Practical Points in Urinary Proteomics

Recent progress in mass spectrometry-based urinary proteomics

Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.

Urinary lipid profile of patients with coronavirus diseases 2019

The coronavirus diseases 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is ongoing. Over 490 million people have been infected with this virus worldwide. Although many patients present with lower respiratory symptoms, some may progress to acute respiratory distress syndrome and even multi-organ damage. Therefore, there is an urgent need to establish treatment and management methods for this infectious disease. Here, we comprehensively analyzed urinary lipid mediators and their metabolites to identify non-invasive biomarkers that reflect the disease status of COVID-19 patients. We diagnosed 16 patients by polymerase chain reaction (PCR) analysis, who presented with mild-to-moderate symptoms, including fever and cough, between May and October 2020 in Japan, and collected their urine samples. Using mass spectrometry, we analyzed the lipid metabolites in these urine samples. In all the urine samples from the patients, 21 types of fatty acids and their metabolites were consistently detected in the samples among the 214 metabolites which were analyzed. Interestingly, urinary levels of fatty acids, docosahexaenoic acid was increased by approximately 3-fold in patients with COVID-19 compared to those in healthy subjects. Metabolites of major proinflammatory lipid mediators, PGE2, TXA2, and PGF2α, were also detected at significantly higher levels in the urine of patients with COVID-19. These observations suggest that urinary lipids can reflect the inflammatory status of patients with COVID-19, which can be a useful index to manage this disease.

Proteomic analysis of inhibitory protein profiles in the urine of children with nephrolithiasis: implication for disease prevention

PURPOSE

In this study we aimed to screen for the presence of biomarkers that are downregulated in children with nephrolithiasis (RS) compared to healthy controls (HC) using a proteomic approach. We hypothesized that RS and HC would display unique inhibitory protein profiles that could be used for comparative pathway analysis.

METHODS

This is a prospective, controlled, pilot study of pooled urine from RS (N = 30, 24 females, mean age 12.95 ± 4.03 years) versus age- and gender-matched HC, using liquid chromatography-mass spectrometry. The criteria for protein selection were: (1) patient/control abundance ratio of < 0.5; and (2) ≤ 0.05 p-value for the Fisher's Exact Test. Results were confirmed by ELISA testing in individual samples.

RESULTS

67 proteins were downregulated in RS group, and 17 of those were significantly different compared to controls. Of those seventeen proteins, five (two actins, annexin A5, keratin 6B, and serpin B4) were completely absent in the urine of stone patients but were found in controls. The remaining twelve proteins were significantly less abundant in the patient's urine compared to healthy controls. Protein-protein interaction modeling of significant proteins identified syndecan-1 as the key node, a protein associated with adhesion pathways. ELISA analysis by subgroups showed statistically significant difference in the urinary excretion of osteopontin (5.1 ± 3.22 ng/mg creatinine vs 14.1 ± 9.5 ng/mg creatinine, p = 0.046) between stone patients with hypocitraturia and controls. Urinary osteopontin concentration was positively correlated with urinary citrate excretion (r = 0.417, p = 0.03).

CONCLUSIONS

Children with RS have a different urinary inhibitory polypeptide profile compared to HC. Decreased urinary excretion of these proteins indicates their potential inhibitory role in renal stone formation, especially of the adhesion phase. Lower concentration of urinary osteopontin in children with nephrolithiasis and hypocitraturia suggests its potential involvement in the pathogenesis of this disease. Further characterization of these proteins in a larger sample is imperative.

Urinary proteome of dogs with renal disease secondary to leishmaniosis

Canine leishmaniosis is frequently associated with the development of renal disease. Its pathogenesis is complex and not fully understood. For this reason, this study aimed to describe the urinary proteome, and identify possible new biomarkers in dogs with kidney disease secondary to leishmaniosis. Urine samples were collected from 20 dogs, 5 from healthy dogs, and 15 from stages Leishvet III and IV. Urine samples were analyzed by UHPLC-MS/MS. The data are available via ProteomeXchange with identifier PXD029165. A total of 951 proteins were obtained. After bioinformatic analysis, 93 urinary proteins were altered in the study group. Enrichment analysis performed on these proteins showed an overrepresentation of the complement activation pathway, among others. Finally, 12 discriminant variables were found in dogs with renal disease secondary to leishmaniosis, highlighting C4a anaphylatoxin, apolipoprotein A-I, haptoglobin, leucine-rich alpha-2-glycoprotein 1, and beta-2-microglobulin. This study is the first to describe the urinary proteomics of dogs with renal disease caused by leishmaniosis, and it provides new possible biomarkers for the diagnosis and monitoring of this disease.

Urinary Biomarkers for Detection of Clinical Endometriosis or Adenomyosis

Endometriosis or adenomyosis can be clinically diagnosed by ultrasound, symptoms, physical examination, and serum CA125. The urinary markers need to be investigated. The aim of our study was to investigate the urinary markers of clinical endometriosis/adenomyosis, and the correlation of serum CA125 was also studied. From the literature, alpha-1 antitrypsin (A1AT), enolase-1, vitamin D binding protein (VDBP), and CA125 in urine and serum were used in our study and measured by enzyme-linked immunosorbent assays (ELISA). Further clinical correlation and detection performance were evaluated. We enrolled 19 normal controls and 33 patients clinically diagnosed with endometriosis/adenomyosis. There were significant differences between studied patients and normal controls, as follows: serum CA125 (130.91 vs. 19.75 U/mL, p = 0.004); urinary CA125-creatinine ratio (5.591 vs. 0.254 ng/mg, p = 0.028); and urinary VDBP-creatinine ratio (28.028 vs. 7.301 ng/mg, p = 0.018). For diagnostic performances, serum CA125 provided the best results, with an area under curve (AUC) of 0.888 (p = 0.001) and accuracy of 86.5%. Other excellent results were also found using urinary VDBP (AUC 0.841, p = 0.001) and A1AT (AUC 0.722, p = 0.011) creatinine ratio. Using three combined biomarkers, serum CA125, urinary VDBP, and A1AT creatinine ratio, provided good detection power (AUC 0.913, p = 0.001, sensitivity 90.9%, specificity 76.5%). Double urine markers used in combination with VDBP and A1AT creatinine ratio also provided good diagnostic performance (AUC 0.809, p = 0.001, sensitivity 81.8%, specificity 76.5%, accuracy 80%). Further development of non-invasive point-of-care tests using these biomarkers could be a fruitful future endeavor.

Systematic analysis of modulating activities of native human urinary Tamm-Horsfall protein on calcium oxalate crystallization, growth, aggregation, crystal-cell adhesion and invasion through extracellular matrix

Functions of Tamm-Horsfall protein (THP), the most abundant human urinary protein, have been studied for decades. However, its precise roles in kidney stone formation remain controversial. In this study, we aimed to clarify the roles of native human urinary THP in calcium oxalate monohydrate (COM) kidney stone formation. THP was purified from the human urine by adsorption method using diatomaceous earth (DE). Its effects on stone formation processes, including COM crystallization, crystal growth, aggregation, crystal-cell adhesion and invasion through extracellular matrix (ECM), were examined. SDS-PAGE and Western blotting confirmed that DE adsorption yielded 84.9% purity of the native THP isolated from the human urine. Systematic analyses revealed that THP (at 0.4-40 μg/ml) concentration-dependently reduced COM crystal size but did not affect the crystal mass during initial crystallization. At later steps, THP concentration-dependently inhibited COM crystal growth and aggregation, and prevented crystal-cell adhesion only at 40 μg/ml. However, THP did not affect crystal invasion through the ECM. Sequence analysis revealed two large calcium-binding domains (residues 65-107 and 108-149) and three small oxalate-binding domains (residues 199-207, 361-368 and 601-609) in human THP. Immunofluorescence study confirmed the binding of THP to COM crystals. Analyses for calcium-affinity and/or oxalate-affinity demonstrated that THP exerted a high affinity with only calcium, not oxalate. Functional validation revealed that saturation of THP with calcium, not with oxalate, could abolish the inhibitory effects of THP on COM crystal growth, aggregation and crystal-cell adhesion. These data highlight the inhibitory roles of the native human urinary THP in COM crystal growth, aggregation and crystal-cell adhesion, which are the important processes for kidney stone formation. Such inhibitory effects of THP are most likely mediated via its high affinity with calcium ions.

Gold nanoparticles-based assays for biodetection in urine

Urine is a biofluid easy to collect through a non-invasive technique that allows collecting a large volume of sample. The use of urine for disease diagnosis is not yet well explored. However, it has gained attention over the last three years. It has been applied in the diagnosis of several illnesses such as kidney disease, bladder cancer, prostate cancer and cardiovascular diseases. In the last decade, gold nanoparticles (Au NPs) have attracted attention in biosensors' development for the diagnosis of diseases due to their electrical and optical properties, ability to conjugate with biomolecules, high sensitivity, and selectivity. Therefore, this article aims to present a comprehensive view of state of the art on the advances made in the quantification of analytes in urinary samples using AuNPs based assays, with a focus on protein analysis. The type of diagnosis methods, the Au NPs synthesis approaches and the strategies for surface modification aiming at selectivity towards the different targets are highlighted.

Optimization of artificial urine formula for in vitro cellular study compared with native urine

Several artificial urine (AU) formulas have been developed to mimic the normal urine. Most of them are protein-free, particularly when secreted proteins (secretome) is to be analyzed. However, the normal urine actually contains a tiny amount of proteins. We hypothesized that urinary proteins at physiologic level play a role in preservation of renal cell biology and function. This study evaluated the effects from supplementation of 0-10% fetal bovine serum (FBS) into the well-established AU-Siriraj protocol on MDCK renal tubular cells. Time to deformation (T_D) was reduced by both native urine and AU-Siriraj without/with FBS compared with complete culture medium (control). Among the native urine and AU-Siriraj without/with FBS, the cells in AU-Siriraj+2.5% FBS had the longest T_D. Supplementation of FBS increased cell death in a dose-dependent manner (but still <10%). Transepithelial electrical resistance (TER) of the polarized cells in the native urine was comparable to the control, whereas that of the cells in AU-Siriraj+2.5% FBS had the highest TER. These data indicate that supplementation of 2.5% FBS into AU-Siriraj can prolong time to deformation and enhance polarization of renal tubular cells. Therefore, AU-Siriraj+2.5% FBS is highly recommended for in vitro study of cell biology and function (when secretome is not subjected to analysis).

Detecting Proteomic Indicators to Distinguish Diabetic Nephropathy from Hypertensive Nephrosclerosis by Integrating Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging with High-Mass Accuracy Mass Spectrometry

INTRODUCTION

Diabetic nephropathy (DN) and hypertensive nephrosclerosis (HN) represent the most common causes of chronic kidney disease (CKD) and many patients progress to -end-stage renal disease. Patients are treated primarily through the management of cardiovas-cular risk factors and hypertension; however patients with HN have a more favorable outcome. A noninvasive clinical approach to separate these two entities, especially in hypertensive patients who also have diabetes, would allow for targeted treatment and more appropriate resource allocation to those patients at the highest risk of CKD progression. Meth-ods: In this preliminary study, high-spatial-resolution matrix-assisted laser desorption/ion-ization (MALDI) mass spectrometry imaging (MSI) was integrated with high-mass accuracy MALDI-FTICR-MS and nLC-ESI-MS/MS analysis in order to detect tissue proteins within kidney biopsies to discriminate cases of DN (n = 9) from cases of HN (n = 9).

RESULTS

Differences in the tryptic peptide profiles of the 2 groups could clearly be detected, with these becoming even more evident in the more severe histological classes, even if this was not evident with routine histology. In particular, 4 putative proteins were detected and had a higher signal intensity within regions of DN tissue with extensive sclerosis or fibrosis. Among these, 2 proteins (PGRMC1 and CO3) had a signal intensity that increased at the latter stages of the disease and may be associated with progression.

DISCUSSION/CONCLUSION

This preliminary study represents a valuable starting point for a future study employing a larger cohort of patients to develop sensitive and specific protein biomarkers that could reliably differentiate between diabetic and hypertensive causes of CKD to allow for improved diagnosis, fewer biopsy procedures, and refined treatment approaches for clinicians.

SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data

Background

Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficult because the data may not be normally distributed and there is often a large fraction of zero values. Although several statistical methods have been proposed, they either require the data normality assumption or are inefficient.

Results

We propose a new semi-parametric differential abundance analysis (SDA) method for metabolomics and proteomics data from MS. The method considers a two-part model, a logistic regression for the zero proportion and a semi-parametric log-linear model for the possibly non-normally distributed non-zero values, to characterize data from each feature. A kernel-smoothed likelihood method is developed to estimate model coefficients and a likelihood ratio test is constructed for differential abundant analysis. The method has been implemented into an R package, SDAMS, which is available at https://www.bioconductor.org/packages/release/bioc/html/SDAMS.html.

Conclusion

By introducing the two-part semi-parametric model, SDA is able to handle both non-normally distributed data and large fraction of zero values in a MS dataset. It also allows for adjustment of covariates. Simulations and real data analyses demonstrate that SDA outperforms existing methods.

Urine and Serum Exosomes as Novel Biomarkers in Detection of Bladder Cancer

Background:

The gold standard for initial clinical diagnosis of bladder cancer involves cystoscopic examination of bladder and histological evaluation of tissues. There is a critical need to identify non-invasive and sensitive biomarkers. Early detection is essential challenge in diagnosis and surveillance of bladder carcinoma. Exosomes are nano- sized vesicles present in many biological fluids and have significant role in cancer. Thus, quantification of exosomes in different stages of bladder cancer may be of critical concern for clinical diagnosis and prognosis.

Methods:

Tumor derived exosomes levels in urine and serum samples of 70 bladder cancer Egyptian patients from stages T0-T3 and 12 healthy control people were measured using ELISA technique.

Results:

When compared to health subjects, exosomes levels in bladder cancer patients were increased in urine and serum samples at different stages of the disease. A gradual increase in tumor derived exosomes in serum (1.21, 3.31, 4.71, 6.47µg/ml) and urine (1.59, 2.84, 4.75, 6.67µg/ml) was observed comparative to invasiveness of tumor (T0-T3). Serum was more specific (100%) sample for detection of exosomes in bladder cancer.

Conclusion:

our findings suggest that tumor derived exosomes may offer a convenient tool for early diagnosis and monitoring of bladder cancer.

Proteomic profiling of urine: implications for lupus nephritis

INTRODUCTION

Lupus nephritis (LN) is a common and significant manifestation, affecting 60% of adults and 80% of children with systemic lupus erythematosus, with up to 30% of patients progressing to end stage renal disease. There remains an unmet need for non-invasive markers of disease activity, damage, and response to therapy. In addition, non-invasive biomarkers that predict therapeutic efficacy are needed to enable cost-effective clinical trials of novel agents. Areas covered: This review examines the methodological aspects of urinary proteomics, the role of proteome profiling in identifying promising urinary biomarkers in LN, and the translation of research findings into clinically useful tools in the management of LN. Expert opinion: Targeted and unbiased proteomics have identified several promising urinary biomarkers that predict LN activity, damage (chronicity), and response to therapy. In particular, a combination of biologically plausible urinary biomarkers termed as RAIL (Renal Activity Index for Lupus) has emerged as an excellent predictor of LN activity as well as response to therapy, being able to predict efficacy within 3 months of therapy. If validated in additional large prospective studies, the RAIL biomarkers will transform the care of patients with LN, allowing for a personalized and predictive approach and improved outcomes.

Proteomics in Psoriasis

Psoriasis has been thought to be driven primarily by innate and adaptive immune systems that can be modified by genetic and environmental factors. Complex interplay between inflammatory cytokines and T-cells, especially Th1 and Th17 cells, leads to abnormal cell proliferation and psoriatic skin lesions. Nevertheless, such mechanisms do not entirely represent the pathogenesis of psoriasis. Moreover, earlier and better biomarkers in diagnostics, prognostics, and monitoring therapeutic outcomes of psoriasis are still needed. During the last two decades, proteomics (a systematic analysis of proteins for their identities, quantities, and functions) has been widely employed to psoriatic research. This review summarizes and discusses all of the previous studies that applied various modalities of proteomics technologies to psoriatic skin disease. The data obtained from such studies have led to (i) novel mechanisms and new hypotheses of the disease pathogenesis; (ii) biomarker discovery for diagnostics and prognostics; and (iii) proteome profiling for monitoring treatment efficacy and drug-induced toxicities.

Proteomics and Metabolomics for AKI Diagnosis

Acute kidney injury (AKI) is a severe and frequent condition in hospitalized patients. Currently, no efficient therapy of AKI is available. Therefore, efforts focus on early prevention and potentially early initiation of renal replacement therapy to improve the outcome in AKI. The detection of AKI in hospitalized patients implies the need for early, accurate, robust, and easily accessible biomarkers of AKI evolution and outcome prediction because only a narrow window exists to implement the earlier-described measures. Even more challenging is the multifactorial origin of AKI and the fact that the changes of molecular expression induced by AKI are difficult to distinguish from those of the diseases associated or causing AKI as shock or sepsis. During the past decade, a considerable number of protein biomarkers for AKI have been described and we expect from recent advances in the field of omics technologies that this number will increase further in the future and be extended to other sorts of biomolecules, such as RNAs, lipids, and metabolites. However, most of these biomarkers are poorly defined by their AKI-associated molecular context. In this review, we describe the state-of-the-art tissue and biofluid proteomic and metabolomic technologies and new bioinformatics approaches for proteomic and metabolomic pathway and molecular interaction analysis. In the second part of the review, we focus on AKI-associated proteomic and metabolomic biomarkers and briefly outline their pathophysiological context in AKI.

Urine proteomic profiling in patients with nephrolithiasis and cystinuria

PURPOSE

The purpose of the study was to assess the differences in the concentration and function of urinary proteins between patients with cystine stones (CYS) and healthy controls (HC). We postulated that CYS and HC groups would demonstrate different proteomic profiles.

METHODS

A pilot study was performed comparing urinary proteomes of 10 patients with CYS and 10 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Proteins which met the selection criteria (i) ≥ 2 unique peptide identifications; (ii) ≥ twofold difference in protein abundance; and (iii) ≤ 0.05 p value for the Fisher's Exact Test were analyzed using Gene Ontology classifications.

RESULTS

Of the 2097 proteins identified by proteomic analysis, 398 proteins were significantly different between CYS and HC. Of those, 191 were involved in transport processes and 61 in inflammatory responses. The majority were vesicle-mediated transport proteins (78.5%), and 1/3 of them were down-regulated; of those, 12 proteins were involved in endosomal transport (including 6 charged multivesicular body proteins (CHMP) and 3 vacuolar sorting-associated proteins) and 9 in transmembrane transport. Myosin-2 and two actin-related proteins were significantly up-regulated in the vesicle-mediated transport group.

CONCLUSION

We provide proteomic evidence of impaired endocytosis, dysregulation of actin and myosin cytoskeleton, and inflammation in CYS. Endosomal transport proteins were down-regulated mainly through defective CHMP. These findings may contribute to further understanding of the pathogenesis of CYS, potentially affecting its management.

Marked increase in urinary excretion of apolipoproteins in children with nephrolithiasis associated with hypercalciuria

BACKGROUND

Using a proteomic approach, we aimed to identify and compare the urinary excretion of proteins involved in lipid transport and metabolism in children with kidney stones and hypercalciuria (CAL), hypocitraturia (CIT), and normal metabolic work-up (NM), and in healthy controls (HCs). Additionally, we aimed to confirm these results using ELISA, and to examine the relationship between the urinary excretion of selected proteins with demographic, dietary, blood, and urinary parameters.

METHODS

Prospective, controlled, pilot study of pooled urine from CAL, CIT, and NM versus age- and gender-matched HCs, using liquid chromatography-mass spectrometry. Relative protein abundance was estimated using spectral counting. Results were confirmed by ELISA performed on individual samples.

RESULTS

Of the 1,813 proteins identified, 230 met the above criteria. Of those, 5 proteins (apolipoprotein A-II [APOA2]; apolipoprotein A-IV [APOA4]; apolipoprotein C-III [APOA3]; fatty acid-binding protein, liver [FABPL]; fatty acid-binding protein, adipocyte [FABP4]) involved in lipid metabolism and transport were found in the CAL group, with significant differences compared with HCs. ELISA analysis indicated statistically significant differences in the urinary excretion of APOC3, APOA4, and FABPL in the CAL group compared with HCs. Twenty-four-hour urinary calcium excretion correlated significantly with concentrations of ApoC3 (r = 0.77, p < 0.001), and FABPL (r = 0.80, p = 0.005).

CONCLUSIONS

We provide proteomic data showing increased urinary excretion of lipid metabolism/transport-related proteins in children with kidney stones and hypercalciuria. These findings suggest that abnormalities in lipid metabolism might play a role in kidney stone formation.

Saikosaponins induced hepatotoxicity in mice via lipid metabolism dysregulation and oxidative stress: a proteomic study

BACKGROUND

Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury.

METHODS

Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice. Serum and liver total triglyceride and cholesterol were used to indicate lipid metabolism homeostasis. Liver ROS, GSH, MDA and iNOS were used to examine the oxidative stress level after SS administration. Western blot was used to detect CYP2E1 expression. A 8-Plex iTRAQ Labeling Coupled with 2D LC - MS/MS technique was applied to analyze the protein expression profiles in livers of mice administered with different doses of SS for different time periods. Gene ontology analysis, cluster and enrichment analysis were employed to elucidate potential mechanism involved. HepG2 cells were used to identify our findings in vitro.

RESULTS

SS dose- and time-dependently induced liver injury in mice, indicated by increased serum AST, ALT and LDH levels. According to proteomic analysis, 487 differentially expressed proteins were identified in mice administrated with different dose of SS for different time periods. Altered proteins were enriched in pathways such as lipid metabolism, protein metabolism, macro molecular transportation, cytoskeleton structure and response to stress. SS enhanced CYP2E1 expression in a time and dose dependent manner, and induced oxidative stress both in vivo and in vitro.

CONCLUSION

Our results identified hepatotoxicity and established dose-time course-liver toxicity relationship in mice model of SS administration and suggested potential mechanisms, including impaired lipid and protein metabolism and oxidative stress. The current study provides experimental evidence for clinical safe use of RB, and also new insights into understanding the mechanism by which SS and RB induced liver injury.

Physiologic changes of urinary proteome by caffeine and excessive water intake

Background:

Diurnal variations and physiologic changes of urinary proteome have been suggested in the urinary proteomics field. However, no clear evidence has been demonstrated. The present study thus aimed to define changes in urinary proteome by physiological stimuli, i.e. caffeine intake and excessive water drinking, both of which cause physiologic diuresis.

Methods:

Urine samples were collected from 30 healthy individuals under three different conditions: (i) morning void as the control; (ii) after drinking a cup of coffee; and (iii) after drinking 1 L of water within 20 min. Thereafter, differentially excreted proteins were analyzed by 2-DE proteomics approach and validated by Western blotting and ELISA.

Results:

Spot matching, quantitative intensity analysis, and ANOVA followed by Tukey’s post-hoc multiple comparisons and the Bonferroni correction revealed significant differences in levels of five protein spots among three different conditions. These proteins were identified by quadrupole time-of-flight mass spectrometry (Q-TOF MS) and/or MS/MS analyses as kininogen 1 isoform 3, β-actin, prostaglandin D synthase (PGDS), fibrinogen α-chain and immunoglobulin light chain. Among these, the decreased level of immunoglobulin was successfully validated by Western blotting and ELISA.

Conclusions:

These data indicated that caffeine intake and excessive water drinking could affect urinary excretion of some proteins and may affect urinary proteome analysis.

Differential human urinary lipid profiles using various lipid-extraction protocols: MALDI-TOF and LIFT-TOF/TOF analyses

Changes in lipid levels/profiles can reflect health status and diseases. Urinary lipidomics, thus, has a great potential in clinical diagnostics/prognostics. Previously, only chloroform and methanol were used for extracting lipids from the urine. The present study aimed to optimize lipid extraction and examine differential lipid classes obtained by various extraction protocols. Urine samples were collected from eight healthy individuals and then pooled. Lipids were extracted by six solvent protocols, including (i) chloroform/methanol (1:1, v/v), (ii) chloroform/methanol (2:1, v/v), (iii) hexane/isopropanol (3:2, v/v), (iv) chloroform, (v) diethyl ether, and (vi) hexane. Lipid profiles of the six extracts were acquired by MALDI-TOF mass spectrometry (MS) and some lipid classes were verified by LIFT-TOF/TOF MS/MS. The data revealed that phosphatidylglycerol (PG) and phosphatidylinositol (PI) could be detected by all six protocols. However, phosphatidylcholine (PC) and sphingomyelin (SM) were detectable only by protocols (i)–(iv), whereas phosphatidylserine (PS) was detectable only by protocols (iii)–(vi), and phosphatidylethanolamine (PE) was detectable only by protocols (v)–(vi). In summary, we have demonstrated differential lipidome profiles yielded by different extraction protocols. These data can serve as an important source for selection of an appropriate extraction method for further highly focused studies on particular lipid classes in the human urine.

A proteomic evaluation of urinary changes associated with cardiopulmonary bypass

Background

The urinary proteome of patients undergoing cardiopulmonary bypass (CPB) may provide important insights into systemic and renal changes associated with the procedure. Such information may ultimately provide a basis to differentiate changes or properties associated with the development of acute kidney injury. While mass spectrometry (MS) analysis offers the potential for in-depth compositional analysis it is often limited in coverage and relative quantitation capacity. The aim of this study was to develop a process flow for the preparation and comparison of the intraoperative urinary proteome.

Methods

Urines were collected from patients at the start of CPB and 1-h into CPB. Pooled samples (n = 5) from each time point were processed using a modified Filter Assisted Sample Preparation protocol. The resulting peptides were analyzed by 2D-LC–MS/MS and by 1D-LC–MS/MS SWATH (Sequential Window acquisition of All Theoretical fragment ion spectra).

Results

The 2D-LC–MS/MS analysis identified 1324 proteins in the two pools, of which 744 were quantifiable. The SWATH approach provided quantitation for 730 proteins, 552 of which overlapped with the common population from the 2D-IDA results. Intensity correlation filtering between the two methods gave 475 proteins for biological interpretation. Proteins displaying greater than threefold changes (>log₂ 1.59) at 1-hour CPB relative to the initiation of CPB (26 down-regulated and 22 up-regulated) were selected for further analysis. Up-regulated proteins were enriched in GO terms related to humoral immune response, predominantly innate immunity (C4b, lactotransferrin, protein S100-A8, cathelicidin, myeloperoxidase) and extracellular matrix reorganization (e.g. MMP-9).

Conclusions

This study describes a scheme for processing urine from patients undergoing CPB for mass spectrometry-based analysis. The introduction of SWATH into the workflow offers a sample and instrument sparing approach to obtaining consistent in-depth sample analysis. The design of the methodology is such that it can be readily applied to large numbers of clinical samples with the potential for automation. The results also suggest that activation of the innate immune responses occur during cardiac bypass surgery.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-016-9118-9) contains supplementary material, which is available to authorized users.

Development and characterization of a pseudo multiple reaction monitoring method for the quantification of human uromodulin in urine

Background: Uromodulin is the most abundant protein in healthy human urine. Recently it has been suggested as a specific biomarker of renal tubular damage. We have developed a novel pseudo multiple reaction monitoring (pseudo MRM) for the protein's quantification in human urine. Results: Selection of two peptides allowed quantification of uromodulin in human urine. The pseudo MRM quantified uromodulin in healthy individuals between 21 and 1344 nM and in autosomal dominant tubulointerstitial kidney disease-UMOD patients between 2 and 25 nM. Conclusion: The pseudo MRM allows greater confidence in assay specificity than traditional MRM methods and quantified uromodulin at concentrations higher than achievable by ELISA. Differences in urinary uromodulin concentration related to the rs4293393 promoter variant in the UMOD gene was confirmed. This method will be used to further investigate uromodulin as a biomarker of renal injury.

Renal Tubular Dysfunction in Pediatric Urolithiasis: Proteomic Evidence

OBJECTIVE

To investigate whether inflammation, oxidation, and tubular injury are present in children with stones (RS) compared with healthy controls (HC) by measuring urinary proteins involved in these processes.

METHODS

Quantitative proteomic comparison of pooled urine from RS (N = 30, 24 females, mean age 12.95 ± 4.03 years) versus age- and gender-matched HC (N = 30), using liquid chromatography-mass spectrometry. Relative protein abundance was estimated using spectral counting. Proteins of interest were selected using the following criteria: (1) ≥5 spectral counts; (2) ≥2-fold difference in spectral counts; and (3) P-value ≤.05 for Fisher's exact test.

RESULTS

Of the 1813 proteins identified, 230 met the above criteria, with 163 proteins upregulated in the RS group and 67 upregulated in HC. Functional analysis revealed 19 inflammatory proteins, 5 proteins involved in oxidative stress, and 5 involved in tubular injury. Of those proteins, NADPH-oxidase, a major source of reactive oxygen species, was only found in the RS group, whereas glutathione S-transferase A2, an important antioxidant enzyme, was more abundant in controls. ELISA analysis confirmed statistically significant differences in the urinary excretion of retinol-binding protein 4, a marker of proximal tubular dysfunction, between stone patients with hypercalciuria and controls.

CONCLUSION

We provide proteomic evidence of oxidative stress, inflammation, and tubular injury in children with renal stones. We speculate that inflammation and changes in the oxidant-antioxidant balance may cause tubular damage in these patients. Targeting these proteins may have therapeutic benefits.

Solifenacin and Tamsulosin Combination Therapy Decreases Urine Nerve Growth Factor/Creatinine Levels in Men

OBJECTIVE

To evaluate urinary nerve growth factor (NGF)/creatinine (Cr) levels from men with symptomatic lower urinary tract symptoms (LUTS) and measure the effect of combination therapy with solifenacin and tamsulosin.

MATERIALS AND METHODS

From January 2012 to February 2014, all male patients referred for evaluation and management of LUTS were screened for enrollment. In all subjects, urinary NGF and Cr levels were measured and normalized to the urinary Cr concentrations (NGF/Cr). Uroflow, postvoid residual, and symptom questionnaires were measured at baseline, 4 weeks, 8 weeks, and 12 weeks after starting combination therapy with solifenacin 5 mg and tamsulosin 0.4 mg. The primary endpoint was urinary NGF and NGF/Cr change from baseline compared with week 12.

RESULTS

Ten patients were recruited into the study. Peak urine flow at baseline 20.3 ± 2.5 ml/s and postvoid residual 45.3 ± 13.6 ml did not significantly change with 3 months of combination treatment 14.9 ± 1.8 ml/s and 58.5 ± 23.9 ml. However, urine NGF/Cr (pg/mg) levels were significantly reduced following treatment with levels of 39.7 ± 6.6 at baseline to 17.9 ± 5.1 at 3 months (P value <.05). The decrease in urine NGF/Cr levels correlated with significant decreases in patient reported outcomes.

CONCLUSION

Male patients with LUTS had decreased urinary NGF/Cr levels after treatment with combination solifenacin and tamsulosin in this novel pilot study. This corresponded with improvement in patient reported outcomes.

The association of urinary nerve growth factor levels with bladder outlet obstruction in women

OBJECTIVES

Nerve growth factor (NGF) has been proposed as a urinary biomarker and previously shown to be elevated in male patients with bladder outlet obstruction (BOO) and other lower urinary tract symptoms. No published studies have examined NGF as a potential urinary biomarker in women with BOO. The aims of this prospective study were to evaluate NGF levels in urine from women with anatomic BOO resulting from pelvic organ prolapse (POP) and/or previous incontinence surgery and to measure the effect associated with surgical or conservative management.

METHODS

From January to September 2012, all female patients referred for evaluation and management of BOO from POP or previous incontinence surgery were screened for enrollment. Inclusion criteria included elevated postvoid residual, valsalva voiding on urodynamics, or urinary peak flow (Qmax) of 12 mL/s or less. A control group of 10 asymptomatic age-matched female volunteers was also recruited. In all subjects, urinary NGF and creatinine (Cr) levels were measured and normalized to the urinary Cr concentrations (NGF/Cr). Urinary NGF levels were measured at 1 month and 3 months after either surgical correction or initiation of clean intermittent catheterization.

RESULTS

A total of 10 female patients with anatomic BOO (mean [SD] age of 66.2 [3.88] years) and 10 female control subjects (mean [SD] age of 62 [7] years) were recruited. Nine patients had POP. Six patients had undergone a previous anti-incontinence procedure. Five patients had both POP and undergone a previous anti-incontinence procedure. The urinary NGF/Cr levels in the study patients with BOO (mean [SE] 20.8 [4.31] pg/mg) were significantly higher (P = 0.0001) than the levels in the age-matched control group (5.6 [0.65] pg/mg). After treatment, the urinary NGF/Cr level significantly decreased to 6.50 (0.57) pg/mg (P = 0.01) CONCLUSIONS: In this study, female patients with anatomic BOO resulting from POP and/or previous incontinence surgery had significantly higher urinary NGF/Cr levels when compared with age-matched controls. After treatment, the urinary NGF/Cr levels significantly decreased.

Application of Proteomics in Cancer Biomarker Discovery: GeLC-MS/MS

Proteomic approaches are being increasingly applied to study multiple facets of healthy and diseased processes. In particular, the application of global proteome profiling in the field of oncology is already starting to shape the diagnostic, prognostic, monitoring, and therapeutic approaches. At the heart of such approaches lies a quest for clinically relevant biomarkers, particularly arising from global analyses of body fluids, as, in major part, they represent easily accessible and noninvasive matrices. A detailed protocol of one of the popular approaches for global proteome profiling, SDS-PAGE-liquid chromatography-tandem mass spectrometry or GeLC-MS/MS, and its application for biomarker discovery in urine is provided here.

An Empirical Approach to Signature Peptide Choice for Selected Reaction Monitoring: Quantification of Uromodulin in Urine

BACKGROUND

Many avenues have been proposed for a seamless transition between biomarker discovery data and selected reaction monitoring (SRM) assays for biomarker validation. Unfortunately, studies with the abundant urinary protein uromodulin have shown that these methods do not converge on a consistent set of surrogate peptides for targeted mass spectrometry. As an alternative, we present an empirical peptide selection work flow for robust protein quantification.

METHODS

We compared the relative SRM signal intensity of 12 uromodulin-derived peptides between tryptic digests of 9 urine samples. Pairwise CVs between the 12 peptides were 0.19-0.99. We used a correlation matrix to identify peptides that reproducibly tracked the amount of uromodulin protein and selected 4 peptides with robust and highly correlated SRM signals. Absolute quantification was performed with stable isotope-labeled versions of these peptides as internal standards and a standard curve prepared from a tryptic digest of purified uromodulin.

RESULTS

Absolute quantification of uromodulin in 40 clinical urine samples yielded interpeptide correlations of ≥0.984 and correlations of ≥0.912 with ELISA data. The SRM assays were linear over >3 orders of magnitude and had typical interdigest CVs of <10%, interinjection CVs of <7%, and intertransition CVs of <7%.

CONCLUSIONS

Comparing the apparent abundance of a plurality of peptides derived from the same target protein makes it possible to select signature peptides that are unaffected by the unpredictable confounding factors inevitably present in biological samples.

Strategy and rationale for urine collection protocols employed in the NEPTUNE study

Background

Glomerular diseases are potentially fatal, requiring aggressive interventions and close monitoring. Urine is a readily-accessible body fluid enriched in molecular signatures from the kidney and therefore particularly suited for routine clinical analysis as well as development of non-invasive biomarkers for glomerular diseases.

Methods

The Nephrotic Syndrome Study Network (NEPTUNE; ClinicalTrials.gov Identifier NCT01209000) is a North American multicenter collaborative consortium established to develop a translational research infrastructure for nephrotic syndrome. This includes standardized urine collections across all participating centers for the purpose of discovering non-invasive biomarkers for patients with nephrotic syndrome due to minimal change disease, focal segmental glomerulosclerosis, and membranous nephropathy. Here we describe the organization and methods of urine procurement and banking procedures in NEPTUNE.

Results

We discuss the rationale for urine collection and storage conditions, and demonstrate the performance of three experimental analytes (neutrophil gelatinase-associated lipocalin [NGAL], retinol binding globulin, and alpha-1 microglobulin) under these conditions with and without urine preservatives (thymol, toluene, and boric acid). We also demonstrate the quality of RNA and protein collected from the urine cellular pellet and exosomes.

Conclusions

The urine collection protocol in NEPTUNE allows robust detection of a wide range of proteins and RNAs from urine supernatant and pellets collected longitudinally from each patient over 5 years. Combined with the detailed clinical and histopathologic data, this provides a unique resource for exploration and validation of new or accepted markers of glomerular diseases.

Trial registration

ClinicalTrials.gov Identifier NCT01209000

Electronic supplementary material

The online version of this article (doi:10.1186/s12882-015-0185-3) contains supplementary material, which is available to authorized users.

Urine proteomic analysis in cystinuric children with renal stones

INTRODUCTION

The gene mutations responsible for cystinuria do not fully explain kidney stone activity, suggesting that specific proteins may serve as promoters of cystine precipitation, aggregation or epithelial adherence. In this study we assessed (1) the differences in the urinary proteins between children with cystinuria and kidney stones (CYS) and healthy controls (HC), with particular attention to the fibrosis-related proteins, and (2) the presence of diagnostic biomarkers for CYS.

MATERIAL AND METHODS

We conducted a pilot study comparing individual urinary proteomes of 2 newly diagnosed children with CYS and 2 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Relative protein abundance was estimated using spectral counting. Proteins of interest in both CYS and HC were selected using the following criteria: i) ≥5 spectral counts; ii) ≥2-fold difference in spectral counts; and iii) ≤0.05 p-value for the Fisher's Exact Test.

DISCUSSION

This study demonstrates a different urinary polypeptide profile in two children with CYS compared to two HC. Of the 623 proteins identified by proteomic analysis, 180 exhibited at least a 2-fold increased relative abundance in CYS compared to HC. Of these, 39 were involved in response to stress, 26 in response to wounding, 21 in inflammatory response, 18 in immune response, and 4 in cellular response to oxidative stress. 133 proteins were found only in children with CYS, 33 of which met the selection criteria. Of these 33 unique proteins, six are known to be associated with fibrosis pathways (Table). The major limitation of this study is the small number of samples that were analyzed. Validation using highly specific methods such as ELISA is needed.

CONCLUSION

We provide proteomic evidence of oxidative injury, inflammation, wound healing and fibrosis in two children with CYS. We speculate that oxidative stress and inflammation may cause remodeling via actin and vimentin pathways, leading to fibrosis. Additionally, we identified ITIH and MMP-9 as potential diagnostic biomarkers and novel therapeutic targets in CYS. These proteins merit further investigation.

Evaluation of urinary protein precipitation protocols for the multidisciplinary approach to the study of chronic pelvic pain research network

Standardization of sample collection, shipping, and storage has been a major focus of biorepositories servicing large, multi-institute studies. The standardization of total protein concentration measurements may also provide an important metric for characterizing biospecimens. The measurement of total protein concentration in urine is challenging because of widely variable sample dilutions obtained in the clinic and the lack of a reference matrix for use with a standard curve and blank subtraction. Urinary proteins are therefore typically precipitated and reconstituted in a reference solution before quantitation. We have tested three different methods for protein precipitation and evaluated them using variability in total protein concentration measurement as a metric. The methods were tested on four urine samples ranging from very concentrated to very dilute. A method using a commercially available kit provided the most reproducible results, with average coefficients of variation <10%. Addition of a freeze/thaw did not lead to significant protein loss or additional variability. Samples were titrated and the measurements obtained appeared to be linearly correlated with sample starting volume. This method was applied to analysis of 77 urine biorepository samples and provided reproducible results when the same sample was assayed on different microwell plates.

Update on Biomarkers for the Detection of Endometriosis

Endometriosis is histologically characterized by the displacement of endometrial tissue to extrauterine locations including the pelvic peritoneum, ovaries, and bowel. An important cause of infertility and pelvic pain, the individual and global socioeconomic burden of endometriosis is significant. Laparoscopy remains the gold standard for the diagnosis of the condition. However, the invasive nature of surgery, coupled with the lack of a laboratory biomarker for the disease, results in a mean latency of 7–11 years from onset of symptoms to definitive diagnosis. Unfortunately, the delay in diagnosis may have significant consequences in terms of disease progression. The discovery of a sufficiently sensitive and specific biomarker for the nonsurgical detection of endometriosis promises earlier diagnosis and prevention of deleterious sequelae and represents a clear research priority. In this review, we describe and discuss the current status of biomarkers of endometriosis in plasma, urine, and endometrium.

Noninvasive effects measurements for air pollution human studies: methods, analysis, and implications

Human exposure studies, compared with cell and animal models, are heavily relied upon to study the associations between health effects in humans and air pollutant inhalation. Human studies vary in exposure methodology, with some work conducted in controlled settings, whereas other studies are conducted in ambient environments. Human studies can also vary in the health metrics explored, as there exists a myriad of health effect end points commonly measured. In this review, we compiled mini reviews of the most commonly used noninvasive health effect end points that are suitable for panel studies of air pollution, broken into cardiovascular end points, respiratory end points, and biomarkers of effect from biological specimens. Pertinent information regarding each health end point and the suggested methods for mobile collection in the field are assessed. In addition, the clinical implications for each health end point are summarized, along with the factors identified that can modify each measurement. Finally, the important research findings regarding each health end point and air pollutant exposures were reviewed. It appeared that most of the adverse health effects end points explored were found to positively correlate with pollutant levels, although differences in study design, pollutants measured, and study population were found to influence the magnitude of these effects. Thus, this review is intended to act as a guide for researchers interested in conducting human exposure studies of air pollutants while in the field, although there can be a wider application for using these end points in many epidemiological study designs.

A methodological approach based on gold-nanoparticles followed by matrix assisted laser desorption ionization time of flight mass spectrometry for the analysis of urine profiling of knee osteoarthritis

The aim of this work is to develop a nanoparticle-based methodology to find out biomarkers of diagnostic for knee osteoarthritis, KOA, through the use of matrix assisted laser desorption ionization time-of-flight-based mass spectrometry profiling. Urine samples used for this study were obtained from KOA patients (42 patients), patients with prosthesis (58 patients), and controls (36 individuals) with no history of joint disease. Gold-nano particle MALDI-based urine profiling was optimized and then applied over the 136 individuals. Jaccard index and 10 different classifiers over MALDI MS datasets were used to find out potential biomarkers. Then, the specificity and sensitivity of the method were evaluated. The presence of ten m/z signals as potential biomarkers in the healthy versus non-healthy approach suggests that patients (KOA and prosthesis) are differentiable from the healthy volunteers through profiling. The automatic diagnostic study confirmed these preliminary conclusions. The sensitivity and the specificity for the urine profiling criteria here reported, achieved by the C4.5 classifier, is 97% and 69% respectively. Thus, it is confirmed the utility of the method proposed in this work as an additional fast, non-expensive and robust test for KOA diagnostic. When the proposed method is compared with those used in common practice it is found that sensitivity is the highest, thus with a low false negative rate for diagnostic KOA patients in the population studied. Specificity is lower but in the range accepted for diagnostic objectives.

Differential regulation of urine proteins in urothelial neoplasm

Urothelial neoplasm of the urinary bladder has a high rate of multifocality and recurrence. To understand this we first need to understand the changes in the molecular level that distinguishes a normal individual from a patient and also a low grade neoplasm from a high grade. In this work we aim to study the urine proteome of Indian patients with urothelial neoplasm categorised on the basis of their p53 immunohistochemistry. The urine samples of pre-operative patients were subjected to two dimensional gel electrophoresis followed by densitometric analysis and spot identification using MALDI mass spectrometry. Our study shows that few proteins such as albumin, alpha 1 antitrypsin, apolipoprotein A1, transferrin, transthyretin, haptoglobin and haemoglobin β chain were upregulated and inter alpha trypsin inhibitor heavy chain was downregulated in the disease samples. Further we have reported that some of these proteins show an association with disease severity. The present study marks the first step in the identification of new diagnostic markers as well as therapeutic targets.

BIOLOGICAL SIGNIFICANCE

Bladder carcinoma is the ninth most common cancer worldwide. It has gained attention within both clinicians and cancer biologists because of its recurrence and mortality rate. Identifying the prognostic factors of progression is a challenge, so that high risk patients who may be a candidate for a radical cystectomy may be identified. In this study we have attempted to study the changes observed in the urinary protein levels of urothelial neoplasm patients. The samples were graded based on p53 immunohistochemistry staining. We have reported eight (8) proteins, mostly highly abundant; those have exhibited differential regulation in case of diseased samples. This study is first of its kind that associates the changes in the urinary protein levels to that of the severity of the disease. We believe that the findings can be used as a stepping stone in the development of a noninvasive prognostic tool for the disease. This article is part of a Special Issue entitled: Proteomics in India.

Proteomics urine analysis of pregnant women suffering from multiple sclerosis

Multiple sclerosis (MScl) frequently is remitted during the third trimester of pregnancy but exacerbated in the first postpartum period. In this context, we investigated protein identification, its abundance, and its change in urine related to these two periods. Using mass spectrometry (LTQ Orbitrap), we identified 1699 tryptic peptides (related to 402 proteins) in urine from 31 MScl and 8 control at these two periods. Pregnancy-related peptides were significantly elevated (p < 0.01) in MScl patients compared with controls (Analysis 1: 531 peptides in MScl and 36 peptides in controls higher abundant in the third trimester compared to postpartum). When comparing the longitudinal differences (Analysis 2), we identified 43 (related to 35 proteins) MScl disease-associated peptides (p < 0.01) with increased or decreased difference ratio in MScl compared with controls. The most discriminating peptides identified were trefoil factor 3 and lysosomal-associated membrane protein 2. Both proteins have a role in the innate immune system. Three proteins with a significant decreased ratio were plasma glutamate carboxypeptidase, Ig mu chain C region, and osteoclast associated immune like receptor. Our results indicate that the protein expression pattern in urine of MScl patients contains information about remote CNS and brain disease processes.

An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis

Purpose

We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies.

Experimental design

Ten urine samples from patients with varying pathologies were each divided and PIs added to one‐half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20–22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D‐PAGE, SELDI‐TOF‐MS, and immunoassay.

Results

Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D‐PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β₂‐microglobulin, or α₁‐microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient‐dependent with most samples showing minimal effects.

Conclusions and clinical relevance

The extent of processing‐induced changes and the benefit of PI addition are patient‐ and sample‐dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results.

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.

Development of quantitative proteomics using iTRAQ based on the immunological response of Galleria mellonella larvae challenged with Fusarium oxysporum microconidia

Galleria mellonella has emerged as a potential invertebrate model for scrutinizing innate immunity. Larvae are easy to handle in host-pathogen assays. We undertook proteomics research in order to understand immune response in a heterologous host when challenged with microconidia of Fusarium oxysporum. The aim of this study was to investigate hemolymph proteins that were differentially expressed between control and immunized larvae sets, tested with F. oxysporum at two temperatures. The iTRAQ approach allowed us to observe the effects of immune challenges in a lucid and robust manner, identifying more than 50 proteins, 17 of them probably involved in the immune response. Changes in protein expression were statistically significant, especially when temperature was increased because this was notoriously affected by F. oxysporum 104 or 106 microconidia/mL. Some proteins were up-regulated upon immune fungal microconidia challenge when temperature changed from 25 to 37°C. After analysis of identified proteins by bioinformatics and meta-analysis, results revealed that they were involved in transport, immune response, storage, oxide-reduction and catabolism: 20 from G. mellonella, 20 from the Lepidoptera species and 19 spread across bacteria, protista, fungi and animal species. Among these, 13 proteins and 2 peptides were examined for their immune expression, and the hypothetical 3D structures of 2 well-known proteins, unannotated for G. mellonella, i.e., actin and CREBP, were resolved using peptides matched with Bombyx mori and Danaus plexippus, respectively. The main conclusion in this study was that iTRAQ tool constitutes a consistent method to detect proteins associated with the innate immune system of G. mellonella in response to infection caused by F. oxysporum. In addition, iTRAQ was a reliable quantitative proteomic approach to detect and quantify the expression levels of immune system proteins and peptides, in particular, it was found that 104 microconidia/mL at 37°C over expressed many more proteins than other treatments.

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

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

Urine sample preparation for proteomic analysis

Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery.

From hundreds to thousands: Widening the normal human Urinome (1)

It is currently unknown how many proteins can be detected in urine. Improving the analytical approach would increase their number and potentially strengthen their predictive potential in diseases. We developed a combination of analytical procedures for maximizing sensitivity and reproducibility of normal human urinary proteome analysis based on ultracentrifugation, vesicles separation, combinatorial peptide ligand libraries (CPLL) and solvent removal of pigments. Proteins were identified by an Orbitrap Velos Mass Spectrometry. Overall, 3429 proteins were characterized: most components (1615) were contained in vesicles while the remaining 1794 were equally distributed among CPLL and butanol insoluble fractions. Several proteins were detected exclusively in one of the phases of the procedure, suggesting that each step is crucial in the fractionation strategy. Many (1724) proteins are described here whose presence in urine has never been reported and represents a potential source of information considering that urine is the unique site of excretion of products of interaction of metabolic processes. Improving the characterization of normal urinary proteome would also represent the basis for the analysis of urine biomarkers in human diseases.

BIOLOGICAL SIGNIFICANCE

Sub-fractionating normal urine by successive steps (vesicle separation, CPLL and solvent treatments) allowed the identification of 3429 proteins, a relevant part (1724) being detected for the first time in urine. Several proteins of new description have been implicated in physiology pathways and in pathologies thus representing a potential source of new information on both metabolic processes and diseases.

The urinary proteome and peptidome of renal cell carcinoma patients: a comparison of different techniques

Renal cell carcinomas, originating from the renal cortex, account for about 80% of kidney primary malignancies. Small localized tumors rarely produce symptoms and diagnosis is often delayed until the disease is advanced. In contrast to other urological cancers, renal cell carcinomas are associated with a high degree of metastases and a low 5-year survival rate. The identification of diagnostic and prognostic markers, especially in the urine, remains an area of intense investigation. Different proteomic strategies have been applied so far to biomarker discovery in urine at the proteome or the peptidome level. Gel-based and gel-free strategies combined with mass spectrometry are the most-used strategies, have different success rates, and will be depicted here. We also prefigure a scenario in which the limitations of a single approach are overcome by applying new and complementary research strategies, relying on the excellent availability coupled to the intrinsic richness typical of urine samples.