The ubiquitin-proteasome pathway is important for dengue virus infection in primary human endothelial cells

Dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) are the most severe forms of dengue virus infection with hemorrhage and plasma leakage. However, pathogenic mechanisms of DHF and DSS remain poorly understood. We therefore investigated host responses as determined by changes in the cellular proteome of primary human endothelial cells upon infection with dengue virus serotype 2 (DEN-2) at a multiplicity of infection (MOI) of 10 for 24 h. Two-dimensional PAGE and quantitative intensity analysis revealed 38 significantly altered protein spots (16 upregulated and 22 downregulated) in DEN-2-infected cells compared to mock controls. These altered proteins were successfully identified by mass spectrometry, including those involved in oxidative stress response, transcription and translation, cytoskeleton assembly, protein degradation, cell growth regulation, apoptosis, cellular metabolism, and antiviral response. The proteomic data were validated by Western blot analyses [upregulated ubiquitin-activating enzyme E1 (UBE1) and downregulated annexin A2] and an immunofluorescence study (upregulated MxA). Interestingly, we found that MxA was colocalized with DEN-2 viral capsid protein, strengthening its role as an antiviral protein. Moreover, we also identified upregulation of a proteasome subunit. Our functional study revealed the significant role of ubiquitination in dengue infection and UBE1 inhibition by its specific inhibitor (UBEI-41) caused a significant reduction in the level of viral protein synthesis and its infectivity. Our findings suggest that various biological processes were triggered in response to dengue infection, particularly antiviral IFN and ubiquitin-proteasome pathways.

Protective effect of mangosteen extract against beta-amyloid-induced cytotoxicity, oxidative stress and altered proteome in SK-N-SH cells

Beta-amyloid (A beta) plays a key role in the pathogenesis of Alzheimer's disease (AD) by inducing neurotoxicity and cell death mainly through production of reactive oxygen species (ROS). Garcinia mangostana L. (mangosteen) has been recognized as a major source of natural antioxidants that could decrease ROS. However, its role in protection of A beta-induced cytotoxicity and apoptosis in neuronal cells remains unclear. We therefore examined such a protective effect of mangosteen extract (ME) by evaluating cell viability using MTT test, ROS level, caspase-3 activity, and cellular proteome. Treating SK-N-SH cells with 5-20 microM A beta((1-42)) for 24 h caused morphologically cytotoxic changes, decreased cell viability and increased ROS level, whereas preincubation with 50-400 microg/mL ME 30 min before the induction by A beta((1-42)) successfully prevented such cytotoxic effects in a dose-dependent manner (completely at 400 microg/mL). The A beta-induced increase in caspase-3 activity was also preventable by 400 microg/mL ME. Proteomic analysis using 2-D gel electrophoresis (n = 5 gels/group) followed by mass spectrometry revealed 63 proteins whose levels were significantly altered by A beta((1-42)) induction. Interestingly, changes in 10 proteins were successfully prevented by the ME pretreatment. In summary, we report herein the significant protective effects of ME against A beta-induced cytotoxicity, increased ROS, and increased caspase activity in SK-N-SH cells. Moreover, proteomic analysis revealed some proteins that might be responsible for these protective effects by ME. Further characterizations of these proteins may lead to identification of novel therapeutic targets for successful prevention and/or decreasing the severity of AD.

Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides.

Red blood cell membrane fragments but not intact red blood cells promote calcium oxalate monohydrate crystal growth and aggregation

PURPOSE

Cell membranes are thought to promote calcium oxalate kidney stone formation but to our knowledge the modulating effect of red blood cell membranes on calcium oxalate crystals has not been previously investigated. Thus, we examined the effects of red blood cell membrane fragments on calcium oxalate monohydrate and calcium oxalate dihydrate crystal growth and aggregation.

MATERIALS AND METHODS

Calcium oxalate monohydrate and calcium oxalate dihydrate crystals were treated with red blood cell membrane fragments or intact red blood cells from a healthy donor. Phase contrast microscopy was performed to evaluate crystal morphology and aggregation. We used ImageMaster 2D Platinum software to evaluate crystal size and spectrophotometric oxalate depletion assay to monitor crystal growth.

RESULTS

Red blood cell membrane fragments had significant promoting activity on calcium oxalate monohydrate crystal growth with an approximately 75% increase in size and aggregation with an approximately 2.5-fold increase in aggregate number compared to the control without membrane fragments or cells. Approximately 50% of calcium oxalate monohydrate crystals were adhered by red blood cell membrane fragments. Intact red blood cells had no significant effect on calcium oxalate monohydrate crystal growth or aggregation but they could transform calcium oxalate monohydrate to calcium oxalate dihydrate crystals. Red blood cell membrane fragments and intact red blood cells had no effect on calcium oxalate dihydrate crystals. The promoting activity of red blood cell membrane fragments on calcium oxalate monohydrate crystal growth was successfully confirmed by spectrophotometric oxalate depletion assay.

CONCLUSIONS

To our knowledge our data provide the first direct evidence that red blood cell membrane fragments are a promoting factor for calcium oxalate monohydrate crystal growth and aggregation. Thus, they may aggravate calcium oxalate stone formation.

Vimentin interacts with heterogeneous nuclear ribonucleoproteins and dengue nonstructural protein 1 and is important for viral replication and release

Our previous study using expression proteomics demonstrated that many proteins, particularly five forms of heterogeneous nuclear ribonucleoproteins (hnRNPs), were up-regulated in human endothelial cells upon dengue virus infection. To address functional significance of these proteins in response to dengue virus infection, we performed a functional proteomics study to identify hnRNPs-interacting proteins in the infected EA.hy926 cells. Immunoprecipitation followed by 2-D PAGE and mass spectrometric analyses revealed 18 and 13 interacting partners of hnRNP C1/C2 and hnRNP K, respectively. Interestingly, vimentin was a common partner for both hnRNP C1/C2 and K. The interaction between vimentin and these hnRNPs was confirmed by reciprocal immunoprecipitation followed by Western blot analysis and also by double immunofluorescence staining. Disruption of vimentin intermediate filament by acrylamide not only dissociated these complexes but also reduced nuclear hnRNPs expression, whereas cytosolic hnRNPs expression was unchanged. We also demonstrated that vimentin was strongly associated with dengue non-structural protein 1 (NS1). Disruption of vimentin intermediate filament not only dissociated this complex but also reduced dengue NS1 expression, as well as viral replication and release. Our data report for the first time that vimentin interacts with hnRNPs and dengue NS1, and plays a crucial role in replication and release of dengue virus.

Comprehensive human urine standards for comparability and standardization in clinical proteome analysis

PURPOSE

Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies.

EXPERIMENTAL DESIGN

We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds.

RESULTS

The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated.

CONCLUSIONS AND CLINICAL RELEVANCE

These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.

Proteomic analysis of proteins bound to adsorption units of extracorporeal liver support system under clinical conditions

Fractionated Plasma Separation, Adsorption and Dialysis (Prometheus) has a well-documented capacity to remove protein-bound organic toxins in patients with liver failure. However, the compositions of adsorbed proteins remain unknown. Elution of both adsorbers constituting Prometheus system was performed following a 6-h session in a patient with acute on chronic liver failure. Sodium dodecylsulphate was employed to elute proteins from the neutral adsorber (P1), while acetic acid was applied to the cationic one (P2). Eluted proteins were resolved by two-dimensional gel electrophoresis (2-DE) and identified by mass spectrometry (MS). Totally, 4113 and 8280 mg of proteins were obtained from P1 and P2 eluates, 2-DE yielded 148 and 163 protein fractions in P1 and P2, respectively. MS identified 18 unique proteins in P1, and 30 unique proteins in P2 sample. Proteins with the highest selective adsorption (as determined by eluate to plasma ratio) included transthyretin (37), trypsin-2 (29), prothrombin (23), hyaluronan-binding protein 2 (13) and plasma retinol-binding protein (8.7), all of which adsorbed to P2. We identified a large number of proteins removed by extracorporeal liver support system. A selective adsorption was demonstrated in a subset of proteins depending on the type of adsorber and proteins' characteristics.

Analysis of differential proteomes in pathogenic and non-pathogenic Leptospira: potential pathogenic and virulence factors

Leptospirosis is a bacterial zoonotic disease caused by spirochetes in the genus Leptospira. To date, factors determining the pathogenicity and virulence of leptospires remain unclear. We performed a gel-based proteomic analysis to evaluate differential leptospiral proteomes in the pathogenic L. interrogans (serovars Australis, Bratislava, Autumnalis, and Icterohaemorrhagiae) and the non-pathogenic L. biflexa (serovar Patoc). Quantitative proteome analysis and MS protein identification revealed 42 forms of 33 unique proteins whose levels were significantly greater in the pathogenic serovars compared with the non-pathogenic serovar. Among the four pathogenic serovars, the more virulent serovar Icterohaemorrhagiae (which is most commonly associated with severe leptospirosis in patients) had significantly greater levels of 14 forms of 12 unique proteins, when compared with the other three pathogenic serovars. Some of these identified proteins may serve as the pathogenic and/or virulence factors of leptospirosis.

Are protease inhibitors required for gel-based proteomics of kidney and urine?

Proteolysis is one of the major problems in collection and storage of biological samples for proteome analysis, particularly when the samples undergo freeze-thaw cycles. The use of protease inhibitors for prevention of such proteolysis in some samples is debated because protease inhibitors may interfere with proteome analysis and whether protease inhibitors are useful for renal and urinary proteomics remains unclear. We therefore performed a systematic evaluation of the use of protease inhibitors in gel-based renal and urinary proteomics. Renal proteins were extracted from porcine kidney tissue and stored at -30 or -70 degrees C without protease inhibitors. After 0, 2, 4, 6, 8, 10, and 12 freeze-thaw cycles, the 2-D proteome profile was examined. Differential spot analysis and ANOVA with Tukey posthoc multiple comparisons revealed significantly quantitative changes in intensity levels of 12 and 7 renal proteins that were stored at -30 and -70 degrees C, respectively, after >or=4 freeze-thaw cycles. Additionally, there were qualitative changes (vertical elongation or streak) in 6 and 1 renal proteins that were stored at -30 and -70 degrees C, respectively. All these changes could be successfully prevented by the addition of 1% (v/v) protease inhibitors cocktail prior to storage. In contrast, neither quantitative nor qualitative changes were observed in urine samples that were stored without protease inhibitors and processed as for kidney samples. From these data, the addition of protease inhibitors is highly recommended for gel-based renal proteomics, but no longer recommended for gel-based urinary proteomics.

Should urine pH be adjusted prior to gel-based proteome analysis?

The urine has become one of the most widely used clinical samples for biomarker discovery. The pH of human urine may vary largely from 4.5 to 8.0. Previously, it was questionable whether the urine pH would affect proteome analysis and whether the urine pH needed to be adjusted prior to proteome analysis remained unclear. We therefore performed a systematic analysis of the effect of urine pH on proteome profile. Midstream second morning and random afternoon urine samples were collected from 5 males and 5 females who were healthy and had no recent medication. After removal of cells and debris by low-speed centrifugation, pH levels of individual samples were measured and urinary proteins were isolated by 75% ethanol precipitation. Equally loaded 100 microg of proteins from individual samples were resolved in 2-DE (linear pH 3-10) and visualized with SYPRO Ruby fluorescence stain. There was no significant correlation between difference in the morning versus afternoon urine pH (DeltapH) and %match of protein spots derived from morning versus afternoon urine samples in individual samples (Pearson's r = 0.074; p = 0.839). In parallel, all individual samples with equal volume were pooled. The pH of the pooled urine was adjusted to 4-10 and urinary proteome profiles were analyzed as for individual samples. ANOVA with Tukey's posthoc multiple comparisons showed no significant differences in total number of detected spots and %match among various pH levels. Our data suggest that the urine pH has no significant effects on urinary proteome profile and thus needs no adjustment prior to gel-based proteome analysis.

Plasma proteome profiling of von Hippel-Lindau disease after total and subtotal nephrectomy: a preliminary study

OBJECTIVES

Common treatment of renal cell carcinoma associated with von Hippel-Lindau (VHL) disease is total (bilateral) or subtotal nephrectomy. Whereas total nephrectomy is associated with absolutely no residual renal function, subtotal nephrectomy frequently leads to chronic kidney disease (CKD) with some residual renal functions. However, molecular mechanisms underlying CKD remain unclear and the diagnosis of CKD is frequently accomplished at its late stage.

DESIGN AND METHODS

We performed a plasma proteomics study to compare the plasma proteome profile of VHL patient who underwent total nephrectomy to the profiles of VHL patient with subtotal nephrectomy and healthy control. Totally 100 mug proteins from each sample was resolved by two-dimensional electrophoresis (2-DE) in triplicate and visualized with SYPRO Ruby fluorescence stain.

RESULTS

The normal plasma proteome profile markedly differed from the profiles of VHL patients. Comparative analysis between total versus subtotal nephrectomized patients revealed significant differences in levels of 20 plasma proteins. Pathway analysis revealed two important networks involving in lipid metabolism, molecular transport, carbohydrate metabolism, cellular growth and proliferation, and small molecule biochemistry, in which these identified and other proteins interplayed.

CONCLUSIONS

Our data identified potential biomarkers for CKD. Further characterization of these identified proteins might also lead to better understanding of molecular mechanisms underlying CKD.

Alterations in cellular proteome and secretome upon differentiation from monocyte to macrophage by treatment with phorbol myristate acetate: insights into biological processes

Monocyte and macrophage are mainly involved in immune response and inflammatory processes. Monocytes circulate in the bloodstream and migrate to various tissues where they can differentiate to macrophages. However, the molecular basis of biological processes involved in this cellular differentiation remains ambiguous. This study was to investigate alterations in cellular and secreted proteins after this differentiation phase. Macrophage was differentiated from U937 human monocytic cell line by treatment with 100 ng/ml phorbol myristate acetate (PMA) for 48 h. Cellular and secreted proteins extracted from PMA-treated cells (macrophages) were compared with those of untreated cells (monocytes) using 2-DE (n=5 gels/condition; stained with Deep Purple fluorescence dye). Quantitative intensity analysis revealed 81 and 67 protein spots whose levels were significantly altered in cellular proteome and secretome. These proteins were subsequently identified by Q-TOF MS and/or MS/MS analyses. The altered levels of cellular elongation factor-2 (EF-2) and secreted alpha-tubulin were confirmed by Western blot analysis. Global protein network analysis demonstrated that these altered proteins were involved in cell death, lipid metabolism, cell morphology, cellular movement, and protein folding. Our data may provide some insights into molecular mechanisms of biological processes upon differentiation from monocytes to macrophages.

Specific adsorption of some complement activation proteins to polysulfone dialysis membranes during hemodialysis

Dialyser bioincompatibility is an important factor contributing to complications of hemodialysis with well known systemic consequences. Here we studied the local processes that occur on dialysis membranes by eluting proteins adsorbed to the polysulfone dialyser membranes of 5 patients after 3 consecutive routine maintenance hemodialysis sessions. At the end of each procedure, a plasma sample was also collected. These eluates and their accompanying plasma samples were separated by 2-dimensional gel electrophoresis; all proteins that were present in all patients were analyzed by tandem mass spectrometry; and a ratio of the relative spot intensity of the eluate to plasma was calculated. Of 153 proteins detected, 84 were found in all patients, 57 of which were successfully identified by mass spectrometry as 38 components of 23 unique proteins. In 10 spots the relative eluate intensity differed significantly from that in the plasma, implying preferential adsorption. These proteins included ficolin-2, clusterin, complement C3c fragment, and apolipoprotein A1. Our finding of a selective binding of ficolin-2 to polysulfone membranes suggests a possible role of the lectin complement pathway in blood-dialyser interactions.

Characterizations of urinary sediments precipitated after freezing and their effects on urinary protein and chemical analyses

One of the obstacles in analyzing frozen urine samples is the formation of uncharacterized precipitates. Frequently, these precipitates are discarded before analysis. Some laboratory data may be erroneous if these precipitates contain important compounds. In the present study, we examined urinary sediments precipitated after overnight storage at -20 degrees C. Although cells and debris were removed before freezing, the precipitates remained, whereas storing the centrifuged urine overnight at 4 degrees C did not result in precipitate formation. There were no significant differences observed among 10 healthy individuals (5 men and 5 women). EDTA (5 mM) could efficiently reduce the amount of precipitates to approximately 25% of the initial amount. The addition of exogenous CaCl2, but not sodium oxalate and NaCl, significantly increased the amount of precipitates in a dose-dependent manner. Linear regression analysis revealed a significant correlation between endogenous urinary calcium level and the amount of precipitates (r = 0.894; P < 0.001). Urine pH also had some effects on the type and amount of precipitates. These precipitates were composed mainly of calcium oxalate dihydrate and amorphous calcium crystals. The results also showed that these precipitates could deplete urinary proteins and calcium ions (23.6 +/- 1.1% decrease). Therefore, these freezer-induced urinary sediments significantly affect protein analysis and measurement of calcium levels in the urine. However, vigorous shaking of the sample at room temperature could redissolve these precipitates. Our data strongly indicate that these freezer-induced precipitates must be taken into account when the frozen urine samples are analyzed.

Altered secretome of Burkholderia pseudomallei induced by salt stress

Burkholderia pseudomallei is a saprophyte found in soil and water. It is a difficult microorganism to kill and can survive in these environments for many years. Mechanisms for its adaptive response to environmental changes remain largely unknown. We performed a proteomics study to examine alterations in secreted proteins (secretome) under a salt stress (with 150 mM NaCl) compared to the normal cultured condition in LB broth. The culture supernatants were filtrated and precipitated with 50% ethanol. The isolated proteins were recovered, separated with 2-D PAGE, and visualized with SYPRO Ruby stain (n=5 gels for each group). Differentially expressed protein spots were identified by Q-TOF MS and/or MS/MS analyses. A total of 42 protein spots representing 37 unique proteins were identified as the altered proteins during the salt stress, including metabolic enzymes, transcription/translation regulators, potential virulence factors, chaperones, phage capsid proteins, drug resistance protein, solute transport regulator, and hypothetical proteins. The presence of secreted GroEL only after NaCl exposure was confirmed by Western blot analysis. The increased level (19-fold) of a beta-lactamase-like protein suggested that the NaCl-exposed bacterium might resist to beta-lactam antibiotics. Functional analysis revealed that the NaCl-exposed bacterium had significantly greater survival rate after a treatment with ceftazidime. Our study provided the first dataset of the secretome of B. pseudomallei and its alterations, which may lead to novel insights into adaptive response of B. pseudomallei during the salt stress.