101
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Bruntz RC, Lane AN, Higashi RM, Fan TWM. Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM). J Biol Chem 2017; 292:11601-11609. [PMID: 28592486 PMCID: PMC5512057 DOI: 10.1074/jbc.r117.776054] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metabolic reprogramming is a hallmark of cancer. The changes in metabolism are adaptive to permit proliferation, survival, and eventually metastasis in a harsh environment. Stable isotope-resolved metabolomics (SIRM) is an approach that uses advanced approaches of NMR and mass spectrometry to analyze the fate of individual atoms from stable isotope-enriched precursors to products to deduce metabolic pathways and networks. The approach can be applied to a wide range of biological systems, including human subjects. This review focuses on the applications of SIRM to cancer metabolism and its use in understanding drug actions.
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Affiliation(s)
- Ronald C Bruntz
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Markey Cancer Center, Lexington, Kentucky 40506; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40506.
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102
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Stryeck S, Birner-Gruenberger R, Madl T. Integrative metabolomics as emerging tool to study autophagy regulation. MICROBIAL CELL (GRAZ, AUSTRIA) 2017; 4:240-258. [PMID: 28845422 PMCID: PMC5568430 DOI: 10.15698/mic2017.08.584] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/01/2017] [Indexed: 12/15/2022]
Abstract
Recent technological developments in metabolomics research have enabled in-depth characterization of complex metabolite mixtures in a wide range of biological, biomedical, environmental, agricultural, and nutritional research fields. Nuclear magnetic resonance spectroscopy and mass spectrometry are the two main platforms for performing metabolomics studies. Given their broad applicability and the systemic insight into metabolism that can be obtained it is not surprising that metabolomics becomes increasingly popular in basic biological research. In this review, we provide an overview on key metabolites, recent studies, and future opportunities for metabolomics in studying autophagy regulation. Metabolites play a pivotal role in autophagy regulation and are therefore key targets for autophagy research. Given the recent success of metabolomics, it can be expected that metabolomics approaches will contribute significantly to deciphering the complex regulatory mechanisms involved in autophagy in the near future and promote understanding of autophagy and autophagy-related diseases in living cells and organisms.
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Affiliation(s)
- Sarah Stryeck
- Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Ruth Birner-Gruenberger
- Research Unit for Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Tobias Madl
- Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
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103
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Li DW, Wang C, Brüschweiler R. Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures. JOURNAL OF BIOMOLECULAR NMR 2017; 68:195-202. [PMID: 28573376 PMCID: PMC7032946 DOI: 10.1007/s10858-017-0119-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 05/24/2017] [Indexed: 05/16/2023]
Abstract
Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications. To better meet these emerging needs, an automated spin-system identification algorithm of TOCSY spectra is introduced that represents the cross-peaks and their connectivities as a mathematical graph, for which all subgraphs are determined that are maximal cliques. Each maximal clique can be assigned to an individual spin system thereby providing a robust deconvolution of the original spectrum for the easy extraction of critical spin system information. The approach is demonstrated for a complex metabolite mixture consisting of 20 compounds and for E. coli cell lysate.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Cheng Wang
- Department of Chemistry and Biochemistry, The Ohio State University, CBEC Building, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, CBEC Building, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
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104
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Matrka MC, Watanabe M, Muraleedharan R, Lambert PF, Lane AN, Romick-Rosendale LE, Wells SI. Overexpression of the human DEK oncogene reprograms cellular metabolism and promotes glycolysis. PLoS One 2017; 12:e0177952. [PMID: 28558019 PMCID: PMC5448751 DOI: 10.1371/journal.pone.0177952] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/05/2017] [Indexed: 12/12/2022] Open
Abstract
The DEK oncogene is overexpressed in many human malignancies including at early tumor stages. Our reported in vitro and in vivo models of squamous cell carcinoma have demonstrated that DEK contributes functionally to cellular and tumor survival and to proliferation. However, the underlying molecular mechanisms remain poorly understood. Based on recent RNA sequencing experiments, DEK expression was necessary for the transcription of several metabolic enzymes involved in anabolic pathways. This identified a possible mechanism whereby DEK may drive cellular metabolism to enable cell proliferation. Functional metabolic Seahorse analysis demonstrated increased baseline and maximum extracellular acidification rates, a readout of glycolysis, in DEK-overexpressing keratinocytes and squamous cell carcinoma cells. DEK overexpression also increased the maximum rate of oxygen consumption and therefore increased the potential for oxidative phosphorylation (OxPhos). To detect small metabolites that participate in glycolysis and the tricarboxylic acid cycle (TCA) that supplies substrate for OxPhos, we carried out NMR-based metabolomics studies. We found that high levels of DEK significantly reprogrammed cellular metabolism and altered the abundances of amino acids, TCA cycle intermediates and the glycolytic end products lactate, alanine and NAD+. Taken together, these data support a scenario whereby overexpression of the human DEK oncogene reprograms keratinocyte metabolism to fulfill energy and macromolecule demands required to enable and sustain cancer cell growth.
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Affiliation(s)
- Marie C. Matrka
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Miki Watanabe
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Ranjithmenon Muraleedharan
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Andrew N. Lane
- Center for Environmental Systems Biochemistry, Dept. Toxicology and Cancer Biology and Markey Cancer Center, Lexington, Kentucky, United States of America
| | - Lindsey E. Romick-Rosendale
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Susanne I. Wells
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
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105
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Kostidis S, Addie RD, Morreau H, Mayboroda OA, Giera M. Quantitative NMR analysis of intra- and extracellular metabolism of mammalian cells: A tutorial. Anal Chim Acta 2017. [PMID: 28622799 DOI: 10.1016/j.aca.2017.05.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolomics analysis of body fluids as well as cells is depended on many factors. While several well-accepted standard operating procedures for the analysis of body fluids are available, the NMR based quantitative analysis of cellular metabolites is less well standardized. Experimental designs depend on the cell type, the quenching protocol and the applied post-acquisition workflow. Here, we provide a tutorial for the quantitative description of the metabolic phenotype of mammalian cells using NMR spectroscopy. We discuss all key steps of the process, starting from the selection of the appropriate culture medium, quenching techniques to arrest metabolism in a reproducible manner, the extraction of the intracellular components and the profiling of the culture medium. NMR data acquisition and methods for both qualitative and quantitative analysis are also provided. The suggested methods cover experiments for adherent cells and cells in suspension. We ultimately describe the application of the discussed workflow to a thyroid cancer cell line. Although this tutorial focuses on mammalian cells, the given guidelines and procedures may be adjusted for the analysis of other cell types.
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Affiliation(s)
- Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands.
| | - Ruben D Addie
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands; Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
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106
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Marshall DD, Powers R. Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:1-16. [PMID: 28552170 PMCID: PMC5448308 DOI: 10.1016/j.pnmrs.2017.01.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 05/02/2023]
Abstract
Metabolomics is undergoing tremendous growth and is being employed to solve a diversity of biological problems from environmental issues to the identification of biomarkers for human diseases. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the analytical tools that are routinely, but separately, used to obtain metabolomics data sets due to their versatility, accessibility, and unique strengths. NMR requires minimal sample handling without the need for chromatography, is easily quantitative, and provides multiple means of metabolite identification, but is limited to detecting the most abundant metabolites (⩾1μM). Conversely, mass spectrometry has the ability to measure metabolites at very low concentrations (femtomolar to attomolar) and has a higher resolution (∼103-104) and dynamic range (∼103-104), but quantitation is a challenge and sample complexity may limit metabolite detection because of ion suppression. Consequently, liquid chromatography (LC) or gas chromatography (GC) is commonly employed in conjunction with MS, but this may lead to other sources of error. As a result, NMR and mass spectrometry are highly complementary, and combining the two techniques is likely to improve the overall quality of a study and enhance the coverage of the metabolome. While the majority of metabolomic studies use a single analytical source, there is a growing appreciation of the inherent value of combining NMR and MS for metabolomics. An overview of the current state of utilizing both NMR and MS for metabolomics will be presented.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States.
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107
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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108
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Gowda GAN, Raftery D. Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity To Evaluate Coenzymes and Antioxidants. Anal Chem 2017; 89:4620-4627. [PMID: 28318242 PMCID: PMC6245939 DOI: 10.1021/acs.analchem.7b00171] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conventional human blood metabolomics employs serum or plasma and provides a wealth of metabolic information therein. However, this approach lacks the ability to measure and evaluate important metabolites such as coenzymes and antioxidants that are present at high concentrations in red blood cells. As an important alternative to serum/plasma metabolomics, we show here that a simple 1H NMR experiment can simultaneously measure coenzymes and antioxidants in extracts of whole human blood, in addition to the nearly 70 metabolites that were shown to be quantitated in serum/plasma recently [ Anal. Chem. 2015 , 87 , 706 - 715 ]. Coenzymes of redox reactions: oxidized/reduced nicotinamide adenine dinucleotide (NAD+ and NADH) and nicotinamide adenine dinucleotide phosphate (NADP+ and NADPH); coenzymes of energy including adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP); and antioxidants, the sum of oxidized and reduced glutathione (GSSG and GSH) can be measured with essentially no additional effort. A new method was developed for detecting many of these unstable species without affecting other blood/blood plasma metabolites. The identities of coenzymes and antioxidants in blood NMR spectra were established combining 1D/2D NMR techniques, chemical shift databases, pH measurements and, finally, spiking with authentic compounds. This is the first study to report identification of major coenzymes and antioxidants and quantify them, simultaneously, with the large pool of other metabolites in human blood using NMR spectroscopy. Considering that the levels of coenzymes and antioxidants represent a sensitive measure of cellular functions in health and numerous diseases, the NMR method presented here potentially opens a new chapter in the metabolomics of blood.
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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109
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Hoffmann F, Li DW, Sebastiani D, Brüschweiler R. Improved Quantum Chemical NMR Chemical Shift Prediction of Metabolites in Aqueous Solution toward the Validation of Unknowns. J Phys Chem A 2017; 121:3071-3078. [PMID: 28388058 DOI: 10.1021/acs.jpca.7b01954] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A quantum-chemistry based protocol, termed MOSS-DFT, is presented for the prediction of 13C and 1H NMR chemical shifts of a wide range of organic molecules in aqueous solution, including metabolites. Molecular motif-specific linear scaling parameters are reported for five different density functional theory (DFT) methods (B97-2/pcS-1, B97-2/pcS-2, B97-2/pcS-3, B3LYP/pcS-2, and BLYP/pcS-2), which were applied to a large set of 176 metabolite molecules. The chemical shift root-mean-square deviations (RMSD) for the best method, B97-2/pcS-3, are 1.93 and 0.154 ppm for 13C and 1H chemical shifts, respectively. Excellent results have been obtained for chemical shifts of methyl and aromatic 13C and 1H that are not directly bonded to a heteroatom (O, N, S, or P) with RMSD values of 1.15/0.079 and 1.31/0.118 ppm, respectively. This study not only demonstrates how NMR chemical shift in aqueous environment can be improved over the commonly used global linear scaling approach, but also allows for motif-specific error estimates, which are useful for an improved chemical shift-based verification of metabolite candidates of metabolomics samples containing unknown components.
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Affiliation(s)
- Felix Hoffmann
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg , von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States
| | - Daniel Sebastiani
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg , von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University , Columbus, Ohio 43210, United States
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110
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Lane AN, Fan TWM. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry. Arch Biochem Biophys 2017; 628:123-131. [PMID: 28263717 DOI: 10.1016/j.abb.2017.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 01/23/2023]
Abstract
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA.
| | - Teresa W-M Fan
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA
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111
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Menni C, Zierer J, Valdes AM, Spector TD. Mixing omics: combining genetics and metabolomics to study rheumatic diseases. Nat Rev Rheumatol 2017; 13:174-181. [PMID: 28148918 DOI: 10.1038/nrrheum.2017.5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metabolomics is an exciting field in systems biology that provides a direct readout of the biochemical activities taking place within an individual at a particular point in time. Metabolite levels are influenced by many factors, including disease status, environment, medications, diet and, importantly, genetics. Thanks to their dynamic nature, metabolites are useful for diagnosis and prognosis, as well as for predicting and monitoring the efficacy of treatments. At the same time, the strong links between an individual's metabolic and genetic profiles enable the investigation of pathways that underlie changes in metabolite levels. Thus, for the field of metabolomics to yield its full potential, researchers need to take into account the genetic factors underlying the production of metabolites, and the potential role of these metabolites in disease processes. In this Review, the methodological aspects related to metabolomic profiling and any potential links between metabolomics and the genetics of some of the most common rheumatic diseases are described. Links between metabolomics, genetics and emerging fields such as the gut microbiome and proteomics are also discussed.
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Affiliation(s)
- Cristina Menni
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Jonas Zierer
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Ana M Valdes
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
- Academic Rheumatology, The University of Nottingham, Clinical Sciences Building, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Tim D Spector
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
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112
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Millard P, Cahoreau E, Heuillet M, Portais JC, Lippens G. 15N-NMR-Based Approach for Amino Acids-Based 13C-Metabolic Flux Analysis of Metabolism. Anal Chem 2017; 89:2101-2106. [DOI: 10.1021/acs.analchem.6b04767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pierre Millard
- LISBP, Université de Toulouse,
CNRS, INRA, INSA, 31077, Toulouse, France
| | - Edern Cahoreau
- LISBP, Université de Toulouse,
CNRS, INRA, INSA, 31077, Toulouse, France
| | - Maud Heuillet
- LISBP, Université de Toulouse,
CNRS, INRA, INSA, 31077, Toulouse, France
| | | | - Guy Lippens
- LISBP, Université de Toulouse,
CNRS, INRA, INSA, 31077, Toulouse, France
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113
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine and
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine and
- Department of Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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114
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Wist J. Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:22-28. [PMID: 27668407 DOI: 10.1002/mrc.4533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/14/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Untargeted strategies have changed the rules of the game in complex mixture analysis, introducing an amazing potential for medical and biological applications that is just starting to be tapped. But with great power come great challenges; although untargeted mixture analysis opens the road for many exciting possibilities, the road is still full of perils. On the one hand, this article highlights some of the difficulties that need to be sorted for mixture analysis by NMR to fulfill its potential, along with insight on how they may be managed. Highlighted key points include the need for 'computer friendly' solutions for sharing data, experimental design and algorithm to facilitate the steady growth of knowledge and modeling ability in the field, and the need for large-scale studies to improve confidence in newly identified biomarkers. On the other hand, the second part of this article presents some breakthroughs in NMR experiments that, when combined, may modify the landscape of mixture analysis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Julien Wist
- Chemistry Department, Universidad del Valle, Cali, Colombia
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115
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Lee S, Wen H, An YJ, Cha JW, Ko YJ, Hyberts SG, Park S. Carbon Isotopomer Analysis with Non-Unifom Sampling HSQC NMR for Cell Extract and Live Cell Metabolomics Studies. Anal Chem 2016; 89:1078-1085. [DOI: 10.1021/acs.analchem.6b02107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sujin Lee
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - He Wen
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Department
of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yong Jin An
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Jin Wook Cha
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Natural
Constituents Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea
| | - Yoon-Joo Ko
- National
Center for Inter-University Research Facilities (NCIRF), Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Sven G. Hyberts
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sunghyouk Park
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
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116
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Bingol K, Li DW, Zhang B, Brüschweiler R. Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server. Anal Chem 2016; 88:12411-12418. [PMID: 28193069 DOI: 10.1021/acs.analchem.6b03724] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the coanalysis of up to three two-dimensional (2D) NMR spectra, namely, 13C-1H HSQC (heteronuclear single quantum coherence spectroscopy), 1H-1H TOCSY (total correlation spectroscopy), and 13C-1H HSQC-TOCSY, for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum, and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
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117
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Serum metabolomics analysis of patients with chikungunya and dengue mono/co-infections reveals distinct metabolite signatures in the three disease conditions. Sci Rep 2016; 6:36833. [PMID: 27845374 PMCID: PMC5109290 DOI: 10.1038/srep36833] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/17/2016] [Indexed: 12/23/2022] Open
Abstract
Chikungunya and dengue are arboviral infections with overlapping clinical symptoms. A subset of chikungunya infection occurs also as co-infections with dengue, resulting in complications during diagnosis and patient management. The present study was undertaken to identify the global metabolome of patient sera infected with chikungunya as mono infections and with dengue as co-infections. Using nuclear magnetic resonance (NMR) spectroscopy, the metabolome of sera of three disease conditions, namely, chikungunya and dengue as mono-infections and when co-infected were ascertained and compared with healthy individuals. Further, the cohorts were analyzed on the basis of age, onset of fever and joint involvement. Here we show that many metabolites in the serum are significantly differentially regulated during chikungunya mono-infection as well as during chikungunya co-infection with dengue. We observed that glycine, serine, threonine, galactose and pyrimidine metabolisms are the most perturbed pathways in both mono and co-infection conditions. The affected pathways in our study correlate well with the clinical manifestation like fever, inflammation, energy deprivation and joint pain during the infections. These results may serve as a starting point for validations and identification of distinct biomolecules that could be exploited as biomarker candidates thereby helping in better patient management.
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118
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Recent advances in high-throughput 13C-fluxomics. Curr Opin Biotechnol 2016; 43:104-109. [PMID: 27838571 DOI: 10.1016/j.copbio.2016.10.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
The rise of high throughput (HT) strain engineering tools accompanying the area of synthetic biology is supporting the generation of a large number of microbial cell factories. A current bottleneck in process development is our limited capacity to rapidly analyze the metabolic state of the engineered strains, and in particular their intracellular fluxes. HT 13C-fluxomics workflows have not yet become commonplace, despite the existence of several HT tools at each of the required stages. This includes cultivation and sampling systems, analytics for isotopic analysis, and software for data processing and flux calculation. Here, we review recent advances in the field and highlight bottlenecks that must be overcome to allow the emergence of true HT 13C-fluxomics workflows.
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119
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Di Gialleonardo V, Tee SS, Aldeborgh HN, Miloushev VZ, Cunha LS, Sukenick GD, Keshari KR. High-Throughput Indirect Quantitation of 13C Enriched Metabolites Using 1H NMR. Anal Chem 2016; 88:11147-11153. [PMID: 27749041 DOI: 10.1021/acs.analchem.6b03307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomics to perform quantitative profiling of low-molecular weight compounds from biological specimens. The measurement of endogenous metabolites using NMR has proven to be a powerful tool to identify new metabolic biomarkers in physiological and pathological conditions, and to study and evaluate treatment efficiency. In this study we present a rapid approach to indirectly quantify 13C enriched molecules using one-dimensional (1D) 1H NMR. We demonstrate this approach using isotopically labeled [1,6-13C]glucose and in four different cell lines. We confirm the applicability of this approach for treatment follow-up, utilizing a renal cancer cell line with rapamycin as a tool compound to study changes in metabolic profiles. Finally, we validate the applicability of this method to study metabolic biomarkers from ex vivo tumor extracts, after infusion, using isotopically enriched glucose. Given the high throughput and increased sensitivity of direct-detect 1H NMR, this analytical approach provides an avenue for simple and rapid metabolic analysis of biological samples including blood, urine, and biopsies.
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Affiliation(s)
- Valentina Di Gialleonardo
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - Sui Seng Tee
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - Hannah N Aldeborgh
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - Vesselin Z Miloushev
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - Lidia S Cunha
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - George D Sukenick
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates
| | - Kayvan R Keshari
- Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United Sates.,Weill Cornell Medical College, New York, New York 10065, United States
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120
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Karlsson M, Jensen PR, Ardenkjaer-Larsen JH, Lerche MH. Difference between Extra- and Intracellular T
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Values of Carboxylic Acids Affects the Quantitative Analysis of Cellular Kinetics by Hyperpolarized NMR. Angew Chem Int Ed Engl 2016; 55:13567-13570. [DOI: 10.1002/anie.201607535] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Magnus Karlsson
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Pernille Rose Jensen
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Jan Henrik Ardenkjaer-Larsen
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Mathilde H. Lerche
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
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121
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Karlsson M, Jensen PR, Ardenkjaer-Larsen JH, Lerche MH. Difference between Extra- and Intracellular T
1
Values of Carboxylic Acids Affects the Quantitative Analysis of Cellular Kinetics by Hyperpolarized NMR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Magnus Karlsson
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Pernille Rose Jensen
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Jan Henrik Ardenkjaer-Larsen
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
| | - Mathilde H. Lerche
- Technical University of Denmark; Department of Electrical Engineering; Center for Hyperpolarization in Magnetic Resonance; Building 349 DK-2800 Kgs Lyngby Denmark
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122
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Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL. Increasing rigor in NMR-based metabolomics through validated and open source tools. Curr Opin Biotechnol 2016; 43:56-61. [PMID: 27643760 DOI: 10.1016/j.copbio.2016.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/30/2016] [Indexed: 01/18/2023]
Abstract
The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies.
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Affiliation(s)
- Hamid R Eghbalnia
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Pedro R Romero
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - William M Westler
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Kumaran Baskaran
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Eldon L Ulrich
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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123
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Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Curr Opin Biotechnol 2016; 43:34-40. [PMID: 27580257 DOI: 10.1016/j.copbio.2016.08.001] [Citation(s) in RCA: 487] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 12/15/2022]
Abstract
The two leading analytical approaches to metabolomics are mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Although currently overshadowed by MS in terms of numbers of compounds resolved, NMR spectroscopy offers advantages both on its own and coupled with MS. NMR data are highly reproducible and quantitative over a wide dynamic range and are unmatched for determining structures of unknowns. NMR is adept at tracing metabolic pathways and fluxes using isotope labels. Moreover, NMR is non-destructive and can be utilized in vivo. NMR results have a proven track record of translating in vitro findings to in vivo clinical applications.
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Affiliation(s)
- John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Rafael Brüschweiler
- Department of Chemistry & Biochemistry, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, USA; Department of Biological Chemistry & Pharmacology, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, USA
| | - Arthur S Edison
- Department of Genetics and Biochemistry, Institute of Bioinformatics and Complex Carbohydrate Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Hamid R Eghbalnia
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588, USA
| | - Daniel Raftery
- Department of Anesthesiology & Pain Medicine, 850 Republican St, University of Washington, Seattle, WA 98109, USA
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8; Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
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124
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Bingol K, Brüschweiler R. Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods. Curr Opin Biotechnol 2016; 43:17-24. [PMID: 27552705 DOI: 10.1016/j.copbio.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 01/10/2023]
Abstract
Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexity of these tasks.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, United States.
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125
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Lane AN, Higashi RM, Fan TWM. Preclinical models for interrogating drug action in human cancers using Stable Isotope Resolved Metabolomics (SIRM). Metabolomics 2016; 12:118. [PMID: 27489532 PMCID: PMC4968890 DOI: 10.1007/s11306-016-1065-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AIMS In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions. BACKGROUND All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy. As metabolism reports directly on the biochemical state of cells and tissues, it can be very sensitive to drugs and/or other environmental changes. This is especially so when metabolic activities are probed by stable isotope tracing methods, which can also provide detailed mechanistic information on drug action. We have developed and been applying Stable Isotope-Resolved Metabolomics (SIRM) to examine metabolic reprogramming of human lung cancer cells in monoculture, in mouse xenograft/explant models, and in lung cancer patients in situ (Lane et al. 2011; T. W. Fan et al. 2011; T. W-M. Fan et al. 2012; T. W. Fan et al. 2012; Xie et al. 2014b; Ren et al. 2014a; Sellers et al. 2015b). We are able to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by O. Warburg (Warburg 1923), which retain the native tissue architecture and heterogeneity with a paired benign versus cancer design under defined cell culture conditions. This platform offers an unprecedented human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (Xie et al. 2014a). As the microenvironment of the target human tissue is retained and individual patient's response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments. CONCLUSIONS AND FUTURE WORK Development of ex vivo human tissue and animal models with humanized organs including bone marrow and liver show considerable promise for analyzing drug responses that are more relevant to humans. Similarly using stable isotope tracer methods with these improved models in advanced stages of the drug development pipeline, in conjunction with tissue biopsy is expected significantly to reduce the high failure rate of experimental drugs in Phase II and III clinical trials.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky
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