PubMed

Related Articles Implementation of a Multicenter Biobanking Collaboration for Next-Generation Sequencing-Based Biomarker Discovery Based on Fresh Frozen Pretreatment Tumor Tissue Biopsies. Oncologist. 2016 Sep 23; Authors: Bins S, Cirkel GA, Gadellaa-van Hooijdonk CG, Weeber F, Nijman IJ, Bruggink AH, van Diest PJ, Willems SM, Veldhuis WB, van den Heuvel MM, de Knegt RJ, Koudijs MJ, van Werkhoven E, Mathijssen RH, Cuppen E, Sleijfer S, Schellens JH, Voest EE, Langenberg MH, de Jonge MJ, Steeghs N, Lolkema MP Abstract BACKGROUND: The discovery of novel biomarkers that predict treatment response in advanced cancer patients requires acquisition of high-quality tumor samples. As cancer evolves over time, tissue is ideally obtained before the start of each treatment. Preferably, samples are freshly frozen to allow analysis by next-generation DNA/RNA sequencing (NGS) but also for making other emerging systematic techniques such as proteomics and metabolomics possible. Here, we describe the first 469 image-guided biopsies collected in a large collaboration in The Netherlands (Center for Personalized Cancer Treatment) and show the utility of these specimens for NGS analysis. PATIENTS AND METHODS: Image-guided tumor biopsies were performed in advanced cancer patients. Samples were fresh frozen, vital tumor cellularity was estimated, and DNA was isolated after macrodissection of tumor-rich areas. Safety of the image-guided biopsy procedures was assessed by reporting of serious adverse events within 14 days after the biopsy procedure. RESULTS: Biopsy procedures were generally well tolerated. Major complications occurred in 2.1%, most frequently consisting of pain. In 7.3% of the percutaneous lung biopsies, pneumothorax requiring drainage occurred. The majority of samples (81%) contained a vital tumor percentage of at least 30%, from which at least 500 ng DNA could be isolated in 91%. Given our preset criteria, 74% of samples were of sufficient quality for biomarker discovery. The NGS results in this cohort were in line with those in other groups. CONCLUSION: Image-guided biopsy procedures for biomarker discovery to enable personalized cancer treatment are safe and feasible and yield a highly valuable biobank. IMPLICATIONS FOR PRACTICE: This study shows that it is safe to perform image-guided biopsy procedures to obtain fresh frozen tumor samples and that it is feasible to use these biopsies for biomarker discovery purposes in a Dutch multicenter collaboration. From the majority of the samples, sufficient DNA could be yielded to perform next-generation sequencing. These results indicate that the way is paved for consortia to prospectively collect fresh frozen tumor tissue. PMID: 27662884 [PubMed - as supplied by publisher]

Related Articles Tetracycline uptake and metabolism by vetiver grass (Chrysopogon zizanioides L. Nash). Environ Sci Pollut Res Int. 2016 Sep 23; Authors: Sengupta A, Sarkar D, Das P, Panja S, Parikh C, Ramanathan D, Bagley S, Datta R Abstract Environmental contamination by antibiotics not only perturbs the ecological balance but also poses a risk to human health by promoting the development of multiantibiotic-resistant bacteria. This study focuses on identifying the biochemical pathways associated with tetracycline (TC) transformation/degradation in vetiver grass that has the potential to be used as a biological remediation system in TC-contaminated water sources. A hydroponic experimental setup was used with four initial TC concentrations (0, 5, 35, 75 ppm), and TC uptake was monitored over a 30-day period. Results show that TC transformation in the media occurred during the first 5 days, where a decrease in the parent compound and an increase in the concentration of the isomers such as epitetracycline (ETC) and anhyrotetracycline (ATC) occurred, and TC disappeared in 20 days in tanks with vetiver grass. However, the isomers ETC and ATC remained in the control tanks for the duration of the trial. Transformation products of TC in plant tissue were analyzed by using ultra HPLC high-resolution Orbitrap mass spectrometery (HRMS/MS), which indicates amide hydrolysis of TC in vetiver roots. Metabolic profiling revealed that glyoxylate metabolism, TCA cycle, biosynthesis of secondary metabolites, tryptophan metabolism, and inositol phosphate metabolism were impacted in vetiver root by TC treatment. PMID: 27662856 [PubMed - as supplied by publisher]

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/09/24PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/09/23PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci. 2016 Sep 20; Authors: Aucamp J, Bronkhorst AJ, Badenhorst CP, Pretorius PJ Abstract The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins. PMID: 27652382 [PubMed - as supplied by publisher]

Related Articles Starving cancer from the outside and inside: separate and combined effects of calorie restriction and autophagy inhibition on Ras-driven tumors. Cancer Metab. 2016;4:18 Authors: Lashinger LM, O'Flanagan CH, Dunlap SM, Rasmussen AJ, Sweeney S, Guo JY, Lodi A, Tiziani S, White E, Hursting SD Abstract BACKGROUND: Calorie restriction (CR) prevents obesity and exerts anticancer effects in many preclinical models. CR is also increasingly being used in cancer patients as a sensitizing strategy prior to chemotherapy regimens. While the beneficial effects of CR are widely accepted, the mechanisms through which CR affects tumor growth are incompletely understood. In many cell types, CR and other nutrient stressors can induce autophagy, which provides energy and metabolic substrates critical for cancer cell survival. We hypothesized that limiting extracellular and intracellular substrate availability by combining CR with autophagy inhibition would reduce tumor growth more effectively than either treatment alone. RESULTS: A 30 % CR diet, relative to control diet, in nude mice resulted in significant decreases in body fat, blood glucose, and serum insulin, insulin-like growth factor-1, and leptin levels concurrent with increased adiponectin levels. In a xenograft model in nude mice involving H-Ras(G12V)-transformed immortal baby mouse kidney epithelial cells with (Atg5 (+/+) ) and without (Atg5 (-/-)) autophagic capacity, the CR diet (relative to control diet) genetically induced autophagy inhibition and their combination, each reduced tumor development and growth. Final tumor volume was greatest for Atg5 (+/+) tumors in control-fed mice, intermediate for Atg5 (+/+) tumors in CR-fed mice and Atg5 (-/-) tumors in control-fed mice, and lowest for Atg5 (-/-) tumors in CR mice. In Atg5 (+/+) tumors, autophagic flux was increased in CR-fed relative to control-fed mice, suggesting that the prosurvival effects of autophagy induction may mitigate the tumor suppressive effects of CR. Metabolomic analyses of CR-fed, relative to control-fed, nude mice showed significant decreases in circulating glucose and amino acids and significant increases in ketones, indicating CR induced negative energy balance. Combining glucose deprivation with autophagy deficiency in Atg5 (-/-) cells resulted in significantly reduced in vitro colony formation relative to glucose deprivation or autophagy deficiency alone. CONCLUSIONS: Combined restriction of extracellular (via CR in vivo or glucose deprivation in vitro) and intracellular (via autophagy inhibition) sources of energy and nutrients suppresses Ras-driven tumor growth more effectively than either CR or autophagy deficiency alone. Interventions targeting both systemic energy balance and tumor-cell intrinsic autophagy may represent a novel and effective anticancer strategy. PMID: 27651895 [PubMed - as supplied by publisher]

Related Articles Impact of early postnatal nutrition on the NMR urinary metabolic profile of infant. J Proteome Res. 2016 Sep 21; Authors: Cesare Marincola F, Corbu S, Lussu M, Noto A, Dessì A, Longo S, Civardi E, Garofoli F, Grenci B, Mongini E, Budelli A, Grinzato A, Fasano F, Fanos V, Stronati M Abstract NMR-based metabolomics was used to compare the metabolic urinary profiles of exclusively breast fed term infants (n=11) with those of a double-blinded controlled trial with 49 formula-fed term newborns randomized to receive either an infant formula enriched by functional ingredients (n=24) or a standard formula (n=25). Anthropometric measurements and urine samples were taken at enrollment (within the first month of life), at around 60 days of life and at the end of study period (average age of 130 days). The metabolic profiles were examined in relation to time and diet strategy. A common age-dependent modification of urine metabolome was observed for the three types of nutrition, mainly characterized by similar temporal trends of choline, betaine, myo-inositol, taurine, and citrate. Contrariwise, differences in the metabolic profiles were identified according to the type of diet (human versus formula milk), while no significant difference was observed between the two formulas. These modifications are discussed mainly in terms of the different composition between milks. Despite the low number of enrolled infants (n=60), these findings pointed out the potential of the metabolomics approach for neonatal nutritional science, and in particular in providing important contributions to the optimization of formula milk. PMID: 27650928 [PubMed - as supplied by publisher]

Related Articles Adipocyte Glucocorticoid Receptor Deficiency Attenuates Aging- and Hfd-Induced Obesity, and Impairs the Feeding-Fasting Transition. Diabetes. 2016 Sep 20; Authors: Mueller KM, Hartmann K, Kaltenecker D, Vettorazzi S, Bauer M, Mauser L, Amann S, Jall S, Fischer K, Esterbauer H, Müller TD, Tschöp MH, Magnes C, Haybaeck J, Scherer T, Bordag N, Tuckermann JP, Moriggl R Abstract Glucocorticoids (GCs) are important regulators of systemic energy metabolism, while aberrant GC action is linked to metabolic dysfunctions. Yet, the extent to which normal and pathophysiologic energy metabolism depend on the glucocorticoid receptor (GR) in adipocytes remains unclear. Here, we demonstrate that adipocyte GR-deficiency in mice significantly impacts systemic metabolism in different energetic states. Plasma metabolomics and biochemical analyses revealed a marked global effect of GR-deficiency on systemic metabolite abundance and thus, substrate partitioning in fed and fasted states. This correlated with a decreased lipolytic capacity of GR-deficient adipocytes under post-absorptive and fasting conditions, resulting from impaired signal transduction from β-adrenergic receptors to adenylate cyclase. Upon prolonged fasting, the impaired lipolytic response resulted in abnormal substrate utilization and lean mass wasting. Conversely, GR-deficiency attenuated aging-/diet-associated obesity, adipocyte hypertrophy and liver steatosis. Systemic glucose tolerance was improved in obese GR-deficient mice, which was associated with increased insulin signaling in muscle and adipose tissue.We conclude that the GR in adipocytes exerts central, but diverging roles in the regulation of metabolic homeostasis depending on the energetic state: The adipocyte GR is indispensable for the feeding-fasting transition, but also promotes adiposity and associated metabolic disorders in fat-fed and aged mice. PMID: 27650854 [PubMed - as supplied by publisher]

Related Articles Discovery, screening and evaluation of a plasma biomarker panel for subjects with psychological suboptimal health state using (1)H-NMR-based metabolomics profiles. Sci Rep. 2016;6:33820 Authors: Tian JS, Xia XT, Wu YF, Zhao L, Xiang H, Du GH, Zhang X, Qin XM Abstract Individuals in the state of psychological suboptimal health keep increasing, only scales and questionnaires were used to diagnose in clinic under current conditions, and symptoms of high reliability and accuracy are destitute. Therefore, the noninvasive and precise laboratory diagnostic methods are needed. This study aimed to develop an objective method through screen potential biomarkers or a biomarker panel to facilitate the diagnosis in clinic using plasma metabolomics. Profiles were based on H-nuclear magnetic resonance ((1)H-NMR) metabolomics techniques combing with multivariate statistical analysis. Furthermore, methods of correlation analysis with Metaboanalyst 3.0 for selecting a biomarker panel, traditional Chinese medicine (TCM) drug intervention for validating the close relations between the biomarker panel and the state and the receiver operating characteristic curves (ROC curves) analysis for evaluation of clinical diagnosis ability were carried out. 9 endogenous metabolites containing trimethylamine oxide (TMAO), glutamine, N-acetyl-glycoproteins, citrate, tyrosine, phenylalanine, isoleucine, valine and glucose were identified and considered as potential biomarkers. Then a biomarker panel consisting of phenylalanine, glutamine, tyrosine, citrate, N-acetyl-glycoproteins and TMAO was selected, which exhibited the highest area under the curve (AUC = 0.971). This study provided critical insight into the pathological mechanism of psychological suboptimal health and would supply a novel and valuable diagnostic method. PMID: 27650680 [PubMed - as supplied by publisher]

Related Articles Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms. J Bioinform Comput Biol. 2016 Sep 9;:1650032 Authors: Deng B, Kim S, Li H, Heath E, Zhang X Abstract Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC[Formula: see text][Formula: see text][Formula: see text]GC-MS) has been used to analyze multiple samples in a metabolomics study. However, due to some uncontrollable experimental conditions, such as the differences in temperature or pressure, matrix effects on samples and stationary phase degradation, there is always a shift of retention times in the two GC columns between samples. In order to correct the retention time shifts in GC[Formula: see text][Formula: see text][Formula: see text]GC-MS, the peak alignment is a crucial data analysis step to recognize the peaks generated by the same metabolite in different samples. Two approaches have been developed for GC[Formula: see text][Formula: see text][Formula: see text]GC-MS data alignment: profile alignment and peak matching alignment. However, these existing alignment methods are all based on a local alignment, resulting that a peak may not be correctly aligned in a dense chromatographic region where many peaks are present in a small region. False alignment will result in false discovery in the downstream statistical analysis. We, therefore, develop a global comparison-based peak alignment method using point matching algorithm (PMA-PA) for both homogeneous and heterogeneous data. The developed algorithm PMA-PA first extracts feature points (peaks) in the chromatography and then searches globally the matching peaks in the consecutive chromatography by adopting the projection of rigid and nonrigid transformation. PMA-PA is further applied to two real experimental data sets, showing that PMA-PA is a promising peak alignment algorithm for both homogenous and heterogeneous data in terms of [Formula: see text]1 score, although it uses only peak location information. PMID: 27650662 [PubMed - as supplied by publisher]

Related Articles Serum metabolomics analysis for early detection of colorectal cancer. J Gastroenterol. 2016 Sep 20; Authors: Uchiyama K, Yagi N, Mizushima K, Higashimura Y, Hirai Y, Okayama T, Yoshida N, Katada K, Kamada K, Handa O, Ishikawa T, Takagi T, Konishi H, Kuriu Y, Nakanishi M, Otsuji E, Itoh Y, Naito Y Abstract BACKGROUND: Although colorectal cancer (CRC) is one of the most common causes of cancer mortality, early-stage detection improves survival rates dramatically. Because cancer impacts important metabolic pathways, the alteration of metabolite levels as a potential biomarker of early-stage cancer has been the focus of many studies. Here, we used CE-TOFMS, a novel and promising method with small injection volume and high resolution, to separate and detect ionic compounds based on the different migration rates of charged metabolites in order to detect metabolic biomarkers in patients with CRC. METHODS: A total of 56 patients with CRC (n = 14 each of Stages I-IV), 60 healthy controls, and 59 patients with colonic adenoma were included in this study. Metabolome analysis was conducted by CE-TOFMS on serum samples of patients and controls using the Advanced Scan package (Human Metabolome Technologies). RESULTS: We obtained 334 metabolites in the serum, of which 139 were identified as known substances. Among these 139 known metabolites, 16 were correlated with CRC stage by upregulation and 44 by downregulation, with benzoic acid (r = -0.649, t = 11.653, p = 6.07599E-24), octanoic acid (r = 0.557, t = 9.183, p = 7.9557E-17), decanoic acid (r = 0.539, t = 8.749, p = 1.24352E-15), and histidine (r = -0.513, t = 8.194, p = 3.90224E-14) exhibiting significant correlation. CONCLUSIONS: To the best of our knowledge, this is the first report to determine the correlation between serum metabolites and CRC stage using CE-TOFMS. Our results show that benzoic acid exhibited excellent diagnostic power and could potentially serve as a novel disease biomarker for CRC diagnosis. PMID: 27650200 [PubMed - as supplied by publisher]

Related Articles Quantification of Water-Soluble Metabolites in Medicinal Mushrooms Using Proton NMR Spectroscopy. Int J Med Mushrooms. 2016;18(5):413-424 Authors: Lo YC, Chien SC, Mishchuk DO, Slupsky CM, Mau JL Abstract The water-soluble metabolites in 5 mushrooms were identified and quantified using proton nuclear magnetic resonance (NMR) spectroscopy and software for targeted metabolite detection and quantification. In total, 35 compounds were found in Agaricus brasiliensis, 25 in Taiwanofungus camphoratus, 23 in Ganoderma lucidum (Taiwan) and Lentinus edodes, and 16 in G. lucidum (China). Total amounts of all identified metabolites in A. brasiliensis, T. camphoratus, G. lucidum, G. lucidum (China), and L. edodes were 149,950.51, 12,834.18, 9,549.09, 2,788.41, and 111,726.51 mg/kg dry weight, respectively. These metabolites were categorized into 4 groups: free amino acids and derivatives, carbohydrates, carboxylic acids, and nucleosides. Carbohydrates were the most abundant metabolites among all 4 groups, with mannitol having the highest concentration among all analyzed metabolites (848-94,104 mg/kg dry weight). Principal components analysis (PCA) showed obvious distinction among the metabolites of the 5 different kinds of mushrooms analyzed in this study. Thus PCA could provide an optional analytical way of identifying and recognizing the compositions of flavor products. Furthermore, the results of this study demonstrate that NMRbased metabolomics is a powerful tool for differentiating between various medicinal mushrooms. PMID: 27649603 [PubMed - as supplied by publisher]

Related Articles Application of natural deep eutectic solvents to the extraction of anthocyanins from Catharanthus roseus with high extractability and stability replacing conventional organic solvents. J Chromatogr A. 2016 Feb 19;1434:50-6 Authors: Dai Y, Rozema E, Verpoorte R, Choi YH Abstract Natural deep eutectic solvents (NADES) have attracted a great deal of attention in recent times as promising green media. They are generally composed of neutral, acidic or basic compounds that form liquids of high viscosity when mixed in certain molar ratio. Despite their potential, viscosity and acid or basic nature of some ingredients may affect the extraction capacity and stabilizing ability of the target compounds. To investigate these effects, extraction with a series of NADES was employed for the analysis of anthocyanins in flower petals of Catharanthus roseus in combination with HPLC-DAD-based metabolic profiling. Along with the extraction yields of anthocyanins their stability in NADES was also studied. Multivariate data analysis indicates that the lactic acid-glucose (LGH), and 1,2-propanediol-choline chloride (PCH) NADES present a similar extraction power for anthocyanins as conventional organic solvents. Furthermore, among the NADES employed, LGH exhibits an at least three times higher stabilizing capacity for cyanidins than acidified ethanol, which facilitates their extraction and analysis process. Comparing NADES to the conventional organic solvents, in addition to their reduced environmental impact, they proved to provide higher stability for anthocyanins, and therefore have a great potential as possible alternatives to those organic solvents in health related areas such as food, pharmaceuticals and cosmetics. PMID: 26822320 [PubMed - indexed for MEDLINE]

Related Articles Analytical methodology using ion-pair liquid chromatography-tandem mass spectrometry for the determination of four di-ester metabolites of organophosphate flame retardants in California human urine. J Chromatogr A. 2016 Feb 19;1434:70-80 Authors: Petropoulou SS, Petreas M, Park JS Abstract Alkyl- and aryl-esters of phosphoric acid (both halogenated and non-halogenated) are mainly used as flame retardants (FRs), among other applications, in furniture and consumer products and they are collectively known as organophosphate flame retardants (OPFRs). The absorption, biotransformation or elimination of many of these chemicals in humans and their possible health effects are not yet well known. A major reason for the limited information is the nature of these compounds, which causes several technical difficulties in their isolation and sensitive determination. A novel analytical liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the accurate and sensitive determination of four urinary OPFR metabolites: bis(1,3-dichloro-2-propyl) phosphate (BDCIPP), bis(2-chloroethyl) phosphate (BCEP), bis(1-chloro-2-propyl) phosphate (BCIPP), and diphenyl phosphate (DPhP), using mixed-mode solid phase extraction and isotope. For the first time all four analytes can be identified in one chromatographic run. An extensive investigation of method development parameters (enzymatic hydrolysis, matrix effects, process efficiency, sources of background interferences, linearity, accuracy, precision, stabilities and limits of detection and quantification) was performed in order to address previously reported method inconsistencies and select a process with the highest accuracy and sensitivity. Chromatographic separation was achieved on a Luna C18 (2) (2.00 mm × 150 mm, 3 μm) with mobile phase 80:20 v/v water: MeOH and MeOH: water 95:5 v/v, both containing 1mM tributylamine and 1mM acetic acid. Limits of detection were 0.025 ng mL(-1) for BDCIPP and BCIPP and 0.1 ng mL(-1) for DPhP and BCEP. Absolute recoveries of all four analytes and their labeled compounds were in the range of 88-107%. The method was tested on 13 adult California urine samples. BCEP was detected at 0.4-15 ng mL(-1) with a geometric mean (GM): 1.9 ng mL(-1); BDCIPP at 0.5-7.3 ng mL(-1), (GM: 2.5 ng mL(-1)) and DPhP at <MDL-5.6 ng mL(-1), (GM: 1.7 ng mL(-1)). BCIPP was detected for the first time in US samples in 92.3% of the samples with two to three times lower values (range <MDL-3.5 ng mL(-1) and GM: 0.4 ng mL(-1)) than the other OPFRs. PMID: 26818234 [PubMed - indexed for MEDLINE]

Related Articles Metabolomic profile related to cardiovascular disease in patients with type 2 diabetes mellitus: A pilot study. Talanta. 2016;148:135-43 Authors: García-Fontana B, Morales-Santana S, Díaz Navarro C, Rozas-Moreno P, Genilloud O, Vicente Pérez F, Pérez del Palacio J, Muñoz-Torres M Abstract Type 2 diabetes mellitus (T2DM) patients have an increased risk of cardiovascular disease (CVD) that represents one of the main causes of mortality in this population. The knowledge of the underlie factors involved in the development of CVD and the discovery of new biomarkers of the disease could help to early identification of high-risk patients. Using liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) we analyzed the serum metabolomic profile of 30 subject distributed according three groups: (i) T2DM patients with CVD; (ii) T2DM patients without CVD; (iii) non-diabetic subjects as controls (C) in order to identify potential biomarkers of the CVD related to T2DM. A partial least squares discriminant analysis (PLS-DA) and one-way analysis of variance (ANOVA) were applied to identify differential metabolites between different groups. Four glycerophospholipids were further identified as potential biomarkers of CVD in T2DM patients. Specifically, a reduction in phosphatidylcholine, lysophosphatidylcholine and lysophosphatidylethanolamine (LPE) serum levels were found in T2DM patients compared to controls, presenting the patients with CVD the lowest serum levels of these metabolites. These results show a generalized reduction of circulating phospholipids species in T2DM patients which is more pronounced in those with CVD providing information of the pathways involved in the pathogenesis and progression of CVD associated to T2DM. PMID: 26653434 [PubMed - indexed for MEDLINE]

Related Articles Omics-Based Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes during Early Infestation by Small Brown Planthopper. Int J Mol Sci. 2015;16(12):28746-64 Authors: Zhang W, Yang L, Li M, Ma B, Yan C, Chen J Abstract The small brown planthopper (SBPH) is one of the destructive pests of rice. Although different biochemical pathways that are involved in rice responding to planthopper infestation have been documented, it is unclear which individual metabolic pathways are responsive to planthopper infestation. In this study, an omics-based comparative transcriptional profiling of two contrasting rice genotypes, an SBPH-resistant and an SBPH-susceptible rice line, was assessed for rice individual metabolic pathways responsive to SBPH infestation. When exposed to SBPH, 166 metabolic pathways were differentially regulated; of these, more than one-third of metabolic pathways displayed similar change patterns between these two contrasting rice genotypes; the difference of change pattern between these two contrasting rice genotypes mostly lies in biosynthetic pathways and the obvious difference of change pattern lies in energy metabolism pathways. Combining the Pathway Tools Omics Viewer with the web tool Venn, 21 and 6 metabolic pathways which potentially associated with SBPH resistance and susceptibility, respectively were identified. This study presents an omics-based comparative transcriptional profiling of SBPH-resistant and SBPH-susceptible rice plants during early infestation by SBPH, which will be very informative in studying rice-insect interaction. The results will provide insight into how rice plants respond to early infestation by SBPH from the biochemical pathways perspective. PMID: 26633389 [PubMed - indexed for MEDLINE]

Related Articles Specific inhibition by synthetic analogs of pyruvate reveals that the pyruvate dehydrogenase reaction is essential for metabolism and viability of glioblastoma cells. Oncotarget. 2015 Nov 24;6(37):40036-52 Authors: Bunik VI, Artiukhov A, Kazantsev A, Goncalves R, Daloso D, Oppermann H, Kulakovskaya E, Lukashev N, Fernie A, Brand M, Gaunitz F Abstract The pyruvate dehydrogenase complex (PDHC) and its phosphorylation are considered essential for oncotransformation, but it is unclear whether cancer cells require PDHC to be functional or silenced. We used specific inhibition of PDHC by synthetic structural analogs of pyruvate to resolve this question. With isolated and intramitochondrial PDHC, acetyl phosphinate (AcPH, KiAcPH = 0.1 μM) was a much more potent competitive inhibitor than the methyl ester of acetyl phosphonate (AcPMe, KiAcPMe = 40 μM). When preincubated with the complex, AcPH also irreversibly inactivated PDHC. Pyruvate prevented, but did not reverse the inactivation. The pyruvate analogs did not significantly inhibit other 2-oxo acid dehydrogenases. Different cell lines were exposed to the inhibitors and a membrane-permeable precursor of AcPMe, dimethyl acetyl phosphonate, which did not inhibit isolated PDHC. Using an ATP-based assay, dependence of cellular viability on the concentration of the pyruvate analogs was followed. The highest toxicity of the membrane-permeable precursor suggested that the cellular action of charged AcPH and AcPMe requires monocarboxylate transporters. The relevant cell-specific transcripts extracted from Gene Expression Omnibus database indicated that cell lines with higher expression of monocarboxylate transporters and PDHC components were more sensitive to the PDHC inhibitors. Prior to a detectable antiproliferative action, AcPH significantly changed metabolic profiles of the investigated glioblastoma cell lines. We conclude that catalytic transformation of pyruvate by pyruvate dehydrogenase is essential for the metabolism and viability of glioblastoma cell lines, although metabolic heterogeneity causes different cellular sensitivities and/or abilities to cope with PDHC inhibition. PMID: 26503465 [PubMed - indexed for MEDLINE]

Related Articles Untargeted metabolomic analysis for the clinical screening of inborn errors of metabolism. J Inherit Metab Dis. 2015 Nov;38(6):1029-39 Authors: Miller MJ, Kennedy AD, Eckhart AD, Burrage LC, Wulff JE, Miller LA, Milburn MV, Ryals JA, Beaudet AL, Sun Q, Sutton VR, Elsea SH Abstract Global metabolic profiling currently achievable by untargeted mass spectrometry-based metabolomic platforms has great potential to advance our understanding of human disease states, including potential utility in the detection of novel and known inborn errors of metabolism (IEMs). There are few studies of the technical reproducibility, data analysis methods, and overall diagnostic capabilities when this technology is applied to clinical specimens for the diagnosis of IEMs. We explored the clinical utility of a metabolomic workflow capable of routinely generating semi-quantitative z-score values for ~900 unique compounds, including ~500 named human analytes, in a single analysis of human plasma. We tested the technical reproducibility of this platform and applied it to the retrospective diagnosis of 190 individual plasma samples, 120 of which were collected from patients with a confirmed IEM. Our results demonstrate high intra-assay precision and linear detection for the majority compounds tested. Individual metabolomic profiles provided excellent sensitivity and specificity for the detection of a wide range of metabolic disorders and identified novel biomarkers for some diseases. With this platform, it is possible to use one test to screen for dozens of IEMs that might otherwise require ordering multiple unique biochemical tests. However, this test may yield false negative results for certain disorders that would be detected by a more well-established quantitative test and in its current state should be considered a supplementary test. Our findings describe a novel approach to metabolomic analysis of clinical specimens and demonstrate the clinical utility of this technology for prospective screening of IEMs. PMID: 25875217 [PubMed - indexed for MEDLINE]

Plasma metabolic profiling analysis of cyclophosphamide-induced cardiotoxicity using metabolomics coupled with UPLC/Q-TOF-MS and ROC curve. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Aug 30;1033-1034:428-435 Authors: Yin J, Xie J, Guo X, Ju L, Li Y, Zhang Y Abstract Cyclophosphamide (CY) is a commonly-used nitrogen mustard alkylating agent, but its clinical application is severely limited by its cardiotoxicity. Since the development of metabolomics, the change of metabolite profiles caused by cyclophosphamide has been studied by metabolomics and has gained much attention. In this study, we analyzed rat plasma samples collected one, three and five days after cyclophosphamide administration using ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Multiple statistical analyses, such as principal component analysis (PCA) and partial least squares - discriminant analysis (PLS-DA), were used to examine metabolite profile changes in plasma samples in order to screen for potential cardiotoxicity biomarkers and metabolic pathways. Levels of a dozen of metabolites changed significantly in plasma from the CY-treated group after one, three, and five days compared with the control group treated with normal saline (NS). Receiver operator characteristic (ROC) curve analysis suggested that the total 16 metabolites play important roles in different times of CY-induced cardiotoxicity respectively. Our results suggest that these metabolites in linoleic acid metabolism and glycerol phospholipid metabolism may be related to CY-induced cardiotoxicity. These metabolites could act as sensitive biomarkers for CY-induced cardiotoxicity and be useful for investigating toxic mechanisms. They may also lay a foundation for clinical use of cyclophosphamide. PMID: 27649503 [PubMed - as supplied by publisher]

Metabolomic signatures of drug response phenotypes for ketamine and esketamine in subjects with refractory major depressive disorder: new mechanistic insights for rapid acting antidepressants. Transl Psychiatry. 2016;6(9):e894 Authors: Rotroff DM, Corum DG, Motsinger-Reif A, Fiehn O, Bottrel N, Drevets WC, Singh J, Salvadore G, Kaddurah-Daouk R Abstract Ketamine, at sub-anesthetic doses, is reported to rapidly decrease depression symptoms in patients with treatment-resistant major depressive disorder (MDD). Many patients do not respond to currently available antidepressants, (for example, serotonin reuptake inhibitors), making ketamine and its enantiomer, esketamine, potentially attractive options for treatment-resistant MDD. Although mechanisms by which ketamine/esketamine may produce antidepressant effects have been hypothesized on the basis of preclinical data, the neurobiological correlates of the rapid therapeutic response observed in patients receiving treatment have not been established. Here we use a pharmacometabolomics approach to map global metabolic effects of these compounds in treatment-refractory MDD patients upon 2 h from infusion with ketamine (n=33) or its S-enantiomer, esketamine (n=20). The effects of esketamine on metabolism were retested in the same subjects following a second exposure administered 4 days later. Two complementary metabolomics platforms were used to provide broad biochemical coverage. In addition, we investigated whether changes in particular metabolites correlated with treatment outcome. Both drugs altered metabolites related to tryptophan metabolism (for example, indole-3-acetate and methionine) and/or the urea cycle (for example, citrulline, arginine and ornithine) at 2 h post infusion (q<0.25). In addition, we observed changes in glutamate and circulating phospholipids that were significantly associated with decreases in depression severity. These data provide new insights into the mechanism underlying the rapid antidepressant effects of ketamine and esketamine, and constitute some of the first detailed metabolomics mapping for these promising therapies. PMID: 27648916 [PubMed - as supplied by publisher]