients with hypertensive nephropathy are needed.

Results

We analyzed urine samples with capillary electrophoresis coupled to a mass-spectrometer from 18 well characterized patients with CKD stage 4–5 (of whom six with hypertensive nephropathy) and 17 healthy controls. Classification scores based on a previously developed panel of 273 urinary peptides were calculated and compared to urine albumin dipstick results. Urinary proteomics classified CKD with a sensitivity of 0.95 and specificity of 1.00. Overall diagnostic accuracy (area under ROC curve) was 0.98, which was better than for albuminuria (0.85, p = 0.02). Results for hypertensive nephropathy were similar to other CKD diagnoses. Adding the proteomic score to an albuminuria model improved detection of rapid kidney function decline (>4 ml/min/1.73 m² per year) substantially: area under ROC curve increased from 0.762 to 0.909 (p = 0.042), and 38% of rapid progressors were correctly reclassified to a higher risk and 55% of slow progressors were correctly reclassified to a lower risk category. Reduced excretion of collagen types I–III, uromodulin, and other indicators of interstitial inflammation, fibrosis and tubular dysfunction were associated with CKD diagnosis and rapid progression. Patients with hypertensive nephropathy displayed the same findings as other types of CKD.

Conclusions

Urinary proteomic analyses had a high diagnostic accuracy for CKD, including hypertensive nephropathy, and strongly improved identification of patients with rapid kidney function decline beyond albuminuria testing.     

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.