Technology Insight: renal proteomics--at the crossroads between promise and problems

One-step sample concentration, purification, and albumin depletion method for urinary proteomics

Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downstream compatibilities with fractionation technologies such as off-gel electrophoresis have not been investigated. We developed a one-step sample preparation workflow that simultaneously (i) concentrates proteins, (ii) purifies by removing salts and other low molecular weight compounds, and (iii) depletes (albumin) from urine samples. This simple and robust workflow can be multiplexed and is compatible with a diverse range of downstream multidimensional separation technologies. Additionally, because of its high reproducibility and flexibility in processing samples with different volumes and concentrations, it has the potential to be used for standardization of urinary proteomics studies, as well as for studying other body fluids of similar complexity.

2-D hydrophilic interaction liquid chromatography-RP separation in urinary proteomics--minimizing variability through improved downstream workflow compatibility

Optimization of every step in a bottom-up urinary proteomics approach was studied with respect to maximize the protein recovery and making the downstream steps in the workflow fully compatible without compromising on the amount of information obtained. Sample enrichment and desalting using centrifugal filtration (5 kDa cut-off) yielded protein recoveries up to 97% when 8 M urea was used. Although yielding lower recoveries (88%), addition of Tris-HCl/NaCl was considered a better choice due to good down-stream compatibility. The consecutive depletion of HSA, using an immunoaffinity column was successfully adapted for use in urine. Separation of the trypsin generated peptides in an off-line 2-D chromatographic system consisting of a hydrophilic interaction liquid chromatography column, followed by a RP chromatography column showed a high peak capacity and good repeatability in addition to a high degree of orthogonality. All operations were modified in order to keep sample handling between every step to a minimum, reducing the variability of each process. In order to test the suitability of the full method in an extensive proteomic experiment, a urine sample from a kidney-transplanted patient was analyzed (n=6). The total variability of the method was identified with RSD values ranging from 11 to 30%. Eventually, we identified a total of 1668 peptides and 438 proteins from a single urine sample despite the use of low-resolution MS/MS equipment. The optimized and "streamlined" complex method has shown potential for use in future urinary proteomic studies.

Molecular diagnostics in transplantation

The past few decades are characterized by an explosive evolution of genetics and molecular cell biology. Advances in chemistry and engineering have enabled increased data throughput, permitting the study of complete sets of molecules with increasing speed and accuracy using techniques such as genomics, transcriptomics, proteomics, and metabolomics. Prediction of long-term outcomes in transplantation is hampered by the absence of sufficiently robust biomarkers and a lack of adequate insight into the mechanisms of acute and chronic alloimmune injury and the adaptive mechanisms of immunological quiescence that may support transplantation tolerance. Here, we discuss some of the great opportunities that molecular diagnostic tools have to offer both basic scientists and translational researchers for bench-to-bedside clinical application in transplantation medicine, with special focus on genomics and genome-wide association studies, epigenetics (DNA methylation and histone modifications), gene expression studies and transcriptomics (including microRNA and small interfering RNA studies), proteomics and peptidomics, antibodyomics, metabolomics, chemical genomics and functional imaging with nanoparticles. We address the challenges and opportunities associated with the newer high-throughput sequencing technologies, especially in the field of bioinformatics and biostatistics, and demonstrate the importance of integrative approaches. Although this Review focuses on transplantation research and clinical transplantation, the concepts addressed are valid for all translational research.

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.

The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease

Aging induces morphological changes of the kidney and reduces renal function. We analyzed the low molecular weight urinary proteome of 324 healthy individuals from 2-73 years of age to gain insight on human renal aging. We observed age-related modification of secretion of 325 out of over 5000 urinary peptides. The majority of these changes were associated with renal development before and during puberty, while 49 peptides were related to aging in adults. We therefore focussed the remainder of the study on these 49 peptides. The majority of these 49 peptides were also markers of chronic kidney disease, suggesting high similarity between aging and chronic kidney disease. Blinded evaluation of samples from healthy volunteers and diabetic nephropathy patients confirmed both the correlation of biomarkers with aging and with renal disease. Identification of a number of these aging-related peptides led us to hypothesize that reduced proteolytic activity is involved in human renal aging. Finally, among the 324 supposedly healthy individuals, some had urinary aging-related peptide excretion patterns typical of an individual significantly older than their actual age. In conclusion, these aging-related biomarkers may allow noninvasive detection of renal lesions in healthy persons and show high resemblance between human aging and chronic kidney disease. This similarity has to be taken into account when searching for biomarkers of renal disease.

Altered expression of calreticulin during the development of fibrosis

Tissue damage following injury leads to inflammation and fibrosis. To understand the molecular mechanisms and the proteins involved in the fibrotic process, we used the well-established unilateral ureteric obstruction rat model and we analyzed the alterations at early and late time intervals using a classical proteomic approach. Data analysis demonstrates a correlation between calreticulin up-regulation and progression of fibrosis. Calreticulin is involved in Ca++ homeostasis but has not been previously implicated in animal models of fibrosis. Proteomic analysis consistently revealed up-regulation of calreticulin in both early and late time intervals. These findings were further confirmed by biochemical and morphological approaches. Next, animal models of lung fibrosis (bleomycin-induced) and heart fibrosis (desmin-null) were examined. In the lung model, calreticulin expression was up-regulated from early time intervals, whereas in the heart model no change in the expression of calreticulin was observed. In addition, TGF-beta, a well known major contributing factor in several fibrotic processes, was found to up-regulate calreticulin in cultured human proximal tubule epithelial cells. The above observations suggest that calreticulin might be involved in fibrotic processes; however the mechanism(s) underlying its possible involvement are yet unresolved.

Prospective, randomized trial comparing short and long intravenous antibiotic treatment of acute pyelonephritis in children: dimercaptosuccinic acid scintigraphic evaluation at 9 months

OBJECTIVE

We report a prospective, randomized, multicenter trial that compared the effect of 3 vs 8 days of intravenous ceftriaxone treatment on the incidence of renal scarring at 6 to 9 months of follow-up in 383 children with a first episode of acute pyelonephritis.

METHODS

After initial treatment with intravenous netilmicin and ceftriaxone, patients were randomly assigned to either 5 days of oral antibiotics (short intravenous treatment) or 5 days of intravenous ceftriaxone (long intravenous treatment). Inclusion criteria were age 3 months to 16 years and first acute pyelonephritis episode, defined by fever of >38.5 degrees C, C-reactive protein level of >20 mg/L, and bacteriuria at >10(5)/mL. All patients underwent 99m technetium-dimercaptosuccinic acid scintigraphy 6 to 9 months after inclusion. A total of 548 children were included, 48 of whom were secondarily excluded and 117 of whom were lost to follow-up or had incomplete data; therefore, 383 children were eligible, 205 of them in the short intravenous treatment group and 178 in the long intravenous treatment group.

RESULTS

At inclusion, median age was 15 months, median duration of fever was 43 hours, and median C-reactive protein level was 122 mg/L. A total of 37% (143 of 383) of patients had a vesicoureteral reflux grades 1 to 3. Patient characteristics at inclusion were similar in both groups, except for a significantly higher proportion of girls in the short intravenous treatment group. The frequency of renal scars at scintigraphy was similar in both groups. Multivariate analysis demonstrated that renal scars were significantly associated with increased renal height at initial ultrasound and with the presence of grade 3 vesicoureteric reflux.

CONCLUSIONS

The incidence of renal scars was similar in patients who received 3 days compared 8 days of intravenous ceftriaxone. Increased renal height at initial ultrasound examination and grade 3 vesicoureteric reflux were significant risk factors for renal scars.

Proteomics for biomarker discovery in acute kidney injury

Acute kidney injury (AKI), previously referred to as acute renal failure, represents a common and devastating problem in clinical medicine. Despite significant improvements in therapeutics, the mortality and morbidity associated with AKI remain high. A major reason for this is the lack of early markers for AKI, and hence an unacceptable delay in initiating therapy. Fortunately, the application of innovative technologies such as functional genomics and proteomics to human and animal models of AKI has uncovered several novel biomarkers and therapeutic targets. The most promising of these are chronicled in this review. These include the identification of biomarker panels in plasma (neutrophil gelatinase-associated lipocalin and cystatin C) and urine (neutrophil gelatinase-associated lipocalin, kidney injury molecule-1, interleukin-18, cystatin C, alpha1-microglobulin, Fetuin-A, Gro-alpha, and meprin). It is likely that the AKI panels will be useful for timing the initial insult, and assessing the duration and severity of AKI. It is also probable that the AKI panels will distinguish between the various etiologies of AKI and predict clinical outcomes. It will be important in future studies to validate the sensitivity and specificity of these biomarker panels in clinical samples from large cohorts and from multiple clinical situations. Such studies will be facilitated markedly by the development of commercial tools for the reproducible measurement of biomarkers across different laboratories.

Chronic hypoxia aggravates renal injury via suppression of Cu/Zn-SOD: a proteomic analysis

Accumulating evidence suggests a pathogenic role of chronic hypoxia in various kidney diseases. Chronic hypoxia in the kidney was induced by unilateral renal artery stenosis, followed 7 days later by observation of tubulointerstitial injury. Proteomic analysis of the hypoxic kidney found various altered proteins. Increased proteins included lipocortin-5, calgizzarin, ezrin, and transferrin, whereas the decreased proteins were alpha(2u)-globulin PGCL1, eukaryotic translation elongation factor 1alpha(2), and Cu/Zn superoxide dismutase (SOD1). Among these proteins, we focused on Cu/Zn-SOD, a crucial antioxidant. Western blot analysis and real-time quantitative PCR analysis confirmed the downregulation of Cu/Zn-SOD in the chronic hypoxic kidney. Furthermore, our laser capture microdissection system showed that the expression of Cu/Zn-SOD was predominant in the tubulointerstitium and was decreased by chronic hypoxia. The tubulointerstitial injury estimated by histology and immunohistochemical markers was ameliorated by tempol, a SOD mimetic. This amelioration was associated with a decrease in levels of the oxidative stress markers 4-hydroxyl-2-nonenal and nitrotyrosine. Our in vitro studies utilizing cultured tubular cells revealed a role of TNF-alpha in downregulation of Cu/Zn-SOD. Since the administration of anti-TNF-alpha antibody ameliorated Cu/Zn-SOD suppression, TNF-alpha seems to be one of the suppressants of Cu/Zn-SOD. In conclusion, our proteomic analysis revealed a decrease in Cu/Zn-SOD, at least partly by TNF-alpha, in the chronic hypoxic kidney. This study, for the first time, uncovered maladaptive suppression of Cu/Zn-SOD as a mediator of a vicious cycle of oxidative stress and subsequent renal injury induced by chronic hypoxia.

Diagnostic Potential of Urine Proteome: A Broken Mirror of Renal Diseases

This brief overview of studies into the urine proteome illustrates its potential value for diagnostic, prognostic, and pathophysiologic discovery. Hypothesis-targeted investigations of individual proteins as well as proteome-wide searches for urinary biomarkers of various diseases and their progression are reviewed. The majority of urine proteins appear as cleavage products that are found not only as free solutes but also in secreted membrane vesicles called exosomes. Described are several recent examples of important diagnostic findings using urine proteomics along with the idea that signature profiles of injury to individual nephron segments can be measured by this technology. Shared are some thoughts on the most challenging step: Integration of seemingly unrelated findings of various protein fragments into a rational pathogenetic pathway(s). The future chance that the centuries-old technique of uroscopy will reveal its secrets using modern proteomic approaches makes gradual improvement.

Diagnostic Tools for Monitoring Kidney Transplant Recipients

Recent advancements in immunobiology have introduced several new diagnostic tools for monitoring kidney transplant recipients. These have been added to more established tests that, although imperfect, remain important benchmarks of diagnostic utility. Both new and old tests can be characterized with regard to their practicality, and as to whether they detect aberrant function or define the cause of dysfunction. Unfortunately, no current test is both practical and specific to a particular disease entity. Accordingly, the diagnosis of graft dysfunction remains dependent on the proper use and interpretation of many studies. This article reviews the current assays that have been evaluated in the clinic for the diagnosis of renal allograft-related diseases. These are limited to assays based on routinely obtainable samples such as blood, biopsy tissue, and urine. Newer studies are presented, along with more mundane assays, to highlight the practical use of studies regardless of their degree of mechanistic sophistication.

Diagnostic potential for urinary proteomics

Urine represents a modified ultrafiltrate of plasma, with protein concentrations typically approximately 1000-fold lower than plasma. Urine’s low protein concentration might suggest it to be a less promising diagnostic specimen than plasma. However, urine can be obtained noninvasively and tests of many urinary proteins are well-established in clinical practice. Proteomic technologies expand opportunities to analyze urinary proteins, identifying more than 1000 proteins and peptides in urine. Urine offers a sampling of most plasma proteins, with increased proportions of low-molecular-weight protein and peptide components. Urine also offers enriched sampling of proteins released along the urinary tract. Although urine presents some challenges as a diagnostic specimen, its diverse range of potential markers offers great potential for diagnosis of both systemic and kidney diseases. Examples of clinical situations where this may be of value are for more sensitive detection of kidney transplant rejection or of renal toxicity of medications.