151
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Bourdon AK, Spano GM, Marshall W, Bellesi M, Tononi G, Serra PA, Baghdoyan HA, Lydic R, Campagna SR, Cirelli C. Metabolomic analysis of mouse prefrontal cortex reveals upregulated analytes during wakefulness compared to sleep. Sci Rep 2018; 8:11225. [PMID: 30046159 PMCID: PMC6060152 DOI: 10.1038/s41598-018-29511-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
By identifying endogenous molecules in brain extracellular fluid metabolomics can provide insight into the regulatory mechanisms and functions of sleep. Here we studied how the cortical metabolome changes during sleep, sleep deprivation and spontaneous wakefulness. Mice were implanted with electrodes for chronic sleep/wake recording and with microdialysis probes targeting prefrontal and primary motor cortex. Metabolites were measured using ultra performance liquid chromatography-high resolution mass spectrometry. Sleep/wake changes in metabolites were evaluated using partial least squares discriminant analysis, linear mixed effects model analysis of variance, and machine-learning algorithms. More than 30 known metabolites were reliably detected in most samples. When used by a logistic regression classifier, the profile of these metabolites across sleep, spontaneous wake, and enforced wake was sufficient to assign mice to their correct experimental group (pair-wise) in 80-100% of cases. Eleven of these metabolites showed significantly higher levels in awake than in sleeping mice. Some changes extend previous findings (glutamate, homovanillic acid, lactate, pyruvate, tryptophan, uridine), while others are novel (D-gluconate, N-acetyl-beta-alanine, N-acetylglutamine, orotate, succinate/methylmalonate). The upregulation of the de novo pyrimidine pathway, gluconate shunt and aerobic glycolysis may reflect a wake-dependent need to promote the synthesis of many essential components, from nucleic acids to synaptic membranes.
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Affiliation(s)
- Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Giovanna Maria Spano
- Department of Psychiatry, University of Wisconsin, Madison, Madison, WI, United States
| | - William Marshall
- Department of Psychiatry, University of Wisconsin, Madison, Madison, WI, United States
| | - Michele Bellesi
- Department of Psychiatry, University of Wisconsin, Madison, Madison, WI, United States.,Department of Experimental and Clinical Medicine, Section of Neuroscience and Cell Biology, Università Politecnica delle Marche, Ancona, Italy
| | - Giulio Tononi
- Department of Psychiatry, University of Wisconsin, Madison, Madison, WI, United States
| | - Pier Andrea Serra
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Helen A Baghdoyan
- Department of Anesthesiology and Psychology, University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ralph Lydic
- Department of Anesthesiology and Psychology, University of Tennessee, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States. .,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN, United States.
| | - Chiara Cirelli
- Department of Psychiatry, University of Wisconsin, Madison, Madison, WI, United States.
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152
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Hsiao JJ, Potter OG, Chu TW, Yin H. Improved LC/MS Methods for the Analysis of Metal-Sensitive Analytes Using Medronic Acid as a Mobile Phase Additive. Anal Chem 2018; 90:9457-9464. [PMID: 29976062 DOI: 10.1021/acs.analchem.8b02100] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Phosphorylated compounds and organic acids with multiple carboxylate groups are commonly observed to have poor peak shapes and signal in LC/MS experiments. The poor peak shape is caused by the presence of trace metals, particularly iron, contributed from a variety of sources within the chromatographic system. To ameliorate this problem, different solvent additives were investigated to reduce the amount of metal in the flow path to achieve better analytical performance for these metal-sensitive compounds. Here, we introduce the use of a solvent additive that can significantly improve the peak shapes and signal of metal-sensitive metabolites for LC/MS analysis. Moreover, the additive is shown to be amenable for other metal-sensitive applications, such as the analysis of phosphopeptides and polar phosphorylated pesticides, where the instruments could be used in either positive or negative analysis mode.
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Affiliation(s)
- Jordy J Hsiao
- Agilent Technologies, Santa Clara , California 95051 , United States
| | - Oscar G Potter
- Agilent Technologies, Santa Clara , California 95051 , United States
| | - Te-Wei Chu
- Agilent Technologies, Santa Clara , California 95051 , United States
| | - Hongfeng Yin
- Agilent Technologies, Santa Clara , California 95051 , United States
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153
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Xie B, Wang Y, Jones DR, Dey KK, Wang X, Li Y, Cho JH, Shaw TI, Tan H, Peng J. Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. Anal Chem 2018; 90:8538-8545. [PMID: 29883117 DOI: 10.1021/acs.analchem.8b01591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High throughput untargeted metabolomics usually relies on complementary liquid chromatography-mass spectrometry (LC-MS) methods to expand the coverage of diverse metabolites, but the integration of those methods is not fully characterized. We systematically investigated the performance of hydrophilic interaction liquid chromatography (HILIC)-MS and nanoflow reverse-phase liquid chromatography (nRPLC)-MS under 8 LC-MS settings, varying stationary phases (HILIC and C18), mobile phases (acidic and basic pH), and MS ionization modes (positive and negative). Whereas nRPLC-MS optimization was previously reported, we found in HILIC-MS (2.1 mm × 150 mm) that the optimal performance was achieved in a 90 min gradient with 100 μL/min flow rate by loading metabolite extracts from 2 mg of cell/tissue samples. Since peak features were highly compromised by contaminants, we used stable isotope labeled yeast to enhance formula identification for comparing different LC-MS conditions. The 8 LC-MS settings enabled the detection of a total of 1050 formulas, among which 78%, 73%, and 62% formulas were recovered by the best combination of 4, 3, and 2 LC-MS settings, respectively. Moreover, these yeast samples were harvested in the presence or absence of nitrogen starvation, enabling quantitative comparisons of altered formulas and metabolite structures, followed by validation with selected synthetic metabolites. The results revealed that nitrogen starvation downregulated amino acid components but upregulated uridine-related metabolism. In summary, this study introduces a thorough evaluation of hydrophilicity and hydrophobicity based LC-MS and provides information for selecting complementary settings to balance throughput and efficiency during metabolomics experiments.
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154
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Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A 2018; 115:E6301-E6309. [PMID: 29915065 DOI: 10.1073/pnas.1804218115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial persisters are subpopulations of phenotypic variants in isogenic cultures that can survive lethal doses of antibiotics. Their tolerances are often attributed to reduced activities of antibiotic targets, which limit corruption and damage in persisters compared with bacteria that die from treatment. However, that model does not hold for nongrowing populations treated with ofloxacin, a fluoroquinolone, where antibiotic-induced damage is comparable between cells that live and those that die. To understand how those persisters achieve this feat, we employed a genetic system that uses orthogonal control of MazF and MazE, a toxin and its cognate antitoxin, to generate model persisters that are uniformly tolerant to ofloxacin. Despite this complete tolerance, MazF model persisters required the same DNA repair machinery (RecA, RecB, and SOS induction) to survive ofloxacin treatment as their nongrowing, WT counterparts and exhibited similar indicators of DNA damage from treatment. Further investigation revealed that, following treatment, the timing of DNA repair was critical to MazF persister survival because, when repair was delayed until after growth and DNA synthesis resumed, survival was compromised. In addition, we found that, with nongrowing, WT planktonic and biofilm populations, stalling the resumption of growth and DNA synthesis after the conclusion of fluoroquinolone treatment with a prevalent type of stress at infection sites (nutrient limitation) led to near complete survival. These findings illustrate that the timing of events, such as DNA repair, following fluoroquinolone treatment is important to persister survival and provide further evidence that knowledge of the postantibiotic recovery period is critical to understanding persistence phenotypes.
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155
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Davila A, Liu L, Chellappa K, Redpath P, Nakamaru-Ogiso E, Paolella LM, Zhang Z, Migaud ME, Rabinowitz JD, Baur JA. Nicotinamide adenine dinucleotide is transported into mammalian mitochondria. eLife 2018; 7:33246. [PMID: 29893687 PMCID: PMC6013257 DOI: 10.7554/elife.33246] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/10/2018] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial NAD levels influence fuel selection, circadian rhythms, and cell survival under stress. It has alternately been argued that NAD in mammalian mitochondria arises from import of cytosolic nicotinamide (NAM), nicotinamide mononucleotide (NMN), or NAD itself. We provide evidence that murine and human mitochondria take up intact NAD. Isolated mitochondria preparations cannot make NAD from NAM, and while NAD is synthesized from NMN, it does not localize to the mitochondrial matrix or effectively support oxidative phosphorylation. Treating cells with nicotinamide riboside that is isotopically labeled on the nicotinamide and ribose moieties results in the appearance of doubly labeled NAD within mitochondria. Analogous experiments with doubly labeled nicotinic acid riboside (labeling cytosolic NAD without labeling NMN) demonstrate that NAD(H) is the imported species. Our results challenge the long-held view that the mitochondrial inner membrane is impermeable to pyridine nucleotides and suggest the existence of an unrecognized mammalian NAD (or NADH) transporter.
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Affiliation(s)
- Antonio Davila
- Department of Physiology, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,PARC, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ling Liu
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, United States
| | - Karthikeyani Chellappa
- Department of Physiology, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Philip Redpath
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Eiko Nakamaru-Ogiso
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Lauren M Paolella
- Department of Physiology, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Zhigang Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Marie E Migaud
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom.,Mitchell Cancer Institute, University of South Alabama, Mobile, United States
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, United States
| | - Joseph A Baur
- Department of Physiology, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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156
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Prebiotic effects of white button mushroom (Agaricus bisporus) feeding on succinate and intestinal gluconeogenesis in C57BL/6 mice. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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157
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Rubat S, Varas I, Sepúlveda R, Almonacid D, González-Nilo F, Agosin E. Increasing the intracellular isoprenoid pool in Saccharomyces cerevisiae by structural fine-tuning of a bifunctional farnesyl diphosphate synthase. FEMS Yeast Res 2018; 17:3869469. [PMID: 28854674 DOI: 10.1093/femsyr/fox032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/16/2017] [Indexed: 11/13/2022] Open
Abstract
Farnesyl diphosphate synthase (FPPS) is a key enzyme responsible for the supply of isoprenoid precursors for several essential metabolites, including sterols, dolichols and ubiquinone. In Saccharomyces cerevisiae, FPPS catalyzes the sequential condensation of two molecules of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP), producing geranyl diphosphate (GPP) and farnesyl diphosphate (FPP). Critical amino acid residues that determine product chain length were determined by a comparative study of strict GPP synthases versus strict FPPS. In silico ΔΔG, i.e. differential binding energy between a protein and two different ligands-of yeast FPPS mutants was evaluated, and F96, A99 and E165 residues were identified as key determinants for product selectivity. A99X variants were evaluated in vivo, S. cerevisiae strains carrying A99R and A99H variants showed significant differences on GPP concentrations and specific growth rates. The FPPS A99T variant produced unquantifiable amounts of FPP and no effect on GPP production was observed. Strains carrying A99Q, A99Y and A99K FPPS accumulated high amounts of DMAPP-IPP, with a decrease in GPP and FPP. Our results demonstrated the relevance of the first residue before FARM (First Aspartate Rich Motif) over substrate consumption and product specificity of S. cerevisiae FPPS in vivo. The presence of A99H significantly modified product selectivity and appeared to be relevant for GPP synthesis.
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Affiliation(s)
- Sebastián Rubat
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
| | - Ignacio Varas
- Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Republica 239, Santiago 8370146, Chile
| | - Romina Sepúlveda
- Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Republica 239, Santiago 8370146, Chile
| | - Daniel Almonacid
- Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Republica 239, Santiago 8370146, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Republica 239, Santiago 8370146, Chile
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
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158
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Campa MF, Techtmann SM, Gibson CM, Zhu X, Patterson M, Garcia de Matos Amaral A, Ulrich N, Campagna SR, Grant CJ, Lamendella R, Hazen TC. Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5989-5999. [PMID: 29683652 DOI: 10.1021/acs.est.8b00239] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.
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Affiliation(s)
- Maria Fernanda Campa
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Stephen M Techtmann
- Department of Biological Sciences , Michigan Technological University , Houghton , Michigan 49931 , United States
| | - Caleb M Gibson
- Department of Chemistry , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Xiaojuan Zhu
- Office of Information Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Megan Patterson
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | | | - Nikea Ulrich
- Department of Biology , Juniata College , Huntingdon , Pennsylvania 16652 , United States
| | - Shawn R Campagna
- Department of Chemistry , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Biological and Small Molecule Mass Spectrometry Core , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Christopher J Grant
- Department of Biology , Juniata College , Huntingdon , Pennsylvania 16652 , United States
| | - Regina Lamendella
- Department of Biology , Juniata College , Huntingdon , Pennsylvania 16652 , United States
| | - Terry C Hazen
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Department of Civil and Environmental Engineering , University of Tennessee , Knoxville , Tennessee 37996-1605 , United States
- Earth & Planetary Sciences , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
- Institute for a Secure and Sustainable Environment , Knoxville , Tennessee 37996 , United States
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159
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Simithy J, Sidoli S, Garcia BA. Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. Proteomics 2018. [PMID: 29512899 DOI: 10.1002/pmic.201700309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromatin fiber is the control panel of eukaryotic cells. Chromatin is mostly composed of DNA, which contains the genetic instruction for cell phenotype, and histone proteins, which provide the scaffold for chromatin folding and part of the epigenetic inheritance. Histone writers/erasers "flag" chromatin regions by catalyzing/removing covalent histone post-translational modifications (PTMs). Histone PTMs chemically contribute to chromatin relaxation or compaction and recruit histone readers to modulate DNA readout. The precursors of protein PTMs are mostly small metabolites. For instance, acetyl-CoA is used for acetylation, ATP for phosphorylation, and S-adenosylmethionine for methylation. Interestingly, PTMs such as acetylation can occur at neutral pH also without their respective enzyme when the precursor is sufficiently concentrated. Therefore, it is essential to differentially quantify the contribution of histone writers/erasers versus the effect of local concentration of metabolites to understand the primary regulation of histone PTM abundance. Aberrant phenotypes such as cancer cells have misregulated metabolism and thus the composition and the modulation of chromatin is not only driven by enzymatic tuning. In this review, the latest advances in mass spectrometry (MS) to analyze histone PTMs and the most adopted quantification methods for related metabolites, both necessary to understand PTM relative changes, are discussed.
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Affiliation(s)
- Johayra Simithy
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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160
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Kang YP, Ward NP, DeNicola GM. Recent advances in cancer metabolism: a technological perspective. Exp Mol Med 2018; 50:1-16. [PMID: 29657324 PMCID: PMC5938018 DOI: 10.1038/s12276-018-0027-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/12/2017] [Indexed: 01/28/2023] Open
Abstract
Cancer cells are highly dependent on metabolic pathways to sustain both their proliferation and adaption to harsh microenvironments. Thus, understanding the metabolic reprogramming that occurs in tumors can provide critical insights for the development of therapies targeting metabolism. In this review, we will discuss recent advancements in metabolomics and other multidisciplinary techniques that have led to the discovery of novel metabolic pathways and mechanisms in diverse cancer types. Researchers now have access to a rapidly growing number of tools for probing the metabolic abnormalities associated with tumor growth. Unrestrained growth puts special demands on cancer cells, and scientists have known for nearly a century that tumor metabolism differs considerably from healthy tissue metabolism. Gina DeNicola and colleagues at the Moffitt Cancer Center and Research Institute, Tampa, USA, have reviewed the technological tools available for monitoring the molecules that power cell growth and survival. These include mass spectrometry, which can generate an extremely detailed census of cellular metabolites in a single experiment. The authors also highlight techniques that can help ‘trap’ short-lived or unstable chemical intermediates for analysis. Other chemical labeling and tracing techniques can illuminate activity of selected metabolic processes in living tumor cells or even in patients, findings that could reveal therapeutic vulnerabilities.
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Affiliation(s)
- Yun Pyo Kang
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Nathan P Ward
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Gina M DeNicola
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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161
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Cope ER, Voy BH, Whitlock BK, Staton M, Lane T, Davitt J, Mulliniks JT. Beta-hydroxybutyrate infusion identifies acutely differentially expressed genes related to metabolism and reproduction in the hypothalamus and pituitary of castrated male sheep. Physiol Genomics 2018; 50:468-477. [PMID: 29625019 DOI: 10.1152/physiolgenomics.00104.2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To identify molecular pathways that couple metabolic imbalances and reproduction, we randomly assigned 10 castrated male sheep to be centrally injected into the lateral ventricle through intracerebroventricular cannulas with 1 ml of β-hydroxybutyric acid sodium salt solution (BHB; 12,800 µmol/l) or saline solution (CON; 0.9% NaCl). Approximately 2 h postinjection, sheep were humanely euthanized, and hypothalamus and pituitary tissues were harvested for transcriptome characterization by RNA sequencing. RNA was extracted from the hypothalamus and pituitary and sequenced at a high depth (hypothalamus: 468,912,732 reads; pituitary: 515,106,092 reads) with the Illumina Hi-Seq 2500 platform and aligned to Bos taurus and Ovis aries genomes. Of the total raw reads, 87% (hypothalamus) and 90.5% (pituitary) mapped to the reference O. aries genome. Within these read sets, ~56% in hypothalamus and 69% in pituitary mapped to either known or putative protein coding genes. Fragments per kilobase of transcripts per million normalized counts were averaged and ranked to identify the transcript expression level. Gene Ontology analysis (DAVID Bioinformatics Resources) was utilized to identify biological process functions related to genes shared between tissues, as well as functional categories with tissue-specific enrichment. Between CON- and BHB-treated sheep, 11 and 44 genes were differentially expressed (adj. P < 0.05) within the pituitary and hypothalamus, respectively. Functional enrichment analyses revealed BHB altered expression of genes in pathways related to stimulus perception, inflammation, and cell cycle control. The set of genes altered by BHB creates a foundation from which to identify the signaling pathways that impact reproduction during metabolic imbalances.
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Affiliation(s)
- Emily R Cope
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee
| | - Brynn H Voy
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee
| | - Brian K Whitlock
- Department of Large Animal Clinical Sciences, University of Tennessee , Knoxville, Tennessee
| | - Meg Staton
- Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, Tennessee
| | - Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, Tennessee
| | - Jack Davitt
- Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, Tennessee
| | - J Travis Mulliniks
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee
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162
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Peng G, Martin RM, Dearth SP, Sun X, Boyer GL, Campagna SR, Lin S, Wilhelm SW. Seasonally Relevant Cool Temperatures Interact with N Chemistry to Increase Microcystins Produced in Lab Cultures of Microcystis aeruginosa NIES-843. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018. [PMID: 29522323 DOI: 10.1021/acs.est.7b06532] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Freshwater cyanobacterial blooms are regularly formed by Microcystis spp., which are well-known producers of the hepatotoxin microcystin. The environmental factors that regulate microcystin synthesis remain unclear. We used reverse transcription-quantitative PCR (RT-qPCR), metabolomics, and toxin profiling (both by LC-MS) to measure the response of Microcystis aeruginosa NIES-843 to nitrogen (N) concentration, N chemistry (nitrate versus urea), and a range of seasonally relevant temperatures. Growth rates at lower temperatures were slower but resulted in increased cellular microcystin content (quota), and at these lower temperatures, N concentration had no effect on toxin production. In contrast, at warmer temperatures, reduction in N concentration increased toxin production, especially when urea was supplied as the nitrogen source. Our culture results demonstrate how temperature may lead to physiological responses ranging from slow growing yet very toxic cells at cool temperatures, to faster growing but less-toxic cells at warmer temperatures. This response represents a key interaction in bloom dynamics. Capturing this phenomenon as a temperature-driven toxin phenotype incorporated into models might improve the ability to predict microcystin biosynthesis during cyanobacterial blooms.
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Affiliation(s)
- Guotao Peng
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security , Tongji University , Shanghai 200092 , China
| | | | | | | | - Gregory L Boyer
- Department of Biochemistry , State University of New York , Syracuse , New York 13210 , United States
| | | | - Sijie Lin
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security , Tongji University , Shanghai 200092 , China
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163
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Bambouskova M, Gorvel L, Lampropoulou V, Sergushichev A, Loginicheva E, Johnson K, Korenfeld D, Mathyer ME, Kim H, Huang LH, Duncan D, Bregman H, Keskin A, Santeford A, Apte RS, Sehgal R, Johnson B, Amarasinghe GK, Soares MP, Satoh T, Akira S, Hai T, de Guzman Strong C, Auclair K, Roddy TP, Biller SA, Jovanovic M, Klechevsky E, Stewart KM, Randolph GJ, Artyomov MN. Electrophilic properties of itaconate and derivatives regulate the IκBζ-ATF3 inflammatory axis. Nature 2018; 556:501-504. [PMID: 29670287 PMCID: PMC6037913 DOI: 10.1038/s41586-018-0052-z] [Citation(s) in RCA: 429] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 03/16/2018] [Indexed: 01/03/2023]
Abstract
Metabolic regulation has been recognized as a powerful principle guiding immune responses. Inflammatory macrophages undergo extensive metabolic rewiring 1 marked by the production of substantial amounts of itaconate, which has recently been described as an immunoregulatory metabolite 2 . Itaconate and its membrane-permeable derivative dimethyl itaconate (DI) selectively inhibit a subset of cytokines 2 , including IL-6 and IL-12 but not TNF. The major effects of itaconate on cellular metabolism during macrophage activation have been attributed to the inhibition of succinate dehydrogenase2,3, yet this inhibition alone is not sufficient to account for the pronounced immunoregulatory effects observed in the case of DI. Furthermore, the regulatory pathway responsible for such selective effects of itaconate and DI on the inflammatory program has not been defined. Here we show that itaconate and DI induce electrophilic stress, react with glutathione and subsequently induce both Nrf2 (also known as NFE2L2)-dependent and -independent responses. We find that electrophilic stress can selectively regulate secondary, but not primary, transcriptional responses to toll-like receptor stimulation via inhibition of IκBζ protein induction. The regulation of IκBζ is independent of Nrf2, and we identify ATF3 as its key mediator. The inhibitory effect is conserved across species and cell types, and the in vivo administration of DI can ameliorate IL-17-IκBζ-driven skin pathology in a mouse model of psoriasis, highlighting the therapeutic potential of this regulatory pathway. Our results demonstrate that targeting the DI-IκBζ regulatory axis could be an important new strategy for the treatment of IL-17-IκBζ-mediated autoimmune diseases.
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Affiliation(s)
- Monika Bambouskova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Laurent Gorvel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vicky Lampropoulou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Ekaterina Loginicheva
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Daniel Korenfeld
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary Elizabeth Mathyer
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Li-Hao Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dustin Duncan
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | | | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Andrea Santeford
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Rajendra S Apte
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Britney Johnson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Takashi Satoh
- Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Shizuo Akira
- Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Tsonwin Hai
- Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA
| | - Cristina de Guzman Strong
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | | | | | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Eynav Klechevsky
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Gwendalyn J Randolph
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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164
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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165
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Miller RA, Shi Y, Lu W, Pirman DA, Jatkar A, Blatnik M, Wu H, Cárdenas C, Wan M, Foskett JK, Park JO, Zhang Y, Holland WL, Rabinowitz JD, Birnbaum MJ. Targeting hepatic glutaminase activity to ameliorate hyperglycemia. Nat Med 2018; 24:518-524. [PMID: 29578539 PMCID: PMC6089616 DOI: 10.1038/nm.4514] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 02/08/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Russell A Miller
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Pfizer Internal Medicine Research Units, Cambridge, Massachusetts, USA
| | - Yuji Shi
- Pfizer Internal Medicine Research Units, Cambridge, Massachusetts, USA
| | - Wenyun Lu
- Chemistry and Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - David A Pirman
- Pfizer Worldwide Research and Development, Groton, Connecticut, USA
| | - Aditi Jatkar
- Pfizer Internal Medicine Research Units, Cambridge, Massachusetts, USA
| | - Matthew Blatnik
- Pfizer Worldwide Research and Development, Groton, Connecticut, USA
| | - Hong Wu
- Pfizer Worldwide Research and Development, Groton, Connecticut, USA
| | - César Cárdenas
- Anatomy and Developmental Biology Program, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,Geroscience Center for Brain Health and Metabolism, Santiago, Chile.,Buck Institute for Research on Aging, Novato, California, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Min Wan
- Pfizer Internal Medicine Research Units, Cambridge, Massachusetts, USA
| | - J Kevin Foskett
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junyoung O Park
- Chemistry and Integrative Genomics, Princeton University, Princeton, New Jersey, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Yiyi Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William L Holland
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joshua D Rabinowitz
- Chemistry and Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Morris J Birnbaum
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Pfizer Internal Medicine Research Units, Cambridge, Massachusetts, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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166
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Schatschneider S, Abdelrazig S, Safo L, Henstra AM, Millat T, Kim DH, Winzer K, Minton NP, Barrett DA. Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in Clostridium autoethanogenum with Uniformly 13C-Labeled Standards Derived from Spirulina. Anal Chem 2018. [PMID: 29533656 DOI: 10.1021/acs.analchem.7b04758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have investigated the applicability of commercially available lyophilized spirulina ( Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze-thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves ( R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood-Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation.
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Affiliation(s)
- Sarah Schatschneider
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Laudina Safo
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anne M Henstra
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Thomas Millat
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Klaus Winzer
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Nigel P Minton
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
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167
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Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FDO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R, Müller-Santos M. PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Front Microbiol 2018; 9:472. [PMID: 29599762 PMCID: PMC5862806 DOI: 10.3389/fmicb.2018.00472] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.
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Affiliation(s)
- Marcelo B Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Cícero S Teixeira
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z T Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luis P S Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Glaucio Valdameri
- Department of Clinical Analysis, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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168
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Abstract
Anesthetic mechanisms that eliminate consciousness and perception of pain are products of the nervous system. Chemical approaches to the study of anesthetic mechanisms have the potential to serve as an ideal interface between basic and clinical neuroscience. There are disproportionately more basic neurochemical studies than clinical studies of anesthetic mechanisms. Even within neuroscience, the study of anesthetic mechanisms is sparse. The Society for Neuroscience hosts one of the world's largest and most vibrant scientific meetings, yet the content themes of that meeting do not include anesthesia. One goal of this chapter is to facilitate neurochemical studies of anesthetic mechanisms by outlining user-friendly descriptions of existing and emerging techniques. The introduction provides a context for chapter goals. The second portion of this chapter focuses on microdialysis methods that enable the humane acquisition of neurochemical samples from intact, behaving animals during anesthetic induction, maintenance, and emergence. No single neurotransmitter and no single brain region regulate the physiological and behavioral traits characteristic of any anesthetic state. This limitation is being addressed via application of new instrumentation and techniques in analytic chemistry. The final third of this chapter highlights selected omics approaches that are now being applied to the neurochemical study of anesthetic mechanisms. We hope that this brief chapter can stimulate basic and clinical metabolomic approaches aiming to elucidate the mechanisms of anesthetic action.
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Affiliation(s)
- Ralph Lydic
- University of Tennessee, Knoxville, TN, United States; Oak Ridge National Laboratory, Oak Ridge, TN, United States.
| | - Helen A Baghdoyan
- University of Tennessee, Knoxville, TN, United States; Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Amanda L May
- University of Tennessee, Knoxville, TN, United States
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169
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Zha H, Cai Y, Yin Y, Wang Z, Li K, Zhu ZJ. SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery. Anal Chem 2018; 90:4062-4070. [PMID: 29485856 DOI: 10.1021/acs.analchem.7b05318] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The complexity of metabolome presents a great analytical challenge for quantitative metabolite profiling, and restricts the application of metabolomics in biomarker discovery. Targeted metabolomics using multiple-reaction monitoring (MRM) technique has excellent capability for quantitative analysis, but suffers from the limited metabolite coverage. To address this challenge, we developed a new strategy, namely, SWATHtoMRM, which utilizes the broad coverage of SWATH-MS technology to develop high-coverage targeted metabolomics method. Specifically, SWATH-MS technique was first utilized to untargeted profile one pooled biological sample and to acquire the MS2 spectra for all metabolites. Then, SWATHtoMRM was used to extract the large-scale MRM transitions for targeted analysis with coverage as high as 1000-2000 metabolites. Then, we demonstrated the advantages of SWATHtoMRM method in quantitative analysis such as coverage, reproducibility, sensitivity, and dynamic range. Finally, we applied our SWATHtoMRM approach to discover potential metabolite biomarkers for colorectal cancer (CRC) diagnosis. A high-coverage targeted metabolomics method with 1303 metabolites in one injection was developed to profile colorectal cancer tissues from CRC patients. A total of 20 potential metabolite biomarkers were discovered and validated for CRC diagnosis. In plasma samples from CRC patients, 17 out of 20 potential biomarkers were further validated to be associated with tumor resection, which may have a great potential in assessing the prognosis of CRC patients after tumor resection. Together, the SWATHtoMRM strategy provides a new way to develop high-coverage targeted metabolomics method, and facilitates the application of targeted metabolomics in disease biomarker discovery. The SWATHtoMRM program is freely available on the Internet ( http://www.zhulab.cn/software.php ).
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Affiliation(s)
- Haihong Zha
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai , 200032 People's Republic of China.,University of Chinese Academy of Sciences , Beijing , 100049 People's Republic of China
| | - Yuping Cai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai , 200032 People's Republic of China.,University of Chinese Academy of Sciences , Beijing , 100049 People's Republic of China
| | - Yandong Yin
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai , 200032 People's Republic of China
| | - Zhuozhong Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai , 200032 People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health , Harbin Medical University , Harbin , 150086 People's Republic of China
| | - Kang Li
- Department of Epidemiology and Biostatistics, School of Public Health , Harbin Medical University , Harbin , 150086 People's Republic of China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai , 200032 People's Republic of China
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170
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Pavlova NN, Hui S, Ghergurovich JM, Fan J, Intlekofer AM, White RM, Rabinowitz JD, Thompson CB, Zhang J. As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid. Cell Metab 2018; 27:428-438.e5. [PMID: 29337136 PMCID: PMC5803449 DOI: 10.1016/j.cmet.2017.12.006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/03/2017] [Accepted: 12/09/2017] [Indexed: 02/09/2023]
Abstract
When mammalian cells are deprived of glutamine, exogenous asparagine rescues cell survival and growth. Here we report that this rescue results from use of asparagine in protein synthesis. All mammalian cell lines tested lacked cytosolic asparaginase activity and could not utilize asparagine to produce other amino acids or biosynthetic intermediates. Instead, most glutamine-deprived cell lines are capable of sufficient glutamine synthesis to maintain essential amino acid uptake and production of glutamine-dependent biosynthetic precursors, with the exception of asparagine. While experimental introduction of cytosolic asparaginase could enhance the synthesis of glutamine and increase tricarboxylic acid cycle anaplerosis and the synthesis of nucleotide precursors, cytosolic asparaginase suppressed the growth and survival of cells in glutamine-depleted medium in vitro and severely compromised the in vivo growth of tumor xenografts. These results suggest that the lack of asparaginase activity represents an evolutionary adaptation to allow mammalian cells to survive pathophysiologic variations in extracellular glutamine.
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Affiliation(s)
- Natalya N Pavlova
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sheng Hui
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan M Ghergurovich
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jing Fan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Craig B Thompson
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Ji Zhang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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171
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Jang C, Hui S, Lu W, Cowan AJ, Morscher RJ, Lee G, Liu W, Tesz GJ, Birnbaum MJ, Rabinowitz JD. The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids. Cell Metab 2018; 27:351-361.e3. [PMID: 29414685 PMCID: PMC6032988 DOI: 10.1016/j.cmet.2017.12.016] [Citation(s) in RCA: 370] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/18/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022]
Abstract
Excessive consumption of sweets is a risk factor for metabolic syndrome. A major chemical feature of sweets is fructose. Despite strong ties between fructose and disease, the metabolic fate of fructose in mammals remains incompletely understood. Here we use isotope tracing and mass spectrometry to track the fate of glucose and fructose carbons in vivo, finding that dietary fructose is cleared by the small intestine. Clearance requires the fructose-phosphorylating enzyme ketohexokinase. Low doses of fructose are ∼90% cleared by the intestine, with only trace fructose but extensive fructose-derived glucose, lactate, and glycerate found in the portal blood. High doses of fructose (≥1 g/kg) overwhelm intestinal fructose absorption and clearance, resulting in fructose reaching both the liver and colonic microbiota. Intestinal fructose clearance is augmented both by prior exposure to fructose and by feeding. We propose that the small intestine shields the liver from otherwise toxic fructose exposure.
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Affiliation(s)
- Cholsoon Jang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Sheng Hui
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Wenyun Lu
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Alexis J Cowan
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Raphael J Morscher
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Gina Lee
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medical School, New York, NY 10065, USA
| | - Wei Liu
- Pfizer Inc. Internal Medicine, Cambridge, MA 02139, USA
| | | | | | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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172
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Wells A, Barrington WT, Dearth S, May A, Threadgill DW, Campagna SR, Voy BH. Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography–Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice. J Proteome Res 2018; 17:1077-1090. [DOI: 10.1021/acs.jproteome.7b00750] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann Wells
- University of Tennessee-Knoxville, UT-ORNL Graduate
School of Genome Science and Technology, Knoxville, Tennessee 37996, United States
| | - William T. Barrington
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, Bryan, Texas 77807, United States
| | - Stephen Dearth
- University of Tennessee-Knoxville, Department of Chemistry, Knoxville, Tennessee 37996, United States
| | - Amanda May
- University of Tennessee-Knoxville, Department of Chemistry, Knoxville, Tennessee 37996, United States
| | - David W. Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, Bryan, Texas 77807, United States
| | - Shawn R. Campagna
- University of Tennessee-Knoxville, UT-ORNL Graduate
School of Genome Science and Technology, Knoxville, Tennessee 37996, United States
- University of Tennessee-Knoxville, Department of Chemistry, Knoxville, Tennessee 37996, United States
| | - Brynn H. Voy
- University of Tennessee-Knoxville, UT-ORNL Graduate
School of Genome Science and Technology, Knoxville, Tennessee 37996, United States
- University of Tennessee-Knoxville, Department of Animal
Science, Knoxville, Tennessee 37996, United States
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173
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Lu W, Wang L, Chen L, Hui S, Rabinowitz JD. Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors. Antioxid Redox Signal 2018; 28:167-179. [PMID: 28497978 PMCID: PMC5737638 DOI: 10.1089/ars.2017.7014] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AIMS Accurate analysis of dinucleotide redox cofactors nicotinamide adenine dinucleotide phosphate reduced (NADPH), nicotinamide adenine dinucleotide phosphate (NADP+), nicotinamide adenine dinucleotide reduced (NADH), and nicotinamide adenine dinucleotide (NAD+) from biological samples is important to understanding cellular redox homeostasis. In this study, we aimed to develop a simple protocol for quenching metabolism and extracting NADPH that avoids interconversion among the reduced forms and the oxidized forms. RESULTS We compared seven different solvents for quenching and extraction of cultured mammalian cells and mouse tissues: a cold aqueous buffer commonly used in enzyme assays with and without detergent, hot aqueous buffer, and cold organic mixtures (80% methanol, buffered 75% acetonitrile, and acidic 40:40:20 acetonitrile:methanol:water with either 0.02 M or 0.1 M formic acid). Extracts were analyzed by liquid chromatography-mass spectrometry (LC-MS). To monitor the metabolite interconversion, cells were grown in 13C6-glucose medium, and unlabeled standards were spiked into the extraction solvents. Interconversion between the oxidized and reduced forms was substantial except for the enzyme assay buffer with detergent, 80% methanol and 40:40:20 acetonitrile:methanol:water, with the 0.1 M formic acid mix giving the least interconversion and best recoveries. Absolute NAD+, NADH, NADP+, and NADPH concentrations in cells and mouse tissues were measured with this approach. INNOVATION We found that the interconversion between the reduced and oxidized forms during extraction is a major barrier to accurately measuring NADPH/NADP+ and NADH/NAD+ ratios. Such interconversion can be monitored by isotope labeling cells and spiking NAD(P)(H) standards. CONCLUSION Extraction with 40:40:20 acetonitrile:methanol:water with 0.1 M formic acid decreases interconversion and, therefore, is suitable for measurement of redox cofactor ratios using LC-MS. This solvent is also useful for general metabolomics. Samples should be neutralized immediately after extraction to avoid acid-catalyzed degradation. When LC-MS is not available and enzyme assays are accordingly used, inclusion of detergent in the aqueous extraction buffer reduces interconversion. Antioxid. Redox Signal. 28, 167-179.
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Affiliation(s)
- Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Lin Wang
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Li Chen
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Sheng Hui
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
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174
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Martin RM, Dearth SP, LeCleir GR, Campagna SR, Fozo EM, Zinser ER, Wilhelm SW. Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium. PLoS One 2017; 12:e0189608. [PMID: 29240841 PMCID: PMC5730168 DOI: 10.1371/journal.pone.0189608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
Microcystins are secondary metabolites produced by several freshwater, bloom-forming cyanobacterial species. Microcystin-producing cyanobacteria co-occur with a complex community of heterotrophic bacteria. Though conflicting, studies suggest that microcystins affect the physiology of heterotrophic bacteria by inducing oxidative stress and increasing cell envelope permeability. Based on these observations, we hypothesized that exposure to microcystin should induce differential expression in genes responding to oxidative and envelope stress and trigger shifts in metabolite pools. We tested this hypothesis by exposing Escherichia coli MG1655 to 1 and 10 mg/L microcystin-LR and monitored global changes to gene expression, cellular metabolite pools, and lipid composition using RNA-sequencing and UPLC-MS. Contrary to reported studies, we observed no evidence that microcystin-LR induced oxidative or cell envelope stress in E. coli under the tested conditions. Our results suggest a potential difference in mechanism by which microcystin-LR interacts with heterotrophic bacteria vs. cyanobacteria.
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Affiliation(s)
- Robbie M. Martin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Stephen P. Dearth
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Gary R. LeCleir
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Erik R. Zinser
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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175
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Tague ED, Bourdon AK, MacDonald A, Lookadoo MS, Kim ED, White WM, Terry PD, Campagna SR, Voy BH, Whelan J. Metabolomics Approach in the Study of the Well-Defined Polyherbal Preparation Zyflamend. J Med Food 2017; 21:306-316. [PMID: 29227176 DOI: 10.1089/jmf.2017.0062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Zyflamend is a highly controlled blend of 10 herbal extracts that synergistically impact multiple cell signaling pathways with anticancer and anti-inflammatory properties. More recently, its effects were shown to also modify cellular energetics, for example, activation of fatty acid oxidation and inhibition of lipogenesis. However, its general metabolic effects in vivo have yet to be explored. The objective of this study was to characterize the tissue specific metabolomes in response to supplementation of Zyflamend in mice, with a comparison of equivalent metabolomics data generated in plasma from humans supplemented with Zyflamend. Because Zyflamend has been shown to activate AMPK, the "energy sensor" of the cell, in vitro, the effects of Zyflamend on adiposity were also tested in the murine model. C57BL/6 mice were fed diets that mimicked the macro- and micronutrient composition of the U.S. diet with and without Zyflamend supplementation at human equivalent doses. Untargeted metabolomics was performed in liver, skeletal muscle, adipose, and plasma from mice consuming Zyflamend and in plasma from humans supplemented with Zyflamend at an equivalent dose. Adiposity in mice was significantly reduced in the Zyflamend-treated animals (compared with controls) without affecting body weight or weight gain. Based on KEGG pathway enrichment, purine and pyrimidine metabolism (potential regulators of AMPK) were particularly responsive to Zyflamend across all tissues, but only in mice. Consistent with the metabolomics data, Zyflamend activated AMPK and inhibited acetyl CoA-carboxylase in adipose tissue, key regulators of lipogenesis. Zyflamend reduces adipose tissue in mice through a mechanism that likely involves the activation of AMPK.
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Affiliation(s)
- Eric D Tague
- 1 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee, USA
| | - Allen K Bourdon
- 1 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee, USA
| | - Amber MacDonald
- 2 Department of Nutrition, University of Tennessee Knoxville , Knoxville, Tennessee, USA
| | - Maggie S Lookadoo
- 1 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee, USA
| | - Edward D Kim
- 3 Department of Surgery, University of Tennessee Medical Center , Knoxville, Tennessee, USA
| | - Wesley M White
- 3 Department of Surgery, University of Tennessee Medical Center , Knoxville, Tennessee, USA
| | - Paul D Terry
- 4 Department of Medicine, University of Tennessee Medical Center , Knoxville, Tennessee, USA
| | - Shawn R Campagna
- 1 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee, USA .,5 Biological Small Molecule Mass Spectrometry Core, University of Tennessee , Knoxville, Tennessee, USA
| | - Brynn H Voy
- 6 Department of Animal Science, University of Tennessee Knoxville , Knoxville, Tennessee, USA
| | - Jay Whelan
- 2 Department of Nutrition, University of Tennessee Knoxville , Knoxville, Tennessee, USA
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176
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Campos CG, Veras HCT, de Aquino Ribeiro JA, Costa PPKG, Araújo KP, Rodrigues CM, de Almeida JRM, Abdelnur PV. New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2646-2657. [PMID: 28879550 DOI: 10.1007/s13361-017-1786-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. Graphical Abstract ᅟ.
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Affiliation(s)
- Christiane Gonçalves Campos
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil
| | - Henrique César Teixeira Veras
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Postgraduate Program in Molecular Biology, Department of Cellular Biology, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | | | - Katiúscia Pereira Araújo
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
| | - Clenilson Martins Rodrigues
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
| | - João Ricardo Moreira de Almeida
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil
- Postgraduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Patrícia Verardi Abdelnur
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Brasília, DF, 70770-901, Brazil.
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil.
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177
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Matsuda F, Toya Y, Shimizu H. Learning from quantitative data to understand central carbon metabolism. Biotechnol Adv 2017; 35:971-980. [DOI: 10.1016/j.biotechadv.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 12/23/2022]
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178
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Bazurto JV, Dearth SP, Tague ED, Campagna SR, Downs DM. Untargeted metabolomics confirms and extends the understanding of the impact of aminoimidazole carboxamide ribotide (AICAR) in the metabolic network of Salmonella enterica. MICROBIAL CELL 2017; 5:74-87. [PMID: 29417056 PMCID: PMC5798407 DOI: 10.15698/mic2018.02.613] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In Salmonella enterica, aminoimidazole carboxamide ribotide (AICAR) is a purine biosynthetic intermediate and a substrate of the AICAR transformylase/IMP cyclohydrolase (PurH) enzyme. When purH is eliminated in an otherwise wild-type strain, AICAR accumulates and indirectly inhibits synthesis of the essential coenzyme thiamine pyrophosphate (TPP). In this study, untargeted metabolomics approaches were used to i) corroborate previously defined metabolite changes, ii) define the global consequences of AICAR accumulation and iii) investigate the metabolic effects of mutations that restore thiamine prototrophy to a purH mutant. The data showed that AICAR accumulation led to an increase in the global regulator cyclic AMP (cAMP) and that disrupting central carbon metabolism could decrease AICAR and/or cAMP to restore thiamine synthesis. A mutant (icc) blocked in cAMP degradation that accumulated cAMP but had wild-type levels of AICAR was used to identify changes in the purH metabolome that were a direct result of elevated cAMP. Data herein describe the use of metabolomics to identify the metabolic state of mutant strains and probe the underlying mechanisms used by AICAR to inhibit thiamine synthesis. The results obtained provide a cautionary tale of using metabolite concentrations as the only data to define the physiological state of a bacterial cell.
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Affiliation(s)
| | - Stephen P Dearth
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996
| | - Eric D Tague
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA 30602
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179
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A New Derivatization Reagent for HPLC-MS Analysis of Biological Organic Acids. Chromatographia 2017; 80:1723-1732. [PMID: 29213145 PMCID: PMC5698372 DOI: 10.1007/s10337-017-3421-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/22/2017] [Accepted: 10/13/2017] [Indexed: 01/08/2023]
Abstract
Small molecules containing carboxylic acid functional groups are ubiquitous throughout biology, playing vital roles in biological chemistry ranging from energy metabolism to cellular signaling. This paper describes a new derivatization reagent, 4-bromo-N-methylbenzylamine, which was selected for its potential to derivatize mono-, di- and tri-carboxylic acids, such as the intermediates of the tricarboxylic acid (TCA) cycle. This derivatization procedure facilitated the use of positive electrospray ionization (ESI) tandem mass spectrometry (MS/MS) detection of derivatized species allowing for clear identification thanks to the easily recognizable isotope pattern of the incorporated bromine. A liquid chromatography (LC)-MS/MS method was developed which provided limits of detection between 0.2 and 44 μg L−1 in under 6 min, depending on the analyte and total analysis time. This method was successfully applied in both in vitro and in vivo models.
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180
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Wu Y, Seyedsayamdost MR. Synergy and Target Promiscuity Drive Structural Divergence in Bacterial Alkylquinolone Biosynthesis. Cell Chem Biol 2017; 24:1437-1444.e3. [PMID: 29033316 DOI: 10.1016/j.chembiol.2017.08.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/21/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
Abstract
Microbial natural products are genetically encoded by dedicated biosynthetic gene clusters (BGCs). A given BGC usually produces a family of related compounds that share a core but contain variable substituents. Though common, the reasons underlying this divergent biosynthesis are in general unknown. Herein, we have addressed this issue using the hydroxyalkylquinoline (HAQ) family of natural products synthesized by Burkholderia thailandensis. Investigations into the detailed functions of two analogs show that they act synergistically in inhibiting bacterial growth. One analog is a nanomolar inhibitor of pyrimidine biosynthesis and at the same time disrupts the proton motive force. A second analog inhibits the cytochrome bc1 complex as well as pyrimidine biogenesis. These results provide a functional rationale for the divergent nature of HAQs. They imply that synergy and target promiscuity are driving forces for the evolution of tailoring enzymes that diversify the products of the HAQ biosynthetic pathway.
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Affiliation(s)
- Yihan Wu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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181
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Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. mSystems 2017; 2:mSystems00093-17. [PMID: 29034330 PMCID: PMC5634791 DOI: 10.1128/msystems.00093-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/17/2017] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence suggests that environmental toxicants may influence inflammation-promoted chronic disease susceptibility during early life. BPA, an environmental endocrine disruptor, can transfer across the placenta and accumulate in fetal gut and liver. However, underlying mechanisms for BPA-induced colonic and liver inflammation are not fully elucidated. In this report, we show how perinatal BPA exposure in rabbits alters gut microbiota and their metabolite profiles, which leads to colonic and liver inflammation as well as to increased gut permeability as measured by elevated serum lipopolysaccharide (LPS) levels in the offspring. Also, perinatal BPA exposure leads to reduced levels of gut bacterial diversity and bacterial metabolites (short-chain fatty acids [SCFA]) and elevated gut permeability—three common early biomarkers of inflammation-promoted chronic diseases. In addition, we showed that SCFA ameliorated BPA-induced intestinal permeability in vitro. Thus, our study results suggest that correcting environmental toxicant-induced bacterial dysbiosis early in life may reduce the risk of chronic diseases later in life. Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is due to alterations in the microbiome and colonic metabolome. The 16S rRNA amplicon sequencing analysis revealed differences in beta diversity with a significant reduction in the relative abundances of short-chain fatty acid (SCFA) producers such as Oscillospira and Ruminococcaceae due to BPA exposure. Furthermore, BPA exposure reduced fecal SCFA levels and increased systemic lipopolysaccharide (LPS) levels. BPA exposure-increased intestinal permeability was ameliorated by the addition of SCFA in vitro. Metabolic fingerprints revealed alterations in global metabolism and amino acid metabolism. Thus, our findings indicate that perinatal BPA exposure may cause gut bacterial dysbiosis and altered metabolite profiles, particularly SCFA profiles, leading to chronic colon and liver inflammation. IMPORTANCE Emerging evidence suggests that environmental toxicants may influence inflammation-promoted chronic disease susceptibility during early life. BPA, an environmental endocrine disruptor, can transfer across the placenta and accumulate in fetal gut and liver. However, underlying mechanisms for BPA-induced colonic and liver inflammation are not fully elucidated. In this report, we show how perinatal BPA exposure in rabbits alters gut microbiota and their metabolite profiles, which leads to colonic and liver inflammation as well as to increased gut permeability as measured by elevated serum lipopolysaccharide (LPS) levels in the offspring. Also, perinatal BPA exposure leads to reduced levels of gut bacterial diversity and bacterial metabolites (short-chain fatty acids [SCFA]) and elevated gut permeability—three common early biomarkers of inflammation-promoted chronic diseases. In addition, we showed that SCFA ameliorated BPA-induced intestinal permeability in vitro. Thus, our study results suggest that correcting environmental toxicant-induced bacterial dysbiosis early in life may reduce the risk of chronic diseases later in life.
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182
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Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A 2017; 114:11404-11409. [PMID: 29073064 DOI: 10.1073/pnas.1706617114] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The enzyme serine hydroxymethyltransferse (SHMT) converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Folate one-carbon units support purine and thymidine synthesis, and thus cell growth. Mammals have both cytosolic SHMT1 and mitochondrial SHMT2, with the mitochondrial isozyme strongly up-regulated in cancer. Here we show genetically that dual SHMT1/2 knockout blocks HCT-116 colon cancer tumor xenograft formation. Building from a pyrazolopyran scaffold that inhibits plant SHMT, we identify small-molecule dual inhibitors of human SHMT1/2 (biochemical IC50 ∼ 10 nM). Metabolomics and isotope tracer studies demonstrate effective cellular target engagement. A cancer cell-line screen revealed that B-cell lines are particularly sensitive to SHMT inhibition. The one-carbon donor formate generally rescues cells from SHMT inhibition, but paradoxically increases the inhibitor's cytotoxicity in diffuse large B-cell lymphoma (DLBCL). We show that this effect is rooted in defective glycine uptake in DLBCL cell lines, rendering them uniquely dependent upon SHMT enzymatic activity to meet glycine demand. Thus, defective glycine import is a targetable metabolic deficiency of DLBCL.
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183
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Wooldridge AL, Bischof RJ, Liu H, Heinemann GK, Hunter DS, Giles LC, Simmons RA, Lien YC, Lu W, Rabinowitz JD, Kind KL, Owens JA, Clifton VL, Gatford KL. Late-gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR. Am J Physiol Regul Integr Comp Physiol 2017; 314:R22-R33. [PMID: 28978515 DOI: 10.1152/ajpregu.00549.2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Perinatal exposures are associated with altered risks of childhood allergy. Human studies and our previous work suggest that restricted growth in utero (IUGR) is protective against allergic disease. The mechanisms are not clearly defined, but reduced fetal abundance and altered metabolism of methyl donors are hypothesized as possible underlying mechanisms. Therefore, we examined whether late-gestation maternal dietary methyl donor and cofactor supplementation of the placentally restricted (PR) sheep pregnancy would reverse allergic protection in progeny. Allergic outcomes were compared between progeny from control pregnancies (CON; n = 49), from PR pregnancies without intervention (PR; n = 28), and from PR pregnancies where the dam was fed a methyl donor plus cofactor supplement from day 120 of pregnancy until delivery (PR + Methyl; n = 25). Both PR and PR + Methyl progeny were smaller than CON; supplementation did not alter birth size. PR was protective against cutaneous hypersensitivity responses to ovalbumin (OVA; P < 0.01 in singletons). Cutaneous hypersensitivity responses to OVA in PR + Methyl progeny were intermediate to and not different from the responses of CON and PR sheep. Cutaneous hypersensitivity responses to house dust mites did not differ between treatments. In singleton progeny, upper dermal mast cell density was greater in PR + Methyl than in PR or CON (each P < 0.05). The differences in the cutaneous allergic response were not explained by treatment effects on circulating immune cells or antibodies. Our results suggest that mechanisms underlying in utero programming of allergic susceptibility by IUGR and methyl donor availability may differ and imply that late-gestation methyl donor supplementation may increase allergy risk.
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Affiliation(s)
- Amy L Wooldridge
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Robert J Bischof
- The Ritchie Centre, Hudson Institute of Medical Research , Clayton, Victoria , Australia.,Department of Physiology, Monash University , Melbourne, Victoria , Australia
| | - Hong Liu
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Gary K Heinemann
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Damien S Hunter
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Lynne C Giles
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,School of Population Health, University of Adelaide , Adelaide, South Australia , Australia
| | - Rebecca A Simmons
- Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Yu-Chin Lien
- Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Princeton, New Jersey
| | - Karen L Kind
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,School of Animal and Veterinary Sciences, University of Adelaide , Adelaide, South Australia , Australia
| | - Julie A Owens
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Vicki L Clifton
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia.,Mater Research Institute-University of Queensland and Translational Research Institute, South Brisbane, Queensland, Australia
| | - Kathryn L Gatford
- Robinson Research Institute, University of Adelaide , Adelaide, South Australia , Australia.,Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
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184
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McClory PJ, Håkansson K. Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition. Anal Chem 2017; 89:10188-10193. [PMID: 28841300 PMCID: PMC5642034 DOI: 10.1021/acs.analchem.7b01225] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions, corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately 6× higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.
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Affiliation(s)
- Phillip J. McClory
- Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109-1055
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109-1055
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185
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Rajeshkumar NV, Yabuuchi S, Pai SG, De Oliveira E, Kamphorst JJ, Rabinowitz JD, Tejero H, Al-Shahrour F, Hidalgo M, Maitra A, Dang CV. Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin. Clin Cancer Res 2017; 23:5639-5647. [PMID: 28611197 PMCID: PMC6540110 DOI: 10.1158/1078-0432.ccr-17-1115] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/23/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Purpose: To identify effective metabolic inhibitors to suppress the aggressive growth of pancreatic ductal adenocarcinoma (PDAC), we explored the in vivo antitumor efficacy of metabolic inhibitors, as single agents, in a panel of patient-derived PDAC xenograft models (PDX) and investigated whether genomic alterations of tumors correlate with the sensitivity to metabolic inhibitors.Experimental Design: Mice with established PDAC tumors from 6 to 13 individual PDXs were randomized and treated, once daily for 4 weeks, with either sterile PBS (vehicle) or the glutaminase inhibitor bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), transaminase inhibitor aminooxyacetate (AOA), pyruvate dehydrogenase kinase inhibitor dichloroacetate (DCA), autophagy inhibitor chloroquine (CQ), and mitochondrial complex I inhibitor phenformin/metformin.Results: Among the agents tested, phenformin showed significant tumor growth inhibition (>30% compared with vehicle) in 5 of 12 individual PDXs. Metformin, at a fivefold higher dose, displayed significant tumor growth inhibition in 3 of 12 PDXs similar to BPTES (2/8 PDXs) and DCA (2/6 PDXs). AOA and CQ had the lowest response rates. Gene set enrichment analysis conducted using the baseline gene expression profile of pancreatic tumors identified a gene expression signature that inversely correlated with phenformin sensitivity, which is in agreement with the phenformin gene expression signature of NIH Library of Integrated Network-based Cellular Signatures (LINCS). The PDXs that were more sensitive to phenformin showed a baseline reduction in amino acids and elevation in oxidized glutathione. There was no correlation between phenformin response and genetic alterations in KRAS, TP53, SMAD4, or PTENConclusions: Phenformin treatment showed relatively higher antitumor efficacy against established PDAC tumors, compared with the efficacy of other metabolic inhibitors and metformin. Phenformin treatment significantly diminished PDAC tumor progression and prolonged tumor doubling time. Overall, our results serve as a foundation for further evaluation of phenformin as a therapeutic agent in pancreatic cancer. Clin Cancer Res; 23(18); 5639-47. ©2017 AACR.
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Affiliation(s)
- N V Rajeshkumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shinichi Yabuuchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shweta G Pai
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth De Oliveira
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jurre J Kamphorst
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, United Kingdom
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey
| | - Héctor Tejero
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | | | - Manuel Hidalgo
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Division of Hematology-Oncology, Rosenberg Clinical Cancer Center, Beth Israel Deaconess Medical Center (BIDMC), Boston, Massachusetts
| | - Anirban Maitra
- Department of Pathology and Translational Molecular Pathology, Sheikh Ahmad Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chi V Dang
- Abramson Cancer Center, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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186
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Zhang Y, Kurupati R, Liu L, Zhou XY, Zhang G, Hudaihed A, Filisio F, Giles-Davis W, Xu X, Karakousis GC, Schuchter LM, Xu W, Amaravadi R, Xiao M, Sadek N, Krepler C, Herlyn M, Freeman GJ, Rabinowitz JD, Ertl HCJ. Enhancing CD8 + T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy. Cancer Cell 2017; 32:377-391.e9. [PMID: 28898698 PMCID: PMC5751418 DOI: 10.1016/j.ccell.2017.08.004] [Citation(s) in RCA: 408] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 02/08/2023]
Abstract
How tumor-infiltrating T lymphocytes (TILs) adapt to the metabolic constrains within the tumor microenvironment (TME) and to what degree this affects their ability to combat tumor progression remain poorly understood. Using mouse melanoma models, we report that CD8+ TILs enhance peroxisome proliferator-activated receptor (PPAR)-α signaling and catabolism of fatty acids (FAs) when simultaneously subjected to hypoglycemia and hypoxia. This metabolic switch partially preserves CD8+ TILs' effector functions, although co-inhibitor expression increases during tumor progression regardless of CD8+ TILs' antigen specificity. Further promoting FA catabolism improves the CD8+ TILs' ability to slow tumor progression. PD-1 blockade delays tumor growth without changing TIL metabolism or functions. It synergizes with metabolic reprogramming of T cells to achieve superior antitumor efficacy and even complete cures.
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Affiliation(s)
- Ying Zhang
- Gene Therapy and Vaccines Program, University of Pennsylvania (U of PA), Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA 19104, USA
| | - Raj Kurupati
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ling Liu
- Lewis-Sigler Institute for Integrative Genomics & Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | | | - Gao Zhang
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Abeer Hudaihed
- Biology Program, Temple University, Philadelphia, PA 19122, USA
| | - Flavia Filisio
- Biology Program, Temple University, Philadelphia, PA 19122, USA
| | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, U of PA, Philadelphia, PA 19104, USA
| | | | | | - Wei Xu
- Department of Medicine, U of PA, Philadelphia, PA 19104, USA
| | - Ravi Amaravadi
- Department of Medicine, U of PA, Philadelphia, PA 19104, USA
| | - Min Xiao
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Norah Sadek
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | | | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics & Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
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187
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Rosebrock AP, Caudy AA. Metabolite Extraction from Saccharomyces cerevisiae for Liquid Chromatography-Mass Spectrometry. Cold Spring Harb Protoc 2017; 2017:pdb.prot089086. [PMID: 28864564 DOI: 10.1101/pdb.prot089086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Prior to mass spectrometric analysis, cellular small molecules must be extracted and separated from interfering components such as salts and culture medium. To ensure minimal perturbation of metabolism, yeast cells grown in liquid culture are rapidly harvested by filtration as described here. Simultaneous quenching of metabolism and extraction is afforded by immediate immersion in low-temperature organic solvent. Samples prepared using this method are suitable for a range of downstream liquid chromatography-mass spectrometry analyses and are stable in solvent for >1 yr at -80°C.
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Affiliation(s)
- Adam P Rosebrock
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada
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188
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Schittmayer M, Birner-Gruenberger R. Resolution Ladder for High-Resolution Mass Spectrometry. Anal Chem 2017; 89:9611-9615. [PMID: 28845970 DOI: 10.1021/acs.analchem.7b02042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution mass spectrometry has become a key technology in life sciences. Since it is often unfeasible to find pairs of analytes with an appropriate mass difference to actually quantify the resolution experimentally, resolution is usually calculated from the shape of a single mass peak. In this study we show that the commonly employed strategy yields a poor measure of true resolution since it does not account for interactions that take place between ions of very similar mass and might be further distorted by signal processing effects. We present a straightforward and easily adaptable method to create a ladder of mass pairs to experimentally quantify actual mass resolution over a wide m/z range, compare the experimental resolution to the single peak based calculated resolution, and demonstrate the applicability of mass resolution ladders to study interactions of similar ions in various types of widely used mass spectrometers.
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Affiliation(s)
- Matthias Schittmayer
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , Stiftingtalstrasse 24, 8010 Graz, Austria.,Institute of Molecular Systems Biology, ETH Zürich , 8093 Zürich, Switzerland.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
| | - Ruth Birner-Gruenberger
- Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz , Stiftingtalstrasse 24, 8010 Graz, Austria.,Omics Center Graz, BioTechMed-Graz , 8010 Graz, Austria
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189
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Hu Y, Zheng Q, Wanek W. Flux Analysis of Free Amino Sugars and Amino Acids in Soils by Isotope Tracing with a Novel Liquid Chromatography/High Resolution Mass Spectrometry Platform. Anal Chem 2017; 89:9192-9200. [PMID: 28776982 PMCID: PMC5605124 DOI: 10.1021/acs.analchem.7b01938] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Soil fluxomics analysis can provide
pivotal information for understanding
soil biochemical pathways and their regulation, but direct measurement
methods are rare. Here, we describe an approach to measure soil extracellular
metabolite (amino sugar and amino acid) concentrations and fluxes
based on a 15N isotope pool dilution technique via liquid
chromatography and high-resolution mass spectrometry. We produced
commercially unavailable 15N and 13C labeled
amino sugars and amino acids by hydrolyzing peptidoglycan isolated
from isotopically labeled bacterial biomass and used them as tracers
(15N) and internal standards (13C). High-resolution
(Orbitrap Exactive) MS with a resolution of 50 000 allowed
us to separate different stable isotope labeled analogues across a
large range of metabolites. The utilization of 13C internal
standards greatly improved the accuracy and reliability of absolute
quantification. We successfully applied this method to two types of
soils and quantified the extracellular gross fluxes of 2 amino sugars,
18 amino acids, and 4 amino acid enantiomers. Compared to the influx
and efflux rates of most amino acids, similar ones were found for
glucosamine, indicating that this amino sugar is released through
peptidoglycan and chitin decomposition and serves as an important
nitrogen source for soil microorganisms. d-Alanine and d-glutamic acid derived from peptidoglycan decomposition exhibited
similar turnover rates as their l-enantiomers. This novel
approach offers new strategies to advance our understanding of the
production and transformation pathways of soil organic N metabolites,
including the unknown contributions of peptidoglycan and chitin decomposition
to soil organic N cycling.
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Affiliation(s)
- Yuntao Hu
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
| | - Qing Zheng
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna , Althanstraße 14, 1090 Vienna, Austria
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190
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Chen L, Ducker GS, Lu W, Teng X, Rabinowitz JD. An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate. Anal Bioanal Chem 2017; 409:5955-5964. [PMID: 28799108 DOI: 10.1007/s00216-017-0514-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022]
Abstract
The cofactor tetrahydrofolate (THF) is used to reduce, oxidize, and transfer one-carbon (1C) units required for the synthesis of nucleotides, glycine, and methionine. Measurement of intracellular THF species is complicated by their chemical instability, signal dilution caused by variable polyglutamation, and the potential for interconversion among these species. Here, we describe a method using negative mode liquid chromatography-mass spectrometry (LC-MS) to measure intracellular folate species from mammalian cells. Application of this method with isotope-labeled substrates revealed abiotic interconversion of THF and methylene-THF, which renders their separate quantitation particularly challenging. Chemical reduction of methylene-THF using deuterated sodium cyanoborohydride traps methylene-THF, which is unstable, as deuterated 5-methyl-THF, which is stable. Together with proper sample handling and LC-MS, this enables effective measurements of five active folate pools (THF, 5-methyl-THF, methylene-THF, methenyl-THF/10-formyl-THF, and 5-formyl-THF) representing the biologically important 1C oxidation states of THF in mammalian cells. Graphical abstract Chemical derivatization with deuterated cyanoborohydride traps unstable methylene-THF as isotope-labeled 5-methyl-THF, enabling accurate quantification by LC-MS.
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Affiliation(s)
- Li Chen
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Gregory S Ducker
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Xin Teng
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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191
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Dulka BN, Bourdon AK, Clinard CT, Muvvala MBK, Campagna SR, Cooper MA. Metabolomics reveals distinct neurochemical profiles associated with stress resilience. Neurobiol Stress 2017; 7:103-112. [PMID: 28828396 PMCID: PMC5552108 DOI: 10.1016/j.ynstr.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/11/2017] [Accepted: 08/05/2017] [Indexed: 11/27/2022] Open
Abstract
Acute social defeat represents a naturalistic form of conditioned fear and is an excellent model in which to investigate the biological basis of stress resilience. While there is growing interest in identifying biomarkers of stress resilience, until recently, it has not been feasible to associate levels of large numbers of neurochemicals and metabolites to stress-related phenotypes. The objective of the present study was to use an untargeted metabolomics approach to identify known and unknown neurochemicals in select brain regions that distinguish susceptible and resistant individuals in two rodent models of acute social defeat. In the first experiment, male mice were first phenotyped as resistant or susceptible. Then, mice were subjected to acute social defeat, and tissues were immediately collected from the ventromedial prefrontal cortex (vmPFC), basolateral/central amygdala (BLA/CeA), nucleus accumbens (NAc), and dorsal hippocampus (dHPC). Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) was used for the detection of water-soluble neurochemicals. In the second experiment, male Syrian hamsters were paired in daily agonistic encounters for 2 weeks, during which they formed stable dominant-subordinate relationships. Then, 24 h after the last dominance encounter, animals were exposed to acute social defeat stress. Immediately after social defeat, tissue was collected from the vmPFC, BLA/CeA, NAc, and dHPC for analysis using UPLC-HRMS. Although no single biomarker characterized stress-related phenotypes in both species, commonalities were found. For instance, in both model systems, animals resistant to social defeat stress also show increased concentration of molecules to protect against oxidative stress in the NAc and vmPFC. Additionally, in both mice and hamsters, unidentified spectral features were preliminarily annotated as potential targets for future experiments. Overall, these findings suggest that a metabolomics approach can identify functional groups of neurochemicals that may serve as novel targets for the diagnosis, treatment, or prevention of stress-related mental illness.
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Affiliation(s)
- Brooke N Dulka
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States
| | - Catherine T Clinard
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Mohan B K Muvvala
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States.,Biological Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN 37996, United States
| | - Matthew A Cooper
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
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192
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Swain-Lenz D, Nikolskiy I, Cheng J, Sudarsanam P, Nayler D, Staller MV, Cohen BA. Causal Genetic Variation Underlying Metabolome Differences. Genetics 2017; 206:2199-2206. [PMID: 28652377 PMCID: PMC5560816 DOI: 10.1534/genetics.117.203752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81, cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype.
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Affiliation(s)
- Devjanee Swain-Lenz
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Missouri 63110
- Department of Genetics, Washington University in St. Louis School of Medicine, Missouri 63110
| | - Igor Nikolskiy
- Department of Chemistry, Washington University in St. Louis, Missouri 63130
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Missouri 63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Priya Sudarsanam
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Missouri 63110
- Department of Genetics, Washington University in St. Louis School of Medicine, Missouri 63110
| | - Darcy Nayler
- Department of Genetics, Washington University in St. Louis School of Medicine, Missouri 63110
| | - Max V Staller
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Missouri 63110
- Department of Genetics, Washington University in St. Louis School of Medicine, Missouri 63110
| | - Barak A Cohen
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Missouri 63110
- Department of Genetics, Washington University in St. Louis School of Medicine, Missouri 63110
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193
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Song Y, Marmion RA, Park JO, Biswas D, Rabinowitz JD, Shvartsman SY. Dynamic Control of dNTP Synthesis in Early Embryos. Dev Cell 2017; 42:301-308.e3. [PMID: 28735680 DOI: 10.1016/j.devcel.2017.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/13/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023]
Abstract
Exponential increase of cell numbers in early embryos requires large amounts of DNA precursors (deoxyribonucleoside triphosphates (dNTPs)). Little is understood about how embryos satisfy this demand. We examined dNTP metabolism in the early Drosophila embryo, in which gastrulation is preceded by 13 sequential nuclear cleavages within only 2 hr of fertilization. Surprisingly, despite the breakneck speed at which Drosophila embryos synthesize DNA, maternally deposited dNTPs can generate less than half of the genomes needed to reach gastrulation. The rest of the dNTPs are synthesized "on the go." The rate-limiting enzyme of dNTP synthesis, ribonucleotide reductase, is inhibited by endogenous levels of deoxyATP (dATP) present at fertilization and is activated as dATP is depleted via DNA polymerization. This feedback inhibition renders the concentration of dNTPs at gastrulation robust, with respect to large variations in maternal supplies, and is essential for normal progression of embryogenesis.
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Affiliation(s)
- Yonghyun Song
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Robert A Marmion
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Junyoung O Park
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Debopriyo Biswas
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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194
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Dolfi SC, Medina DJ, Kareddula A, Paratala B, Rose A, Dhami J, Chen S, Ganesan S, Mackay G, Vazquez A, Hirshfield KM. Riluzole exerts distinct antitumor effects from a metabotropic glutamate receptor 1-specific inhibitor on breast cancer cells. Oncotarget 2017; 8:44639-44653. [PMID: 28591718 PMCID: PMC5546507 DOI: 10.18632/oncotarget.17961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
Recent evidence suggests that glutamate signaling plays an important role in cancer. Riluzole is a glutamate release inhibitor and FDA-approved drug for the treatment of amyotrophic lateral sclerosis. It has been investigated as an inhibitor of cancer cell growth and tumorigenesis with the intention of repurposing it for the treatment of cancer. Riluzole is thought to act by indirectly inhibiting glutamate signaling. However, the specific effects of riluzole in breast cancer cells are not well understood. In this study, the anti-cancer effects of riluzole were explored in a panel of breast cancer cell lines in comparison to the metabotropic glutamate receptor 1-specific inhibitor BAY 36-7620. While both drugs inhibited breast cancer cell proliferation, there were distinct functional effects suggesting that riluzole action may be metabotropic glutamate receptor 1-independent. Riluzole induced mitotic arrest independent of oxidative stress while BAY 36-7620 had no measurable effect on mitosis. BAY 36-7620 had a more pronounced and significant effect on DNA damage than riluzole. Riluzole altered cellular metabolism as demonstrated by changes in oxidative phosphorylation and cellular metabolite levels. These results provide a better understanding of the functional action of riluzole in the treatment of breast cancer.
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Affiliation(s)
- Sonia C Dolfi
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Daniel J Medina
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Aparna Kareddula
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Bhavna Paratala
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Ashley Rose
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Jatinder Dhami
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Suzie Chen
- Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Shridar Ganesan
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
| | - Gillian Mackay
- CRUK Beatson Institute, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - Alexei Vazquez
- CRUK Beatson Institute, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - Kim M Hirshfield
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, USA
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195
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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196
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Schwaiger M, Rampler E, Hermann G, Miklos W, Berger W, Koellensperger G. Anion-Exchange Chromatography Coupled to High-Resolution Mass Spectrometry: A Powerful Tool for Merging Targeted and Non-targeted Metabolomics. Anal Chem 2017; 89:7667-7674. [PMID: 28581703 DOI: 10.1021/acs.analchem.7b01624] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, simultaneous targeted metabolic profiling by isotope dilution and non-targeted fingerprinting is proposed for cancer cell studies. The novel streamlined metabolomics workflow was established using anion-exchange chromatography (IC) coupled to high-resolution mass spectrometry (MS). The separation time of strong anion-exchange (2 mm column, flow rate 380 μL min-1, injection volume 5 μL) could be decreased to 25 min for a target list comprising organic acids, sugars, sugar phosphates, and nucleotides. Internal standardization by fully 13C labeled Pichia pastoris extracts enabled absolute quantification of the primary metabolites in adherent cancer cell models. Limits of detection (LODs) in the low nanomolar range and excellent intermediate precisions of the isotopologue ratios (on average <5%, N = 5, over 40 h) were observed. As a result of internal standardization, linear dynamic ranges over 4 orders of magnitude (5 nM-50 μM, R2 > 0.99) were obtained. Experiments on drug-sensitive versus resistant SW480 cancer cells showed the feasibility of merging analytical tasks into one analytical run. Comparing fingerprinting with and without internal standard proved that the presence of the 13C labeled yeast extract required for absolute quantification was not detrimental to non-targeted data evaluation. Several interesting metabolites were discovered by accurate mass and comparing MS2 spectra (acquired in ddMS2 mode) with spectral libraries. Significant differences revealed distinct metabolic phenotypes of drug-sensitive and resistant SW480 cells.
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Affiliation(s)
- Michaela Schwaiger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , Waehringer Strasse 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , Waehringer Strasse 38, 1090 Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , Waehringer Strasse 38, 1090 Vienna, Austria.,ISOtopic Solutions , Waehringerstrasse 38, 1090 Vienna, Austria
| | - Walter Miklos
- Institute of Cancer Research, Department of Internal Medicine I, Medical University of Vienna , Borschkegasse 8a, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Department of Internal Medicine I, Medical University of Vienna , Borschkegasse 8a, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , Waehringer Strasse 38, 1090 Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna , Althanstrasse 14, 1090 Vienna, Austria
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197
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McReynolds MR, Wang W, Holleran LM, Hanna-Rose W. Uridine monophosphate synthetase enables eukaryotic de novo NAD + biosynthesis from quinolinic acid. J Biol Chem 2017; 292:11147-11153. [PMID: 28559281 DOI: 10.1074/jbc.c117.795344] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/25/2017] [Indexed: 11/06/2022] Open
Abstract
NAD+ biosynthesis is an attractive and promising therapeutic target for influencing health span and obesity-related phenotypes as well as tumor growth. Full and effective use of this target for therapeutic benefit requires a complete understanding of NAD+ biosynthetic pathways. Here, we report a previously unrecognized role for a conserved phosphoribosyltransferase in NAD+ biosynthesis. Because a required quinolinic acid phosphoribosyltransferase (QPRTase) is not encoded in its genome, Caenorhabditis elegans are reported to lack a de novo NAD+ biosynthetic pathway. However, all the genes of the kynurenine pathway required for quinolinic acid (QA) production from tryptophan are present. Thus, we investigated the presence of de novo NAD+ biosynthesis in this organism. By combining isotope-tracing and genetic experiments, we have demonstrated the presence of an intact de novo biosynthesis pathway for NAD+ from tryptophan via QA, highlighting the functional conservation of this important biosynthetic activity. Supplementation with kynurenine pathway intermediates also boosted NAD+ levels and partially reversed NAD+-dependent phenotypes caused by mutation of pnc-1, which encodes a nicotinamidase required for NAD+ salvage biosynthesis, demonstrating contribution of de novo synthesis to NAD+ homeostasis. By investigating candidate phosphoribosyltransferase genes in the genome, we determined that the conserved uridine monophosphate phosphoribosyltransferase (UMPS), which acts in pyrimidine biosynthesis, is required for NAD+ biosynthesis in place of the missing QPRTase. We suggest that similar underground metabolic activity of UMPS may function in other organisms. This mechanism for NAD+ biosynthesis creates novel possibilities for manipulating NAD+ biosynthetic pathways, which is key for the future of therapeutics.
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Affiliation(s)
- Melanie R McReynolds
- From the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wenqing Wang
- From the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lauren M Holleran
- From the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wendy Hanna-Rose
- From the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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198
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Abstract
Orbitraps are high-resolution ion-trap mass spectrometers that are widely used in metabolomics. While the mass accuracy and resolving power of orbitraps have been extensively documented, their spectral accuracy, i.e., accuracy in measuring the abundances of isotopic peaks, remains less studied. In analyzing spectra of unlabeled metabolites, we discovered a systematic under representation of heavier natural isotopic species, especially for high molecular weight metabolites (∼20% under-measurement of [M + 1]/[M + 0] ratio at m/z 600). We hypothesize that these discrepancies arise for metabolites far from the lower limit of the mass scan range, due to the weaker containment in the C-trap that results in suboptimal trajectories inside the Orbitrap analyzer. Consistent with this, spectral fidelity was restored by dividing the mass scan range (initially 75 m/z to 1000 m/z) into two scan events, one for lower molecular weight and the other for higher molecular weight metabolites. Having thus obtained accurate mass spectra at high resolution, we found that natural isotope correction for high-resolution labeling data requires more sophisticated algorithms than typically employed: the correction algorithm must take into account whether isotopologues with the same nominal mass are resolved. We present an algorithm and associated open-source code, named AccuCor, for this purpose. Together, these improvements in instrument parameters and natural isotope correction enable more accurate measurement of metabolite labeling and thus metabolic flux.
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Affiliation(s)
- Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
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199
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Choi J, Rajagopal A, Xu YF, Rabinowitz JD, O’Shea EK. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. PLoS One 2017; 12:e0176085. [PMID: 28520786 PMCID: PMC5435139 DOI: 10.1371/journal.pone.0176085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Furthermore, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.
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Affiliation(s)
- Joonhyuk Choi
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Abbhirami Rajagopal
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yi-Fan Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Erin K. O’Shea
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
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200
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The mitochondrial respiratory chain is essential for haematopoietic stem cell function. Nat Cell Biol 2017; 19:614-625. [PMID: 28504706 PMCID: PMC5474760 DOI: 10.1038/ncb3529] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022]
Abstract
Adult and fetal hematopoietic stem cells (HSCs) display a glycolytic phenotype, which is required for maintenance of stemness; however, whether mitochondrial respiration is required to maintain HSC function is not known. Here we report that loss of the mitochondrial complex III subunit Rieske iron sulfur protein (RISP) in fetal mouse HSCs allows them to proliferate but impairs their differentiation, resulting in anemia and prenatal death. RISP null fetal HSCs displayed impaired respiration resulting in a decreased NAD+/NADH ratio. RISP null fetal HSCs and progenitors exhibited an increase in both DNA and histone methylation associated with increases in 2-hydroxyglutarate (2-HG), a metabolite known to inhibit DNA and histone demethylases. RISP inactivation in adult HSCs also impaired respiration resulting in loss of quiescence concomitant with severe pancytopenia and lethality. Thus, respiration is dispensable for adult or fetal HSC proliferation, but essential for fetal HSC differentiation and maintenance of adult HSC quiescence.
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