PubMed

Related Articles Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics. 2017 Apr;17(7): Authors: Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH Abstract The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality, precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies. PMID: 27688154 [PubMed - indexed for MEDLINE]

Related Articles Defective postreperfusion metabolic recovery directly associates with incident delayed graft function. Kidney Int. 2016 Jul;90(1):181-91 Authors: Wijermars LG, Schaapherder AF, de Vries DK, Verschuren L, Wüst RC, Kostidis S, Mayboroda OA, Prins F, Ringers J, Bierau J, Bakker JA, Kooistra T, Lindeman JH Abstract Delayed graft function (DGF) following kidney transplantation affects long-term graft function and survival and is considered a manifestation of ischemia reperfusion injury. Preclinical studies characterize metabolic defects resulting from mitochondrial damage as primary driver of ischemia reperfusion injury. In a comprehensive approach that included sequential establishment of postreperfusion arteriovenous concentration differences over the human graft, metabolomic and genomic analysis in tissue biopsies taken before and after reperfusion, we tested whether the preclinical observations translate to the context of clinical DGF. This report is based on sequential studies of 66 eligible patients of which 22 experienced DGF. Grafts with no DGF immediately recovered aerobic respiration as indicated by prompt cessation of lactate release following reperfusion. In contrast, grafts with DGF failed to recover aerobic respiration and showed persistent adenosine triphosphate catabolism indicated by a significant persistently low post reperfusion tissue glucose-lactate ratio and continued significant post-reperfusion lactate and hypoxanthine release (net arteriovenous difference for lactate and hypoxanthine at 30 minutes). The metabolic data for the group with DGF point to a persistent post reperfusion mitochondrial defect, confirmed by functional (respirometry) and morphological analyses. The archetypical mitochondrial stabilizing peptide SS-31 significantly preserved mitochondrial function in human kidney biopsies following simulated ischemia reperfusion. Thus, development of DGF is preceded by a profound post-reperfusion metabolic deficit resulting from severe mitochondrial damage. Strategies aimed at preventing DGF should be focused on safeguarding a minimally required post-reperfusion metabolic competence. PMID: 27188504 [PubMed - indexed for MEDLINE]

Related Articles System-based proteomic and metabonomic analysis of the Df(16)A(+/-) mouse identifies potential miR-185 targets and molecular pathway alterations. Mol Psychiatry. 2017 Mar;22(3):384-395 Authors: Wesseling H, Xu B, Want EJ, Holmes E, Guest PC, Karayiorgou M, Gogos JA, Bahn S Abstract Deletions on chromosome 22q11.2 are a strong genetic risk factor for development of schizophrenia and cognitive dysfunction. We employed shotgun liquid chromatography-mass spectrometry (LC-MS) proteomic and metabonomic profiling approaches on prefrontal cortex (PFC) and hippocampal (HPC) tissue from Df(16)A(+/-) mice, a model of the 22q11.2 deletion syndrome. Proteomic results were compared with previous transcriptomic profiling studies of the same brain regions. The aim was to investigate how the combined effect of the 22q11.2 deletion and the corresponding miRNA dysregulation affects the cell biology at the systems level. The proteomic brain profiling analysis revealed PFC and HPC changes in various molecular pathways associated with chromatin remodelling and RNA transcription, indicative of an epigenetic component of the 22q11.2DS. Further, alterations in glycolysis/gluconeogenesis, mitochondrial function and lipid biosynthesis were identified. Metabonomic profiling substantiated the proteomic findings by identifying changes in 22q11.2 deletion syndrome (22q11.2DS)-related pathways, such as changes in ceramide phosphoethanolamines, sphingomyelin, carnitines, tyrosine derivates and panthothenic acid. The proteomic findings were confirmed using selected reaction monitoring mass spectrometry, validating decreased levels of several proteins encoded on 22q11.2, increased levels of the computationally predicted putative miR-185 targets UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT1) and kinesin heavy chain isoform 5A and alterations in the non-miR-185 targets serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform, neurofilament light chain and vesicular glutamate transporter 1. Furthermore, alterations in the proteins associated with mammalian target of rapamycin signalling were detected in the PFC and with glutamatergic signalling in the hippocampus. Based on the proteomic and metabonomic findings, we were able to develop a schematic model summarizing the most prominent molecular network findings in the Df(16)A(+/-) mouse. Interestingly, the implicated pathways can be linked to one of the most consistent and strongest proteomic candidates, (OGT1), which is a predicted miR-185 target. Our results provide novel insights into system-biological mechanisms associated with the 22q11DS, which may be linked to cognitive dysfunction and an increased risk to develop schizophrenia. Further investigation of these pathways could help to identify novel drug targets for the treatment of schizophrenia. PMID: 27001617 [PubMed - indexed for MEDLINE]

Prediction of liver toxicity and mode of action using metabolomics in vitro in HepG2 cells. Arch Toxicol. 2017 Sep 30;: Authors: Ramirez T, Strigun A, Verlohner A, Huener HA, Peter E, Herold M, Bordag N, Mellert W, Walk T, Spitzer M, Jiang X, Sperber S, Hofmann T, Hartung T, Kamp H, van Ravenzwaay B Abstract Liver toxicity is a leading systemic toxicity of drugs and chemicals demanding more human-relevant, high throughput, cost effective in vitro solutions. In addition to contributing to animal welfare, in vitro techniques facilitate exploring and understanding the molecular mechanisms underlying toxicity. New 'omics technologies can provide comprehensive information on the toxicological mode of action of compounds, as well as quantitative information about the multi-parametric metabolic response of cellular systems in normal and patho-physiological conditions. Here, we combined mass-spectroscopy metabolomics with an in vitro liver toxicity model. Metabolite profiles of HepG2 cells treated with 35 test substances resulted in 1114 cell supernatants and 3556 intracellular samples analyzed by metabolomics. Control samples showed relative standard deviations of about 10-15%, while the technical replicates were at 5-10%. Importantly, this procedure revealed concentration-response effects and patterns of metabolome changes that are consistent for different liver toxicity mechanisms (liver enzyme induction/inhibition, liver toxicity and peroxisome proliferation). Our findings provide evidence that identifying organ toxicity can be achieved in a robust, reliable, human-relevant system, representing a non-animal alternative for systemic toxicology. PMID: 28965233 [PubMed - as supplied by publisher]

New chemotype of selective and potent inhibitors of human delta 24-dehydrocholesterol reductase. Eur J Med Chem. 2017 Sep 12;140:305-320 Authors: Müller C, Hemmers S, Bartl N, Plodek A, Körner A, Mirakaj V, Giera M, Bracher F Abstract The enzyme Δ(24)-dehydrocholesterol reductase (DHCR24) catalyzes the reduction of the Δ(24)-double bond in the side chain of cholesterol precursors. Recent biochemical investigations fuel the hope that inhibition of DHCR24, resulting in an accumulation of desmosterol, can open new therapeutic options for treating hepatitis C virus infections, certain forms of cancer and atherosclerosis. In turn, there is a high need for selective, potent and non-toxic inhibitors of DHCR24. Previous reports as well as our re-evaluation showed that established DHCR24 inhibitors are not suitable for this purpose. Based on the lathosterol-derived amide MGI-21 (IC50 823 nM for inhibition of overall cholesterol biosynthesis in HL-60 cells) we performed a systematic variation of the side chain functionality and identified the steroidal 3,22-diols 29 and 30, as well as several esters thereof, as extremely potent (IC50 < 5 nM), selective, and non-toxic DHCR24 inhibitors. In mice, diester 27 (SH-42) led to a significant increase in plasma desmosterol levels. The new inhibitors described here are valuable tools for investigating the therapeutic potential of DHCR24 inhibition. PMID: 28964935 [PubMed - as supplied by publisher]

Do lipids shape the eukaryotic cell cycle? Biochim Biophys Acta. 2017 Sep 27;: Authors: Furse S, Shearman GC Abstract Successful passage through the cell cycle presents a number of structural challenges to the cell. Inceptive studies carried out in the last five years have produced clear evidence of modulations in the lipid profile (lipidome) of eukaryotes as a function of the cell cycle. This mounting body of evidence indicates that lipids play key roles in the structural transformations seen across this most fundamental of biological processes. The accumulation of this evidence coincides with a revolution in our understanding of how lipid composition regulates a plethora of biological processes ranging from protein activity through to cellular signaling and membrane compartmentalisation. In this review, we discuss evidence from biological, chemical and physical studies of the lipid fraction across the cell cycle that demonstrate that lipids are well-developed cellular components at the heart of the biological machinery responsible for managing progress through the cell cycle. Furthermore, we discuss the mechanisms by which this careful control is exercised. PMID: 28964796 [PubMed - as supplied by publisher]

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow. Cell Syst. 2017 Sep 26;: Authors: Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U, Ralser M, Patil KR Abstract Many microorganisms live in communities and depend on metabolites secreted by fellow community members for survival. Yet our knowledge of interspecies metabolic dependencies is limited to few communities with small number of exchanged metabolites, and even less is known about cellular regulation facilitating metabolic exchange. Here we show how yeast enables growth of lactic acid bacteria through endogenous, multi-component, cross-feeding in a readily established community. In nitrogen-rich environments, Saccharomyces cerevisiae adjusts its metabolism by secreting a pool of metabolites, especially amino acids, and thereby enables survival of Lactobacillus plantarum and Lactococcus lactis. Quantity of the available nitrogen sources and the status of nitrogen catabolite repression pathways jointly modulate this niche creation. We demonstrate how nitrogen overflow by yeast benefits L. plantarum in grape juice, and contributes to emergence of mutualism with L. lactis in a medium with lactose. Our results illustrate how metabolic decisions of an individual species can benefit others. PMID: 28964698 [PubMed - as supplied by publisher]

Comprehensive lipid and metabolite profiling of children with and without familial hypercholesterolemia: A cross-sectional study. Atherosclerosis. 2017 Sep 21;266:48-57 Authors: Christensen JJ, Ulven SM, Retterstøl K, Narverud I, Bogsrud MP, Henriksen T, Bollerslev J, Halvorsen B, Aukrust P, Holven KB Abstract BACKGROUND AND AIMS: Individuals with familial hypercholesterolemia (FH) have elevated low-density lipoprotein cholesterol (LDL-C), accelerated atherosclerosis, and premature cardiovascular disease. Whereas children with lifestyle-induced dyslipidemias often present with complex lipid abnormalities, children with FH have isolated hypercholesterolemia. However, to the best of our knowledge, a comprehensive profiling of FH children is lacking. Therefore, we aimed to characterize the lipid-related and metabolic alterations associated with elevated LDL-C in children with FH and healthy children. METHODS: We measured plasma metabolites in children with FH (n = 47) and in healthy children (n = 57) using a high-throughput nuclear magnetic resonance (NMR) spectroscopy platform, and compared the differences between FH and healthy children. RESULTS: Both statin treated (n = 17) and non-statin treated FH children (n = 30) had higher levels of atherogenic ApoB-containing lipoproteins and lipids, and lipid fractions in lipoprotein subclasses, compared to healthy children (n = 57). FH children displayed alterations in HDL particle concentration and lipid content, compared with healthy children. Interestingly, the small HDL particles were characterized by higher content of cholesteryl esters, and lower levels of free cholesterol and phospholipids. Furthermore, plasma fatty acids were higher in non-statin treated FH children, particularly linoleic acid. Finally, acetoacetate and acetate were lower in FH children compared with healthy children. CONCLUSIONS: Hypercholesterolemia in children associates with diverse metabolic repercussions and is more complex than previously believed. In particular, we found that hypercholesterolemia in FH children was paralleled not only by increased atherogenic ApoB-containing lipoproteins and lipid fractions, but also alterations in HDL subfractions that suggest impaired reverse cholesterol transport. PMID: 28963918 [PubMed - as supplied by publisher]

Development of an LC-MS/MS method with protein G purification strategy for quantifying bevacizumab in human plasma. Anal Bioanal Chem. 2017 Sep 29;: Authors: Chiu HH, Tsai IL, Lu YS, Lin CH, Kuo CH Abstract Biopharmaceutical products such as protein drugs and monoclonal antibodies (mAb) are currently of great interest with monoclonal antibody drugs being one of the fastest growing categories of biopharmaceutical products. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has gained high interest for measuring mAb drugs in biological samples in recent years due to its high selectivity. Bevacizumab is a humanized immunoglobulin G (IgG) mAb drug against human vascular endothelial cell growth factor A (VEGF-A). It is used for treating many types of cancers. Recent studies have indicated that clinical outcomes vary among patients treated with bevacizumab and produce various side effects, such as vascular disorders. In this study, we developed an LC-MS/MS method to quantify bevacizumab concentration. We selected readily available and economic materials for sample preparation to facilitate its wider use in clinical fields.-Protein G was used to trap bevacizumab from human plasma. In place of an extended stable isotope-labeled internal standard (SIL-IS), the IgG-based drug-IS tocilizumab was used because of its better calibration performance. The method was validated in terms of its precision, accuracy, linearity, and sensitivity. The accuracies which were expressed as percentage recoveries for three concentration levels were within 92.8 ± 3.2 to 112.7 ± 4.5%. Repeatability and intermediate precision in terms of peak area ratios were lower than 5.2 and 12.9% RSD, respectively. The application to patients' sample measurements revealed a wide individual variability of drug concentrations, and the proposed simple and general method may facilitate personalized medicine for improving therapeutic efficacy and safety. Graphical abstract ᅟ. PMID: 28963670 [PubMed - as supplied by publisher]

Herbicide glufosinate inhibits yeast growth and extends longevity during wine fermentation. Sci Rep. 2017 Sep 29;7(1):12414 Authors: Vallejo B, Picazo C, Orozco H, Matallana E, Aranda A Abstract Glufosinate ammonium (GA) is a widely used herbicide that inhibits glutamine synthetase. This inhibition leads to internal amino acid starvation which, in turn, causes the activation of different nutrient sensing pathways. GA also inhibits the enzyme of the yeast Saccharomyces cerevisiae in such a way that, although it is not used as a fungicide, it may alter yeast performance in industrial processes like winemaking. We describe herein how GA indeed inhibits the yeast growth of a wine strain during the fermentation of grape juice. In turn, GA extends longevity in a variety of growth media. The biochemical analysis indicates that GA partially inhibits the nutrient sensing TORC1 pathway, which may explain these phenotypes. The GCN2 kinase mutant is hypersensitive to GA. Hence the control of translation and amino acid biosynthesis is required to also deal with the damaging effects of this pesticide. A global metabolomics analysis under winemaking conditions indicated that an increase in amino acid and in polyamines occurred. In conclusion, GA affects many different biochemical processes during winemaking, which provides us with some insights into both the effect of this herbicide on yeast physiology and into the relevance of the metabolic step for connecting nitrogen and carbon metabolism. PMID: 28963559 [PubMed - in process]

Effect of light-load resistance exercise on postprandial amino acid transporter expression in elderly men. Physiol Rep. 2017 Sep;5(18): Authors: Agergaard J, Bülow J, Jensen JK, Reitelseder S, Bornø A, Drummond MJ, Schjerling P, Holm L Abstract An impaired amino acid sensing is associated with age-related loss of skeletal muscle mass. We tested whether light-load resistance exercise (LL-RE) affects postprandial amino acid transporter (AAT) expression in aging skeletal muscle. Untrained, healthy men (age: +65 years) were subjected to 13 h of supine rest. After 2 1/2 h of rest, unilateral LL-RE was conducted (leg extensions, 10 sets of 36 repetitions) at 16% 1RM Thereafter, the subjects were randomized into groups that orally ingested 40 g of whey protein either as hourly drinks (4 g per drink) (PULSE, N = 10) or two boluses (28 g at 0 h and 12 g at 7 h) (BOLUS, N = 10), or hourly isocaloric maltodextrin drinks (placebo, N = 10). Quadriceps muscle biopsies were taken at 0, 3, 7, and 10 h postexercise from both the resting and exercised leg, from which the membrane protein and mRNA expression of select AATs were analyzed by Western Blot and RT-PCR, respectively. LAT1 and PAT1 protein expression increased in response to LL-RE in the PULSE group, and SNAT2 and PAT1 protein expression increased in the BOLUS group when plasma BCAA concentration was low. In all three groups, LL-RE increased LAT1 mRNA expression, whereas a time course decrease in SNAT2 mRNA expression was observed. LL-RE increased membrane-associated AAT protein expression and mRNA expression. Altered AAT protein expression was only seen in groups that ingested whey protein, with the greatest effect observed after hourly feeding. This points toward an importance of AATs in the anabolic response following LL-RE and protein intake. PMID: 28963124 [PubMed - in process]

Comprehensive Metabolomic Profiling and Incident Cardiovascular Disease: A Systematic Review. J Am Heart Assoc. 2017 Sep 28;6(10): Authors: Ruiz-Canela M, Hruby A, Clish CB, Liang L, Martínez-González MA, Hu FB Abstract BACKGROUND: Metabolomics is a promising tool of cardiovascular biomarker discovery. We systematically reviewed the literature on comprehensive metabolomic profiling in association with incident cardiovascular disease (CVD). METHODS AND RESULTS: We searched MEDLINE and EMBASE from inception to January 2016. Studies were eligible if they pertained to adult humans; followed an agnostic and/or comprehensive approach; used serum or plasma (not urine or other biospecimens); conducted metabolite profiling at baseline in the context of examining prospective disease; and included myocardial infarction, stroke, and/or CVD death in the CVD outcome definition. We identified 12 original articles (9 cohort and 3 nested case-control studies); participant numbers ranged from 67 to 7256. Mass spectrometry was the predominant analytical method. The number and chemical diversity of metabolites were very heterogeneous, ranging from 31 to >10 000 features. Four studies used untargeted profiling. Different types of metabolites were associated with CVD risk: acylcarnitines, dicarboxylacylcarnitines, and several amino acids and lipid classes. Only tiny improvements in CVD prediction beyond traditional risk factors were observed using these metabolites (C index improvement ranged from 0.006 to 0.05). CONCLUSIONS: There are a limited number of longitudinal studies assessing associations between comprehensive metabolomic profiles and CVD risk. Quantitatively synthesizing the literature is challenging because of the widely varying analytical tools and the diversity of methodological and statistical approaches. Although some results are promising, more research is needed, notably standardization of metabolomic techniques and statistical approaches. Replication and combinations of novel and holistic methodological approaches would move the field toward the realization of its promise. PMID: 28963102 [PubMed - in process]

The Art of Measuring Steroids: Principles and Practice of Current Hormonal Steroid Analysis. J Steroid Biochem Mol Biol. 2017 Sep 26;: Authors: Wudy SA, Schuler G, Sánchez-Guijo A, Hartmann MF Abstract Steroids are small and highly important structural or signalling molecules in living organisms and their metabolism is complex. Due to the multiplicity of enzymes involved there are many different steroid related disorders. E.g., an individual enzyme defect is rather rare but can share various clinical symptoms and can thus be hardly diagnosed clinically. Therefore, reliable hormonal determination still presents the most reasonable initial diagnostic approach and helps to avoid uncritical and expensive attempts at molecular diagnostic testing. It also presents a backbone of monitoring these complex patients. In science, reliable hormone measurement is indispensable for the elucidation of new mechanisms of steroid hormone actions. Steroid analytics is highly challenging and should never be considered trivial. Most common methods for steroid determination comprise traditionally immunoassay, or more recently, mass spectrometry based methods. It is absolutely necessary that clinicians and scientists know the methods they are applying by heart. With the introduction of automated direct assays, a loss of quality could be observed over the last two decades in the field of steroid immunoassays. This review wants to meet the need for profound information and orientation in the field of steroid analysis. The pros and cons of the most important methods, such as immunoassays and mass spectrometry based methods will be discussed. The focus of the latter will lie on gas chromatography-mass spectrometry (GC-MS) as well as liquid chromatography-mass spectrometry (LC-MS). Selected analytical applications from our Deutsche Forschungsgemeinschaft Research Group FOR 1369 "Sulfated Steroids in Reproduction" will illustrate the contents. In brief, immunoassays have for long presented the traditional technique for steroid analysis. They are easy to set up. Only one analyte can be measured per immunoassay. Specificity problems can arise and caution has to be exerted especially regarding direct assays lacking purification steps. Mass spectrometry based methods provide structural information on the analyte and thus higher specificity. In combination with chromatographic techniques, they permit the simultaneous determination of a multitude of analytes. Highest specificity can be obtained using GC-MS, a sophisticated but most powerful tool for characterizing steroid metabolomes. LC-MS is a true high throughput technique and highly suited for detecting complex steroids. GC-MS and LC-MS are not competing but complementary techniques. Since reliable steroid determination requires extremely high expertise in the field of analytics as well as steroid biochemistry, it is recommended that collaborations and networking with highly specialized centers of expertise are developed. PMID: 28962971 [PubMed - as supplied by publisher]

Hexokinases link DJ-1 to the PINK1/parkin pathway. Mol Neurodegener. 2017 Sep 29;12(1):70 Authors: Hauser DN, Mamais A, Conti MM, Primiani CT, Kumaran R, Dillman AA, Langston RG, Beilina A, Garcia JH, Diaz-Ruiz A, Bernier M, Fiesel FC, Hou X, Springer W, Li Y, de Cabo R, Cookson MR Abstract BACKGROUND: Early onset Parkinson's disease is caused by variants in PINK1, parkin, and DJ-1. PINK1 and parkin operate in pathways that preserve mitochondrial integrity, but the function of DJ-1 and how it relates to PINK1 and parkin is poorly understood. METHODS: A series of unbiased high-content screens were used to analyze changes at the protein, RNA, and metabolite level in rodent brains lacking DJ-1. Results were validated using targeted approaches, and cellular assays were performed to probe the mechanisms involved. RESULTS: We find that in both rat and mouse brains, DJ-1 knockout results in an age-dependent accumulation of hexokinase 1 in the cytosol, away from its usual location at the mitochondria, with subsequent activation of the polyol pathway of glucose metabolism in vivo. Both in the brain and in cultured cells, DJ-1 deficiency is associated with accumulation of the phosphatase PTEN that antagonizes the kinase AKT. In cells, addition of an inhibitor of AKT (MK2206) or addition of a peptide to dissociate association of hexokinases from mitochondria both inhibit the PINK1/parkin pathway, which works to maintain mitochondrial integrity. CONCLUSION: Hexokinases are an important link between three major genetic causes of early onset Parkinson's disease. Because aging is associated with deregulated nutrient sensing, these results help explain why DJ-1 is associated with age-dependent disease. PMID: 28962651 [PubMed - in process]

From the Cover: Metabolism Modulation in Different Organs by Silver Nanoparticles: An NMR Metabolomics Study of a Mouse Model. Toxicol Sci. 2017 Oct 01;159(2):422-435 Authors: Jarak I, Carrola J, Barros AS, Gil AM, Pereira ML, Corvo ML, Duarte IF Abstract Although silver nanoparticles (AgNPs) are widely disseminated and show great potential in the biomedical field, there is a recognized need to better understand their action at the metabolic and functional levels. In this work, we have used NMR metabolomics, together with conventional clinical chemistry and histological examination, to characterize multi-organ and systemic metabolic responses to AgNPs intravenously administered to mice at 8 mg/kg body weight (a dose not eliciting overt toxicity). The major target organs of AgNPs accumulation, liver and spleen, showed the greatest metabolic changes, in a clear 2-stage response. In particular, the liver of dosed mice was found to switch from glycogenolysis and lipid storage, at 6 h postinjection, to glycogenesis and lipolysis, at subsequent times up to 48 h. Moreover, metabolites related to antioxidative defense, immunoregulation and detoxification seemed to play a crucial role in avoiding major hepatic damage. The spleen showed several early changes, including depletion of several amino acids, possibly reflecting impairment of hemoglobin recycling, while only a few differences remained at 48 h postinjection. In the heart, the metabolic shift towards TCA cycle intensification and increased ATP production possibly reflected a beneficial adaptation to the presence of AgNPs. On the other hand, the TCA cycle appeared to be down regulated in the lungs of injected mice, which showed signs of inflammation. Thekidneys showed the mildest metabolic response to AgNPs. Overall, this study has shown that NMR metabolomics is a powerful tool to monitor invivo metabolic responses to nanoparticles, revealing unforeseen effects. PMID: 28962526 [PubMed - in process]

Sucrose and Starch Content Negatively Correlates with PSII Maximum Quantum Efficiency in Tomato (Solanum lycopersicum) Exposed to Abnormal Light/Dark Cycles and Continuous Light. Plant Cell Physiol. 2017 Aug 01;58(8):1339-1349 Authors: Velez-Ramirez AI, Carreño-Quintero N, Vreugdenhil D, Millenaar FF, van Ieperen W Abstract Light is most important to plants as it fuels photosynthesis and provides clues about the environment. If provided in unnatural long photoperiods, however, it can be harmful and even lethal. Tomato (Solanum lycopersicum), for example, develops mottled chlorosis and necrosis when exposed to continuous light. Understanding the mechanism of these injuries is valuable, as important pathways regulating photosynthesis, such as circadian, retrograde and light signaling pathways are probably involved. Here, we use non-targeted metabolomics and transcriptomics analysis as well as hypothesis-driven experiments with continuous light-tolerant and -sensitive tomato lines to explore the long-standing proposed role of carbohydrate accumulation in this disorder. Analysis of metabolomics and transcriptomics data reveals a clear effect of continuous light on sugar metabolism and photosynthesis. A strong negative correlation between sucrose and starch content with the severity of continuous light-induced damage quantified as the maximum quantum efficiency of PSII (Fv/Fm) was found across several abnormal light/dark cycles, supporting the hypothesis that carbohydrates play an important role in the continuous light-induced injury. We postulate that the continuous light-induced injury in tomato is caused by down-regulation of photosynthesis, showing characteristics of both cytokinin-regulated senescence and light-modulated retrograde signaling. Molecular mechanisms linking carbohydrate accumulation with down-regulation of carbon-fixing enzymes are discussed. PMID: 28961989 [PubMed - in process]

PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics. 2017 Aug 14;: Authors: Gloaguen Y, Morton F, Daly R, Gurden R, Rogers S, Wandy J, Wilson D, Barrett M, Burgess K Abstract Summary: The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of the experiment along with associated metadata; and the Metabolite Page, which provides a list of each metabolite accompanied by 'evidence cards', which provide a variety of criteria behind metabolite annotation including peak shapes, intensities in different sample groups and database information. Availability: PiMP is available at http://polyomics.mvls.gla.ac.uk , and access is freely available on request. 50 GB of space is allocated for data storage, with unrestricted number of samples and analyses per user. Source code is available at https://github.com/RonanDaly/pimp and licensed under the GPL. Contact: karl.burgess@glasgow.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online. PMID: 28961954 [PubMed - as supplied by publisher]

A large-scale, multi-center serum metabolite biomarkers identification study for the early detection of hepatocellular carcinoma. Hepatology. 2017 Sep 28;: Authors: Luo P, Yin P, Hua R, Tan Y, Li Z, Qiu G, Yin Z, Xie X, Wang X, Chen W, Zhou L, Wang X, Li Y, Chen H, Gao L, Lu X, Wu T, Wang H, Niu J, Xu G Abstract Hepatocellular carcinoma (HCC) is the third most lethal cancer worldwide. The lack of effective biomarkers for the early detection of HCC results in unsatisfactory curative treatments. Here, metabolite biomarkers were identified and validated for HCC diagnosis. A total of 1448 subjects, mainly including normal controls and patients with chronic hepatitis B virus infection, liver cirrhosis, and HCC were recruited from multi-center in China. Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics methods were used to characterize the subjects' serum metabolic profiles and to screen and validate the HCC biomarkers. A serum metabolite biomarker panel including phenylalanyl-tryptophan and glycocholate, was defined. This panel had a higher diagnostic performance than did α-fetoprotein (AFP) in differentiating HCC from a high-risk population of cirrhosis, such as area under the receiver-operating characteristic curve (AUC) of 0.930, 0.892, 0.807 for panel versus 0.657, 0.725, 0.650 for AFP in the discovery, test and cohort 1 of the validation set, respectively. In the nested case-control study, this panel had high sensitivity (rang 80.0-70.3%) to detect preclinical HCC, and its combination with AFP provided better risk prediction of preclinical HCC before clinical diagnosis. Besides, this panel showed a larger AUC than did AFP (0.866 versus 0.682) to distinguish small-HCC, and 80.6% of the AFP false-negative patients with HCC were correctly diagnosed using this panel in the test set, which was corroborated by the validation set. The specificity and biological relevance of the identified biomarkers were further evaluated using sera from other two cancers and HCC tissue specimens, respectively. CONCLUSIONS: The discovered and validated serum metabolite biomarker panel exhibits good diagnostic performance for the early detection of HCC from at-risk populations. This article is protected by copyright. All rights reserved. PMID: 28960374 [PubMed - as supplied by publisher]

Related Articles [Action mechanism of Mahuang Xixin Fuzi decoction for mice with influenza based on metabolomics information]. Zhongguo Zhong Yao Za Zhi. 2017 Feb;42(4):763-771 Authors: Sun QH, Zhang J, Li ZZ, Du BX, Jiang HQ, Yang Y, Lv QT, Rong R Abstract This study aimed to analyze the endogenous metabolite changes in the serum of mice infected with H1N1 virus after intervention by Mahuang-Xixin-Fuzi decoction (MXF) based on metabolomics method, investigate potential biomarkers and related metabolic pathways, and explore the therapeutic mechanism of MXF through metabolomics technology. Thirty-six Kunming (KM) mice were randomly divided into three groups: normal group, model group and MXF group. Influenza virus H1N1 was used by nasal drip to establish influenza mice model. The mice in MXF group were orally administrated with MXF for 6 consecutive days after inoculation, and the other two groups were given with equal volume of saline solution in the same way. Body weight, rectal temperature, morbidity and mortality were recorded daily. Serum samples were collected 24 hours after the last administration for HPLC-TOF-MS analysis. The results showed that as compared with the normal group, the body weight and rectal temperature were decreased in model group, and their lung index and mortality rate were significantly increased (P<0.05); MXF had good therapeutic effects on the abnormity of body weight, rectal temperature, lung index and high mortality rate of mice infected with H1N1 virus. The original data collected from the serum samples were analyzed with R language, MPP, SIMCA-P and other software, and significant changes were found in 14 kinds of endogenous substances from mice serum (P<0.05). As compared with model group, the potential metabolic markers in MXF group recovered to normal levels to a certain degree after being intervened by MXF. Further analysis with MetPA data platform showed that, the pathways involved in 14 metabolites included glucose metabolism, arachidonic acid metabolism, glycerophospholipids and sphingolipids metabolism etc. The metabolomics study and pharmacological experiment showed that MXF might play a role of efficacy by improving glucose metabolism, regulating arachidonic acid metabolism, glycerophospholipid and sphingolipid metabolic pathways. PMID: 28959850 [PubMed - in process]

Related Articles Differential cellular metabolite alterations in HaCaT cells caused by exposure to the aryl hydrocarbon receptor-binding polycyclic aromatic hydrocarbons chrysene, benzo[a]pyrene and dibenzo[a,l]pyrene. Toxicol Rep. 2016;3:763-773 Authors: Potratz S, Jungnickel H, Grabiger S, Tarnow P, Otto W, Fritsche E, von Bergen M, Luch A Abstract Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the human environment. Since they are present in crude oilfractions used for the production of rubber and plastics, consumers may come into direct dermal contacts with these compounds (e.g., via tool handles) on a daily basis. Some individual PAHs are identified as genotoxic mutagens thereby prompting particular toxicological and environmental concern. Among this group, benzo[a]pyrene (BAP) constitutes a model carcinogen which is also used as reference compound for risk assessment purposes. It acts as a strong agonist of the aryl hydrocarbon receptor (AHR) and becomes metabolically activated toward mutagenic and carcinogenic intermediates by cytochrome P450-dependent monooxygenases (CYPs). While BAP has been exhaustively characterized with regard to its toxicological properties, there is much less information available for other PAHs. We treated an AHR-proficient immortal human keratinocyte cell line (i.e., HaCaT) with three selected PAHs: BAP, chrysene (CRY) and dibenzo[a,l]pyrene (DALP). Compound-mediated alterations of endogenous metabolites were investigated by an LC-MS/MS-based targeted approach. To examine AHR-dependent changes of the measured metabolites, AHR-deficient HaCaT knockdown cells (AHR-KD) were used for comparison. Our results reveal that 24 metabolites are sufficient to separate the PAH-exposed cells from untreated controls by application of a multivariate model. Alterations in the metabolomics profiles caused by each PAH show influences on the energy and lipid metabolism of the cells indicating reduced tricarboxylic acid (TCA) cycle activity and β-oxidation. Up-regulation of sphingomyelin levels after exposure to BAP and DALP point to pro-apoptotic processes caused by these two potent PAHs. Our results suggest that in vitro metabolomics can serve as tool to develop bioassays for application in hazard assessment. PMID: 28959603 [PubMed]