Early prediction of acute renal injury using urinary proteomics

Urinary proteome profiling for stratifying patients with familial Parkinson's disease

The prevalence of Parkinson's disease (PD) is increasing but the development of novel treatment strategies and therapeutics altering the course of the disease would benefit from specific, sensitive, and non‐invasive biomarkers to detect PD early. Here, we describe a scalable and sensitive mass spectrometry (MS)‐based proteomic workflow for urinary proteome profiling. Our workflow enabled the reproducible quantification of more than 2,000 proteins in more than 200 urine samples using minimal volumes from two independent patient cohorts. The urinary proteome was significantly different between PD patients and healthy controls, as well as between LRRK2 G2019S carriers and non‐carriers in both cohorts. Interestingly, our data revealed lysosomal dysregulation in individuals with the LRRK2 G2019S mutation. When combined with machine learning, the urinary proteome data alone were sufficient to classify mutation status and disease manifestation in mutation carriers remarkably well, identifying VGF, ENPEP, and other PD‐associated proteins as the most discriminating features. Taken together, our results validate urinary proteomics as a valuable strategy for biomarker discovery and patient stratification in PD.

Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery

Sensitive and specific diagnostic and prognostic biomarkers for prostate cancer (PCa) are urgently needed. Urine samples are a non-invasive means to obtain abundant and readily accessible “liquid biopsies”. Herein we used urine liquid biopsies to identify and characterize a novel group of urine-enriched RNAs and metabolites in patients with PCa and normal individuals with or without benign prostatic disease. Differentially expressed RNAs were identified in urine samples by deep sequencing and metabolites in urine were measured by mass spectrometry. mRNA and metabolite profiles were distinct in patients with benign and malignant disease. Integrated analysis of urinary gene expression and metabolite signatures unveiled an aberrant glutamate metabolism and tricarboxylic acid (TCA) cycle node in prostate cancer-derived cells. Functional validation supported a role for glutamate metabolism and glutamate oxaloacetate transaminase 1 (GOT1)-dependent redox balance in PCa, which could be exploited for novel biomarkers and therapies. In this study, we discovered cancer-specific changes in urinary RNAs and metabolites, paving the way for the development of sensitive and specific urinary PCa diagnostic biomarkers either alone or in combination. Our methodology was based on single void urine samples (i.e., without prostatic massage). The integrated analysis of metabolomic and transcriptomic data from these liquid biopsies revealed a glutamate metabolism and tricarboxylic acid cycle node that was specific to prostate-derived cancer cells and cancer-specific metabolic changes in urine.

Urine proteomics study reveals potential biomarkers for the differential diagnosis of cholangiocarcinoma and periductal fibrosis

Cholangiocarcinoma (CCA) is a primary malignant tumor of the epithelial lining of biliary track associated with endemic Opisthorchis viverrini (Ov) infection in northeastern Thailand. Ov-associated periductal fibrosis (PDF) is the precancerous lesion for CCA, and can be detected by ultrasonography (US) to facilitate early detection. However, US cannot be used to distinguish PDF from cancer. Therefore, the objective of this study was to discover and qualify potential urine biomarkers for CCA detection in at-risk population. Biomarker discovery was conducted on pooled urine samples, 42 patients per group, with PDF or normal bile duct confirmed by ultrasound. After depletion of high abundance proteins, 338 urinary proteins were identified from the 3 samples (normal-US, PDF-US, CCA). Based on fold change and literature review, 70 candidate proteins were selected for qualification by multiple reaction monitoring mass spectrometry (MRM-MS) in 90 individual urine samples, 30 per group. An orthogonal signal correction projection to latent structures discriminant analysis (O-PLS-DA) multivariate model constructed from the 70 candidate biomarkers significantly discriminated CCA from normal and PDF groups (P = 0.003). As an independent validation, the expression of 3 candidate proteins was confirmed by immunohistochemistry in CCA tissues: Lysosome associated membrane glycoprotein 1 (LAMP1), lysosome associated membrane glycoprotein 2 (LAMP2) and cadherin-related family member 2 (CDHR2). Further evaluation of these candidate biomarkers in a larger cohort is needed to support their applicability in a clinical setting for screening and monitoring early CCA and for CCA surveillance.

[Acute kidney injury: from creatinine to KIM‑1?]

In addition to the early detection of an acute kidney injury (AKI), several problems or questions have to be addressed. These include the identification of the etiology, the severity (functional or structural), the prognosis (recovery or transition to chronic renal failure), the course of the disease (dialysis or not), and the identification of specific treatment options for AKI. The following article provides an overview of established and new AKI biomarkers as well as an outlook on the potential of future biomarker-associated models of AKI.

The role of the tubular biomarkers NAG, kidney injury molecule-1 and neutrophil gelatinase-associated lipocalin in patients with chest pain before contrast media exposition

Aim: We evaluated the role of the tubular biomarkers N-acetyl-ß-D-glucosaminidase (NAG), kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) in patients with chest pain. Methods: Serum and urine samples were collected of 223 patients and 47 healthy controls. None of them was exposed to contrast media. Results: NAG showed among others significant correlation with N-terminal pro brain natriuretic peptide (NTproBNP), troponin I and creatinine. KIM-1 and NGAL showed weaker correlations. NAG was significantly elevated in all subgroups of acute coronary syndrome (ACS) compared with chest wall syndrome and controls. NAG was an independent predictor for the diagnosis of myocardial infarction. Conclusion: NAG may demonstrate the presence of acute tubular injury due to cardiac impairment already in the emergency department. NAG should be evaluated as marker of acute cardiorenal syndrome in patients with chest pain.

Proteomics for Biomarker Identification and Clinical Application in Kidney Disease

Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein. In addition, proteomic biomarkers could also be useful to choose the most suitable therapeutic targets. This review focuses on the current status of proteomic biomarkers from animal models (5/6 nephrectomy, unilateral ureteral obstruction, and diabetic nephropathy) and human studies (chronic kidney disease, glomerular diseases, transplantation, dialysis, acute and drug-induced kidney injury) to assess relevant findings and clinical usefulness. Current issues and problems related to the discovery, validation, and clinical application of proteomic biomarkers are discussed. We also describe several proteomic strategies highlighting technologic advancements, specimen selection, data processing and analysis. This review might provide help in future proteomic studies to improve the diagnosis and management of kidney disease.

The nephrologist of tomorrow: towards a kidney-omic future

Omics refers to the collective technologies used to explore the roles and relationships of the various types of molecules that make up the phenotype of an organism. Systems biology is a scientific discipline that endeavours to quantify all of the molecular elements of a biological system. Therefore, it reflects the knowledge acquired by omics in a meaningful manner by providing insights into functional pathways and regulatory networks underlying different diseases. The recent advances in biotechnological platforms and statistical tools to analyse such complex data have enabled scientists to connect the experimentally observed correlations to the underlying biochemical and pathological processes. We discuss in this review the current knowledge of different omics technologies in kidney diseases, specifically in the field of pediatric nephrology, including biomarker discovery, defining as yet unrecognized biologic therapeutic targets and linking omics to relevant standard indices and clinical outcomes. We also provide here a unique perspective on the field, taking advantage of the experience gained by the large-scale European research initiative called "Systems Biology towards Novel Chronic Kidney Disease Diagnosis and Treatment" (SysKid). Based on the integrative framework of Systems biology, SysKid demonstrated how omics are powerful yet complex tools to unravel the consequences of diabetes and hypertension on kidney function.

Renal injury in neonates: use of "omics" for developing precision medicine in neonatology

Preterm birth is associated with increased risks of morbidity and mortality along with increased healthcare costs. Advances in medicine have enhanced survival for preterm infants but the overall incidence of major morbidities has changed very little. Abnormal renal development is an important consequence of premature birth. Acute kidney injury (AKI) in the neonatal period is multifactorial and may increase lifetime risk of chronic kidney disease.Traditional biomarkers in newborns suffer from considerable confounders, limiting their use for early identification of AKI. There is a need to develop novel biomarkers that can identify, in real time, the evolution of renal dysfunction in an early diagnostic, monitoring and prognostic fashion. Use of "omics", particularly metabolomics, may provide valuable information regarding functional pathways underlying AKI and prediction of clinical outcomes.The emerging knowledge generated by the application of "omics" (genomics, proteomics, metabolomics) in neonatology provides new insights that can help to identify markers of early diagnosis, disease progression, and identify new therapeutic targets. Additionally, omics will have major implications in the field of personalized healthcare in the future. Here, we will review the current knowledge of different omics technologies in neonatal-perinatal medicine including biomarker discovery, defining as yet unrecognized biologic therapeutic targets, and linking of omics to relevant standard indices and long-term outcomes.

The Kidney in Critical Cardiac Disease: Proceedings From the 10th International Conference of the Pediatric Cardiac Intensive Care Society

The field of cardiac intensive care continues to advance in tandem with congenital heart surgery. The focus of intensive care unit care has now shifted to that of morbidity reduction and eventual elimination. Acute kidney injury (AKI) after cardiac surgery is associated with adverse outcomes, including prolonged intensive care and hospital stays, diminished quality of life, and increased long-term mortality. Acute kidney injury occurs frequently, complicating the care of both postoperative patients and those with heart failure. Patients who become fluid overloaded and/or require dialysis are at high risk of mortality, but even minor degrees of AKI portend a significant increase in mortality and morbidity. Clinicians continue to seek methods of early diagnosis and risk stratification of AKI to prevent its adverse sequelae. Previous conventional wisdom that survivors of AKI fully recover renal function without subsequent consequences may be flawed.

Acute Kidney Injury and Cardiorenal Syndromes in Pediatric Cardiac Intensive Care

OBJECTIVES

The objectives of this review are to discuss the definition, diagnosis, and pathophysiology of acute kidney injury and its impact on immediate, short-, and long-term outcomes. In addition, the spectrum of cardiorenal syndromes will be reviewed including the pathophysiology on this interaction and its impact on outcomes.

DATA SOURCE

MEDLINE and PubMed.

CONCLUSION

The field of cardiac intensive care continues to advance in tandem with congenital heart surgery. As mortality has become a rare occurrence, the focus of cardiac intensive care has shifted to that of morbidity reduction. Acute kidney injury adversely impact outcomes of patients following surgery for congenital heart disease as well as in those with heart failure (cardiorenal syndrome). Patients who become fluid overloaded and/or require dialysis are at a higher risk of mortality, but even minor degrees of acute kidney injury portend a significant increase in mortality and morbidity. Clinicians continue to seek methods of early diagnosis and risk stratification of acute kidney injury to prevent its adverse sequelae.

Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases

Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.

Urinary neutrophil gelatinase-associated lipocalin for diagnosis and estimating activity in lupus nephritis: a meta-analysis

Urinary neutrophil gelatinase-associated lipocalin (uNGAL) is relatively specific in lupus nephritis (LN) patients. However, its diagnostic value has not been evaluated. The aim of this review was to determine the value of uNGAL for diagnosis and estimating activity in LN. A comprehensive search was performed on PubMed, EMBASE, Web of Knowledge, Cochrane electronic databases through December 2014. Meta-analysis of sensitivity and specificity was performed with a random-effects model. Additionally, summary receiver operating characteristic (SROC) curves and area under the curve (AUC) values were calculated. Fourteen studies were selected for this review. With respect to diagnosing LN, the pooled sensitivity and specificity were 73.6% (95% confidence interval (CI), 61.9–83.3) and 78.1% (95% CI, 69.0–85.6), respectively. The SROC-AUC value was 0.8632. Regarding estimating LN activity, the pooled sensitivity and specificity were 66.2% (95% CI, 60.4–71.7) and 62.1% (95% CI, 57.9–66.3), respectively. The SROC-AUC value was 0.7583. In predicting renal flares, the pooled sensitivity and specificity were 77.5% (95% CI, 68.1–85.1) and 65.3% (95% CI, 60.0–70.3), respectively. The SROC-AUC value was 0.7756. In conclusion, this meta-analysis indicates that uNGAL has relatively fair sensitivity and specificity in diagnosing LN, estimating LN activity and predicting renal flares, suggesting that uNGAL is a potential biomarker in diagnosing LN and monitoring LN activity.

Genomic and Proteomic Characterization of Acute Kidney Injury

The incidence and severity of acute kidney injury (AKI) is rising globally, and the associated morbidity and mortality remain high despite promising advances in experimental therapeutics. The reasons include (a) an incomplete understanding of the complex pathophysiology, (b) an inability to reliably identify risk factors for AKI and (c) a lack of biomarkers for the early prediction of AKI and its outcomes. Functional genomics, bioinformatics and proteomics have begun to uncover candidates that are emerging as biomarkers and therapeutic targets. This review will update the reader on current technologies in genomics (including targeted sequencing, genome wide association studies and transcriptome profiling) and proteomics (including gel electrophoresis and mass spectrometry methods) and their application on human AKI.

The urinary proteome and metabonome differ from normal in adults with mitochondrial disease

We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin; established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.

Cardiopulmonary bypass changes the plasma proteome in children undergoing tetralogy of Fallot repair

Introduction:

Cardiopulmonary bypass (CPB) can be associated with deleterious clinical effects. However, the impact of CPB on inflammatory, immunological and other homeostatic pathways remains poorly understood. We investigated the impact of CPB on the plasma proteome in children undergoing tetralogy of Fallot repair.

Methods:

Blood samples were taken from 20 children prior to and at the end of CPB and 6h, 12h and 24h after CPB. Plasma was analysed by liquid chromatography-mass spectrometry (LC-MS) in a label-free, untargeted approach. Data were analysed using Genedata software to identify peptides that were differentially expressed (p<0.01 above a false discovery rate). Proteins were identified from peptides that demonstrated differential expression.

Results:

The proteins that were found to be differentially expressed were haptoglobin isoform 1 preproprotein, isoform 2 of semaphorin-6C, vitamin D-binding protein, inter-alpha-trypsin inhibitor, ceruloplasmin, apolipoprotein B100 and fibrinogen alpha.

Conclusion:

CPB alters the plasma proteome with differences most apparent at 6h and 12h post CPB. There was a return to baseline with no proteins differentially regulated by 24h.

Proteomics in paediatric cardiac surgery: is a personalised approach feasible?

The incidence of congenital cardiac abnormalities remains high. Paediatric patients with congenital cardiac defects often require surgery at a young age. The surgeries are often long and complex, rendering this population particularly vulnerable to the deleterious effects of cardiopulmonary bypass and cardiac surgery. The search for cardioprotective strategies is ongoing in an attempt to reduce the morbidity in this population. In the post-genomic era, it is apparent that simply determining the genomic sequences holds little diagnostic potential and means to determine progression of disease and response to treatment. The field of proteomics is expanding and application of proteomic techniques in the clinical setting holds great potential to advance our understanding of the proteomic changes involved in specific disease stages. This review will assess the application of proteomic techniques in the setting of paediatric cardiac surgery and highlight the need to obtain a clear understanding of the role of various proteins in children with cardiac conditions. The success and challenges of the available proteomic technology will be discussed as well as the future potential of proteomic methods for advancing our understanding of protein changes in children requiring cardiac surgery.

SELDI-TOF-MS proteomic profiling of serum, urine, and amniotic fluid in neural tube defects

Neural tube defects (NTDs) are common birth defects, whose specific biomarkers are needed. The purpose of this pilot study is to determine whether protein profiling in NTD-mothers differ from normal controls using SELDI-TOF-MS. ProteinChip Biomarker System was used to evaluate 82 maternal serum samples, 78 urine samples and 76 amniotic fluid samples. The validity of classification tree was then challenged with a blind test set including another 20 NTD-mothers and 18 controls in serum samples, and another 19 NTD-mothers and 17 controls in urine samples, and another 20 NTD-mothers and 17 controls in amniotic fluid samples. Eight proteins detected in serum samples were up-regulated and four proteins were down-regulated in the NTD group. Four proteins detected in urine samples were up-regulated and one protein was down-regulated in the NTD group. Six proteins detected in amniotic fluid samples were up-regulated and one protein was down-regulated in the NTD group. The classification tree for serum samples separated NTDs from healthy individuals, achieving a sensitivity of 91% and a specificity of 97% in the training set, and achieving a sensitivity of 90% and a specificity of 97% and a positive predictive value of 95% in the test set. The classification tree for urine samples separated NTDs from controls, achieving a sensitivity of 95% and a specificity of 94% in the training set, and achieving a sensitivity of 89% and a specificity of 82% and a positive predictive value of 85% in the test set. The classification tree for amniotic fluid samples separated NTDs from controls, achieving a sensitivity of 93% and a specificity of 89% in the training set, and achieving a sensitivity of 90% and a specificity of 88% and a positive predictive value of 90% in the test set. These suggest that SELDI-TOF-MS is an additional method for NTDs pregnancies detection.

How has urinary proteomics contributed to the discovery of early biomarkers of acute kidney injury?

In the past decade, analysis of the urinary proteome (urinary proteomics) has intensified in response to the need for novel biomarkers that support early diagnosis of kidney diseases. In particular, this also applies to acute kidney injury, which is a heterogeneous complex syndrome with a still-increasing incidence at the intensive care unit. Unfortunately, this major need remains largely unmet to date. The current report aims to explain why attempts to implement urinary proteomic-discovered acute kidney injury diagnostic candidates in the intensive care unit setting have not yet led to success. Subsequently, some key notes are provided that should enhance the chance of translating selected urinary proteomic candidates to valuable tools for the nephrologist and intensivist in the near future.

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.

Renal neutrophil gelatinase-associated lipocalin and kidney injury molecule-1 expression in children with acute kidney injury and Henoch-Schönlein purpura nephritis

The aim of this study was to investigate the expression of neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1) in the serum, urine and renal tissues of children with acute kidney injury (AKI) and Henoch-Schönlein purpura nephritis (A-on-C). A prospective single-center evaluation of the serum, urine and renal NGAL and KIM-1 levels was performed in a cohort of children. Blood and 5-ml urine samples were collected from each patient for the analysis of NGAL and KIM-1 levels using an ELISA. In addition, the expression of NGAL and KIM-1 in the kidney was examined using immunohistochemistry in patients with A-on-C and HSPN. The expression of serum cystatin C, β2-macroglobulin and serum creatinine (SCr), as well as urinary β2-MG and SCr, in the patients with A-on-C was significantly higher than that of HSPN patients, and the expression of NGAL and KIM-1 in the serum and urine in the A-on-C patients was also significantly higher than that of HSPN patients. However, there were no significant differences in the urine protein levels between the two groups. NGAL and KIM-1 were expressed in renal tubular epithelial cells, and the expression of NGAL and KIM-1 in the A-on-C patients was significantly higher than that in HSPN patients. In addition, the urine NGAL and KIM-1 levels were negatively correlated with glomerular filtration rate, but there was no significant correlation between the urine NGAL/KIM-1 and urine protein levels. The changes in serum and urine NGAL and KIM-1 levels may be applied to the diagnosis of A-on-C.

Proteomics in acute kidney injury--current status and future promise

Pediatric acute kidney injury (AKI) is associated with increased morbidity, mortality and associated healthcare costs. Unfortunately, there are currently no effective therapies available, and this has been attributed in part to the late diagnosis of AKI. Therefore, significant efforts have been made to develop early diagnostic tools for AKI in the hope that early identification of renal injury will allow for effective therapeutic intervention. Different transcriptomic, proteomic and metabolomic technologies offer unbiased approaches to identifying novel biomarkers of AKI. This review will provide an overview of non-invasive pediatric AKI biomarkers. It will focus on unbiased technologies by using examples of biomarkers identified with "-omic" technologies and different methodological and implementation challenges will be highlighted. Finally, emerging proteomic techniques that may be applicable to biomarker discovery will be presented. Ultimately, the development of novel biomarkers of AKI may lead to the early diagnosis and effective therapeutic intervention of AKI to improve patient outcomes.

Urinary neutrophil gelatinase-associated lipocalin as a marker of severe lupus nephritis in children

INTRODUCTION

More than 60% of children with systemic lupus erythematosus (SLE) develop lupus nephritis (LN). Neutrophil gelatinase-associated lipocalin (NGAL) is a protein secreted by leukocytes during inflammation and is overexpressed in the kidneys following ischemic and nephrotoxic damage.

AIM

To study urinary and serum NGAL in children with SLE and investigate their possible role as markers of renal involvement. Methods Urinary and serum levels of NGAL were assessed in 33 children with active SLE (22 with and 11 without LN) and compared to 15 matched controls.

RESULTS

Children with SLE had elevated urinary NGAL as compared to controls (P<0.001). Levels of urinary NGAL were higher in patients with LN than those without LN (P<0.001). In patients with LN, serum levels of NGAL were not significantly different from controls (P=0.4) and urinary NGAL correlated with the renal score of the Systemic Lupus Erythematosus Disease Activity Index (r=0.5, P=0.02) but not with serum NGAL (P=0.5). Urinary NGAL was significantly predictive of class III and IV LN (P=0.005) with 91% sensitivity and 70% specificity to levels ≥ 10.07 ng/mg creatinine. Conclusions Urinary NGAL is a sensitive marker of proliferative nephritis in juvenile SLE.

Acute kidney injury and critical cardiac disease

The field of cardiac intensive care continues to advance in tandem with congenital heart surgery. The survival of patients with critical congenital heart disease is seldom in question. Consequently, the focus has now shifted to that of morbidity reduction and eventual elimination. Acute kidney injury (AKI) after cardiac surgery is associated with adverse outcomes, including prolonged intensive care and hospital stays, diminished quality of life, and increased long-term mortality. Acute kidney injury occurs frequently, complicating 30% to 40% of adult and pediatric cardiac surgeries. Patients who require dialysis are at high risk of mortality, but even minor degrees of postoperative AKI portend a significant increase in mortality and morbidity.

Paediatric normative data for urine NGAL/creatinine ratio

AIM

The objective of this study was to establish age-dependent urine NGAL (neutrophil gelatinase-associated lipocalin)/creatinine ratio values in healthy children and adolescents.

METHODS

The study was performed using a random sample of 172 healthy children and adolescents (M-88, F-84), aged median 9.75 (0.2-17.9) years. Urine NGAL concentration was measured using a commercially available ELISA kit (R&D Systems, USA).

RESULTS

Median concentrations of urine NGAL/creatinine in particular age groups were analysed using anova. The differences between the youngest group of children under the age of 6 years and the rest of examined population were statistically significant. There were no differences in urine NGAL/creatinine between other age groups. Statistically significant negative correlation between urine NGAL/creatinine and age of subjects was found (r = -0.29, p < 0.05).

CONCLUSION

In the study, normative values of urine NGAL/creatinine for subjects aged 0.2-17.9 years have been established. These data may help clinicians and researchers to improve the interpretation of urine NGAL/creatinine ratio in children and adolescents. However, further studies using numerous data should be conducted to add reference values for urine NGAL partitioned by age and gender.

Characterization of the perfusate proteome of human donor kidneys

BACKGROUND

Preservation of deceased donor kidneys by hypothermic machine perfusion results in superior transplant outcomes as compared with static cold storage and provides the opportunity to measure biomarkers of cellular injury in perfusate samples. Identification of biomarkers predicting early graft dysfunction so far has met with limited success.

METHODS

Two-dimensional difference gel electrophoresis and mass spectrometry were used to explore the proteome of perfusate samples from machine-perfused human donor kidneys (N = 18) and to discover novel biomarkers of ischaemic acute kidney injury.

RESULTS

Thirty-two protein spots were successfully identified, representing 19 unique proteins that were derived from renal tissue and from residual plasma in the renal microcirculation. Two unidentified protein spots were significantly up-regulated, whereas one protein spot--identified as haptoglobin--was significantly down-regulated in the perfusate of ischaemically injured kidneys from donors after cardiac death as compared with kidneys from brain-dead donors who had not suffered warm ischaemic injury. Furthermore, two protein spots were up-regulated in kidneys that never functioned after transplantation, whereas one spot was up-regulated--identified as α1-antitrypsin--in kidneys with delayed graft function.

CONCLUSIONS

We provide the first description of the renal perfusate proteome and present preliminary evidence of differentially expressed biomarkers in human donor kidneys with different levels of acute ischaemic injury. Their diagnostic value for the selection of marginal kidneys in clinical transplantation should be determined in future studies.

Marking renal injury: can we move beyond serum creatinine?

Acute kidney injury (AKI) is a prevalent and devastating condition associated with significant morbidity and mortality. Despite marked improvements in clinical care, the outcomes for subjects with AKI have shown limited improvement in the past 50 years. A major factor inhibiting clinical progress in this field has been the inability to accurately predict and diagnose early kidney dysfunction. The current gold standard clinical and biochemical criteria for diagnosis of AKI, Risk Injury Failure Loss End-stage renal disease, and its modification, Acute Kidney Injury Network criteria, rely on urine output and serum creatinine, which are insensitive, nonspecific, and late markers of disease. The recent development of a variety of analytic mass spectrometry-based platforms have enabled separation, characterization, detection, and quantification of proteins (proteomics) and metabolites (metabolomics). These high-throughput platforms have raised hopes of identifying novel protein and metabolite markers, and recent efforts have led to several promising novel markers of AKI. However, substantial challenges remain, including the need to systematically evaluate incremental performance of these markers over and beyond current clinical and biochemical criteria for AKI. We discuss the basic issues surrounding AKI biomarker development, highlight the most promising markers currently under development, and discuss the barriers toward widespread clinical implementation of these markers.

Kidney and heart interactions during cardiorenal syndrome: a molecular and clinical pathogenic framework

The heart and kidney are physiologically interconnected. Cardiorenal syndrome (CRS) is a pathological disorder where acute or chronic dysfunction in one organ may induce dysfunction in the other one. Although classical studies have proposed a role for hypertension, dyslipidemia and endothelial dysfunction, CRS should be considered as a complex molecular interplay of neurohumoral pathway activation including the sympathetic nervous system, the renin angiotensin aldosterone axis, the endothelin system and the arginine vasopressin system. This activation may induce vascular inflammation, oxidative stress, accelerated atherosclerosis, cardiac hypertrophy and both myocardial and intrarenal fibrosis with progression of CRS treatment. More recently, epigenetics has opened new pathogenic molecular routes for CRS. This will lead to a more rapid development of novel, safe and effective clinical therapies.

Searching for new biomarkers of renal diseases through proteomics

BACKGROUND

Technological advances have resulted in a renaissance of proteomic studies directed at finding markers of disease progression, diagnosis, or responsiveness to therapy. Renal diseases are ideally suited for such research, given that urine is an easily accessible biofluid and its protein content is derived mainly from the kidney. Current renal prognostic markers have limited value, and renal biopsy remains the sole method for establishing a diagnosis. Mass spectrometry instruments, which can detect thousands of proteins at nanomolar (or even femtomolar) concentrations, may be expected to allow the discovery of improved markers of progression, diagnosis, or treatment responsiveness.

CONTENT

In this review we describe the strengths and limitations of proteomic methods and the drawbacks of existing biomarkers, and provide an overview of opportunities in the field. We also highlight several proteomic studies of biomarkers of renal diseases selected from the plethora of studies performed.

SUMMARY

It is clear that the field of proteomics has not yet fulfilled its promise. However, ongoing efforts to standardize sample collection and preparation, improve study designs, perform multicenter validations, and create joint industry-regulatory bodies offer promise for the recognition of novel molecules that could change clinical nephrology forever.

Discovery and initial validation of α 1-B glycoprotein fragmentation as a differential urinary biomarker in pediatric steroid-resistant nephrotic syndrome

PURPOSE

In this cross-sectional pilot study we set out to discover a non-invasive biomarker that could distinguish steroid-resistant nephrotic syndrome (SRNS) from steroid-sensitive nephrotic syndrome (SSNS).

EXPERIMENTAL DESIGN

Urine and clinical data were collected from patients with idiopathic nephrotic syndrome and healthy controls. Using SELDI-TOF-MS, we identified an 11-fold upregulated 13.8 kDa fragment of α 1-B glycoprotein (A1BG) in urine in SRNS. To validate our findings, A1BG was detected by Western blot. Creatinine was measured and transformed to glomerular filtration rate (GFR) by the new Schwartz formula and classified to chronic kidney disease (CKD) stage. p-Values were determined by unpaired t-test and Mann-Whitney rank sum test. Microalbumin was also measured to determine albumin/creatinine ratios.

RESULTS

The 13.8 kDa A1BG was present in 7 of 19 patients with SRNS; but absent in all SSNS (n=15) and controls (n=10). The A1BG(+) patients had lower GFR than A1BG(-) patients (p<0.009) and tended to have higher CKD stage.

CONCLUSION AND CLINICAL RELEVANCE

The 13.8 kDa A1BG fragment had a high discriminatory power for steroid resistance in pediatric nephrotic syndrome, but is only present in a subset of patients. Additional longitudinal studies are required to determine the usefulness of this biomarker as a non-invasive predictive marker of therapeutic response.

Acute kidney injury: controversies revisited

This paper addresses the epidemiology of AKI specifically in relation to recent changes in AKI classification and revisits the controversies regarding the timing of initiation of dialysis and the use of peritoneal dialysis as a renal replacement therapy for AKI. In summary, the new RIFLE/AKIN classifications of AKI have facilitated more uniform diagnosis of AKI and clinically significant risk stratification. Regardless, the issue of timing of dialysis initiation still remains unanswered and warrants further examination. Furthermore, peritoneal dialysis as a treatment modality for AKI remains underutilised in spite of potential beneficial effects. Future research should be directed at identifying early reliable biomarkers of AKI, which in conjunction with RIFLE/AKIN classifications of AKI could facilitate well-designed large randomised controlled trials of early versus late initiation of dialysis in AKI. In addition, further studies of peritoneal dialysis in AKI addressing dialysis dose and associated complications are required for this therapy to be accepted more widely by clinicians.

Analysis of urinary proteomic patterns for type 2 diabetic nephropathy by ProteinChip

OBJECTIVE

To detect urinary proteomic profiling of patients with type 2 diabetes by using ProteinChip array technology, for searching new potential biomarkers in early diagnosis of type 2 diabetic nephropathy (T2DN).

METHODS

A total of 95 urine samples from type 2 diabetic patients with normoalbuminuria (DM, n=30), microalbuminuria (DNl, n=25) and macroalbuminuria (DN2, n=20), and healthy controls (n=20) were analyzed by SELDI-TOF-MS (the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry) technology combined with bioinformatics tools.

RESULTS

Over 300 proteins or peptides from 1 to 80 kDa were obtained using ProteinChip. About 40 of them with the m/z values from 2008.78 to 79176.55 Da were significantly differentiated between type 2 diabetic patients and control subjects. Four proteins of mass 2797.03, 4545.77, 4984.03 and 9083.71 Da were selected as the potential biomarkers for T2DN with sensitivity of 88% and specificity of 96.7%.

CONCLUSION

ProteinChip technology can help to discover new biomarkers and provide a novel non-invasive tool to early diagnosis of T2DN.

Identification of proteomic signatures of mantle cell lymphoma, small lymphocytic lymphoma, and marginal zone lymphoma biopsies by surface enhanced laser desorption/ionization-time of flight mass spectrometry

Mantle cell lymphoma (MCL), small lymphocytic lymphoma (SLL), and marginal zone lymphoma (MZL) are small B-cell non-Hodgkin lymphomas (NHLs) that may be difficult to distinguish. In order to identify specific proteomic biomarkers, differential proteomic analysis of these three NHLs was performed using surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). Whole cell lysates obtained from 18 MCL, 20 SLL, and 20 MZL biopsies were applied on two different ProteinChips (cationic and anionic). Hierarchical clustering and discriminating scores combined with an innovative bio-informatics microdissection strategy allowed us to distinguish specific lymphoma proteomic signatures based on the expression of 37 protein peaks. SELDI-assisted protein purification combined with nano-liquid chromatography (LC) quadrupole-time of flight tandem mass spectrometry (Q-TOF MS/MS) was used to identify proteins overexpressed in both MCL and SLL tumors. Among them two histones, H2B and H4, were identified in MCL tumor biopsies and the signal recognition particle 9 kDa protein, SRP9, in SLL tumor biopsies.

Proteomic analysis of acute kidney injury: biomarkers to mechanisms

Acute kidney injury (AKI) is a devastating clinical condition, both in terms of mortality and costs, and is occurring with increasing incidence. Despite better clinical care, the outcomes of AKI have changed little in the last 50 years. This lack of progress is due in part to a lack of early diagnostic biomarkers and a poor understanding of the disease mechanisms. This review will focus on the rapid progress being made in both the understanding of AKI and the promising panel of early biomarkers for AKI that have come out of both direct proteomic analysis of body fluids of AKI patients and more targeted proteomic approaches using clues from other methods such as transcriptomics. This review concludes with a discussion of the future of proteomics and personalized medicine in AKI and the challenges presented in translating these exciting proteomic results to the clinic.

Urinary proteome analysis enables assessment of renoprotective treatment in type 2 diabetic patients with microalbuminuria

Background

Previously the angiotensin II receptor blocker Irbesartan has been demonstrated to reduce the risk for progression from microalbuminuria to macroalbuminuria in type 2 diabetic patients. The purpose of this study was to evaluate the effect of treatment with Irbesartan in type 2 diabetic patients with microalbuminuria on the urinary proteome.

Methods

High-resolution capillary-electrophoresis coupled to mass-spectrometry (CE-MS) was used to profile the low-molecular-weight proteome in urine of a subgroup of patients from a two year randomized irbesartan versus placebo therapy trial, which included hypertensive type 2 diabetic patients with microalbuminuria on ongoing antihypertensive medication (IRMA2-substudy).

Results

We demonstrate that the therapy with 300 mg Irbesartan daily over a period of two years results in significant changes of the urinary proteome. Both, a classifier developed previously that consists of urinary peptides indicative of chronic kidney disease, as well as several individual peptides changed significantly after treatment. These changes were not observed in the placebo-treated individuals. Most prominent are changes of urinary collagen fragments associated with progression of diabetic nephropathy, indicating normalization in urinary peptides.

Conclusion

CE-MS analysis of urine enabled identification of peptides as potential surrogate markers for renoprotection in microalbuminuric type 2 diabetic patients, which show persistent improvement after longterm treatment with Irbesartan. The results suggest that a major benefit of treatment by Irbesartan may be improvement of collagen turnover, reduction of fibrosis. They further suggest that urinary proteome analysis could be utilized to assess potential benefit of therapeutic intervention, providing statistically significant results even on a small population.

Proteomic identification of early biomarkers of acute kidney injury after cardiac surgery in children

BACKGROUND

Serum creatinine is a delayed marker of acute kidney injury (AKI). Our purpose is to discover and validate novel early urinary biomarkers of AKI after cardiac surgery.

STUDY DESIGN

Diagnostic test study.

SETTING & PARTICIPANTS

Children undergoing cardiopulmonary bypass surgery. The test set included 15 participants with AKI and 15 matched controls (median age, 1.5 year) of 45 participants without AKI. The validation set included 365 children (median age, 1.9 year).

INDEX TESTS

Biomarkers identified using proteomic profiling: α(1)-microglobulin, α(1)-acid glycoprotein, and albumin.

REFERENCE TEST

AKI, defined as ≥50% increase in serum creatinine level from baseline within 3 days of surgery.

RESULTS

Proteomic profiling using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) showed 3 protein peaks that appeared consistently within 2 hours in children who developed AKI after cardiopulmonary bypass surgery. The proteins were identified as α(1)-microglobulin, α(1)-acid glycoprotein, and albumin. Using clinical assays, results were confirmed in a test set and validated in an independent prospective cohort. In the validation set, 135 (37%) developed AKI, in whom there was a progressive increase in urinary biomarker concentrations with severity of AKI. Areas under the curve for urinary α(1)-microglobulin, α(1)-acid glycoprotein, and albumin at 6 hours after cardiac surgery were 0.84 (95% CI, 0.79-0.89), 0.87 (95% CI, 0.83-0.91), and 0.76 (95% CI, 0.71-0.81), respectively. Participants with increasing quartiles of biomarkers showed increasing lengths of hospital stays and durations of AKI (P < 0.001).

LIMITATIONS

Single-center study of children with normal kidney function at recruitment. The SELDI-TOF MS technique has limited sensitivity for the detection of proteins greater than the 20-kDa range.

CONCLUSIONS

Urinary α(1)-microglobulin, α(1)-acid glycoprotein, and albumin represent early, accurate, inexpensive, and widely available biomarkers of AKI after cardiac surgery. They also offer prognostic information about the duration of AKI and length of hospitalization after cardiac surgery.

Urinary proteomics as a novel tool for biomarker discovery in kidney diseases

Urine has become one of the most attractive biofluids in clinical proteomics, for its procurement is easy and noninvasive and it contains sufficient proteins and peptides. Urinary proteomics has thus rapidly developed and has been extensively applied to biomarker discovery in clinical diseases, especially kidney diseases. In this review, we discuss two important aspects of urinary proteomics in detail, namely, sample preparation and proteomic technologies. In addition, data mining in urinary proteomics is also briefly introduced. At last, we present several successful examples on the application of urinary proteomics for biomarker discovery in kidney diseases, including diabetic nephropathy, IgA nephropathy, lupus nephritis, renal Fanconi syndrome, acute kidney injury, and renal allograft rejection.

Identification of diagnostic urinary biomarkers for acute kidney injury

Acute kidney injury (AKI) is an important cause of death among hospitalized patients. The 2 most common causes of AKI are acute tubular necrosis (ATN) and prerenal azotemia (PRA). Appropriate diagnosis of the disease is important but often difficult. We analyzed urine proteins by 2-dimensional gel electrophoresis from 38 patients with AKI. Patients were randomly assigned to a training set, an internal test set, or an external validation set. Spot abundances were analyzed by artificial neural networks to identify biomarkers that differentiate between ATN and PRA. When the trained neural network algorithm was tested against the training data, it identified the diagnosis for 16 of 18 patients in the training set and all 10 patients in the internal test set. The accuracy was validated in the novel external set of patients where conditions of 9 of 10 patients were correctly diagnosed including 5 of 5 with ATN and 4 of 5 with PRA. Plasma retinol-binding protein was identified in 1 spot and a fragment of albumin and plasma retinol-binding protein in the other. These proteins are candidate markers for diagnostic assays of AKI.

Tubular proteinuria in acute kidney injury: a critical evaluation of current status and future promise

The diagnosis and prognosis of acute kidney injury (AKI) by current clinical means is inadequate. Biomarkers of kidney injury that are easily measured and unaffected by physiological variables could revolutionize the management of AKI. Our objective was to systematically review the diagnostic and prognostic utility of urine and serum biomarkers of AKI in humans. We searched MEDLINE, PubMed and EMBASE databases (January 2000–August 2009) for biomarker studies that could be classified into the following categories: (a) confirmation of the diagnosis of established AKI, (b) early prediction of AKI, and (c) prognostication of AKI. We identified 54 manuscripts published since 2000 that met our inclusion and exclusion criteria. Urinary interleukin-18 (IL-18), kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL) and N-acetyl- β-d-glucosaminidase (NAG) are potentially useful biomarkers for the diagnosis of established AKI. Urinary NGAL, IL-18, and liver-type fatty acid binding protein, and serum NGAL and cystatin C represent the most promising biomarkers for early prediction of AKI. Urinary cystatin C, α1-microglobulin, NAG and retinol-binding protein may be useful to predict severity and outcomes of AKI. In conclusion, we identified several studies of promising biomarkers for the diagnosis, prediction and prognostication of AKI. However, we note several limitations, including small sample sizes, inadequate gold standard, exclusion of patients with chronic kidney disease, incomplete statistical analyses, utilization of research-based assays and a paucity of studies examining prediction for clinical outcomes. Future studies will need to address these limitations in order for further progress to be made.

A review of experimental design best practices for proteomics based biomarker discovery: focus on SELDI-TOF

Surface Enhanced Laser/Desorption Ionization-time of flight (SELDI-TOF) mass spectrometry is a technique uniquely suited to the study of the urine proteome due to its salt tolerance, high-throughput, and small sample requirements. However, due to the extreme sensitivity of the technique, sample collection and storage conditions, as well as instrument protocols and analysis conditions, must be rigorously controlled to ensure that data generated and collected is accurate and free from artifacts. Robust and reproducible data sets can be generated and compared between clinical sites when experimental protocols are carefully standardized. This chapter aims to review known factors that cause irreproducible results so that the experiments may be designed with appropriate sample and process controls for successful biomarker discovery. A suggested protocol follows the review. A number of issues for study design are discussed and these are generally applicable to biomarker discovery experiments.

Cell-specific biomarkers in renal medicine and research

Histopathology is the gold standard for defining renal injury, but it is invasive, time-consuming and expensive, plus it is seldom used in subjects with mild renal injury. Using biomarkers linked to distinct, defined cell types and tissues provides a direct link to histopathology without its drawbacks, plus it provides increased sensitivity, and specificity. The nephron consists of several sections, each with its own specific biomarkers; therefore, by the use of a battery of tests injuries can be localised to distinct areas of it. Using urine samples simplifies repeated sampling from the same subject or animal leading to better defined toxicokinetics and disease monitoring.Serum creatinine is the most widely used renal biomarker in spite of its known shortcomings. Cell-specific biomarkers are more specific and sensitive and have been known for over 40 years, but they are still underused in renal medicine and research. In particular, while many studies have shown cell-specific biomarkers to be valuable in diagnosis, there are few studies where they have been used to guide therapy or linked to quantitative changes in the kidney. Furthermore, the great majority of cell-specific biomarkers are from the proximal tubule, which may have hindered research into the study of conditions where the distal tubules are affected. Recently, the range of biomarkers and their applications has been expanded by the introduction of indicators of cellular regeneration.This chapter will discuss how using biomarkers with a known cellular origin, renal effects may be found earlier and at lower levels of injury. Their use in both renal medicine and drug research will be presented. Knowledge of these existing markers lays the foundation for evaluation, comparison, and characterisation of new markers that will be identified in the future.

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.

Recent progress of proteomics in critical illness

Critical illness, such as sepsis or septic shock with multiple organ dysfunction syndrome, is the leading cause of morbidity and mortality in intensive care units. The complexity of critical illness requires a robust methodology to explore the underlying mechanisms. Proteomics represents a powerful postgenomic biotechnology used for simultaneous examination of a large number of proteins or the proteome. Recent progress in proteomic techniques allows thorough evaluation of molecular changes associated with critical illness, thereby permitting to identify novel biomarkers and therapeutic targets. This review provides an update on the recent progress and potential of rapidly evolving proteomics approach to facilitate new discoveries in the field of critical care medicine.

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.