PubMed

Related Articles Lipidomic Analysis of Chlamydomonas reinhardtii under Nitrogen and Sulfur Deprivation. PLoS One. 2015;10(9):e0137948 Authors: Yang D, Song D, Kind T, Ma Y, Hoefkens J, Fiehn O Abstract Chlamydomonas reinhardtii accumulates lipids under complete nutrient starvation conditions while overall growth in biomass stops. In order to better understand biochemical changes under nutrient deprivation that maintain production of algal biomass, we used a lipidomic assay for analyzing the temporal regulation of the composition of complex lipids in C. reinhardtii in response to nitrogen and sulfur deprivation. Using a chip-based nanoelectrospray direct infusion into an ion trap mass spectrometer, we measured a diversity of lipid species reported for C. reinhardtii, including PG phosphatidylglycerols, PI Phosphatidylinositols, MGDG monogalactosyldiacylglycerols, DGDG digalactosyldiacylglycerols, SQDG sulfoquinovosyldiacylglycerols, DGTS homoserine ether lipids and TAG triacylglycerols. Individual lipid species were annotated by matching mass precursors and MS/MS fragmentations to the in-house LipidBlast mass spectral database and MS2Analyzer. Multivariate statistics showed a clear impact on overall lipidomic phenotypes on both the temporal and the nutrition stress level. Homoserine-lipids were found up-regulated at late growth time points and higher cell density, while triacyclglycerols showed opposite regulation of unsaturated and saturated fatty acyl chains under nutritional deprivation. PMID: 26375463 [PubMed - as supplied by publisher]

Related Articles SCK-3: TARGET METABOLOMICS FOR IMPROVING EARLY PREDICTION OF DEATH IN PATIENTS WITH SEPTIC SHOCK. Shock. 2015 Oct;44 Suppl 2:19-20 Authors: Cambiaghi A, Brunelli L, Caironi P, Ferrario M, Gattinoni L, Latini R, Masson S, Ristagno G, Pastorelli R Abstract INTRODUCTION: Elucidation of early metabolic signatures that predict survival in septic shock might help clinicians in prioritizing individual patient treatment. In this preliminary investigation, we examined plasma metabolome and clinical features in a subset of 20 patients with septic shock, enrolled in the multicenter Albumin Italian Outcome Sepsis (ALBIOS, NCT00707122). METHODS: Patients were divided into two groups according to their 28-days and 90-days survival. A mass spectrometry-based metabolomic approach was used to quantify acylcarnitines, aminoacids, biogenic amines, glycerophospolipids, sphingolipids, sugars. Metabolites were measured one day (d1) and one week (d7) after ICU admission. RESULTS: Profiles of specific metabolites differed markedly between survivors and non-survivors. An overall decrease from d1 to d7 in levels of different species of lysophosphatidylcholines (LPC) and phosphatidylcholines (PC) was observed together with a significant increase in kynurenine (KYN), in non-survivors compared to survivors both at 28- and 90-days (Wilcoxon test p < 0.05, FDR < 0.05). Data-mining techniques were then used to highlight metabolite levels associated with mortality. Twenty-eight days mortality was associated at d1 with increased levels of diacyl-PC-C38:1, butyrylacylcarnitine, but decreased diacyl-PC-C40:6 and diacyl-alkyl-PC-38:0; whereas at d7 with increased diacyl-PC-C42:4, KYN and decreased diacyl-alkyl-PC40:1, LPC-C24:0. Ninety-days mortality was associated only at d7 with elevation of KYN, diacyl-PC-C44:3 and reduction of diacyl- alkyl-PC40:1, LPC-C24:0. CONCLUSION: Our preliminary results suggest that increased KYN, that may contribute to hypotension in sepsis, as well as alterations of different LPC and PC species, able to modulate immune and inflammatory responses, might represent not only a risk factor for septic shock patients but important pathophysiologic mechanisms deserving further investigation. PMID: 26375122 [PubMed - as supplied by publisher]

Related Articles Top-down MALDI-in-source decay-FTICR mass spectrometry of isotopically resolved proteins. Anal Chem. 2015 Mar 17;87(6):3429-37 Authors: Nicolardi S, Switzar L, Deelder AM, Palmblad M, van der Burgt YE Abstract An accurate mass measurement of a known protein provides information on potential amino acid deletions and post-translational modifications. Although this field is dominated by strategies based on electrospray ionization, mass spectrometry (MS) methods using matrix-assisted laser desorption/ionization (MALDI) have the advantage of yielding predominantly singly charged precursor ions, thus avoiding peak overlap from different charge states of multiple species. Such MALDI-MS methods require mass measurement at ultrahigh resolution, which is provided by Fourier transform ion cyclotron resonance (FTICR) mass analyzers. Recently, using a MALDI-FTICR-MS platform equipped with a 15 T magnet, we reported on the mass analysis of intact human serum peptides and small proteins with isotopic resolution up to ∼15 kDa and identified new proteoforms from an accurate measurement of mass distances. In the current study, we have used this FTICR system after an upgrade with a novel dynamically harmonized ICR cell, i.e., ParaCell, for mapping isotopically resolved intact proteins up to about 17 kDa and performed top-down MALDI in-source decay (ISD) analysis. Standard proteins myoglobin (m/z-value 16,950) and ribonuclease B (m/z-value 14,900) were measured with resolving powers of 62,000 and 61,000, respectively. Furthermore, it will be shown that (singly charged) MALDI-ISD fragment ions can be measured at isotopic resolution up to m/z-value 12,000 (e.g., resolving power 39,000 at m/z-value 12,000) providing more reliable identifications. Moreover, examples are presented of pseudo-MS(3) experiments on ISD fragment ions from RNase B by collisional-induced dissociation (CID). PMID: 25719938 [PubMed - indexed for MEDLINE]

Related Articles Essential role for oxidative phosphorylation in cancer progression. Cell Metab. 2015 Jan 6;21(1):11-2 Authors: Maiuri MC, Kroemer G Abstract Cancers are often affected by derangements in mitochondrial (mt) function, as well as mtDNA mutations. In this issue, Tan et al. (2015) demonstrate that only mtDNA-depleted cancer cells capable of recovering mtDNA from the host form metastasizing cancers in vivo, revealing an essential requirement for oxidative phosphorylation in tumor progression. PMID: 25565201 [PubMed - indexed for MEDLINE]

Related Articles Metabolomic analysis of plasma and liver from surplus arginine fed Atlantic salmon. Front Biosci (Elite Ed). 2015;7:67-78 Authors: Andersen SM, Assaad HI, Lin G, Wang J, Aksnes A, Wu G, Espe M Abstract The aim of this study was to determine the metabolic effect of surplus arginine (36.1 g/kg dry matter) compared to a control diet with required arginine (21.1 g/kg dry matter) in adult Atlantic salmon (Salmo salar L.). Although the feeding trial had no significant effect on growth, there were significant differences in the metabolite profile in both plasma and liver in experimental group as compared to the control group. There was increased concentrations of biliverdin, PGF-2 alpha, oxidized glutathione, selenocysteine, two monoacylglycerols and a tripeptide in the liver as well as decreased concentrations of valine and a vitamin D3 metabolite in plasma of arginine supplemented fish. These results indicate that while surplus arginine does not affect growth or body weight, it induces metabolic changes in Atlantic salmon. PMID: 25553364 [PubMed - indexed for MEDLINE]

Related Articles Plasma metabolite profiles following trauma-hemorrhage: effect of posttreatment with resveratrol. Shock. 2015 Feb;43(2):172-7 Authors: Wang YR, Tsai YF, Lau YT, Yu HP Abstract Resveratrol (RSV) has been shown to inhibit the inflammatory reaction and ameliorate the organ damage resulting from trauma-hemorrhage (TH). However, the effects of RSV on the metabolomic profiles under these conditions remain unclear. The aim of this study was to determine the metabolomic profiles of plasma in TH rats and to evaluate the therapeutic effects of RSV using high-performance liquid chromatography-mass spectrometry. Thirty male Sprague-Dawley rats were divided into sham operation (n = 10), sham-operation plus RSV treatment (n = 10), TH (n = 10), and TH plus RSV treatment (n = 10) groups. Plasma samples were obtained at 24 h after surgery. Electrospray ionization-tandem mass spectrometry was used to characterize the plasma metabolomes. The systemic analyses of plasma metabolomes and their targets were determined using a number of computational approaches, including principal component analysis, partial least squares discriminant analysis, and heat map analysis. Using these methods, the effects of RSV on the metabolomic profiles in animals that underwent trauma-hemorrhagic injury were determined. These approaches allowed a clear discrimination of the pathophysiological characteristics among the groups. The results demonstrate RSV treatment significantly reduced the metabolic derangements caused by TH. Compared with the sham-operated rats, the plasma levels of carnitine in the TH rats were relatively lower, but the levels of acetylcarnitine and butyrylcarnitine were higher, suggesting that RSV ameliorated the deranged carnitine metabolism in TH rats. There was a statistically significant increase in carnitine. In addition, RSV treatment reduced ketoacidosis and protein degradation, as evidenced by the attenuation of the elevated plasma branched-chain amino acid levels in the TH rats. Our study showed that the alterations of the metabolomic profiles in the rats subjected to trauma-hemorrhagic shock were attenuated by RSV treatment. In view of the metabolomic evidence, we conclude that RSV exerts beneficial effects in trauma-hemorrhagic shock injury and that these effects are partially mediated by improving energy metabolism and reducing protein degradation. PMID: 25300031 [PubMed - indexed for MEDLINE]

Related Articles High-throughput nucleoside phosphate monitoring in mammalian cell fed-batch cultivation using quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Biotechnol J. 2015 Jan;10(1):190-8 Authors: Steinhoff RF, Ivarsson M, Habicher T, Villiger TK, Boertz J, Krismer J, Fagerer SR, Soos M, Morbidelli M, Pabst M, Zenobi R Abstract Current methods for monitoring multiple intracellular metabolite levels in parallel are limited in sample throughput capabilities and analyte selectivity. This article presents a novel high-throughput method based on matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) for monitoring intracellular metabolite levels in fed-batch processes. The MALDI-TOF-MS method presented here is based on a new microarray sample target and allows the detection of nucleoside phosphates and various other metabolites using stable isotope labeled internal standards. With short sample preparation steps and thus high sample throughput capabilities, the method is suitable for monitoring mammalian cell cultures, such as antibody producing hybridoma cell lines in industrial environments. The method is capable of reducing the runtime of standard LC-UV methods to approximately 1 min per sample (including 10 technical replicates). Its performance is exemplarily demonstrated in an 8-day monitoring experiment of independently controlled fed-batches, containing an antibody producing mouse hybridoma cell culture. The monitoring profiles clearly confirmed differences between cultivation conditions. Hypothermia and hyperosmolarity were studied in four bioreactors, where hypothermia was found to have a positive effect on the longevity of the cell culture, whereas hyperosmolarity lead to an arrest of cell proliferation. The results are in good agreement with HPLC-UV cross validation experiments. Subsequent principal component analysis (PCA) clearly separates the different bioreactor conditions based on the measured mass spectral profiles. This method is not limited to any cell line and can be applied as a process analytical tool in biotechnological processes. PMID: 25139677 [PubMed - indexed for MEDLINE]

A serum metabolomic fingerprint of bevacizumab and temsirolimus combination as first-line treatment of metastatic renal cell carcinoma. Br J Cancer. 2015 Sep 15; Authors: Jobard E, Blanc E, Négrier S, Escudier B, Gravis G, Chevreau C, Elena-Herrmann B, Trédan O Abstract BACKGROUND: Renal cell carcinoma is one of the most chemoresistant cancers, and its metastatic form requires administration of targeted therapies based on angiogenesis or mTOR inhibitors. Understanding how these treatments impact the human metabolism is essential to predict the host response and adjust personalised therapies. We present a metabolomic investigation of serum samples from patients with metastatic RCC (mRCC) to identify metabolic signatures associated with targeted therapies. METHODS: Pre-treatment and serial on-treatment sera were available for 121 patients participating in the French clinical trial TORAVA, in which 171 randomised patients with mRCC received a bevacizumab and temsirolimus combination (experimental arm A) or a standard treatment: either sunitinib (B) or interferon-α+bevacizumab (C). Metabolic profiles were obtained using nuclear magnetic resonance spectroscopy and compared on-treatment or between treatments. RESULTS: Multivariate statistical modelling discriminates serum profiles before and after several weeks of treatment for arms A and C. The combination A causes faster changes in patient metabolism than treatment C, detectable after only 2 weeks of treatment. Metabolites related to the discrimination include lipids and carbohydrates, consistently with the known RCC metabolism and side effects of the drugs involved. Comparison of the metabolic profiles for the three arms shows that temsirolimus, an mTOR inhibitor, is responsible for the faster host metabolism modification observed in the experimental arm. CONCLUSIONS: In mRCC, metabolomics shows a faster host metabolism modification induced by a mTOR inhibitor as compared with standard treatments. These results should be confirmed in larger cohorts and other cancer types.British Journal of Cancer advance online publication, 15 September 2015; doi:10.1038/bjc.2015.322 www.bjcancer.com. PMID: 26372698 [PubMed - as supplied by publisher]

Changes in the human plasma and urinary metabolome associated with acute dietary exposure to sucrose and the identification of potential biomarkers of sucrose intake. Mol Nutr Food Res. 2015 Aug 27; Authors: Beckmann M, Joosen AM, Clarke MM, Mugridge O, Frost G, Engel B, Taillart K, Lloyd AJ, Draper J, Lodge JK Abstract SCOPE: The intake of sucrose is of public health concern but limited information is available on the metabolic effects of short-term exposure. Our aim was to use metabolomics to investigate the metabolic impact of acute sucrose exposure. METHODS AND RESULTS: We performed a randomized, parallel, single-dose feeding study on healthy females (n = 90, aged 29.9 ± 4.7 years, BMI 23.3 ± 2.5 kg/m(2) ) consuming either 0, 50, or 100 g sucrose in 500 mL water. Blood and urine samples were taken before and 24 h post sucrose intake. Urine and plasma samples underwent detailed metabolite profiling analysis using established protocols. Flow-injection electrospray MS fingerprinting analysis showed that 3 h after intake was the most informative time point in urine and plasma and out of 120 explanatory signals, highlighted 16 major metabolite signals in urine and 25 metabolite signals in plasma that were discriminatory and correlated with sucrose intake over time. The main confirmed metabolites positively correlated with intake were sucrose, fructose, and erythronic acid, while those negatively correlating with intake included fatty acids and derivatives, acyl-carnitines, and ketone bodies. GC-TOF-MS profiling analysis confirmed the fingerprinting data. CONCLUSION: Acute exposure to sucrose identified a number of metabolites correlated with sucrose intake and several compounds attributed to metabolic fasting. PMID: 26372606 [PubMed - as supplied by publisher]

Differential amniotic fluid cytokine profile in women with chorioamnionitis with and without funisitis. J Matern Fetal Neonatal Med. 2015 Sep 15;:1-5 Authors: Revello R, Alcaide MJ, Dudzik D, Abehsera D, Bartha JL Abstract OBJECTIVES: To evaluate whether the amniotic fluid (AF) cytokine profile in women with chorioamnionitis may differentiate between those with and without funisitis. SUBJECTS AND METHODS: Forty women at high risk of chorioamnionitis were studied. Gestational age at study was 26.94. Amniocentesis, universal and specific polymerase chain reaction, and microbiological cultures were performed. AF IL-1β, IL-2, IL-4, IL-6, IL 8, IL-10, IL-12, TNF-alpha, IFN-gamma, and MMP-8 were measured by multiplex assay. After delivery, the placenta and umbilical cord were studied histologically. Comparisons were made between three groups: controls, and chorioamnionitis with and without funisitis. RESULTS: In 25 cases, the histological findings were normal (61.5%). The remaining 15 composed of 9 cases of chorioamnionitis alone (9/40; 23.1%) and 6 cases of chorioamnionitis plus funisitis (6/40; 15.4%). All AF cytokine levels were significantly higher in the cases with chorioamnionitis in comparison to controls, except for IFN-gamma. The comparisons between the three groups showed significant differences between chorioamnionitis alone and chorioamnionitis plus funisitis in IL-1β, IL-6, IL-10, IL-12, IL-8, and TNF-alpha, with the levels being higher when funisitis was present. Logistic regression found a powerful predictive model for funisitis including the following cytokinesIL-4, IL-10, IL-12, and IL-8. CONCLUSIONS: Measurements of AF interleukins 4, 10, 12, and 8 allow to identify cases with funisitisin women at high risk of chorioamnionitis. PMID: 26372455 [PubMed - as supplied by publisher]

Theoretical evaluation of peak capacity improvements by use of liquid chromatography combined with drift tube ion mobility-mass spectrometry. J Chromatogr A. 2015 Sep 5; Authors: Causon TJ, Hann S Abstract In the domain of liquid phase separations, the quality of separation obtainable is most readily gauged by consideration of classical chromatographic peak capacity theory. Column-based multidimensional strategies for liquid chromatography remain the most attractive and practical route for increasing the number of spatially resolved components in order to reduce stress on necessary mass spectrometric detection. However, the stress placed on a chromatographic separation step as a second dimension in a comprehensive online methodology (i.e. online LC×LC) is rather high. As an alternative to online LC×LC combinations, coupling of HPLC with ion mobility spectrometry hyphenated to mass spectrometry (IMS-MS) has emerged as an attractive approach to permit comprehensive sampling of first dimension chromatographic peaks and subsequent introduction to an orthogonal IMS separation prior to measurement of ions by a mass spectrometer. In the present work, utilization of classical peak capacity and ion mobility theory allows theoretical assessment of the potential of two- (LC×IMS-MS) or even three-dimensional (LC×LC×IMS-MS) experimental setups to enhance peak capacity and, therefore, the number of correctly annotated features within the framework of complex, non-targeted analysis problems frequently addressed using HPLC-MS strategies. Theoretical calculations indicate that newly-available drift tube IMS-MS instrumentation can yield peak capacities of between 10 and 40 using nitrogen drift gas for typical non-targeted metabolomic, lipidomic and proteomic applications according to the expected reduced mobilities of components in the respective samples. Theoretically, this approach can significantly improve the overall peak capacity of conventional HPLC-(MS) methodologies to in excess of 10(4) depending upon the column length and gradient time employed. A more elaborate combination of LC×LC×IMS-MS would improve the ion suppression limitation and possibly allow access to theoretically even higher peak capacities, but such a combination may render the IMS separation practically redundant as well as imparting the well-known dilution problems associated with LC×LC. Finally, some predictions for the separation of co-eluted isobaric compounds can also be made by considering the required peak-to-peak resolution for acceptable IMS separation. The here-described theoretical predication approach can be used to aid method development for HPLC×IMS-MS and is also accompanied by some practical considerations that should be contemplated in associated non-targeted analysis workflows. PMID: 26372446 [PubMed - as supplied by publisher]

Integrative analysis of proteomics and metabolomics of anaphylactoid reaction induced by Xuesaitong injection. J Chromatogr A. 2015 Sep 8; Authors: Xu Y, Dou D, Ran X, Liu C, Chen J Abstract Injection with natural compounds is an important method in the application of natural medicine, but its adverse drug reactions (ADRs) occur frequently, particularly the anaphylactoid reaction, which accounts for more than 77% of all reactions and has become a serious threat to public health. Here, the Xuesaitong injection (XSTI) was employed as an example to elucidate its anaphylactoid mechanism and look for potential biomarkers to assay the anaphylactoid reaction of herbal medicine injection by proteomics and metabolomics. These results disclosed that 13 differential proteins and 28 metabolites, which were further approved using the ELISA method and reference standards, respectively, were suggested as potential biomarkers to examine the anaphylactoid mechanism. The up-regulated expression of Gpx1, Sc5b9, C4d and down-regulated expression of F12, Kng1, C2 and C6 revealed that the XSTI-induced anaphylactoid reaction occurs via direct stimulation, complement and the kallikrein-kinin pathway. In addition, substances that induce an anaphylactoid effect include histamine, LTB4, uric acid and other drugs, which have been confirmed to be involved in arginine and proline metabolism, histidine metabolism, arachidonic acid metabolism purine metabolism and the TCA cycle. Furthermore, separation experiments have indicated that 10-kDa molecules of XSTI are the main allergenic factor inducing an anaphylactoid reaction. PMID: 26372445 [PubMed - as supplied by publisher]

Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. Proc Natl Acad Sci U S A. 2015 Sep 14; Authors: Kurita KL, Glassey E, Linington RG Abstract Traditional natural products discovery using a combination of live/dead screening followed by iterative bioassay-guided fractionation affords no information about compound structure or mode of action until late in the discovery process. This leads to high rates of rediscovery and low probabilities of finding compounds with unique biological and/or chemical properties. By integrating image-based phenotypic screening in HeLa cells with high-resolution untargeted metabolomics analysis, we have developed a new platform, termed Compound Activity Mapping, that is capable of directly predicting the identities and modes of action of bioactive constituents for any complex natural product extract library. This new tool can be used to rapidly identify novel bioactive constituents and provide predictions of compound modes of action directly from primary screening data. This approach inverts the natural products discovery process from the existing ‟grind and find" model to a targeted, hypothesis-driven discovery model where the chemical features and biological function of bioactive metabolites are known early in the screening workflow, and lead compounds can be rationally selected based on biological and/or chemical novelty. We demonstrate the utility of the Compound Activity Mapping platform by combining 10,977 mass spectral features and 58,032 biological measurements from a library of 234 natural products extracts and integrating these two datasets to identify 13 clusters of fractions containing 11 known compound families and four new compounds. Using Compound Activity Mapping we discovered the quinocinnolinomycins, a new family of natural products with a unique carbon skeleton that cause endoplasmic reticulum stress. PMID: 26371303 [PubMed - as supplied by publisher]

Contribution of Colonic Fermentation and Fecal Water Toxicity to the Pathophysiology of Lactose-Intolerance. Nutrients. 2015;7(9):7505-22 Authors: Windey K, Houben E, Deroover L, Verbeke K Abstract Whether or not abdominal symptoms occur in subjects with small intestinal lactose malabsorption might depend on differences in colonic fermentation. To evaluate this hypothesis, we collected fecal samples from subjects with lactose malabsorption with abdominal complaints (LM-IT, n = 11) and without abdominal complaints (LM-T, n = 8) and subjects with normal lactose digestion (NLD, n = 15). Lactose malabsorption was diagnosed using a (13)C-lactose breath test. Colonic fermentation was characterized in fecal samples at baseline and after incubation with lactose for 3 h, 6 h and 24 h through a metabolomics approach using gas chromatography-mass spectrometry (GC-MS). Fecal water cytotoxicity was analyzed using a colorimetric assay. Fecal water cytotoxicity was not different between the three groups (Kruskall-Wallis p = 0.164). Cluster analysis of the metabolite patterns revealed separate clusters for NLD, LM-T and LM-IT samples at baseline and after 24 h incubation with lactose. Levels of 5-methyl-2-furancarboxaldehyde were significantly higher in LM-IT and LM-T compared to NLD whereas those of an unidentified aldehyde were significantly higher in LM-IT compared to LM-T and NLD. Incubation with lactose increased short chain fatty acid (SCFA) concentrations more in LM-IT and LM-T compared to NLD. In conclusion, fermentation patterns were clearly different in NLD, LM-IT and LM-T, but not related to differences in fecal water cytotoxicity. PMID: 26371036 [PubMed - in process]

First Trimester Urine and Serum Metabolomics for Prediction of Preeclampsia and Gestational Hypertension: A Prospective Screening Study. Int J Mol Sci. 2015;16(9):21520-38 Authors: Austdal M, Tangerås LH, Skråstad RB, Salvesen K, Austgulen R, Iversen AC, Bathen TF Abstract Hypertensive disorders of pregnancy, including preeclampsia, are major contributors to maternal morbidity. The goal of this study was to evaluate the potential of metabolomics to predict preeclampsia and gestational hypertension from urine and serum samples in early pregnancy, and elucidate the metabolic changes related to the diseases. Metabolic profiles were obtained by nuclear magnetic resonance spectroscopy of serum and urine samples from 599 women at medium to high risk of preeclampsia (nulliparous or previous preeclampsia/gestational hypertension). Preeclampsia developed in 26 (4.3%) and gestational hypertension in 21 (3.5%) women. Multivariate analyses of the metabolic profiles were performed to establish prediction models for the hypertensive disorders individually and combined. Urinary metabolomic profiles predicted preeclampsia and gestational hypertension at 51.3% and 40% sensitivity, respectively, at 10% false positive rate, with hippurate as the most important metabolite for the prediction. Serum metabolomic profiles predicted preeclampsia and gestational hypertension at 15% and 33% sensitivity, respectively, with increased lipid levels and an atherogenic lipid profile as most important for the prediction. Combining maternal characteristics with the urinary hippurate/creatinine level improved the prediction rates of preeclampsia in a logistic regression model. The study indicates a potential future role of clinical importance for metabolomic analysis of urine in prediction of preeclampsia. PMID: 26370975 [PubMed - in process]

Metabolomics-Based Screening of Biofilm-Inhibitory Compounds against Pseudomonas aeruginosa from Burdock Leaf. Molecules. 2015;20(9):16266-77 Authors: Lou Z, Tang Y, Song X, Wang H Abstract Screening of anti-biofilm compounds from the burdock leaf based on metabolomics is reported here. The crystal violet assay indicated 34% ethanol elution fraction of burdock leaf could completely inhibit biofilm formation of Pseudomonas aeruginosa at 1 mg·mL(-1). Then, the chemical composition of burdock leaf fraction was analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and 11 active compounds (chlorogenic acid, caffeic acid, p-coumaric acid, quercetin, ursolic acid, rutin, cynarin, luteolin, crocin, benzoic acid, and Tenacissoside I) were identified. Lastly, UPLC-MS analysis was employed to obtain the metabolic fingerprints of burdock leaf fractions before and after inhibiting the biofilm of Pseudomonas aeruginosa. The metabolic fingerprints were transformed to data, analyzed with PLS-DA (partial least squares discriminant analysis) and the peaks whose area was significantly changed were found out. Thus, 81 compounds were screened as potential anti-biofilm ingredients. Among them, rutin, ursolic acid, caffeic acid, p-coumaric acid and quercetin were identified and confirmed as the main anti-biofilm compounds in burdock leaf. The study provided basic anti-biofilm profile data for the compounds in burdock leaf, as well as provided a convenient method for fast screening of anti-biofilm compounds from natural plants. PMID: 26370951 [PubMed - in process]

In-Depth Characterization of Protein Disulfide Bonds by Online Liquid Chromatography-Electrochemistry-Mass Spectrometry. J Am Soc Mass Spectrom. 2015 Sep 14; Authors: Switzar L, Nicolardi S, Rutten JW, Oberstein SA, Aartsma-Rus A, van der Burgt YE Abstract Disulfide bonds are an important class of protein post-translational modifications, yet this structurally crucial modification type is commonly overlooked in mass spectrometry (MS)-based proteomics approaches. Recently, the benefits of online electrochemistry-assisted reduction of protein S-S bonds prior to MS analysis were exemplified by successful characterization of disulfide bonds in peptides and small proteins. In the current study, we have combined liquid chromatography (LC) with electrochemistry (EC) and mass analysis by Fourier transform ion cyclotron resonance (FTICR) MS in an online LC-EC-MS platform to characterize protein disulfide bonds in a bottom-up proteomics workflow. A key advantage of a LC-based strategy is the use of the retention time in identifying both intra- and interpeptide disulfide bonds. This is demonstrated by performing two sequential analyses of a certain protein digest, once without and once with electrochemical reduction. In this way, the "parent" disulfide-linked peptide detected in the first run has a retention time-based correlation with the EC-reduced peptides detected in the second run, thus simplifying disulfide bond mapping. Using this platform, both inter- and intra-disulfide-linked peptides were characterized in two different proteins, ß-lactoglobulin and ribonuclease B. In order to prevent disulfide reshuffling during the digestion process, proteins were digested at a relatively low pH, using (a combination of) the high specificity proteases trypsin and Glu-C. With this approach, disulfide bonds in ß-lactoglobulin and ribonuclease B were comprehensively identified and localized, showing that online LC-EC-MS is a useful tool for the characterization of protein disulfide bonds. Graphical Abstract ᅟ. PMID: 26369777 [PubMed - as supplied by publisher]

Negative prognostic impact of regulatory T cell infiltration in surgically resected esophageal cancer post-radiochemotherapy. Oncotarget. 2015 Aug 28;6(25):20840-50 Authors: Vacchelli E, Semeraro M, Enot DP, Chaba K, Poirier Colame V, Dartigues P, Perier A, Villa I, Rusakiewicz S, Gronnier C, Goéré D, Mariette C, Zitvogel L, Kroemer G Abstract Ever accumulating evidence indicates that the long-term effects of radiotherapy and chemotherapy largely depend on the induction (or restoration) of an anticancer immune response. Here, we investigated this paradigm in the context of esophageal carcinomas treated by neo-adjuvant radiochemotherapy, in a cohort encompassing 196 patients. We found that the density of the FOXP3+ regulatory T cell (Treg) infiltrate present in the residual tumor (or its scar) correlated with the pathological response (the less Tregs the more pronounced was the histological response) and predicted cancer-specific survival. In contrast, there was no significant clinical impact of the frequency of CD8+ cytotoxic T cells. At difference with breast or colorectal cancer, a loss-of-function allele of toll like receptor 4 (TLR4) improved cancer-specific survival of patients with esophageal cancer. While a loss-of-function allele of purinergic receptor P2X, ligand-gated ion channel, 7 (P2RX7) failed to affect cancer-specific survival, its presence did correlate with an increase in Treg infiltration. Altogether, these results corroborate the notion that the immunosurveillance seals the fate of patients with esophageal carcinomas treated with conventional radiochemotherapy. PMID: 26369701 [PubMed - in process]

Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC Plant Biol. 2015;15(1):220 Authors: Hagel JM, Mandal R, Han B, Han J, Dinsmore DR, Borchers CH, Wishart DS, Facchini PJ Abstract BACKGROUND: Recent progress toward the elucidation of benzylisoquinoline alkaloid (BIA) metabolism has focused on a small number of model plant species. Current understanding of BIA metabolism in plants such as opium poppy, which accumulates important pharmacological agents such as codeine and morphine, has relied on a combination of genomics and metabolomics to facilitate gene discovery. Metabolomics studies provide important insight into the primary biochemical networks underpinning specialized metabolism, and serve as a key resource for metabolic engineering, gene discovery, and elucidation of governing regulatory mechanisms. Beyond model plants, few broad-scope metabolomics reports are available for the vast number of plant species known to produce an estimated 2500 structurally diverse BIAs, many of which exhibit promising medicinal properties. RESULTS: We applied a multi-platform approach incorporating four different analytical methods to examine 20 non-model, BIA-accumulating plant species. Plants representing four families in the Ranunculales were chosen based on reported BIA content, taxonomic distribution and importance in modern/traditional medicine. One-dimensional (1)H NMR-based profiling quantified 91 metabolites and revealed significant species- and tissue-specific variation in sugar, amino acid and organic acid content. Mono- and disaccharide sugars were generally lower in roots and rhizomes compared with stems, and a variety of metabolites distinguished callus tissue from intact plant organs. Direct flow infusion tandem mass spectrometry provided a broad survey of 110 lipid derivatives including phosphatidylcholines and acylcarnitines, and high-performance liquid chromatography coupled with UV detection quantified 15 phenolic compounds including flavonoids, benzoic acid derivatives and hydroxycinnamic acids. Ultra-performance liquid chromatography coupled with high-resolution Fourier transform mass spectrometry generated extensive mass lists for all species, which were mined for metabolites putatively corresponding to BIAs. Different alkaloids profiles, including both ubiquitous and potentially rare compounds, were observed. CONCLUSIONS: Extensive metabolite profiling combining multiple analytical platforms enabled a more complete picture of overall metabolism occurring in selected plant species. This study represents the first time a metabolomics approach has been applied to most of these species, despite their importance in modern and traditional medicine. Coupled with genomics data, these metabolomics resources serve as a key resource for the investigation of BIA biosynthesis in non-model plant species. PMID: 26369413 [PubMed - in process]

Related Articles Age-related proteostasis and metabolic alterations in Caspase-2-deficient mice. Cell Death Dis. 2015;6:e1597 Authors: Wilson CH, Shalini S, Filipovska A, Richman TR, Davies S, Martin SD, McGee SL, Puccini J, Nikolic A, Dorstyn L, Kumar S Abstract Ageing is a complex biological process for which underlying biochemical changes are still largely unknown. We performed comparative profiling of the cellular proteome and metabolome to understand the molecular basis of ageing in Caspase-2-deficient (Casp2(-/-)) mice that are a model of premature ageing in the absence of overt disease. Age-related changes were determined in the liver and serum of young (6-9 week) and aged (18-24 month) wild-type and Casp2(-/-) mice. We identified perturbed metabolic pathways, decreased levels of ribosomal and respiratory complex proteins and altered mitochondrial function that contribute to premature ageing in the Casp2(-/-) mice. We show that the metabolic profile changes in the young Casp2(-/-) mice resemble those found in aged wild-type mice. Intriguingly, aged Casp2(-/-) mice were found to have reduced blood glucose and improved glucose tolerance. These results demonstrate an important role for caspase-2 in regulating proteome and metabolome remodelling during ageing. PMID: 25611376 [PubMed - indexed for MEDLINE]