PubMed

Metabolomics Applied to the Pancreatic Islet. Arch Biochem Biophys. 2015 Jun 24; Authors: Gooding JR, Jensen MV, Newgard CB Abstract Metabolomics, the characterization of the set of small molecules in a biological system, is advancing research in multiple areas of islet biology. Measuring a breadth of metabolites simultaneously provides a broad perspective on metabolic changes as the islets respond dynamically to glucose or environmental stressors. As a result, metabolomics has the potential to provide new mechanistic insights into islet physiology and pathophysiology. Here we summarize advances in our understanding of islet physiology and the etiologies of type-1 and type-2 diabetes derived from metabolomics studies. PMID: 26116790 [PubMed - as supplied by publisher]

Related Articles Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics. 2015;16(1):477 Authors: Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH Abstract BACKGROUND: The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber. RESULTS: Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA. CONCLUSIONS: The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length. PMID: 26116072 [PubMed - as supplied by publisher]

Related Articles Magnetic resonance spectroscopy of paragangliomas: new insights into in vivo metabolomics. Endocr Relat Cancer. 2015 Jun 26; Authors: Varoquaux A, Le Fur Y, Imperiale A, Reyre A, Montava M, Fakhry N, Namer IJ, Moulin G, Pacak K, Guye M, Taieb D Abstract OBJECTIVE: Paragangliomas (PGLs) can be associated with mutations in genes of the tricarboxylic acid (TCA) cycle. Succinate dehydrogenase mutations (SDHx) are the prime examples of genetically determined TCA cycle defects with accumulation of succinate. Succinate, which acts as an oncometabolite, can be detected by ex-vivo metabolomics approaches. The aim of this study was to evaluate the potential role of proton MR spectroscopy (167 H-MRS) for identifying SDHx-related PGLs in vivo and non-invasively. METHODS: Eight patients were prospectively evaluated with single voxel 168 H-MRS. MR spectra from 8 tumors (4 SDHx-related PGLs, 2 sporadic PGLs, 1 cervical schwannoma, and 1 cervical neurofibroma) were acquired and interpreted qualitatively. RESULTS: Compared to other tumors, a succinate resonance peak was detected only in SDHx72 related tumor patients. Spectra quality was considered good in 3 cases, medium in 2 cases, poor in 2 cases, and uninterpretable in the latter case. Smaller lesions had lower spectra quality compared to larger lesions. Jugular PGLs also exihibited a poorer spectra quality compared to other locations. CONCLUSIONS: 176 H-MRS has always been challenging in terms of its technical requisites. This is even more true for the evaluation of head and neck tumors. However, 177 H-MRS might be added to the classical MR sequences for metabolomic characterization of PGLs. In vivo detection of succinate might guide genetic testing, characterize SDHx variants of unknown significance (in the absence of available tumor sample), and even optimize a selection of appropriate therapies. PMID: 26115958 [PubMed - as supplied by publisher]

Metabolomics analysis identifies novel plasma biomarkers of cystic fibrosis pulmonary exacerbation. Pediatr Pulmonol. 2015 Jun 26; Authors: Laguna TA, Reilly CS, Williams CB, Welchlin C, Wendt CH Abstract BACKGROUND: Cystic fibrosis (CF) lung disease is characterized by infection, inflammation, lung function decline, and intermittent pulmonary exacerbations. However, the link between pulmonary exacerbation and lung disease progression remains unclear. Global metabolomic profiling can provide novel mechanistic insight into a disease process in addition to putative biomarkers for future study. Our objective was to investigate how the plasma metabolomic profile changes between CF pulmonary exacerbation and a clinically well state. METHODS: Plasma samples and lung function data were collected from 25 CF patients during hospitalization for a pulmonary exacerbation and during quarterly outpatient clinic visits. In collaboration with Metabolon, Inc., the metabolomic profiles of matched pair plasma samples, one during exacerbation and one at a clinic visit, were analyzed using gas and liquid chromatography coupled with mass spectrometry. Compounds were identified by comparison to a library of standards. Mixed effects models that controlled for nutritional status and lung function were used to test for differences and principal components analysis was performed. RESULTS: Our population had a median age of 27 years (14-39) and had a median FEV1 % predicted of 65% (23-105%). 398 total metabolites were identified and after adjustment for confounders, five metabolites signifying perturbations in nucleotide (hypoxanthine), nucleoside (N4-acetylcytidine), amino acid (N-acetylmethionine), carbohydrate (mannose), and steroid (cortisol) metabolism were identified. Principal components analysis provided good separation between the two clinical phenotypes. CONCLUSIONS: Our findings provide putative metabolite biomarkers for future study and allow for hypothesis generation about the pathophysiology of CF pulmonary exacerbation. Pediatr Pulmonol. © 2015 Wiley Periodicals, Inc. PMID: 26115542 [PubMed - as supplied by publisher]

Amino acid analysis using chromatography-mass spectrometry: An inter platform comparison study. J Pharm Biomed Anal. 2015 Jun 5;114:398-407 Authors: Krumpochova P, Bruyneel B, Molenaar D, Koukou A, Wuhrer M, Niessen WM, Giera M Abstract The analysis of amino acids has become a central task in many aspects. While amino acid analysis has traditionally mainly been carried out using either gas chromatography (GC) in combination with flame ionization detection or liquid chromatography (LC) with either post-column derivatization using ninhydrin or pre-column derivatization using o-phthalaldehyde, many of today's analysis platforms are based on chromatography in combination with mass spectrometry (MS). While derivatization is mandatory for the GC-based analysis of amino acids, several LC platforms have emerged, particularly in the dawn of targeted metabolite profiling using hydrophilic interaction liquid chromatography (HILIC) coupled to MS, allowing the analysis of underivatized amino acids. Among the numerous analytical platforms available for amino acid analysis today, we here compare three prominent approaches, being GC-MS and LC-MS after amino acid derivatization using chloroformate and HILIC-MS of underivatized amino acids. We compare and discuss practical issues as well as performance characteristics, e.g., the use of (13)C-labeled internal standards, of the different platforms and present data on their practical implementation in our laboratory. Finally, we compare the real-life applicability of all three platforms for a complex biological sample. While all three platforms are very-well suited for the analysis of complex biological samples they all show advantages and disadvantages for some analytes as discussed in detail in this manuscript. PMID: 26115383 [PubMed - as supplied by publisher]

Enantioselective Metabolism and Interference on Tryptophan Metabolism of Myclobutanil in Rat Hepatocytes. Chirality. 2015 Jun 26; Authors: Wang Y, Qiu J, Zhu W, Wang X, Zhang P, Wang D, Zhou Z Abstract Myclobutanil, (RS)-2-(4-chlorophenyl)-2-(1H-1, 2, 4-triazol-1-ylmethyl) hexanenitrile is a widely used triazole fungicide. In this study, enantioselective metabolism and cytotoxicity were investigated in rat hepatocytes by chiral HPLC-MS/MS and the methyl tetrazolium (MTT) assay, respectively. Furthermore, tryptophan metabolism disturbance in rat hepatocytes after myclobutanil exposure was also evaluated by target metabolomics method. The half-life (t1/2) of (+)-myclobutanil was 10.66 h, whereas that for (-)-myclobutanil was 15.07 h. Such results indicated that the metabolic process of myclobutanil in rat hepatocytes was enantioselective with an enrichment of (-)-myclobutanil. For the cytotoxicity research, the calculated EC50 (12h) values for rac-myclobutanil, (+)- and (-)-myclobutanil were 123.65, 150.65 and 152.60 µM, respectively. The results of tryptophan metabolites profiling showed that the levels of kynurenine (KYN) and XA were both up-regulated compared to the control, suggesting the activation effect of the KYN pathway by myclobutanil and its enantiomers which may provide an important insight into its toxicity mechanism. The data presented here could be useful for the environmental hazard assessment of myclobutanil. Chirality 00:000-000, 2015. © 2015 Wiley Periodicals, Inc. PMID: 26115377 [PubMed - as supplied by publisher]

Metabolomic Analysis of the Skeletal Muscle of Mice Overexpressing PGC-1α. PLoS One. 2015;10(6):e0129084 Authors: Hatazawa Y, Senoo N, Tadaishi M, Ogawa Y, Ezaki O, Kamei Y, Miura S Abstract Peroxisome proliferator-activated receptor (PPAR) γ coactivator 1α (PGC-1α) is a coactivator of various nuclear receptors and other transcription factors whose expression increases in the skeletal muscle during exercise. We have previously made transgenic mice overexpressing PGC-1α in the skeletal muscle (PGC-1α-Tg mice). PGC-1α upregulates the expression of genes associated with red fibers, mitochondrial function, fatty acid oxidation, and branched chain amino acid (BCAA) degradation. However, global analyses of the actual metabolic products have not been investigated. In this study, we conducted metabolomic analysis of the skeletal muscle in PGC-1α-Tg mice by capillary electrophoresis with electrospray ionization time-of-flight mass spectrometry. Principal component analysis and hierarchical cluster analysis showed clearly distinguishable changes in the metabolites between PGC-1α-Tg and wild-type control mice. Changes were observed in metabolite levels of various metabolic pathways such as the TCA cycle, pentose phosphate pathway, nucleotide synthesis, purine nucleotide cycle, and amino acid metabolism, including BCAA and β-alanine. Namely, metabolic products of the TCA cycle increased in PGC-1α-Tg mice, with increased levels of citrate (2.3-fold), succinate (2.2-fold), fumarate (2.8-fold), and malate (2.3-fold) observed. Metabolic products associated with the pentose phosphate pathway and nucleotide biosynthesis also increased in PGC-1α-Tg mice. Meanwhile, BCAA levels decreased (Val, 0.7-fold; Leu, 0.8-fold; and Ile, 0.7-fold), and Glu (3.1-fold) and Asp (2.2-fold) levels increased. Levels of β-alanine and related metabolites were markedly decreased in PGC-1α-Tg mice. Coordinated regulation of the TCA cycle and amino acid metabolism, including BCAA, suggests that PGC-1α plays important roles in energy metabolism. Moreover, our metabolomics data showing the activation of the purine nucleotide pathway, malate-aspartate shuttle, as well as creatine metabolism, which are known to be active during exercise, further suggests that PGC-1α regulates metabolism in exercise. Thus, we demonstrated the roles of PGC-1α in the skeletal muscle at the metabolite level. PMID: 26114427 [PubMed - as supplied by publisher]

Related Articles Single cell-type comparative metabolomics of epidermal bladder cells from the halophyte Mesembryanthemum crystallinum. Front Plant Sci. 2015;6:435 Authors: Barkla BJ, Vera-Estrella R Abstract One of the remarkable adaptive features of the halophyte Mesembryanthemum crystallinum are the specialized modified trichomes called epidermal bladder cells (EBC) which cover the leaves, stems, and peduncle of the plant. They are present from an early developmental stage but upon salt stress rapidly expand due to the accumulation of water and sodium. This particular plant feature makes it an attractive system for single cell type studies, with recent proteomics and transcriptomics studies of the EBC establishing that these cells are metabolically active and have roles other than sodium sequestration. To continue our investigation into the function of these unusual cells we carried out a comprehensive global analysis of the metabolites present in the EBC extract by gas chromatography Time-of-Flight mass spectrometry (GC-TOF) and identified 194 known and 722 total molecular features. Statistical analysis of the metabolic changes between control and salt-treated samples identified 352 significantly differing metabolites (268 after correction for FDR). Principal components analysis provided an unbiased evaluation of the data variance structure. Biochemical pathway enrichment analysis suggested significant perturbations in 13 biochemical pathways as defined in KEGG. More than 50% of the metabolites that show significant changes in the EBC, can be classified as compatible solutes and include sugars, sugar alcohols, protein and non-protein amino acids, and organic acids, highlighting the need to maintain osmotic homeostasis to balance the accumulation of Na(+) and Cl(-) ions. Overall, the comparison of metabolic changes in salt treated relative to control samples suggests large alterations in M. crystallinum epidermal bladder cells. PMID: 26113856 [PubMed]

Related Articles Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains. PLoS One. 2014;9(10):e111006 Authors: Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo ML, Sültmann H, Trauner M, Denk H, Zatloukal K, Lehrach H, Wierling C Abstract BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) has a broad spectrum of disease states ranging from mild steatosis characterized by an abnormal retention of lipids within liver cells to steatohepatitis (NASH) showing fat accumulation, inflammation, ballooning and degradation of hepatocytes, and fibrosis. Ultimately, steatohepatitis can result in liver cirrhosis and hepatocellular carcinoma. METHODOLOGY AND RESULTS: In this study we have analyzed three different mouse strains, A/J, C57BL/6J, and PWD/PhJ, that show different degrees of steatohepatitis when administered a 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) containing diet. RNA-Seq gene expression analysis, protein analysis and metabolic profiling were applied to identify differentially expressed genes/proteins and perturbed metabolite levels of mouse liver samples upon DDC-treatment. Pathway analysis revealed alteration of arachidonic acid (AA) and S-adenosylmethionine (SAMe) metabolism upon other pathways. To understand metabolic changes of arachidonic acid metabolism in the light of disease expression profiles a kinetic model of this pathway was developed and optimized according to metabolite levels. Subsequently, the model was used to study in silico effects of potential drug targets for steatohepatitis. CONCLUSIONS: We identified AA/eicosanoid metabolism as highly perturbed in DDC-induced mice using a combination of an experimental and in silico approach. Our analysis of the AA/eicosanoid metabolic pathway suggests that 5-hydroxyeicosatetraenoic acid (5-HETE), 15-hydroxyeicosatetraenoic acid (15-HETE) and prostaglandin D2 (PGD2) are perturbed in DDC mice. We further demonstrate that a dynamic model can be used for qualitative prediction of metabolic changes based on transcriptomics data in a disease-related context. Furthermore, SAMe metabolism was identified as being perturbed due to DDC treatment. Several genes as well as some metabolites of this module show differences between A/J and C57BL/6J on the one hand and PWD/PhJ on the other. PMID: 25347188 [PubMed - indexed for MEDLINE]

Related Articles A gas chromatography-mass spectrometry-based metabolomic approach for the characterization of goat milk compared with cow milk. J Dairy Sci. 2014 Oct;97(10):6057-66 Authors: Scano P, Murgia A, Pirisi FM, Caboni P Abstract In this work, the polar metabolite pool of commercial caprine milk was studied by gas chromatography-mass spectrometry and multivariate statistical data analysis. Experimental data were compared with those of cow milk and the discriminant analysis correctly classified milk. By the same means, differences due to heat treatments (UHT or pasteurization) on milk samples were also investigated. Results of the 2 discriminant analyses were combined, with the aim of finding the discriminant metabolites unique for each class and shared by 2 classes. Valine and glycine were specific to goat milk, talose and malic acid to cow milk, and hydroxyglutaric acid to pasteurized samples. Glucose and fructose were shared by cow milk and UHT-treated samples, whereas ribose was shared by pasteurized and goat milk. Other discriminant variables were not attributed to specific metabolites. Furthermore, with the aim to reduce food fraud, the issue of adulteration of caprine milk by addition of cheaper bovine milk has been also addressed. To this goal, mixtures of goat and cow milk were prepared by adding the latter in a range from 0 to 100% (vol/vol) and studied by multivariate regression analysis. The error in the level of cow milk detectable was approximately 5%. These overall results demonstrated that, through the combined approach of gas chromatography-mass spectrometry and multivariate statistical data analysis, we were able to discriminate between milk typologies on the basis of their polar metabolite profiles and to propose a new analytical method to easily discover food fraud and to protect goat milk uniqueness. The use of appropriate visualization tools improved the interpretation of multivariate model results. PMID: 25108860 [PubMed - indexed for MEDLINE]

Related Articles Association between the bovine milk metabolome and rennet-induced coagulation properties of milk. J Dairy Sci. 2014 Oct;97(10):6076-84 Authors: Sundekilde UK, Gustavsson F, Poulsen NA, Glantz M, Paulsson M, Larsen LB, Bertram HC Abstract The milk metabolomes of 407 individual Swedish Red dairy cows were analyzed by nuclear magnetic resonance spectroscopy as part of the Danish-Swedish Milk Genomics Initiative. By relating these metabolite profiles to total milk protein concentration and rheological measurements of rennet-induced milk coagulation together using multivariate data analysis techniques, we were able to identify several different associations of the milk metabolome to technological properties of milk. Several novel correlations of milk metabolites to protein content and rennet-induced coagulation properties were demonstrated. Metabolites associated with the prediction of total protein content included choline, N-acetyl hexosamines, creatinine, glycerophosphocholine, glutamate, glucose 1-phosphate, galactose 1-phosphate, and orotate. In addition, levels of lactate, acetate, glutamate, creatinine, choline, carnitine, galactose 1-phosphate, and glycerophosphocholine were significantly different when comparing noncoagulating and well-coagulating milks. These findings suggest that the mentioned metabolites are associated with milk protein content and rennet-induced coagulation properties and may act as quality markers for cheese milk. PMID: 25087032 [PubMed - indexed for MEDLINE]

Related Articles Effects of bud load on quality of Beogradska besemena and Thompson seedless table grapes and cultivar differentiation based on chemometrics of analytical indices. J Sci Food Agric. 2012 Feb;92(3):645-53 Authors: Baiano A, Terracone C Abstract BACKGROUND: The effects of bud load on the quality of Beogradska besemena and Thompson seedless table grape cultivars were studied. Two pruning treatments were imposed: 44 and 18 buds per vine for Beogradska besemena and 44 and 22 buds per vine for Thompson seedless. RESULTS: In Beogradska besemena the reduction of bud load decreased titratable acidity (-4%), skin dry weight (-16%) and malic and citric acid contents (-43 and - 20%) and increased tartaric acid content (14%). The decrease in pulp antioxidant activity (-36%) was related to the decrease in hydroxycinnamoyl tartaric acid content (-13%). Concerning skin, the reduction of bud load decreased catechin and caffeoyl tartaric acid contents (-42 and - 40%) and significantly increased rutin and quercetin-3-O-glucopyranoside contents as specific compounds and flavonoids and proanthocyanidins (9 and 21%) as classes of compounds, thus causing an increase in antioxidant activity (6%). In Thompson seedless the reduction of bud load increased soluble solid content (7%), acidity (9%) and concentrations of the three organic acids (7, 3 and 14%). The increase in pulp antioxidant activity (25%) could be attributed to the increase in total phenolics (69%). The reduction of bud load caused a significant decrease in quercetin-3-O-glucopyranoside (-26%) and antioxidant activity (-15%) in skin. Principal component analysis allowed good separation between samples of the two cultivars, independently of bud level. CONCLUSION: The results indicate that the effects of different bud loads are cultivar-dependent. Bud load and genotype differences were shown to dramatically impact the quality and antioxidant properties of table grape. PMID: 21969062 [PubMed - indexed for MEDLINE]

The Utility of Commonly Used Laboratory Tests to Screen for Excessive Alcohol Use in Clinical Practice. Alcohol Clin Exp Res. 2015 Jun 25; Authors: Gough G, Heathers L, Puckett D, Westerhold C, Ren X, Yu Z, Crabb DW, Liangpunsakul S Abstract BACKGROUND: This current study was undertaken to carefully assess the accuracy of routinely used laboratory tests in detecting excessive/recent alcohol use. We also determined the kinetics of these markers in subjects who underwent an intensive alcohol rehabilitation program. METHODS: The study cohort consisted of 210 nonexcessive drinkers, 272 excessive drinkers, and 76 with alcoholic cirrhosis. To determine the kinetics of these markers during alcohol abstinence, we followed 45 subjects with history of excessive alcohol use for 12 weeks during the intensive alcohol treatment program. RESULTS: Percentage of carbohydrate deficient transferrin (%CDT) provided the highest diagnostic performance (area under the curve [AUC] 0.77) followed by gamma-glutamyl transferase (GGT) (AUC 0.68) to detect excessive drinkers. The percentage of excessive drinkers with aspartate aminotransferase:alanine aminotransferase (AST:ALT) > 2 was only 2%, whereas 51% of subjects with alcoholic cirrhosis had AST:ALT > 2. In the multivariate analysis, the levels of GGT and %CDT were associated with the level of alcohol consumed during the past 30 days. The levels of GGT, mean corpuscular volume (MCV), and %CDT were significantly lower compared to those at baseline before alcohol rehabilitation, whereas the AST, ALT, and AST:ALT ratio were unchanged. The percent reduction was ~2.7% (for MCV), 19% (for GGT), and 43% (for %CDT) at the end of the 12-week follow-up compared to the baseline. CONCLUSIONS: %CDT are useful markers to screen for excessive alcohol use and for follow-up of abstinence. Most subjects with excessive alcohol use do not have a high AST:ALT ratio. Rather, the AST:ALT > 2 is suggestive of alcoholic cirrhosis. The performance of the %CDT to screen for heavy alcohol use is still not ideal. Further research to identify the noninvasive marker(s) (i.e., using proteomic or metabolomics approach) should be considered. PMID: 26110815 [PubMed - as supplied by publisher]

(1)H NMR-Based Metabolomics and Neurotoxicity Study of Cerebrum and Cerebellum in Rats Treated with Cinnabar, a Traditional Chinese Medicine. OMICS. 2015 Jun 25; Authors: Wei L, Xue R, Zhang P, Wu Y, Li X, Pei F Abstract Cinnabar, an important traditional Chinese mineral medicine, has been widely used as a Chinese patent medicine ingredient for sedative therapy. Nevertheless, the neurotoxic effects of cinnabar have also been noted. In this study, (1)H NMR-based metabolomics, combined with multivariate pattern recognition, were applied to investigate the neurotoxic effects of cinnabar after intragastrical administration (dosed at 2 and 5 g/kg body weight) on male Wistar rats. The metabolite variations induced by cinnabar were characterized by increased levels of glutamate, glutamine, myo-inositol, and choline, as well as decreased levels of GABA, taurine, NAA, and NAAG in tissue extracts of the cerebellum and cerebrum. These findings suggested that cinnabar induced glutamate excitotoxicity, neuronal cell loss, osmotic state changes, membrane fluidity disruption, and oxidative injury in the brain. We also show here that there is a dose- and time-dependent neurotoxicity of cinnabar, and that cerebellum was more sensitive to cinnabar induction than cerebrum. This work illustrates the utility and reliability of (1)H NMR-based metabolomics approach for examining the potential neurotoxic effects of cinnabar and other traditional Chinese medicines. PMID: 26110755 [PubMed - as supplied by publisher]

Related Articles Metabolic Signature Profiling as a Diagnostic and Prognostic Tool in Pediatric Plasmodium falciparum Malaria. Open Forum Infect Dis. 2015 Apr;2(2):ofv062 Authors: Surowiec I, Orikiiriza J, Karlsson E, Nelson M, Bonde M, Kyamanwa P, Karenzi B, Bergström S, Trygg J, Normark J Abstract Background.  Accuracy in malaria diagnosis and staging is vital to reduce mortality and post infectious sequelae. In this study, we present a metabolomics approach to diagnostic staging of malaria infection, specifically Plasmodium falciparum infection in children. Methods.  A group of 421 patients between 6 months and 6 years of age with mild and severe states of malaria with age-matched controls were included in the study, 107, 192, and 122, individuals, respectively. A multivariate design was used as basis for representative selection of 20 patients in each category. Patient plasma was subjected to gas chromatography-mass spectrometry analysis, and a full metabolite profile was produced from each patient. In addition, a proof-of-concept model was tested in a Plasmodium berghei in vivo model where metabolic profiles were discernible over time of infection. Results.  A 2-component principal component analysis revealed that the patients could be separated into disease categories according to metabolite profiles, independently of any clinical information. Furthermore, 2 subgroups could be identified in the mild malaria cohort who we believe represent patients with divergent prognoses. Conclusions.  Metabolite signature profiling could be used both for decision support in disease staging and prognostication. PMID: 26110164 [PubMed]

Related Articles Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics. 2015;11(4):872-894 Authors: Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS Abstract The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition. PMID: 26109927 [PubMed - as supplied by publisher]

Related Articles A hypothetical astrocyte-microglia lactate shuttle derived from a (1)H NMR metabolomics analysis of cerebrospinal fluid from a cohort of South African children with tuberculous meningitis. Metabolomics. 2015;11(4):822-837 Authors: Mason S, van Furth AM, Mienie LJ, Engelke UF, Wevers RA, Solomons R, Reinecke CJ Abstract Tuberculosis meningitis (TBM) is the most severe form of extra-pulmonary tuberculosis and is particularly intense in small children; there is no universally accepted algorithm for the diagnosis and substantiation of TB infection, which can lead to delayed intervention, a high risk factor for morbidity and mortality. In this study a proton magnetic resonance ((1)H NMR)-based metabolomics analysis and several chemometric methods were applied to data generated from lumber cerebrospinal fluid (CSF) samples from three experimental groups: (1) South African infants and children with confirmed TBM, (2) non-meningitis South African infants and children as controls, and (3) neurological controls from the Netherlands. A total of 16 NMR-derived CSF metabolites were identified, which clearly differentiated between the controls and TBM cases under investigation. The defining metabolites were the combination of perturbed glucose and highly elevated lactate, common to some other neurological disorders. The remaining 14 metabolites of the host's response to TBM were likewise mainly energy-associated indicators. We subsequently generated a hypothesis expressed as an "astrocyte-microglia lactate shuttle" (AMLS) based on the host's response, which emerged from the NMR-metabolomics information. Activation of microglia, as implied by the AMLS hypothesis, does not, however, present a uniform process and involves intricate interactions and feedback loops between the microglia, astrocytes and neurons that hamper attempts to construct basic and linear cascades of cause and effect; TBM involves a complex integration of the responses from the various cell types present within the CNS, with microglia and the astrocytes as main players. PMID: 26109926 [PubMed - as supplied by publisher]

Related Articles Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study. Metabolomics. 2015;11(4):807-821 Authors: Martin JC, Maillot M, Mazerolles G, Verdu A, Lyan B, Migné C, Defoort C, Canlet C, Junot C, Guillou C, Manach C, Jabob D, Bouveresse DJ, Paris E, Pujos-Guillot E, Jourdan F, Giacomoni F, Courant F, Favé G, Le Gall G, Chassaigne H, Tabet JC, Martin JF, Antignac JP, Shintu L, Defernez M, Philo M, Alexandre-Gouaubau MC, Amiot-Carlin MJ, Bossis M, Triba MN, Stojilkovic N, Banzet N, Molinié R, Bott R, Goulitquer S, Caldarelli S, Rutledge DN Abstract The metabo-ring initiative brought together five nuclear magnetic resonance instruments (NMR) and 11 different mass spectrometers with the objective of assessing the reliability of untargeted metabolomics approaches in obtaining comparable metabolomics profiles. This was estimated by measuring the proportion of common spectral information extracted from the different LCMS and NMR platforms. Biological samples obtained from 2 different conditions were analysed by the partners using their own in-house protocols. Test #1 examined urine samples from adult volunteers either spiked or not spiked with 32 metabolite standards. Test #2 involved a low biological contrast situation comparing the plasma of rats fed a diet either supplemented or not with vitamin D. The spectral information from each instrument was assembled into separate statistical blocks. Correlations between blocks (e.g., instruments) were examined (RV coefficients) along with the structure of the common spectral information (common components and specific weights analysis). In addition, in Test #1, an outlier individual was blindly introduced, and its identification by the various platforms was evaluated. Despite large differences in the number of spectral features produced after post-processing and the heterogeneity of the analytical conditions and the data treatment, the spectral information both within (NMR and LCMS) and across methods (NMR vs. LCMS) was highly convergent (from 64 to 91 % on average). No effect of the LCMS instrumentation (TOF, QTOF, LTQ-Orbitrap) was noted. The outlier individual was best detected and characterised by LCMS instruments. In conclusion, untargeted metabolomics analyses report consistent information within and across instruments of various technologies, even without prior standardisation. PMID: 26109925 [PubMed - as supplied by publisher]

Related Articles Training needs in metabolomics. Metabolomics. 2015;11(4):784-786 Authors: Weber RJ, Winder CL, Larcombe LD, Dunn WB, Viant MR PMID: 26109924 [PubMed - as supplied by publisher]

Related Articles Histone Deacetylase 4 promotes cholestatic liver injury in the absence of Prohibitin-1. Hepatology. 2015 Jun 25; Authors: Barbier-Torres L, Beraza N, Fernández-Tussy P, Lopitz-Otsoa F, Fernández-Ramos D, Zubiete-Franco I, Varela-Rey M, Delgado TC, Gutiérrez V, Anguita J, Pares A, Banales JM, Villa E, Caballería J, Alvarez L, Lu SC, Mato JM, Martínez-Chantar ML Abstract Prohibitin 1 (PHB1) is an evolutionary conserved pleiotropic protein that participates in diverse processes depending on its subcellular localization and interactome. Recent data have indicated a diverse role for PHB1 in the pathogenesis of obesity, cancer and inflammatory bowel disease, among others. Data presented here suggest that PHB1 is also linked to cholestatic liver disease. PHB1 expression is markedly reduced in patients with primary billiary cirrhosis and biliary atresia and Alagille syndrome, two major pediatric cholestatic conditions. In the experimental model of bile duct ligation, silencing of PHB1 induced liver fibrosis, reduced animal survival and induced bile duct proliferation. Importantly, the modulatory effect of PHB1 is not dependent on its known mitochondrial function. Importantly,d PHB1 interacts with Histone Deacetylase 4 (HDAC4) in the presence of bile acids. Hence, PHB1 depletion leads to increased nuclear HDAC4 content and its associated epigenetic changes. Remarkably, HDAC4 silencing and the administration of the HDAC inhibitor parthenolide during obstructive cholestasis in vivo promote genomic reprogramming leading to the regression of the fibrotic phenotype in the liver-specific Phb1 KO mice. CONCLUSION: Our data identify PHB1 as an important mediator of cholestatic liver injury regulating the activity of HDAC4, which controls specific epigenetic marks. These results identify potential novel strategies to treat liver injury and fibrosis, particularly as a consequence of chronic cholestasis. This article is protected by copyright. All rights reserved. PMID: 26109312 [PubMed - as supplied by publisher]