PubMed

Metabolomics and Mycobacterial Disease: Don't Forget the Bioinformatics. Ann Am Thorac Soc. 2016 Jan;13(1):141-142 Authors: Collins JM, Kempker RR, Ziegler TR, Blumberg HM, Jones DP PMID: 26730872 [PubMed - as supplied by publisher]

Serum metabolomics study of Traditional Chinese medicine formula intervention to polycystic ovary syndrome. J Pharm Biomed Anal. 2015 Dec 17;120:127-133 Authors: Lu C, Zhao X, Li Y, Li Y, Yuan C, Xu F, Meng X, Hou L, Xu G Abstract Polycystic ovary syndrome (PCOS) is a most common, heterogeneous, complex endocrinopathy disease. Traditional Chinese medicine (TCM) has been used in the treatment of PCOS for many years. However, the mechanism underlying TCM remains obscure and challenging. In this study, 30 PCOS subjects were separated into normoinsulinemic group (NI=13) and hyperinsulinemic group (HI=17), and treated for three menstrual cycles with TCM Formula, Bushen Huatan Formula (BHF). A metabolomics approach based on ultra-high-performance liquid chromatography (UPLC) coupled with linear ion trap Orbi-trap mass spectrometer (LTQ Orbi-trap MS) is used to investigate serum metabolic changes of TCM intervention to PCOS. After BHF intervention for three menstrual cycles, the serum levels of glycerophosphorylethanolamine (GPEA), creatine, creatinine decreased in both NI and HI groups. Furthermore, in NI group, the main manifestation was the changes of phospholipid metabolism. While in HI group, lysine, phenol sulfate, phe-phe etc. decreased, and ornithine, proline, betaine, acetylcholine etc. increased. Combined with clinical biochemical data, BHF was proved effective to PCOS by reducing the inflammatory reaction and oxidative stress. This study also illustrates that the LC-MS based metabolomic approach is a helpful tool to evaluate curative effect and to understand the mechanisms of TCM. PMID: 26730509 [PubMed - as supplied by publisher]

Related Articles The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development. Plant J. 2016 Jan 5; Authors: Dekkers BJ, He H, Hanson J, Willems LA, Jamar DC, Cueff G, Rajjou L, Hilhorst HW, Bentsink L Abstract The seed expressed gene DELAY OF GERMINATION (DOG) 1 is absolutely required for the induction of dormancy. Next to a non-dormant phenotype, the dog1-1 mutant is also characterized by a reduced seed longevity suggesting that DOG1 may affect additional seed processes as well. This aspect however, has been hardly studied and is poorly understood. To uncover additional roles of DOG1 in seeds we performed a detailed analysis of the dog1 mutant using both transcriptomics and metabolomics to investigate the molecular consequences of a dysfunctional DOG1 gene. Further, we used a genetic approach taking advantage of the weak aba insensitive (abi) 3-1 allele as a sensitized genetic background in a cross with dog1-1. DOG1 affects the expression of hundreds of genes including LATE EMBRYOGENESIS ABUNDANT and HEAT SHOCK PROTEIN genes which are affected by DOG1 partly via control of ABI5 expression. Furthermore, the content of a subset of primary metabolites, which normally accumulate during seed maturation, was found to be affected in the dog1-1 mutant. Surprisingly, the abi3-1 dog1-1 double mutant produced green seeds which are highly ABA insensitive, phenocopying severe abi3 mutants, indicating that dog1-1 acts as an enhancer of the weak abi3-1 allele and thus revealing a genetic interaction between both genes. Analysis of the dog1 and dog1 abi3 mutants revealed additional seed phenotypes and therefore we hypothesize that DOG1 function is not limited to dormancy but that it is required for multiple aspects of seed maturation, in part by interfering with ABA signalling components. This article is protected by copyright. All rights reserved. PMID: 26729600 [PubMed - as supplied by publisher]

Related Articles The Art of Destruction: Optimizing Collision Energies in Quadrupole-Time of Flight (Q-TOF) Instruments for Glycopeptide-Based Glycoproteomics. J Am Soc Mass Spectrom. 2016 Jan 4; Authors: Hinneburg H, Stavenhagen K, Schweiger-Hufnagel U, Pengelley S, Jabs W, Seeberger PH, Silva DV, Wuhrer M, Kolarich D Abstract In-depth site-specific investigations of protein glycosylation are the basis for understanding the biological function of glycoproteins. Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. However, the depth of information is highly dependent on the applied analytical tools, including glycopeptide fragmentation regimes and automated data analysis. Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. A linear dependency of m/z-ratio and optimal fragmentation energy was found, showing that with increasing m/z-ratio, more energy is required for glycopeptide fragmentation. Based on these optimized fragmentation parameters, a method combining lower- and higher-energy CID was developed, allowing the online acquisition of glycan and peptide-specific fragments within a single tandem MS experiment. We validated this method analyzing a set of human immunoglobulins (IgA1+2, sIgA, IgG1+2, IgE, IgD, IgM) as well as bovine fetuin. These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. The Q-TOF based glycopeptide analysis platform presented here opens the way to a range of different applications in glycoproteomics research as well as biopharmaceutical development and quality control. Graphical Abstract ᅟ. PMID: 26729457 [PubMed - as supplied by publisher]

Related Articles ChainRank, a chain prioritisation method for contextualisation of biological networks. BMC Bioinformatics. 2016;17(1):17 Authors: Tényi Á, de Atauri P, Gomez-Cabrero D, Cano I, Clarke K, Falciani F, Cascante M, Roca J, Maier D Abstract BACKGROUND: Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of biological associations, which are suitable for systems analyses. However, these networks usually lack both, context specificity in time and space as well as the distinctive borders, which are usually assigned in the classical pathway view of molecular events (e.g. signal transduction). This complexity and high interconnectedness call for automated techniques that can identify smaller targeted subnetworks specific to a given research context (e.g. a disease scenario). RESULTS: Our method, named ChainRank, finds relevant subnetworks by identifying and scoring chains of interactions that link specific network components. Scores can be generated from integrating multiple general and context specific measures (e.g. experimental molecular data from expression to proteomics and metabolomics, literature evidence, network topology). The performance of the novel ChainRank method was evaluated on recreating selected signalling pathways from a human protein interaction network. Specifically, we recreated skeletal muscle specific signaling networks in healthy and chronic obstructive pulmonary disease (COPD) contexts. The analysis showed that ChainRank can identify main mediators of context specific molecular signalling. An improvement of up to factor 2.5 was shown in the precision of finding proteins of the recreated pathways compared to random simulation. CONCLUSIONS: ChainRank provides a framework, which can integrate several user-defined scores and evaluate their combined effect on ranking interaction chains linking input data sets. It can be used to contextualise networks, identify signaling and regulatory path amongst targeted genes or to analyse synthetic lethality in the context of anticancer therapy. ChainRank is implemented in R programming language and freely available at https://github.com/atenyi/ChainRank . PMID: 26729273 [PubMed - in process]

Related Articles Differential Targeting of SLC30A10/ZnT10 Heterodimers to Endolysosomal Compartments Modulates EGF-induced MEK/ERK1/2 Activity. Traffic. 2016 Jan 5; Authors: Zhao Y, Feresin RG, Falcon-Perez JM, Salazar G Abstract The solute carrier 30A (SLC30A) family of zinc exporters transports zinc into the lumen of intracellular organelles in order to prevent zinc toxicity. We reported that formation of tyrosine dimers is required for ZnT3 zinc transport activity and targeting to synaptic-like microvesicles (SLMVs) in PC12 cells and the formation of ZnT3/ZnT10 heterodimers. Here, we focus on ZnT10 to determine the role of heterodimerization in the sorting of ZnTs in the endolysosomal pathway. Using cell fractionation, immunoprecipitation and immunofluorescence approaches, we found that ZnT10 resides in transferrin receptor and Rab5 positive endosomes and forms covalent heterodimers and oligomers with ZnT2, ZnT3 and ZnT4. The interaction of ZnT10 with ZnT3, mediated by dityrosine bonds, was unable to target ZnT10 into SLMVs in vitro or into synaptic vesicles isolated from mouse brain in vivo. However, ZnT3/ZnT10 heterodimers regulate epidermal growth factor receptor (EGF-R) signaling by increasing the phosphorylation of mitogen activated protein kinase kinase (MEK) and extracellular signal regulated kinase (ERK1/2), but not EGF-R, C-Raf or Akt phosphorylation in response to EGF. Further, mutation of tyrosine 4 in ZnT10 reduced ZnT3/ZnT10 dityrosine-mediated heterodimerization and zinc transport, as well as MEK and ERK1/2 phosphorylation, which were also reduced by the zinc chelator TPEN. Phosphorylation of these kinases is likely to occur in the cytosol since no differences in phosphorylation were observed in membrane fractions of control and ZnT3/ZnT10 expressing cells. We propose that ZnT10 plays a role in signal transduction, which is mediated by homo and heterodimerization with other ZnTs. PMID: 26728129 [PubMed - as supplied by publisher]

Related Articles Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries. Am J Clin Nutr. 2015 Oct;102(4):905-13 Authors: Edmands WM, Ferrari P, Rothwell JA, Rinaldi S, Slimani N, Barupal DK, Biessy C, Jenab M, Clavel-Chapelon F, Fagherazzi G, Boutron-Ruault MC, Katzke VA, Kühn T, Boeing H, Trichopoulou A, Lagiou P, Trichopoulos D, Palli D, Grioni S, Tumino R, Vineis P, Mattiello A, Romieu I, Scalbert A Abstract BACKGROUND: An improved understanding of the contribution of the diet to health and disease risks requires accurate assessments of dietary exposure in nutritional epidemiologic studies. The use of dietary biomarkers may improve the accuracy of estimates. OBJECTIVE: We applied a metabolomic approach in a large cohort study to identify novel biomarkers of intake for a selection of polyphenol-containing foods. The large chemical diversity of polyphenols and their wide distribution over many foods make them ideal biomarker candidates for such foods. DESIGN: Metabolic profiles were measured with the use of high-resolution mass spectrometry in 24-h urine samples from 481 subjects from the large European Prospective Investigation on Cancer and Nutrition cohort. Peak intensities were correlated to acute and habitual dietary intakes of 6 polyphenol-rich foods (coffee, tea, red wine, citrus fruit, apples and pears, and chocolate products) measured with the use of 24-h dietary recalls and food-frequency questionnaires, respectively. RESULTS: Correlation (r > 0.3, P < 0.01 after correction for multiple testing) and discriminant [pcorr (1) > 0.3, VIP > 1.5] analyses showed that >2000 mass spectral features from urine metabolic profiles were significantly associated with the consumption of the 6 selected foods. More than 80 polyphenol metabolites associated with the consumption of the selected foods could be identified, and large differences in their concentrations reflecting individual food intakes were observed within and between 4 European countries. Receiver operating characteristic curves showed that 5 polyphenol metabolites, which are characteristic of 5 of the 6 selected foods, had a high predicting ability of food intake. CONCLUSION: Highly diverse food-derived metabolites (the so-called food metabolome) can be characterized in human biospecimens through this powerful metabolomic approach and screened to identify novel biomarkers for dietary exposures, which are ultimately essential to better understand the role of the diet in the cause of chronic diseases. PMID: 26269369 [PubMed - indexed for MEDLINE]

Neuroprotection by selective neuronal deletion of Atg7 in neonatal brain injury. Autophagy. 2016 Jan 4;:0 Authors: Xie C, Ginet V, Sun Y, Koike M, Zhou K, Li T, Li H, Li Q, Wang X, Uchiyama Y, Truttmann AC, Kroemer G, Puyal J, Blomgren K, Zhu C Abstract Perinatal asphyxia induces neuronal cell death and brain injury, and is often associated with irreversible neurological deficits in children. There is an urgent need to elucidate the neuronal death mechanisms occurring after neonatal hypoxia-ischemia (HI). We here investigated the selective neuronal deletion of the Atg7 (autophagy related 7) gene on neuronal cell death and brain injury in a mouse model of severe neonatal hypoxia-ischemia. Neuronal deletion of Atg7 prevented HI-induced autophagy, resulted in 42% decrease of tissue loss compared to wild-type mice after the insult, and reduced cell death in multiple brain regions, including apoptosis, as shown by decreased caspase-dependent and -independent cell death. Moreover, we investigated the lentiform nucleus of human newborns who died after severe perinatal asphyxia and found increased neuronal autophagy after severe hypoxic-ischemic encephalopathy compared to control uninjured brains, as indicated by the numbers of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3)-, LAMP1 (lysosomal-associated membrane protein 1)-, and CTSD (cathepsin D)-positive cells. These findings reveal that selective neuronal deletion of Atg7 is strongly protective against neuronal death and overall brain injury occurring after HI and suggest that inhibition of HI-enhanced autophagy should be considered as a potential therapeutic target for the treatment of human newborns developing severe hypoxic-ischemic encephalopathy. PMID: 26727396 [PubMed - as supplied by publisher]

Primary Metabolism, Phenylpropanoids and Antioxidant Pathways Are Regulated in Potato as a Response to Potato virus Y Infection. PLoS One. 2016;11(1):e0146135 Authors: Kogovšek P, Pompe-Novak M, Petek M, Fragner L, Weckwerth W, Gruden K Abstract Potato production is one of the most important agricultural sectors, and it is challenged by various detrimental factors, including virus infections. To control losses in potato production, knowledge about the virus-plant interactions is crucial. Here, we investigated the molecular processes in potato plants as a result of Potato virus Y (PVY) infection, the most economically important potato viral pathogen. We performed an integrative study that links changes in the metabolome and gene expression in potato leaves inoculated with the mild PVYN and aggressive PVYNTN isolates, for different times through disease development. At the beginning of infection (1 day post-inoculation), virus-infected plants showed an initial decrease in the concentrations of metabolites connected to sugar and amino-acid metabolism, the TCA cycle, the GABA shunt, ROS scavangers, and phenylpropanoids, relative to the control plants. A pronounced increase in those metabolites was detected at the start of the strong viral multiplication in infected leaves. The alterations in these metabolic pathways were also seen at the gene expression level, as analysed by quantitative PCR. In addition, the systemic response in the metabolome to PVY infection was analysed. Systemic leaves showed a less-pronounced response with fewer metabolites altered, while phenylpropanoid-associated metabolites were strongly accumulated. There was a more rapid onset of accumulation of ROS scavengers in leaves inoculated with PVYN than those inoculated with PVYNTN. This appears to be related to the lower damage observed for leaves of potato infected with the milder PVYN strain, and at least partially explains the differences between the phenotypes observed. PMID: 26727123 [PubMed - as supplied by publisher]

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper. J Extracell Vesicles. 2015;4:30087 Authors: Lener T, Gimona M, Aigner L, Börger V, Buzas E, Camussi G, Chaput N, Chatterjee D, Court FA, Del Portillo HA, O'Driscoll L, Fais S, Falcon-Perez JM, Felderhoff-Mueser U, Fraile L, Gho YS, Görgens A, Gupta RC, Hendrix A, Hermann DM, Hill AF, Hochberg F, Horn PA, de Kleijn D, Kordelas L, Kramer BW, Krämer-Albers EM, Laner-Plamberger S, Laitinen S, Leonardi T, Lorenowicz MJ, Lim SK, Lötvall J, Maguire CA, Marcilla A, Nazarenko I, Ochiya T, Patel T, Pedersen S, Pocsfalvi G, Pluchino S, Quesenberry P, Reischl IG, Rivera FJ, Sanzenbacher R, Schallmoser K, Slaper-Cortenbach I, Strunk D, Tonn T, Vader P, van Balkom BW, Wauben M, Andaloussi SE, Théry C, Rohde E, Giebel B Abstract Extracellular vesicles (EVs), such as exosomes and microvesicles, are released by different cell types and participate in physiological and pathophysiological processes. EVs mediate intercellular communication as cell-derived extracellular signalling organelles that transmit specific information from their cell of origin to their target cells. As a result of these properties, EVs of defined cell types may serve as novel tools for various therapeutic approaches, including (a) anti-tumour therapy, (b) pathogen vaccination, (c) immune-modulatory and regenerative therapies and (d) drug delivery. The translation of EVs into clinical therapies requires the categorization of EV-based therapeutics in compliance with existing regulatory frameworks. As the classification defines subsequent requirements for manufacturing, quality control and clinical investigation, it is of major importance to define whether EVs are considered the active drug components or primarily serve as drug delivery vehicles. For an effective and particularly safe translation of EV-based therapies into clinical practice, a high level of cooperation between researchers, clinicians and competent authorities is essential. In this position statement, basic and clinical scientists, as members of the International Society for Extracellular Vesicles (ISEV) and of the European Cooperation in Science and Technology (COST) program of the European Union, namely European Network on Microvesicles and Exosomes in Health and Disease (ME-HaD), summarize recent developments and the current knowledge of EV-based therapies. Aspects of safety and regulatory requirements that must be considered for pharmaceutical manufacturing and clinical application are highlighted. Production and quality control processes are discussed. Strategies to promote the therapeutic application of EVs in future clinical studies are addressed. PMID: 26725829 [PubMed]

PHO13 Deletion-Induced Transcriptional Activation Prevents Sedoheptulose Accumulation during Xylose Metabolism in Engineered Saccharomyces cerevisiae. Metab Eng. 2015 Dec 25; Authors: Xu H, Kim S, Sorek H, Lee Y, Jeong D, Kim JY, Oh EJ, Yun EJ, Wemmer DE, Kim KH, Kim SR, Jin YS Abstract The deletion of PHO13 (pho13Δ) in Saccharomyces cerevisiae, encoding a phosphatase enzyme of unknown specificity, results in the transcriptional activation of genes related to the pentose phosphate pathway (PPP) such as TAL1 encoding transaldolase. It has been also reported that the pho13Δ mutant of S. cerevisiae expressing a heterologous xylose pathway can metabolize xylose efficiently compared to its parental strain. However, the interaction between the pho13Δ-induced transcriptional changes and the phenotypes of xylose fermentation was not understood. Thus we investigated the global metabolic changes in response to pho13Δ when cells were exponentially growing on xylose. Among the 134 intracellular metabolites that we identified, the 98% reduction of sedoheptulose was found to be the most significant change in the pho13Δ mutant as compared to its parental strain. Because sedoheptulose-7-phosphate (S7P), a substrate of transaldolase, reduced significantly in the pho13Δ mutant as well, we hypothesized that limited transaldolase activity in the parental strain might cause dephosphorylation of S7P, leading to carbon loss and inefficient xylose metabolism. Mutants overexpressing TAL1 at different degrees were constructed, and their TAL1 expression levels and xylose consumption rates were positively correlated. Moreover, as TAL1 expression levels increased, intracellular sedoheptulose concentration dropped significantly. Therefore, we concluded that TAL1 upregulation, preventing the accumulation of sedoheptulose, is the most critical mechanism for the improved xylose metabolism by the pho13Δ mutant of engineered S. cerevisiae. PMID: 26724864 [PubMed - as supplied by publisher]

Related Articles STAT3 Inhibition Enhances the Therapeutic Efficacy of Immunogenic Chemotherapy by Stimulating Type 1 Interferon Production by Cancer Cells. Cancer Res. 2015 Sep 15;75(18):3812-22 Authors: Yang H, Yamazaki T, Pietrocola F, Zhou H, Zitvogel L, Ma Y, Kroemer G Abstract STAT3 is an oncogenic transcription factor with potent immunosuppressive functions. We found that pharmacologic inhibition of STAT3 or its selective knockout in cancer cells improved the tumor growth-inhibitory efficacy of anthracycline-based chemotherapies. This combined effect of STAT3 inhibition/depletion and anthracyclines was only found in tumors growing on immunocompetent (not in immunodeficient) mice. As compared with Stat3-sufficient control tumors, Stat3(-/-) cancer cells exhibited an increased infiltration by dendritic cells and cytotoxic T lymphocytes after chemotherapy. Anthracyclines are known to induce several stress pathways that enhance the immunogenicity of dying and dead cancer cells, thereby stimulating a dendritic cell-dependent and T lymphocyte-mediated anticancer immune response. Among these therapy-relevant stress pathways, Stat3(-/-) cancer cells manifested one significant improvement, namely an increase in the expression of multiple type-1 interferon-responsive genes, including that of the chemokines Cxcl9 and Cxcl10. This enhanced type-1 interferon response could be suppressed by reintroducing wild-type Stat3 (but not a transactivation-deficient mutant Stat3(Y705F)) into the tumor cells. This maneuver also abolished the improved chemotherapeutic response of Stat3(-/-) cancers. Finally, the neutralization of the common type-1 interferon receptor or that of the chemokine receptor CXCR3 (which binds CXCL9 and CXCL10) abolished the difference in the chemotherapeutic response between Stat3(-/-) and control tumors. Altogether, these results suggest that STAT3 inhibitors may improve the outcome of chemotherapy by enhancing the type-1 interferon response of cancer cells. PMID: 26208907 [PubMed - indexed for MEDLINE]

Related Articles A Threshold Level of Intratumor CD8+ T-cell PD1 Expression Dictates Therapeutic Response to Anti-PD1. Cancer Res. 2015 Sep 15;75(18):3800-11 Authors: Ngiow SF, Young A, Jacquelot N, Yamazaki T, Enot D, Zitvogel L, Smyth MJ Abstract Despite successes, thus far, a significant proportion of the patients treated with anti-PD1 antibodies have failed to respond. We use mouse tumor models of anti-PD1 sensitivity and resistance and flow cytometry to assess tumor-infiltrating immune cells immediately after therapy. We demonstrate that the expression levels of T-cell PD1 (PD1(lo)), myeloid, and T-cell PDL1 (PDL1(hi)) in the tumor microenvironment inversely correlate and dictate the efficacy of anti-PD1 mAb and function of intratumor CD8(+) T cells. In sensitive tumors, we reveal a threshold for PD1 downregulation on tumor-infiltrating CD8(+) T cells below which the release of adaptive immune resistance is achieved. In contrast, PD1(hi) T cells in resistant tumors fail to be rescued by anti-PD1 therapy and remain dysfunctional unless intratumor PDL1(lo) immune cells are targeted. Intratumor Tregs are partly responsible for the development of anti-PD1-resistant tumors and PD1(hi) CD8(+) T cells. Our analyses provide a framework to interrogate intratumor CD8(+) T-cell PD1 and immune PDL1 levels and response in human cancer. PMID: 26208901 [PubMed - indexed for MEDLINE]

Related Articles Associations of multiple lipoprotein and apolipoprotein measures with worsening of glycemia and incident type 2 diabetes in 6607 non-diabetic Finnish men. Atherosclerosis. 2015 May;240(1):272-7 Authors: Fizelova M, Miilunpohja M, Kangas AJ, Soininen P, Kuusisto J, Ala-Korpela M, Laakso M, Stančáková A Abstract OBJECTIVE: We investigated the association of various lipoprotein traits, apolipoproteins and their ratios with the deterioration of glycemia, incident type 2 diabetes, insulin resistance and insulin secretion in a large population-based Metabolic Syndrome Men (METSIM) Study. RESEARCH DESIGN AND METHODS: The METSIM Study includes 10,197 Finnish men, aged 45-73 years, and examined in 2005-2010. From 6607 non-diabetic participants without statin treatment at baseline, 386 developed incident type 2 diabetes during a 5.9-year follow-up. A total of 3330 non-diabetic participants without statin treatment had both baseline and follow-up visit data, and were included in statistical analyses of the worsening of glycemia. RESULTS: Compared to single lipid and lipoprotein measurements, lipoprotein and apolipoprotein ratios were better predictors of the glucose area under the curve and incident type 2 diabetes after adjustment for confounding factors. The apolipoprotein B/LDL cholesterol ratio was the strongest predictor of the worsening of glycemia, whereas the apolipoprotein A1/HDL cholesterol ratio was the strongest predictor of incident type 2 diabetes. The associations of lipoprotein traits, apolipoproteins and their ratios with insulin sensitivity were stronger than those with insulin secretion. CONCLUSIONS: The apolipoprotein B/LDL cholesterol and apolipoprotein A1/HDL cholesterol ratios were the strongest predictors of the worsening of glycemia and incident type 2 diabetes, respectively. PMID: 25818853 [PubMed - indexed for MEDLINE]

Related Articles The relations between metabolic variations and genetic evolution of different species. Anal Biochem. 2015 May 15;477:105-14 Authors: Li Z, Lin C, Xu J, Wu H, Feng J, Huang H Abstract Metabonomics has been applied in many bio-related scientific fields. Nevertheless, some animal research works are shown to fail when they are extended to humans. Therefore, it is essential to figure out suitable animal modeling to mimic human metabolism so that animal findings can serve humans. In this study, two kinds of commonly selected body fluids, serum and urine, from humans and various experimental animals were characterized by integration of nuclear magnetic resonance (NMR) spectroscopy with multivariate statistical analysis to identify the interspecies metabolic differences and similarities at a baseline physiological status. Our results highlight that the dairy cow and pig may be an optimal choice for transportation and biodistribution studies of drugs and that the Kunming (KM) mouse model may be the most effective for excretion studies of drugs, whereas the Sprague-Dawley (SD) rat could be the most suitable candidate for animal modeling under overall considerations. The biochemical pathways analyses further provide an interconnection between genetic evolution and metabolic variations, where species evolution most strongly affects microbial biodiversity and, consequently, has effects on the species-specific biological substances of biosynthesis and corresponding biological activities. Knowledge of the metabolic effects from species difference will enable the construction of better models for disease diagnosis, drug metabolism, and toxicology research. PMID: 25728943 [PubMed - indexed for MEDLINE]

Related Articles High-throughput quantitative and qualitative analysis of microsomal incubations by cocktail analysis with an ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometer system. Bioanalysis. 2015;7(6):671-83 Authors: Backfisch G, Reder-Hilz B, Hoeckels-Messemer J, Angstenberger J, Sydor J, Laplanche L, Schulz M Abstract BACKGROUND: Metabolite identification studies are very resource intensive and also are rarely performed in early discovery. Here, we report the validation of an ultraperformance liquid chromatography-high-resolution mass spectrometry (UPLC-HRMS) platform for generating high-throughput stability data with structure elucidation in a single injection. MATERIALS & METHODS: Tandem mass spectrometry spectra were obtained for quantitative analysis using a generic information-dependent acquisition method from pooled microsomal samples incubated at low compound concentrations. RESULTS: A good correlation was observed between clearance determined using UPLC-HRMS and UPLC-triple-quadrupole analysis. Structural elucidation performed with MassMetaSite™ (Molecular Discovery, Perugia, Italy) software identified 85% of the major metabolites of eight marketed drugs and over 100 internal compounds under these conditions. CONCLUSION: For the first time, a high-throughput quantitative-qualitative workflow was established using a cocktail approach for sample analysis with UPLC-HRMS in order to enable metabolite identification in early discovery projects. PMID: 25517264 [PubMed - indexed for MEDLINE]

Mannose metabolism in recombinant CHO cells and its effect on IgG glycosylation. Biotechnol Bioeng. 2016 Jan 1; Authors: Slade PG, Caspary RG, Nargund S, Huang CJ Abstract Understanding the causes of high-mannose (HM) glycosylation of recombinant IgG in CHO cells would facilitate the production of therapeutics. CHO cells grown with mannose as the major carbon source demonstrated a dramatic increase in total HM glycosylation in recombinant IgG, with no effect on cell growth, viability or titer. Quantitative metabolomics and (13) C flux analysis were used to explore the mechanism for increased HM glycosylation and understand the metabolism of mannose in CHO cells. It was demonstrated that mannose was a good carbon source for CHO cell growth and IgG production, readily entering both glycolysis and the TCA Cycle. Previous mechanisms for increased HM glycosylation during antibody production have been attributed to changes in pH, osmolality, increased specific productivity, and nutrient limitation. The results from this study propose a novel mechanism where an increased carbon flux in the GDP-mannose synthetic pathway increased the intracellular concentration of mannose-containing metabolites. The abnormally high concentration of mannose and mannose-metabolites were shown to inhibit α-mannosidase activity and it was proposed that this inhibition in the ER and Golgi caused the production of IgG with increased high-mannose glycosylation. This article is protected by copyright. All rights reserved. PMID: 26724786 [PubMed - as supplied by publisher]

Related Articles Sequencing the exposome: A call to action. Toxicol Rep. 2016;3:29-45 Authors: Jones DP Abstract The exposome is a complement to the genome that includes non-genetic causes of disease. Multiple definitions are available, with salient points being global inclusion of exposures and behaviors, and cumulative integration of associated biologic responses. As such, the concept is both refreshingly simple and dauntingly complex. This article reviews high-resolution metabolomics (HRM) as an affordable approach to routinely analyze samples for a broad spectrum of environmental chemicals and biologic responses. HRM has been successfully used in multiple exposome research paradigms and is suitable to implement in a prototype universal exposure surveillance system. Development of such a structure for systematic monitoring of environmental exposures is an important step toward sequencing the exposome because it builds upon successes of exposure science, naturally connects external exposure to body burden and partitions the exposome into workable components. Practical results would be repositories of quantitative data on chemicals according to geography and biology. This would support new opportunities for environmental health analysis and predictive modeling. Complementary approaches to hasten development of exposome theory and associated biologic response networks could include experimental studies with model systems, analysis of archival samples from longitudinal studies with outcome data and study of relatively short-lived animals, such as household pets (dogs and cats) and non-human primates (common marmoset). International investment and cooperation to sequence the human exposome will advance scientific knowledge and also provide an important foundation to control adverse environmental exposures to sustain healthy living spaces and improve prediction and management of disease. PMID: 26722641 [PubMed - as supplied by publisher]

Related Articles Making sense of blood-based proteomics and metabolomics in psychiatric research. Int J Neuropsychopharmacol. 2015 Dec 30; Authors: Guest PC, Guest FL, Martins-de-Souza D Abstract This manuscript describes the basics of proteomic and metabolic profiling of blood serum and plasma from patients with psychiatric disorders. It will also explain the rationale behind the use of these body fluids due to need for user friendly and rapid tests in the clinic with simple sampling procedures. It has emerged over the last 15 years or so that psychiatric disorders are whole body diseases and the bloodstream is a means of molecular transport and therefore provides a conduit for two way communication with the brain. Here we also describe some of the basic biomarker findings from studies of serum or plasma from patients with psychiatric disorders like schizophrenia, major depression and bipolar disorder. Finally, we will discuss potential future advancements in this area which includes the development of held devices containing miniature proteomic and metabolic assays which can be used for facilitating diagnosis in a point-of-care setting and yield results in less than 15 minutes from a single drop of blood. PMID: 26721951 [PubMed - as supplied by publisher]

Related Articles Cigarette smoking behaviour and blood metabolomics. Int J Epidemiol. 2015 Dec 31; Authors: Gu F, Derkach A, Freedman ND, Landi MT, Albanes D, Weinstein SJ, Mondul AM, Matthews CE, Guertin KA, Xiao Q, Zheng W, Shu XO, Sampson JN, Moore SC, Caporaso NE Abstract BACKGROUND: Identifying circulating metabolites related to cigarette smoking may provide insight into the biological mechanisms of smoking-related diseases and the nature of addiction. However, previous studies are limited, generally small, and have largely targeted a priori metabolites. METHODS: We examined associations between cigarette smoking and metabolites using an untargeted metabolomics approach in 892 men and women from four studies including participants from Italy, USA, China and Finland. We examined associations between individual log-transformed metabolites and two key smoking phenotypes (current smoking status and cigarettes per day [cig/day]) using linear regression. Fixed-effect meta-analysis was used to combine results across studies. Strict Bonferroni thresholds were used as our significance criteria. We further examined associated metabolites with other metrics of smoking behaviuor (current versus former, former versus never, smoking duration and years since quitting) in the US study. RESULTS: We identified a total of 25 metabolites associated with smoking behaviours; 24 were associated with current smoking status and eight with cig/day. In addition to three well-established nicotine metabolites (cotinine, hydroxycotinine, cotinine N-oxide), we found an additional 12 xenobiotic metabolites involved in benzoatic (e.g. 3-ethylphenylsulphate) or xanthine metabolism (e.g. 1-methylurate), three amino acids (o-cresol sulphate, serotonin, indolepropionate), two lipids (scyllo-inositol, pregnenolone sulphate), four vitamins or cofactors [e.g. bilirubin (Z,Z)], and one carbohydrate (oxalate). CONCLUSIONS: We identified associations between cigarette smoking and a diverse range of metabolites. Our findings, with further validation in future studies, have implications regarding aetiology and study design of smoking-related diseases. PMID: 26721601 [PubMed - as supplied by publisher]