Urine 2DE proteome analysis in healthy condition and kidney disease

Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview

Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.

New biomarkers of Kawasaki disease identified by urine proteomic analysis

Kawasaki disease (KD) is an acute systemic vasculitis that mainly afflicts infants and young children. The symptoms of KD are similar to those of various febrile diseases. Here, we attempted to develop accurate diagnostic biomarkers of KD by performing urine proteomic analysis of samples from healthy controls, patients with KD, and patients with another febrile disease, pneumonia (two patients). We identified differentially expressed proteins (DEPs) in KD as compared to normal controls. We also constructed functional annotation and protein-protein interaction (PPI) networks of DEPs in KD and pneumonia. DEPs common to both KD and pneumonia were identified, as well as DEPs specific to KD. Compared to normal control, 43 and 62 DEPs were identified in KD and pneumonia, respectively. Serine hydroxymethyltransferase 1 is a hub protein of the KD-specific PPI network. Thirteen DEPs common to both KD and pneumonia and 30 DEPs specific to KD were identified. Of these, the expression of eight DEPs could cluster normal and pneumonia samples into one group and cluster KD samples into another group based on hierarchical clustering. Our study identified several DEPs that may play a role in KD and that may serve as diagnostic biomarkers to distinguish patients with KD from both normal control and other febrile diseases.

Analytical techniques for characterization of biological molecules - proteins and aptamers/oligonucleotides

With the advent of the high-throughput technologies and exciting times for biology, the discipline of analytical methodology is experiencing a surge in the growth and the scope. Over the years, multitude of analytical techniques have evolved from a work-intensive, low sensitivity and high volume of reagent and sample consumption endeavor to automated, better selectivity, lower limit of quantification and cost-effective techniques for biological research. In this review, we give an overview of the currently available wide range of cell-based and noncell based and structural based analytical techniques, their principle and biological applications. The analytical techniques discussed in this paper includes surface plasmon resonance, electrophoresis, enzyme linked immunosorbent assay, Western blotting, flow cytometry, fluorescence activated cell sorting, mass spectrometry, nuclear magnetic resonance and x-ray crystallography.

Missense mutations have unexpected consequences: The McArdle disease paradigm

McArdle disease is a disorder of muscle glycogen metabolism caused by mutations in the PYGM gene, encoding for the muscle-specific isoform of glycogen phosphorylase (M-GP). The activity of this enzyme is completely lost in patients' muscle biopsies, when measured with a standard biochemical test which, does not allow to determine M-GP protein levels. We aimed to determine M-GP protein levels in the muscle of McArdle patients, by studying biopsies of 40 patients harboring a broad spectrum of PYGM mutations and 22 controls. Lack of M-GP protein was found in muscle in the vast majority (95%) of patients, irrespective of the PYGM genotype, including those carrying missense mutations, with few exceptions. M-GP protein biosynthesis is not being produced by PYGM mutations inducing premature termination codons (PTC), neither by most PYGM missense mutations. These findings explain the lack of PYGM genotype-phenotype correlation and have important implications for the design of molecular-based therapeutic approaches.

The Spectrum of Kidney Diseases in Children Associated with Low Molecular Weight Proteinuria

BACKGROUND

Proteinuria, in addition to haematuria, is the most important laboratory parameter in patients with nephro-urological diseases. Low molecular weight proteinuria (LMWP) is of particular importance because some diseases genetic and tubulointerstitial are diagnosed based on its presence.

AIM

The purpose of this study is to describe the clinical features, the course and outcome of pediatric patients with a renal disease associated with LMWP.

MATERIAL AND METHODS

This retrospective observational study included 250 pediatric patients with various kidney diseases in which the type of proteinuria was defined by 4-20% gradient gel sodium dodecyl sulphate polyacrylamide gel (SDS-PAG) electrophoresis.

RESULTS

Isolated LMWP was detected in 12% of patients, while mixed glomerulotubular proteinuria was detected in 18% of patients. It was detected in all patients with the Dent-1/2 disease, Lowe's syndrome and secondary Fanconi syndrome. Transient LMWP was also detected in a series of 12 patients with distal renal tubular acidosis. In patients with nephrotic syndrome, it was associated with corticoresistence and unfavourable clinical course.

CONCLUSION

This study contributes to the understanding of the clinical spectrum of various kidney diseases associated with LMWP, their natural course, and the effect of therapy.

Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems

Liquid chromatography-mass spectrometry (LC-MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin based depletion column followed by either protein In-gel enzymatic digestion or protein in-solution enzymatic digestion and then analysis by one-dimensional reverse-phase chromatography or two-dimensional strong cation exchange (SCX)-reverse-phase chromatography (RPC).

Urinary Kininogen-1 and Retinol binding protein-4 respond to Acute Kidney Injury: predictors of patient prognosis?

Implementation of therapy for acute kidney injury (AKI) depends on successful prediction of individual patient prognosis. Clinical markers as serum creatinine (sCr) have limitations in sensitivity and early response. The aim of the study was to identify novel molecules in urine which show altered levels in response to AKI and investigate their value as predictors of recovery. Changes in the urinary proteome were here investigated in a cohort of 88 subjects (55 AKI patients and 33 healthy donors) grouped in discovery and validation independent cohorts. Patients’ urine was collected at three time points: within the first 48 h after diagnosis(T1), at 7 days of follow-up(T2) and at discharge of Nephrology(T3). Differential gel electrophoresis was performed and data were confirmed by Western blot (WB), liquid chromatography/mass spectrometry (LC-MS/MS) and enzyme-linked immunosorbent assay (ELISA). Retinol binding protein 4 (RBP4) and kininogen-1 (KNG1) were found significantly altered following AKI. RBP4 increased at T1, and progressively decreased towards normalization. Maintained decrease was observed for KNG1 from T1. Individual patient response along time revealed RBP4 responds to recovery earlier than sCr. In conclusion, KNG1 and RBP4 respond to AKI. By monitoring RBP4, patient’s recovery can be anticipated pointing to a role of RBP4 in prognosis evaluation.

Urinary alpha-1 antitrypsin and CD59 glycoprotein predict albuminuria development in hypertensive patients under chronic renin-angiotensin system suppression

BACKGROUND

Hypertension is a multi-factorial disease of increasing prevalence and a major risk factor for cardiovascular mortality even in the presence of adequate treatment. Progression of cardiovascular disease (CVD) occurs frequently during chronic renin-angiotensin-system (RAS) suppression, and albuminuria is a marker of CV risk. High prevalence of albuminuria in treated hypertensive patients has been demonstrated, but there are no available markers able to predict evolution. The aim of this study was the identification of novel indicators of albuminuria progression measurable in urine of diabetic and non-diabetic patients.

METHODS

1143 hypertensive patients under chronic treatment were followed for a minimum period of 3 years. Among them, 105 diabetic and non-diabetic patients were selected and classified in three groups according to albuminuria development during follow-up: (a) patients with persistent normoalbuminuria; (b) patients developing de novo albuminuria; (c) patients with maintained albuminuria. Differential urine analysis was performed by 2D gel electrophoresis (2D-DIGE) and further confirmed by liquid chromatography-mass spectrometry. Non-parametric statistical tests were applied.

RESULTS

CD59 glycoprotein and alpha-1 antitrypsin (AAT) resulted already altered in patients developing albuminuria de novo, with a similar response in those with maintained albuminuria. A prospective study in a sub-group of normoalbuminuric patients who were clinically followed up for at least 1 year from urine sampling, revealed CD59 and AAT proteins significantly varied in the urine collected from normoalbuminurics who will negatively progress, serving as predictors of future albuminuria development.

CONCLUSIONS

CD59 and AAT proteins are significantly altered in hypertensive patients developing albuminuria. Interestingly, CD59 and AAT are able to predict, in normoalbuminuric individuals, who will develop albuminuria in the future, being potential predictors of vascular damage and CV risk. These findings contribute to early identify patients at risk of developing albuminuria even when this classical predictor is still in the normal range, constituting a novel strategy towards a prompt and more efficient therapeutic intervention with better outcome.

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.

Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine

Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.

Quantitative mass spectrometry of urinary biomarkers

The effectiveness of treatment of renal diseases is limited because the lack of diagnostic, prognostic and therapeutic markers. Despite the more than a decade of intensive investigation of urinary biomarkers, no new clinical biomarkers were approved. This is in part because the early expectations toward proteomics in biomarkers discovery were significantly higher than the capability of technology at the time. However, during the last decade, proteomic technology has made dramatic progress in both the hardware and software methods. In this review we are discussing modern quantitative methods of mass-spectrometry and providing several examples of their applications for discovery and validation of renal disease biomarkers. We are optimistic about future prospects for the development of novel of specific clinical urinary biomarkers.