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Wong A. High-resolution magic-angle spinning NMR metabolic profiling with spatially localized spectroscopy under slow sample spinning. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6302-6308. [PMID: 37965882 DOI: 10.1039/d3ay01812a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Owing to its feasibility and versatility, High-Resolution Magic-Angle Spinning (HRMAS) NMR spectroscopy is considered an essential analytical technique in metabolomics for assessing the biochemical composition of tissue samples. Localized profiling with HRMAS has recently emerged and shown promise for spatial resolution of metabolic profiles within the sampling tissues. However, the requisite sample spinning in a few kHz can perturb the tissues spatially and morphologically. This study explored a simple approach to slow sample spinning experiments at 500 Hz without needing pulse-assist sideband suppression experiments to acquire localized spectral data. Slow-spinning localized one-and two-dimensional spectroscopy, including Total Correlation Spectroscopy (TOCSY), were explored on soft tissues for metabolic profiling. We also examined inhomogeneous radiofrequency B1 field distribution across the sampling volume, which can affect the quantification analysis.
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Affiliation(s)
- Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France.
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2
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Stabinska J, Müller-Lutz A, Wittsack HJ, Tell C, Rump LC, Ertas N, Antoch G, Ljimani A. Two point Dixon-based chemical exchange saturation transfer (CEST) MRI in renal transplant patients on 3 T. Magn Reson Imaging 2022; 90:61-69. [PMID: 35476934 DOI: 10.1016/j.mri.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE To assess the performance of two point (2-pt) Dixon-based chemical exchange saturation transfer (CEST) imaging for fat suppression in renal transplant patients. METHODS The 2-pt Dixon-based CEST MRI was validated in an egg-phantom and in fourteen renal transplant recipients (5 females and 9 males; age range: 23-78 years; mean age: 51 ± 16.8). All CEST experiments were performed on a 3 T clinical MRI scanner using a dual-echo CEST sequence. The 2-pt Dixon technique was applied to generate water-only CEST images at different frequency offsets, which were further used to calculate the z-spectra. The magnetization transfer ratio asymmetry (MTRasym) values in the frequency ranges of hydroxyl, amine and amide protons were estimated in the renal cortex and medulla. RESULTS Results of the in vitro experiments suggest that the 2-pt Dixon technique enables effective fat peak removal and does not introduce additional asymmetries to the z-spectrum. Accordingly, our results in vivo show that the fat-corrected amide proton transfer (APT) effect in the kidney is significantly higher compared to that obtained from the CEST data acquired close to the in-phase condition both in the renal cortex (-0.1 [0.7] vs. -0.7 [1.2], P = 0.029) and medulla (0.3 [0.8] vs. 0.01 [1.3], P = 0.049), indicating that the 2-pt Dixon-based CEST method increases the specificity of the APT contrast by correcting the fat-induced artifacts. CONCLUSION Combination of the dual-echo CEST acquisition with Dixon post-processing provides effective water-fat separation, allowing more accurate quantification of the APT CEST effect in the transplanted kidney.
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Affiliation(s)
- Julia Stabinska
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Anja Müller-Lutz
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Hans-Jörg Wittsack
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Christian Tell
- Department of Nephrology, Medical Faculty, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Lars Christian Rump
- Department of Nephrology, Medical Faculty, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Neslihan Ertas
- Department of Vascular and Endovascular Surgery, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Gerald Antoch
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
| | - Alexandra Ljimani
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
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3
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Loo RL, Chan Q, Nicholson JK, Holmes E. Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine- N-oxide. J Proteome Res 2022; 21:560-589. [PMID: 35142516 DOI: 10.1021/acs.jproteome.1c00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
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Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
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4
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Wang H, Falcoz S, Berteau JP. Long-Chain Fatty Acids in Bones and Their Link to Submicroscopic Vascularization Network: NMR Assignment and Relaxation Studies under Magic Angle Spinning Conditions in Intramuscular Bones of Atlantic Herring Fish. J Phys Chem B 2021; 125:4585-4595. [PMID: 33914538 DOI: 10.1021/acs.jpcb.1c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-lasting proton signals in bones are identified as long-chain fatty acids, including saturated, mono-, and di-unsaturated fatty acids, with direct nuclear magnetic resonance evidence. We used intramuscular bones from Atlantic Herring fish to avoid interference from lipid-rich marrows. The key is to recognize that these signals are from mobile phase materials and study them with J-coupled correlation spectroscopies under magic angle spinning conditions. We kept extensive 1H-spin-echo records that allowed us to examine the effect of magic angle spinning on the transverse relaxation time of water and lipids over time. While it is impossible to distinguish based on chemical shifts, the relaxation data suggest that the signals are more consistent with the interpretation of phospholipid membranes than triglycerides in lipid droplets. In particular, the simultaneous T2 changes in water and lipids suggest that the centrifugal impact of magic angle spinning alters the lipid's structure in very tight spaces. Additional evidence of phospholipid membranes came from the choline-γ resonance at 3.2 ppm in fresh samples, which disappears with magic angle spinning. Thus, the fatty acid signals are at least partially from membrane bilayer structures, and we propose that they are linked to the submicroscopic vascularization channels similar to the dense canaliculi network in mammalian bones. Our detection of phospholipids from bones depended critically on two factors: (1) the elimination of the overwhelming triglyceride signals from marrows and (2) the preservation of water that biomembranes require. The relaxation data reveal aspects of lipid fluidity that have not been elucidated by previous order parameter studies on model membranes. Relaxation times have long been considered difficult to interpret. A robust and renewed understanding may be beneficial.
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Affiliation(s)
- Hsin Wang
- Department of Chemistry and Biochemistry, The City College of New York and CUNY Institute for Macromolecular Assemblies, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Steve Falcoz
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, New York 10314, United States
| | - Jean-Philippe Berteau
- Department of Physical Therapy, The College of Staten Island, 2800 Victory Blvd, Staten Island, New York 10314, United States.,New York Centre for Biomedical Engineering, City University of New York - City College of New York, New York, New York 10031, United States.,Nanosciences Initiative, City University of New York - Advance Science Research Center, New York, New York 10031, United States
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Asampille G, Cheredath A, Joseph D, Adiga SK, Atreya HS. The utility of nuclear magnetic resonance spectroscopy in assisted reproduction. Open Biol 2020; 10:200092. [PMID: 33142083 PMCID: PMC7729034 DOI: 10.1098/rsob.200092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Infertility affects approximately 15-20% of individuals of reproductive age worldwide. Over the last 40 years, assisted reproductive technology (ART) has helped millions of childless couples. However, ART is limited by a low success rate and risk of multiple gestations. Devising methods for selecting the best gamete or embryo that increases the ART success rate and prevention of multiple gestation has become one of the key goals in ART today. Special emphasis has been placed on the development of non-invasive approaches, which do not require perturbing the embryonic cells, as the current morphology-based embryo selection approach has shortcomings in predicting the implantation potential of embryos. An observed association between embryo metabolism and viability has prompted researchers to develop metabolomics-based biomarkers. Nuclear magnetic resonance (NMR) spectroscopy provides a non-invasive approach for the metabolic profiling of tissues, gametes and embryos, with the key advantage of having a minimal sample preparation procedure. Using NMR spectroscopy, biologically important molecules can be identified and quantified in intact cells, extracts or secretomes. This, in turn, helps to map out the active metabolic pathways in a system. The present review covers the contribution of NMR spectroscopy in assisted reproduction at various stages of the process.
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Affiliation(s)
- Gitanjali Asampille
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Aswathi Cheredath
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - David Joseph
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Satish K. Adiga
- Department of Clinical Embryology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
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Important Considerations for Sample Collection in Metabolomics Studies with a Special Focus on Applications to Liver Functions. Metabolites 2020; 10:metabo10030104. [PMID: 32178364 PMCID: PMC7142637 DOI: 10.3390/metabo10030104] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolomics has found numerous applications in the study of liver metabolism in health and disease. Metabolomics studies can be conducted in a variety of biological matrices ranging from easily accessible biofluids such as urine, blood or feces, to organs, tissues or even cells. Sample collection and storage are critical steps for which standard operating procedures must be followed. Inappropriate sample collection or storage can indeed result in high variability, interferences with instrumentation or degradation of metabolites. In this review, we will first highlight important general factors that should be considered when planning sample collection in the study design of metabolomic studies, such as nutritional status and circadian rhythm. Then, we will discuss in more detail the specific procedures that have been described for optimal pre-analytical handling of the most commonly used matrices (urine, blood, feces, tissues and cells).
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7
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Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 519] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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8
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Lucas-Torres C, Huber G, Ichikawa A, Nishiyama Y, Wong A. HR-μMAS NMR-Based Metabolomics: Localized Metabolic Profiling of a Garlic Clove with μg Tissues. Anal Chem 2018; 90:13736-13743. [DOI: 10.1021/acs.analchem.8b04150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | - Gaspard Huber
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | | | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
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9
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Amberg A, Riefke B, Schlotterbeck G, Ross A, Senn H, Dieterle F, Keck M. NMR and MS Methods for Metabolomics. Methods Mol Biol 2017; 1641:229-258. [PMID: 28748468 DOI: 10.1007/978-1-4939-7172-5_13] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabolomics, i.e., NMR, UPLC-MS, and GC-MS, have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabolomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation to determining the measurement details of all analytical platforms, and finally to discussing the corresponding specific steps of data analysis.
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Affiliation(s)
| | - Björn Riefke
- Investigational Toxicology, Metabolic Profiling and Clinical Pathology, Bayer Pharma AG, Muellerstr. 178, Berlin, 13353, Germany.
| | - Götz Schlotterbeck
- School of Life Sciences, Institute for Chemistry and Bioanalytics, University of Applied Sciences, Northwestern Switzerland, Muttenz, Switzerland
| | - Alfred Ross
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Hans Senn
- Heythrop College UCL, Kensington Square, London W85HN, UK
| | - Frank Dieterle
- New Products and Medical, Near Patient Testing, Novartis, Basel, Switzerland
| | - Matthias Keck
- Analytical Development 1, Bayer Pharma AG, Wupperal, 42096, Germany
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Ouldamer L, Nadal-Desbarats L, Chevalier S, Body G, Goupille C, Bougnoux P. NMR-Based Lipidomic Approach To Evaluate Controlled Dietary Intake of Lipids in Adipose Tissue of a Rat Mammary Tumor Model. J Proteome Res 2016; 15:868-78. [DOI: 10.1021/acs.jproteome.5b00788] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lobna Ouldamer
- INSERM UMR1069, 10 Boulevard Tonnellé, 37044 Tours, France
- François-Rabelais University, 10 Boulevard
Tonnellé, 37044 Tours, France
| | - Lydie Nadal-Desbarats
- François-Rabelais University, 10 Boulevard
Tonnellé, 37044 Tours, France
- INSERM UMR930, 10 Boulevard Tonnellé, 37044 Tours, France
| | - Stephan Chevalier
- INSERM UMR1069, 10 Boulevard Tonnellé, 37044 Tours, France
- François-Rabelais University, 10 Boulevard
Tonnellé, 37044 Tours, France
| | - Gilles Body
- François-Rabelais University, 10 Boulevard
Tonnellé, 37044 Tours, France
| | | | - Philippe Bougnoux
- INSERM UMR1069, 10 Boulevard Tonnellé, 37044 Tours, France
- François-Rabelais University, 10 Boulevard
Tonnellé, 37044 Tours, France
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11
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Hart CD, Tenori L, Luchinat C, Di Leo A. Metabolomics in Breast Cancer: Current Status and Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:217-34. [DOI: 10.1007/978-3-319-22909-6_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Pothirajan P, Ravindran S, George A, Magin RL, Kotecha M. Magnetic resonance spectroscopy and imaging can differentiate between engineered bone and engineered cartilage. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:3929-32. [PMID: 25570851 DOI: 10.1109/embc.2014.6944483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In the situation when both cartilage and its underlying bone are damaged, osteochondral tissue engineering is being developed to provide a solution. In such cases, the ability to non-invasively monitor and differentiate the development of both cartilage and bone tissues is important. Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) have been widely used to non-invasively assess tissue-engineered cartilage and tissue-engineered bone. The purpose of this work is to assess differences in MR properties of tissue-engineered bone and tissue-engineered cartilage generated from the same cell-plus-scaffold combination at the early stage of tissue growth. We developed cartilage and bone tissue constructs by seeding human marrow stromal cells (HMSCs, 2 million/ml) in 1:1 collagen/chitosan gel for four weeks. The chondrogenic or osteogenic differentiation of cells was directed with the aid of a culture medium containing chondrogenic or osteogenic growth factors, respectively. The proton and sodium NMR and waterproton T1, T2 and diffusion MRI experiments were performed on these constructs and the control collagen/chitosan gel using a 9.4 T ((1)H freq. = 400 MHz) and a 11.7 T ((1)H freq. = 500 MHz) NMR spectrometers. In all cases, the development of bone and cartilage was found to be clearly distinguishable using NMR and MRI. We conclude that MRS and MRI are powerful tools to assess growing osteochondral tissue regeneration.
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Wang P, Wang Q, Yang B, Zhao S, Kuang H. The Progress of Metabolomics Study in Traditional Chinese Medicine Research. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2015; 43:1281-310. [DOI: 10.1142/s0192415x15500731] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Traditional Chinese medicine (TCM) has played important roles in health protection and disease treatment for thousands of years in China and has gained the gradual acceptance of the international community. However, many intricate issues, which cannot be explained by traditional methods, still remain, thus, new ideas and technologies are needed. As an emerging system biology technology, the holistic view adopted by metabolomics is similar to that of TCM, which allows us to investigate TCM with complicated conditions and multiple factors in depth. In this paper, we tried to give a timely and comprehensive update about the methodology progression of metabolomics, as well as its applications, in different fields of TCM studies including quality control, processing, safety and efficacy evaluation. The herbs investigated by metabolomics were selected for detailed examination, including Anemarrhena asphodeloides Bunge, Atractylodes macrocephala Kidd, Pinellia ternate, etc.; furthermore, some valuable results have been obtained and summarized. In conclusion, although the study of metabolomics is at the early phase and requires further scrutiny and validation, it still provides bright prospects to dissect the synergistic action of multiple components from TCM. Overall, with the further development of analytical techniques, especially multi-analysis techniques, we expect that metabolomics will greatly promote TCM research and the establishment of international standards, which is beneficial to TCM modernization.
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Affiliation(s)
- Pengcheng Wang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Qiuhong Wang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Shan Zhao
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Haixue Kuang
- Key Laboratory of Chinese Materia Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, Harbin, P.R. China
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The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. Methods Mol Biol 2015; 1277:161-93. [PMID: 25677154 DOI: 10.1007/978-1-4939-2377-9_13] [Citation(s) in RCA: 316] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted.
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Mori T, Tsuboi Y, Ishida N, Nishikubo N, Demura T, Kikuchi J. Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of (13)C-labeled Plant Metabolites and Lignocellulose. Sci Rep 2015; 5:11848. [PMID: 26143886 PMCID: PMC4491710 DOI: 10.1038/srep11848] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 06/08/2015] [Indexed: 01/18/2023] Open
Abstract
Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components.
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Affiliation(s)
- Tetsuya Mori
- 1] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan [2] Biotechnology Laboratory, Toyota Central R&D Labs, Inc., 41-1, Nagakute 480-1192, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Nobuhiro Ishida
- Biotechnology Laboratory, Toyota Central R&D Labs, Inc., 41-1, Nagakute 480-1192, Japan
| | - Nobuyuki Nishikubo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Taku Demura
- 1] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Biomass Engineering Program, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Jun Kikuchi
- 1] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [3] Biomass Engineering Program, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako 351-0198, Japan [4] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Misawa T, Date Y, Kikuchi J. Human Metabolic, Mineral, and Microbiota Fluctuations Across Daily Nutritional Intake Visualized by a Data-Driven Approach. J Proteome Res 2015; 14:1526-34. [DOI: 10.1021/pr501194k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Takuma Misawa
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
- Biomass
Engineering Program, RIKEN Research Cluster for Innovation, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Dumas ME, Davidovic L. Metabolic Profiling and Phenotyping of Central Nervous System Diseases: Metabolites Bring Insights into Brain Dysfunctions. J Neuroimmune Pharmacol 2015; 10:402-24. [PMID: 25616565 DOI: 10.1007/s11481-014-9578-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/26/2014] [Indexed: 12/13/2022]
Abstract
Metabolic phenotyping corresponds to the large-scale quantitative and qualitative analysis of the metabolome i.e., the low-molecular weight <1 KDa fraction in biological samples, and provides a key opportunity to advance neurosciences. Proton nuclear magnetic resonance and mass spectrometry are the main analytical platforms used for metabolic profiling, enabling detection and quantitation of a wide range of compounds of particular neuro-pharmacological and physiological relevance, including neurotransmitters, secondary messengers, structural lipids, as well as their precursors, intermediates and degradation products. Metabolic profiling is therefore particularly indicated for the study of central nervous system by probing metabolic and neurochemical profiles of the healthy or diseased brain, in preclinical models or in human samples. In this review, we introduce the analytical and statistical requirements for metabolic profiling. Then, we focus on key studies in the field of metabolic profiling applied to the characterization of animal models and human samples of central nervous system disorders. We highlight the potential of metabolic profiling for pharmacological and physiological evaluation, diagnosis and drug therapy monitoring of patients affected by brain disorders. Finally, we discuss the current challenges in the field, including the development of systems biology and pharmacology strategies improving our understanding of metabolic signatures and mechanisms of central nervous system diseases.
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Affiliation(s)
- Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, SW7 2AZ, UK
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André M, Dumez JN, Rezig L, Shintu L, Piotto M, Caldarelli S. Complete protocol for slow-spinning high-resolution magic-angle spinning NMR analysis of fragile tissues. Anal Chem 2014; 86:10749-54. [PMID: 25286333 DOI: 10.1021/ac502792u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
High-resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR) is an essential tool to characterize a variety of semisolid systems, including biological tissues, with virtually no sample preparation. The "non-destructive" nature of NMR is typically compromised, however, by the extreme centrifugal forces experienced under conventional HR-MAS frequencies of several kilohertz. These features limit the usefulness of current HR-MAS approaches for fragile samples. Here, we introduce a full protocol for acquiring high-quality HR-MAS NMR spectra of biological tissues at low spinning rates (down to a few hundred hertz). The protocol first consists of a carefully designed sample preparation, which yields spectra without significant spinning sidebands at low spinning frequency for several types of sample holders, including the standard disposable inserts classically used in HR-MAS NMR-based metabolomics. Suppression of broad spectral features is then achieved using a modified version of the recently introduced PROJECT experiment with added water suppression and rotor synchronization, which deposits limited power in the sample and which can be suitably rotor-synchronized at low spinning rates. The performance of the slow HR-MAS NMR procedure is demonstrated on conventional (liver tissue) and very delicate (fish eggs) samples, for which the slow-spinning conditions are shown to preserve the structural integrity and to minimize intercompartmental leaks of metabolites. Taken together, these results expand the applicability and reliability of HR-MAS NMR spectroscopy. These results have been obtained at 400 and 600 MHz and suggest that high-quality slow HR-MAS spectra can be expected at higher magnetic fields using the described protocol.
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Affiliation(s)
- Marion André
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301 , Avenue de la Terrasse, 91190 Gif sur Yvette, France
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Serum metabonomic analysis of protective effects of Curcuma aromatica oil on renal fibrosis rats. PLoS One 2014; 9:e108678. [PMID: 25265289 PMCID: PMC4181651 DOI: 10.1371/journal.pone.0108678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/24/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Curcuma aromatica oil is a traditional herbal medicine demonstrating protective and anti-fibrosis activities in renal fibrosis patients. However, study of its mechanism of action is challenged by its multiple components and multiple targets that its active agent acts on. METHODOLOGY/PRINCIPAL FINDINGS Nuclear magnetic resonance (NMR)-based metabonomics combined with clinical chemistry and histopathology examination were performed to evaluate intervening effects of Curcuma aromatica oil on renal interstitial fibrosis rats induced by unilateral ureteral obstruction. The metabolite levels were compared based on integral values of serum 1H NMR spectra from rats on 3, 7, 14, and 28 days after the medicine administration. Time trajectory analysis demonstrated that metabolic profiles of the agent-treated rats were restored to control levels after 7 days of dosage. The results confirmed that the agent would be an effective anti-fibrosis medicine in a time-dependent manner, especially in early renal fibrosis stage. Targeted metabolite analysis showed that the medicine could lower levels of lipid, acetoacetate, glucose, phosphorylcholine/choline, trimethylamine oxide and raise levels of pyruvate, glycine in the serum of the rats. Serum clinical chemistry and kidney histopathology examination dovetailed well with the metabonomics data. CONCLUSIONS/SIGNIFICANCES The results substantiated that Curcuma aromatica oil administration can ameliorate renal fibrosis symptoms by inhibiting some metabolic pathways, including lipids metabolism, glycolysis and methylamine metabolism, which are dominating targets of the agent working in vivo. This study further strengthens the novel analytical approach for evaluating the effect of traditional herbal medicine and elucidating its molecular mechanism.
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Izquierdo-García JL, Naz S, Nin N, Rojas Y, Erazo M, Martínez-Caro L, García A, de Paula M, Fernández-Segoviano P, Casals C, Esteban A, Ruíz-Cabello J, Barbas C, Lorente JA. A Metabolomic Approach to the Pathogenesis of Ventilator-induced Lung Injury. Anesthesiology 2014; 120:694-702. [PMID: 24253045 DOI: 10.1097/aln.0000000000000074] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Global metabolic profiling using quantitative nuclear magnetic resonance spectroscopy (MRS) and mass spectrometry (MS) is useful for biomarker discovery. The objective of this study was to discover biomarkers of acute lung injury induced by mechanical ventilation (ventilator-induced lung injury [VILI]), by using MRS and MS. METHODS Male Sprague-Dawley rats were subjected to two ventilatory strategies for 2.5 h: tidal volume 9 ml/kg, positive end-expiratory pressure 5 cm H2O (control, n = 14); and tidal volume 25 ml/kg and positive end-expiratory pressure 0 cm H2O (VILI, n = 10). Lung tissue, bronchoalveolar lavage fluid, and serum spectra were obtained by high-resolution magic angle spinning and H-MRS. Serum spectra were acquired by high-performance liquid chromatography coupled to quadupole-time of flight MS. Principal component and partial least squares analyses were performed. RESULTS Metabolic profiling discriminated characteristics between control and VILI animals. As compared with the controls, animals with VILI showed by MRS higher concentrations of lactate and lower concentration of glucose and glycine in lung tissue, accompanied by increased levels of glucose, lactate, acetate, 3-hydroxybutyrate, and creatine in bronchoalveolar lavage fluid. In serum, increased levels of phosphatidylcholine, oleamide, sphinganine, hexadecenal and lysine, and decreased levels of lyso-phosphatidylcholine and sphingosine were identified by MS. CONCLUSIONS This pilot study suggests that VILI is characterized by a particular metabolic profile that can be identified by MRS and MS. The metabolic profile, though preliminary and pending confirmation in larger data sets, suggests alterations in energy and membrane lipids.SUPPLEMENTAL DIGITAL CONTENT IS AVAILABLE IN THE TEXT.
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Affiliation(s)
- José L Izquierdo-García
- From the Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain (J.L.I.-G., N.N., Y.R., L.M.-C., M.d.P., P.F.-S., C.C., A.E., J.R.-C., and J.A.L.); Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.L.I.-G. and J.R.-C.); Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain (S.N., M.E., A.G., and C.B.); Hospital Universitario de Torrejón, Madrid, Spain (N.N.); Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain (Y.R., L.M.-C., M.d.P., P.F.-S., A.E., and J.A.L.); Universidad Complutense de Madrid, Madrid, Spain (C.C. and J.R.-C.); and Universidad Europea de Madrid, Madrid, Spain (J.A.L.)
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21
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A metabolomic perspective on coeliac disease. Autoimmune Dis 2014; 2014:756138. [PMID: 24665364 PMCID: PMC3934717 DOI: 10.1155/2014/756138] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/30/2013] [Accepted: 10/20/2013] [Indexed: 12/16/2022] Open
Abstract
Metabolomics is an "omic" science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. In the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. A metabolomics investigation of coeliac disease (CD) revealed that a metabolic fingerprint for CD can be defined, which accounts for three different but complementary components: malabsorption, energy metabolism, and alterations in gut microflora and/or intestinal permeability. In this review, we will discuss the major advancements in metabolomics of CD, in particular with respect to the role of gut microbiome and energy metabolism.
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Abstract
Metabolite extraction is a key step in metabolomic analyses, particularly for untargeted studies. The extraction determines the types of metabolites that will be detected and the analytical platform to be used. In this chapter we describe two protocols aimed at detecting polar metabolites from biological samples; the first is aimed at detecting reduced species by LC/MS, and the second satisfies the requirements for both NMR and LC/MS analysis simultaneously.
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Sun G, Wang J, Zhang J, Ma C, Shao C, Hao J, Zheng J, Feng X, Zuo C. High-resolution magic angle spinning (1)H magnetic resonance spectroscopy detects choline as a biomarker in a swine obstructive chronic pancreatitis model at an early stage. MOLECULAR BIOSYSTEMS 2013; 10:467-74. [PMID: 24342968 DOI: 10.1039/c3mb70406h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chronic pancreatitis (CP) is a progressive inflammatory and fibrotic disease of the pancreas which encompasses a variety of clinical syndromes ranging from mild to life-threatening complications. Metabolomics has increasingly been applied to identify biomarkers for disease diagnosis with particular interest in diseases at an early stage. In this study, we tested a swine obstructive CP model by subtotal ligation of the main pancreatic duct, and the metabolic profiles of the Bama miniature swine pancreas were investigated using high-resolution magic angle spinning proton magnetic resonance spectroscopy (HR MAS (1)H MRS) combined with principal components analysis (PCA). Increases in lactate and choline for mild CP and decreases in glycerophosphocholine, phosphocholine, betaine and glycine were observed from normal pancreas to mild, moderate and severe CP. PCA results showed visual separations among the groups. The increase of choline at an early stage of CP and the decrease of glycerophosphocholine, phosphocholine, betaine and glycine reveal the pathogenesis of CP at a molecular level. The MRS results presented here demonstrate the potential of metabolic profiles in discriminating a normal pancreas from different stages of CP, which may be used to achieve CP early diagnosis and timely intervention to prevent irreversible destruction of the pancreas.
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Affiliation(s)
- Gaofeng Sun
- Department of Nuclear Medicine, Changhai Hospital of the Second Military Medical University, Room 182., Building 10., 168 Changhai Rd., Shanghai, China200433.
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Vettukattil R, Gulati M, Sjøbakk TE, Jakola AS, Kvernmo NAM, Torp SH, Bathen TF, Gulati S, Gribbestad IS. Differentiating diffuse World Health Organization grade II and IV astrocytomas with ex vivo magnetic resonance spectroscopy. Neurosurgery 2013; 72:186-95; discussion 195. [PMID: 23147779 DOI: 10.1227/neu.0b013e31827b9c57] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The prognosis and treatment of astrocytomas, which are primary brain tumors, vary depending on the grade of the tumor, necessitating a precise preoperative classification. Magnetic resonance spectroscopy (MRS) provides information about metabolites in tissues and is an emerging noninvasive tool to improve diagnostic accuracy in patients with intracranial neoplasia. OBJECTIVE To investigate whether ex vivo MRS could differentiate World Health Organization grade II (A-II) and IV astrocytomas (glioblastomas; GBM) and to correlate MR spectral profiles with clinical parameters. METHODS Patients with A-II and GBM (n = 58) scheduled for surgical resection were enrolled. Tumor specimens were collected during surgery and stored in liquid nitrogen before being analyzed with high-resolution magic angle spinning MRS. The tumors were histopathologically classified according to World Health Organization criteria as GBM (n = 48) and A-II (n = 10). RESULTS Multivariate analysis of ex vivo proton high-resolution magic angle spinning spectra MRS showed differences in the metabolic profiles of different grades of astrocytomas. A-II had higher levels of glycerophosphocholine and myo-inositol than GBM. The latter had more phosphocholine, glycine, and lipids. We observed a significant metabolic difference between recurrent and nonrecurrent GBM (P < .001). Primary GBM had more phosphocholine than recurrent GBM. A significant correlation (P < .001) between lipid and lactate signals and histologically estimated percentage of necrosis was observed in GBM. Spectral profiles were not correlated with age, survival, or magnetic resonance imaging-defined tumor volume. CONCLUSION Ex vivo MRS can differentiate astrocytomas based on their metabolic profiles.
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Affiliation(s)
- Riyas Vettukattil
- Department of Circulation and Medical Imaging, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
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Dumas ME, Davidovic L. Metabolic phenotyping and systems biology approaches to understanding neurological disorders. F1000PRIME REPORTS 2013; 5:18. [PMID: 23755365 PMCID: PMC3672944 DOI: 10.12703/p5-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput metabolic profiling and the study of the metabolome are particularly important in brain research where small molecules or metabolites play fundamental signalling roles: neurotransmitters, signalling lipids, osmolytes and even ions. Metabolic profiling has shown that metabolic perturbations in the brain go beyond alterations of neurotransmission and that variations in brain metabolic homeostasis are associated with neurological disorders. In this report, we will focus on recent developments in the field of metabolic phenotyping that have contributed to unravelling the pathophysiology of neurological diseases. Also, we will highlight the necessity of implementing systems biology approaches to integrate metabolic data and tackle the structural and functional complexity of the brain in normal and pathological conditions.
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Affiliation(s)
- Marc-Emmanuel Dumas
- Imperial College London, Biomolecular Medicine, Department of Surgery and Cancer, Faculty of MedicineSir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZUK
| | - Laetitia Davidovic
- Institut de Pharmacologie Moléculaire et CellulaireCNRS UMR 7275, 660 route des Lucioles, 06560 ValbonneFrance
- Université de Nice-Sophia AntipolisNiceFrance
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Wong A, Li X, Sakellariou D. Refined Magic-Angle Coil Spinning Resonator for Nanoliter NMR Spectroscopy: Enhanced Spectral Resolution. Anal Chem 2013; 85:2021-6. [DOI: 10.1021/ac400188b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alan Wong
- CEA Saclay, DSM, IRAMIS, UMR
CEA/CNRS 3299 − SIS2M, Laboratoire Structure et Dynamique par
Résonance Magnétique, F-91191, Gif-sur-Yvette Cedex,
France
| | - Xiaonan Li
- CEA Saclay, DSM, IRAMIS, UMR
CEA/CNRS 3299 − SIS2M, Laboratoire Structure et Dynamique par
Résonance Magnétique, F-91191, Gif-sur-Yvette Cedex,
France
| | - Dimitris Sakellariou
- CEA Saclay, DSM, IRAMIS, UMR
CEA/CNRS 3299 − SIS2M, Laboratoire Structure et Dynamique par
Résonance Magnétique, F-91191, Gif-sur-Yvette Cedex,
France
- Ecole Normale Supérieure, 24 rue Lhomond, F-75005 Paris,
France
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Yang Y, Yang L, Zhang Y, Gu X, Xu D, Fang F, Sun A, Wang K, Yu Y, Zuo J, Ge J. Taurine detected using high-resolution magic angle spinning (1)H nuclear magnetic resonance: A potential indicator of early myocardial infarction. Exp Ther Med 2012; 5:683-688. [PMID: 23408155 PMCID: PMC3570233 DOI: 10.3892/etm.2012.857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/13/2012] [Indexed: 11/06/2022] Open
Abstract
Magnetic resonance spectroscopy (MRS) is a unique non-invasive method for detecting cardiac metabolic changes. However, MRS in cardiac diagnosis is limited due to insensitivity and low efficiency. Taurine (Tau) is the most abundant free amino acid in the myocardium. We hypothesized that Tau levels may indicate myocardial ischemia and early infarction. Sprague-Dawley rats were divided into seven groups according to different time points during the course of myocardial ischemia, which was induced by left anterior descending coronary artery ligation. Infarcted myocardial tissue was obtained for high-resolution magic angle spinning (1)H nuclear magnetic resonance (NMR) analysis. Results were validated via high-performance liquid chromatography. The Tau levels in the ischemic myocardial tissue were reduced significantly within 5 min compared with those in the control group (relative ratio from 20.27±6.48 to 8.81±0.04, P<0.05) and were maintained for 6 h post-ischemia. Tau levels declined more markedly (56.5%) than creatine levels (48.5%) at 5 min after ligation. This suggests that Tau may have potential as an indicator in the early detection of myocardial ischemia by (1)H MRS.
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Affiliation(s)
- Yunlong Yang
- Zhongshan Hospital of Fudan University, Shanghai Institute of Cardiovascular Disease, Shanghai 200032; ; Department of Cellular & Genetic Medicine, Shanghai Medical School, Fudan University, Shanghai 200032
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Hu JZ, Rommereim DN, Minard KR, Woodstock A, Harrer BJ, Wind RA, Phipps RP, Sime PJ. Metabolomics in lung inflammation:a high-resolution (1)h NMR study of mice exposedto silica dust. Toxicol Mech Methods 2012; 18:385-98. [PMID: 20020862 DOI: 10.1080/15376510701611032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
ABSTRACT Here we report the first (1)H NMR metabolomics studies on excised lungs and bronchoalveolar lavage fluid (BALF) from mice exposed to crystalline silica. High-resolution (1)H NMR metabolic profiling on intact excised lungs was performed using slow magic angle sample spinning (slow-MAS) (1)H PASS (phase-altered spinning sidebands) at a sample spinning rate of 80 Hz. Metabolic profiling on BALF was completed using fast magic angle spinning at 2 kHz. Major findings are that the relative concentrations of choline, phosphocholine (PC), and glycerophosphocholine (GPC) were statistically significantly increased in silica-exposed mice compared to sham controls, indicating an altered membrane choline phospholipids metabolism (MCPM). The relative concentrations of glycogen/glucose, lactate, and creatine were also statistically significantly increased in mice exposed to silica dust, suggesting that cellular energy pathways were affected by silica dust. Elevated levels of glycine, lysine, glutamate, proline, and 4-hydroxyproline were also increased in exposed mice, suggesting the activation of a collagen pathway. Furthermore, metabolic profiles in mice exposed to silica dust were found to be spatially heterogeneous, consistent with regional inflammation revealed by in vivo magnetic resonance imaging (MRI).
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Affiliation(s)
- Jian Zhi Hu
- Pacific Northwest National Laboratory, Richland, WA
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Zhao L, Gao H, Zhao Y, Lin D. Metabonomic analysis of the therapeutic effect of Zhibai Dihuang Pill in treatment of streptozotocin-induced diabetic nephropathy. JOURNAL OF ETHNOPHARMACOLOGY 2012; 142:647-656. [PMID: 22687255 DOI: 10.1016/j.jep.2012.05.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 05/15/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zhibai Dihuang Pill (ZDP) is one of ancient traditional Chinese medicines (TCMs), which is usually used for the treatment of kidney deficiency for thousands of years in China. AIM OF THE STUDY Traditional Chinese medicines (TCMs) usually operate in vivo through multi-components, multi-ways and multi-targets. However, the molecular mechanisms of TCMs remain unclear. In the present work, nuclear magnetic resonance (NMR)-based metabonomic analysis was used to evaluate the therapeutic effect of Zhibai Dihuang Pill (ZDP) on diabetic nephropathy (DN) rats induced by streptozotocin and to address the underlying molecular mechanism. MATERIALS AND METHODS Male rats were divided into three groups: control, DN and ZDP-treated DN (ZDP-DN), respectively. Based on (1)H NMR spectra of sera, urine and kidney extracts from the rats, principle component analysis (PCA) was performed to identify different metabolic profiles. Kidney portions and serum and urine samples were also subjected to histopathological or biochemical examination. RESULTS PCA scores plots demonstrate that the cluster of DN rats is separated from that of control rats, while some of ZDP-DN rats are located close to control rats, indicating that metabolic profiles of these ZDP-DN rats are restored toward those of control rats. Our results illustrate that ZDP treatment could lower the levels of lipids and 3-hydrobutyrate, and raise the level of lactate in sera of DN rats. Moreover, ZDP treatment could also reduce the levels of glucose, 3-hydrobutyrate and lactate, enhance the level of betaine in kidney tissues. CONCLUSION Our study indicates that ZDP treatment can ameliorate DN symptoms by intervening in some dominating metabolic pathways, such as inhibiting glucose and lipid metabolism, enhancing methylamine metabolism. Our work may be of benefit to both evaluation of the therapeutic effect of TCM and elucidation of the underlying molecular mechanism.
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Affiliation(s)
- Liangcai Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Metabolomics: Concept, methods and potential prospect in marine biology. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5237-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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A metabolomic approach for diagnosis of experimental sepsis. Intensive Care Med 2011; 37:2023-32. [PMID: 21976186 DOI: 10.1007/s00134-011-2359-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
BACKGROUND The search for reliable diagnostic biomarkers of sepsis remains necessary. Assessment of global metabolic profiling using quantitative nuclear magnetic resonance (NMR)-based metabolomics offers an attractive modern methodology for fast and comprehensive determination of multiple circulating metabolites and for defining the metabolic phenotype of sepsis. OBJECTIVE To develop a novel NMR-based metabolomic approach for diagnostic evaluation of sepsis. METHODS Male Sprague-Dawley rats (weight 325-375 g) underwent cecal ligation and puncture (n = 14, septic group) or sham procedure (n = 14, control group) and 24 h later were euthanized. Lung tissue, bronchoalveolar lavage (BAL) fluid, and serum samples were obtained for (1)H NMR and high-resolution magic-angle spinning analysis. Unsupervised principal components analysis was performed on the processed spectra, and a predictive model for diagnosis of sepsis was constructed using partial least-squares discriminant analysis. RESULTS NMR-based metabolic profiling discriminated characteristics between control and septic rats. Characteristic metabolites changed markedly in septic rats as compared with control rats: alanine, creatine, phosphoethanolamine, and myoinositol concentrations increased in lung tissue; creatine increased and myoinositol decreased in BAL fluid; and alanine, creatine, phosphoethanolamine, and acetoacetate increased whereas formate decreased in serum. A predictive model for diagnosis of sepsis using these metabolites classified cases with sensitivity and specificity of 100%. CONCLUSIONS NMR metabolomic analysis is a potentially useful technique for diagnosis of sepsis. The concentrations of metabolites involved in energy metabolism and in the inflammatory response change in this model of sepsis.
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Izquierdo-García JL, Villa P, Kyriazis A, del Puerto-Nevado L, Pérez-Rial S, Rodriguez I, Hernandez N, Ruiz-Cabello J. Descriptive review of current NMR-based metabolomic data analysis packages. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:263-270. [PMID: 21920221 DOI: 10.1016/j.pnmrs.2011.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/14/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Jose L Izquierdo-García
- CIBERES, CIBER Enfermedades Respiratorias, Departartamento Química-Física II, Facultad Farmacia, Universidad Complutense de Madrid, Madrid, Spain.
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33
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Zhao L, Gao H, Lian F, Liu X, Zhao Y, Lin D. 1H-NMR-based metabonomic analysis of metabolic profiling in diabetic nephropathy rats induced by streptozotocin. Am J Physiol Renal Physiol 2011; 300:F947-56. [DOI: 10.1152/ajprenal.00551.2010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Elucidation of the metabolic profiling in diabetic nephropathy (DN) rats is of great assistance for understanding the pathogenesis of DN. In this study, 1H-nuclear magnetic resonance (NMR)-based metabonomics combined with HPLC measurements was used to quantitatively analyze the metabolic changes in urine and kidney extracts from diabetic 2-wk and 8-wk rats induced by streptozotocin (STZ). Pattern recognition analysis of either urine or kidney extracts indicated that the two diabetic groups were separated obviously from the control group, suggesting that the metabolic profiles of the diabetic groups were markedly different from the control. The diabetic 8-wk rats showed lower levels of creatine, dimethylamine, and higher levels of ascorbate, succinate, lactate, citrate, allantoin, 2-ketoglutarate, and 3-hydrobutyrate (3-HB) in the urine samples. Moreover, the diabetic 8-wk rats displayed lower levels of succinate, creatine, myo-inositol, alanine, lactate, and ATP, and higher levels of 3-HB and glucose in the kidney extracts. The observed metabolic changes imply the enhanced pathways of either lipid or ketone body synthesis and decreased pathways of either tricarboxylic acid cycle or glycolysis in DN rats compared with the control. Our results suggest that the energy metabolic changes are associated with the pathogenic process of DN.
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Affiliation(s)
- Liangcai Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai
- The First Affiliated Hospital, Guangxi Medical University, Guangxi, China
| | - Hongchang Gao
- School of Pharmacy, Wenzhou Medical College, Wenzhou; and
| | - Fulin Lian
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai
| | - Xia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai
| | - Yongxiang Zhao
- The First Affiliated Hospital, Guangxi Medical University, Guangxi, China
| | - Donghai Lin
- The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai
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Kolokolova TN, Savel’ev OY, Sergeev NM. Metabolic analysis of human biological fluids by 1H NMR spectroscopy. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934808020020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Hu JZ. Slow magic angle sample spinning: a non- or minimally invasive method for high-resolution 1H nuclear magnetic resonance (NMR) metabolic profiling. Methods Mol Biol 2011; 708:335-364. [PMID: 21207300 DOI: 10.1007/978-1-61737-985-7_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
High-resolution (1)H magic angle spinning nuclear magnetic resonance (NMR), using a sample spinning rate of several kilohertz or more (i.e., high-resolution magic angle spinning (hr-MAS)), is a well-established method for metabolic profiling in intact tissues without the need for sample extraction. The only shortcoming with hr-MAS is that it is invasive and is thus unusable for non-destructive detections. Recently, a method called slow MAS, using the concept of two-dimensional NMR spectroscopy, has emerged as an alternative method for non- or minimally invasive metabolomics in intact tissues, including live animals, due to the slow or ultra-slow sample spinning used. Although slow MAS is a powerful method, its applications are hindered by experimental challenges. Correctly designing the experiment and choosing the appropriate slow MAS method both require a fundamental understanding of the operation principles, in particular the details of line narrowing due to the presence of molecular diffusion. However, these fundamental principles have not yet been fully disclosed in previous publications. The goal of this chapter is to provide an in-depth evaluation of the principles associated with slow MAS techniques by emphasizing the challenges associated with a phantom sample consisting of glass beads and H(2)O, where an unusually large magnetic susceptibility field gradient is obtained.
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Affiliation(s)
- Jian Zhi Hu
- Pacific Northwest National Laboratory, Richland, WA, USA.
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36
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Dieterle F, Riefke B, Schlotterbeck G, Ross A, Senn H, Amberg A. NMR and MS methods for metabonomics. Methods Mol Biol 2011; 691:385-415. [PMID: 20972767 DOI: 10.1007/978-1-60761-849-2_24] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Metabonomics, also often referred to as "metabolomics" or "metabolic profiling," is the systematic profiling of metabolites in bio-fluids or tissues of organisms and their temporal changes. In the last decade, metabonomics has become increasingly popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabonomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabonomics, i.e., NMR, LC-MS, UPLC-MS, and GC-MS have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabonomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation, to determining the measurement details of all analytical platforms, and finally, to discussing the corresponding specific steps of data analysis.
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Affiliation(s)
- Frank Dieterle
- Molecular Diagnostics, Novartis Pharma AG, Basel, Switzerland
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37
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Interactions between immunity and metabolism - contributions from the metabolic profiling of parasite-rodent models. Parasitology 2010; 137:1451-66. [PMID: 20602847 DOI: 10.1017/s0031182010000697] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A combined interdisciplinary research strategy is even more crucial in immunology than in many other biological sciences in order to comprehend the closely linked interactions between cell proliferation, molecular signalling and gene rearrangements. Because of the multi-dimensional nature of the immune system, an abundance of different experimental approaches has developed, with a main focus on cellular and molecular mechanisms. The role of metabolism in immunity has been underexplored so far, and yet researchers have made important contributions in describing associations of immune processes and metabolic pathways, such as the central role of the l-arginine pathway in macrophage activation or the immune regulatory functions of the nucleotides. Furthermore, metabolite supplement studies, including nutritional administration and labelled substrates, have opened up new means of manipulating immune mechanisms. Metabolic profiling has introduced a reproducible platform for systemic assessment of changes at the small-molecule level within a host organism, and specific metabolic fingerprints of several parasitic infections have been characterized by 1H NMR spectroscopy. The application of multivariate statistical methods to spectral data has facilitated recovery of biomarkers, such as increased acute phase protein signals, and enabled direct correlation to the relative cytokine levels, which encourages further application of metabolic profiling to explore immune regulatory systems.
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38
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Beckonert O, Coen M, Keun HC, Wang Y, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc 2010; 5:1019-32. [PMID: 20539278 DOI: 10.1038/nprot.2010.45] [Citation(s) in RCA: 302] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolic profiling, metabolomic and metabonomic studies require robust study protocols for any large-scale comparisons and evaluations. Detailed methods for solution-state NMR spectroscopy have been summarized in an earlier protocol. This protocol details the analysis of intact tissue samples by means of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy and we provide a detailed description of sample collection, preparation and analysis. Described here are (1)H NMR spectroscopic techniques such as the standard one-dimensional, relaxation-edited, diffusion-edited and two-dimensional J-resolved pulse experiments, as well as one-dimensional (31)P NMR spectroscopy. These are used to monitor different groups of metabolites, e.g., sugars, amino acids and osmolytes as well as larger molecules such as lipids, non-invasively. Through the use of NMR-based diffusion coefficient and relaxation times measurements, information on molecular compartmentation and mobility can be gleaned. The NMR methods are often combined with statistical analysis for further metabonomics analysis and biomarker identification. The standard acquisition time per sample is 8-10 min for a simple one-dimensional (1)H NMR spectrum, giving access to metabolite information while retaining tissue integrity and hence allowing direct comparison with histopathology and MRI/MRS findings or the evaluation together with biofluid metabolic-profiling data.
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Affiliation(s)
- Olaf Beckonert
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London, UK
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39
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Hong YS, Coen M, Rhode CM, Reily MD, Robertson DG, Holmes E, Lindon JC, Nicholson JK. Chemical shift calibration of 1H MAS NMR liver tissue spectra exemplified using a study of glycine protection of galactosamine toxicity. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S47-S53. [PMID: 19856339 DOI: 10.1002/mrc.2521] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
High-resolution (1)H magic angle spinning (MAS) NMR spectroscopy is a useful tool for analysing intact tissues as a component of metabonomic studies. The effect of referencing MAS NMR spectra to the chemical shifts of glucose or to that or trimethylsilylpropionic acid on the resultant multivariate statistical models have been investigated. It is shown that referencing to known chemical shifts of either alpha-glucose or beta-glucose in (1)H MAS NMR-based metabolic data of intact liver tissues is preferred. This has been exemplified in studies of galactosamine toxicity in the rat where co-administration of glycine ameliorates the toxic response. This approach leads to better aligned sets of spectra and reduces the inter-sample variability in multivariate statistical models. If glucose is not present in the tissue under study, then a number of alternative internal reference chemical shifts are presented. Finally, the chemical shift difference between that of the anomeric H1 proton of alpha-glucose and residual water is confirmed as a suitable internal temperature calibration method.
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Affiliation(s)
- Young-Shick Hong
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7 2AZ, UK
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40
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Abstract
Metabonomics is rapidly evolving through advances in analytical technologies together with the development of new hyphenated approaches that are increasingly being applied to analyze complex biological systems. Improvements in analytical performance, such as increased sensitivity and selectivity, are providing greater resolution to analytical datasets and the rich potential of metabonomics as a systems biology tool of choice is becoming clear. However, such improvements are resulting in datasets becoming increasingly demanding in terms of data handling and interpretation, and the degree to which metabonomics continues to develop will be dependent on how chemometrics and data-handling approaches keep pace with continually improving analytical technologies. This review provides an overview of the field of metabonomics, with a particular focus on the analytical techniques that are chiefly employed and the chemometric methods that have found most use. However, in addition, we mention less widely used analytical methods and suggest that advanced statistical methods will play a larger role in the future.
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41
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Zhang Q, Hu JZ, Rommereim DN, Murphy MK, Phipps RP, Huso DL, Dicello JF. Application of high-resolution 1H MAS NMR spectroscopy to the analysis of intact bones from mice exposed to gamma radiation. Radiat Res 2009; 172:607-16. [PMID: 19883229 PMCID: PMC2796857 DOI: 10.1667/rr1715.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Herein we demonstrate that high-resolution magic angle spinning (MAS) 1H NMR can be used to profile the pathology of bone marrow rapidly and with minimal sample preparation. The spectral resolution obtained allows several metabolites to be analyzed quantitatively. The level of NMR-detectable metabolites in the epiphysis + metaphysis sections of mouse femur were significantly higher than that observed in the diaphysis of the same femur. The major metabolite damage to bone marrow resulting from either 3.0 Gy or 7.8 Gy of whole-body gamma radiation 4 days after exposure were (1) decreased total choline content, (2) increased fatty acids in bone marrow, and (3) decreased creatine content. These results suggest that the membrane choline phospholipid metabolism (MCPM) pathway and the fatty acid biosynthesis pathway were altered as a result of radiation exposure. We also found that the metabolic damage induced by radiation in the epiphysis + metaphysis sections of mouse femur was higher than that of the diaphysis of the same femur. Traditional histopathology analysis was also carried out to correlate radiation damage with changes in metabolites. Importantly, the molecular information gleaned from high-resolution MAS 1H NMR complements the pathology data.
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Affiliation(s)
- Qibin Zhang
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Jian Zhi Hu
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | | | - Mark K. Murphy
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Richard P. Phipps
- University of Rochester School of Medicine and Dentistry, Lung Biology and Disease Program and Department of Environmental Medicine, Rochester, New York 14642
| | - David L. Huso
- Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205
| | - John F. Dicello
- Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205
- Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, California 92354
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42
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Saric J, Li JV, Wang Y, Keiser J, Veselkov K, Dirnhofer S, Yap IKS, Nicholson JK, Holmes E, Utzinger J. Panorganismal metabolic response modeling of an experimental Echinostoma caproni infection in the mouse. J Proteome Res 2009; 8:3899-911. [PMID: 19489577 PMCID: PMC2724024 DOI: 10.1021/pr900185s] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 12/19/2022]
Abstract
Metabolic profiling of host tissues and biofluids during parasitic infections can reveal new biomarker information and aid the elucidation of mechanisms of disease. The multicompartmental metabolic effects of an experimental Echinostoma caproni infection have been characterized in 12 outbred female mice infected orally with 30 E. caproni metacercariae each, using a further 12 uninfected animals as a control group. Mice were killed 36 days postinfection and brain, intestine (colon, ileum, jejeunum), kidney, liver, and spleen were removed. Metabolic profiles of tissue samples were measured using high-resolution magic angle spinning (1)H NMR spectroscopy and biofluids measured by applying conventional (1)H NMR spectroscopy. Spectral data were analyzed via principal component analysis, partial least-squares-derived methods and hierarchical projection analyses. Infection-induced metabolic changes in the tissues were correlated with altered metabolite concentrations in the biofluids (urine, plasma, fecal water) using hierarchical modeling and correlation analyses. Metabolic descriptors of infection were identified in liver, renal cortex, intestinal tissues but not in spleen, brain or renal medulla. The main physiological change observed in the mouse was malabsorption in the small intestine, which was evidenced by decreased levels of various amino acids in the ileum, for example, alanine, taurine, glutamine, and branched chain amino acids. Furthermore, altered gut microbial activity or composition was reflected by increased levels of trimethylamine in the colon. Our modeling approach facilitated in-depth appraisal of the covariation of the metabolic profiles of different biological matrices and found that urine and plasma most closely reflected changes in ileal compartments. In conclusion, an E. caproni infection not only results in direct localized (ileum and jejenum) effects, but also causes remote metabolic changes (colon and several peripheral organs), and therefore describes the panorganismal metabolic response of the infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jürg Utzinger
- Correspondence should be addressed to: Jürg Utzinger, Department of Public Health and Epidemiology, Swiss Tropical Institute, P.O. Box, CH-4002 Basel, Switzerland. Tel: +41 61 284-8129; fax: +41 61 284-8105; e-mail:
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43
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Avni R, Mangoubi O, Bhattacharyya R, Degani H, Frydman L. Magnetization transfer magic-angle-spinning z-spectroscopy of excised tissues. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:1-9. [PMID: 19409825 DOI: 10.1016/j.jmr.2009.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Accepted: 03/11/2009] [Indexed: 05/27/2023]
Abstract
NMR experiments devised to aid in analyses of tissues include magnetization transfer (MT), which can highlight the signals of biological macromolecules through cross-relaxation and/or chemical exchange processes with the bulk (1)H water resonance, and high-resolution magic-angle-spinning (HRMAS) methods, akin to those used in solid-state NMR to introduce additional spectral resolution via the averaging of spin anisotropies. This paper explores the result of combining these methodologies, and reports on MT "z-spectroscopy" between water and cell components in excised tissues under a variety of HRMAS conditions. Main features arising from the resulting (1)H "MTMAS" experiments include strong spinning sideband manifolds centered at the liquid water shift, high-resolution isotropic features coinciding with aliphatic and amide proton resonances, and a second sideband manifold arising as spinning speeds are increased. Interpretations are given for the origin of these various features, including simulations shedding further light onto the nature of MT NMR signals observed for tissue samples. Concurrently, histological examinations are reported validating the limits of HRMAS NMR procedures to the analysis of tissue samples preserved in a number of different ways.
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Affiliation(s)
- Reut Avni
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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44
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Hu JZ, Sears JA, Kwak JH, Hoyt DW, Wang Y, Peden CHF. An isotropic chemical shift-chemical shift anisotropic correlation experiment using discrete magic angle turning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 198:105-110. [PMID: 19246221 DOI: 10.1016/j.jmr.2009.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 01/15/2009] [Accepted: 01/22/2009] [Indexed: 05/27/2023]
Abstract
An isotropic-anisotropic shift 2D correlation spectroscopy is introduced that combines the advantages of both magic angle turning (MAT) and magic angle hopping (MAH) technologies. In this new approach, denoted DMAT for "discrete magic angle turning", the sample rotates clockwise followed by an anticlockwise rotation of exactly the same amount with each rotation less or equal than 360 degrees but greater than 240 degrees , with the rotation speed being constant only for times related to the evolution dimension. This back and forth rotation is repeated and synchronized with a special radio frequency (RF) pulse sequence to produce an isotropic-anisotropic shift 2D correlation spectrum. For any spin-interaction of rank-2 such as chemical shift anisotropy, isotropic magnetic susceptibility interaction, and residual homo-nuclear dipolar interaction in biological fluid samples, the projection along the isotropic dimension is a high resolution spectrum. Since a less than 360 degrees sample rotation is involved, the design potentially allows for in situ control over physical parameters such as pressure, flow conditions, feed compositions, and temperature so that true in situ NMR investigations can be carried out.
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Affiliation(s)
- Jian Zhi Hu
- Institute for Interfacial Catalysis, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K8-98, Richland, WA 99352, USA.
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45
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Righi V, Durante C, Cocchi M, Calabrese C, Di Febo G, Lecce F, Pisi A, Tugnoli V, Mucci A, Schenetti L. Discrimination of Healthy and Neoplastic Human Colon Tissues by ex Vivo HR-MAS NMR Spectroscopy and Chemometric Analyses. J Proteome Res 2009; 8:1859-69. [DOI: 10.1021/pr801094b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Valeria Righi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Caterina Durante
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Marina Cocchi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Carlo Calabrese
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Giulio Di Febo
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Ferdinando Lecce
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Annamaria Pisi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Vitaliano Tugnoli
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Adele Mucci
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Luisa Schenetti
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
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Metabonomic analysis identifies molecular changes associated with the pathophysiology and drug treatment of bipolar disorder. Mol Psychiatry 2009; 14:269-79. [PMID: 18256615 DOI: 10.1038/sj.mp.4002130] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bipolar affective disorder is a severe and debilitating psychiatric condition characterized by the alternating mood states of mania and depression. Both the molecular pathophysiology of the disorder and the mechanism of action of the mainstays of its treatment remain largely unknown. Here, (1)H NMR spectroscopy-based metabonomic analysis was performed to identify molecular changes in post-mortem brain tissue (dorsolateral prefrontal cortex) of patients with a history of bipolar disorder. The observed changes were then compared to metabolic alterations identified in rat brain following chronic oral treatment with either lithium or valproate. This is the first study to use (1)H NMR spectroscopy to study post-mortem bipolar human brain tissue, and it is the first to compare changes in disease brain with changes induced in rat brain following mood stabilizer treatment. Several metabolites were found to be concordantly altered in both the animal and human tissues. Glutamate levels were increased in post-mortem bipolar brain, while the glutamate/glutamine ratio was decreased following valproate treatment, and gamma-aminobutyric acid levels were increased after lithium treatment, suggesting that the balance of excitatory/inhibitory neurotransmission is central to the disorder. Both creatine and myo-inositol were increased in the post-mortem brain but depleted with the medications. Lastly, the level of N-acetyl aspartate, a clinically important metabolic marker of neuronal viability, was found to be unchanged following chronic mood stabilizer treatment. These findings promise to provide new insight into the pathophysiology of bipolar disorder and may be used to direct research into novel therapeutic strategies.
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Khaitovich P, Lockstone HE, Wayland MT, Tsang TM, Jayatilaka SD, Guo AJ, Zhou J, Somel M, Harris LW, Holmes E, Pääbo S, Bahn S. Metabolic changes in schizophrenia and human brain evolution. Genome Biol 2008; 9:R124. [PMID: 18681948 PMCID: PMC2575514 DOI: 10.1186/gb-2008-9-8-r124] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/22/2008] [Accepted: 08/05/2008] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite decades of research, the molecular changes responsible for the evolution of human cognitive abilities remain unknown. Comparative evolutionary studies provide detailed information about DNA sequence and mRNA expression differences between humans and other primates but, in the absence of other information, it has proved very difficult to identify molecular pathways relevant to human cognition. RESULTS Here, we compare changes in gene expression and metabolite concentrations in the human brain and compare them to the changes seen in a disorder known to affect human cognitive abilities, schizophrenia. We find that both genes and metabolites relating to energy metabolism and energy-expensive brain functions are altered in schizophrenia and, at the same time, appear to have changed rapidly during recent human evolution, probably as a result of positive selection. CONCLUSION Our findings, along with several previous studies, suggest that the evolution of human cognitive abilities was accompanied by adaptive changes in brain metabolism, potentially pushing the human brain to the limit of its metabolic capabilities.
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Affiliation(s)
- Philipp Khaitovich
- Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road, Shanghai, 200031, PR China.
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Hosch W, Junghanss T, Stojkovic M, Brunetti E, Heye T, Kauffmann GW, Hull WE. Metabolic viability assessment of cystic echinococcosis using high-field 1H MRS of cyst contents. NMR IN BIOMEDICINE 2008; 21:734-754. [PMID: 18384178 DOI: 10.1002/nbm.1252] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cystic echinococcosis is a worldwide disease caused by larval stages of the parasite Echinococcus granulosus (canine tapeworm). In clinical practice, staging of cyst development by ultrasonography (US) has allowed treatment options to be tailored to individual patient needs. However, the empirical correlation between cyst morphology and parasite viability is not always dependable and has, until now, required confirmation by invasive assessment of cyst content by light microscopy (LM), for example. Alternatively, high-field 1H MRS may be used to examine cyst fluid ex vivo and prepare detailed quantitative metabolite profiles, enabling a multivariate metabolomics approach to cyst staging. One-dimensional and two-dimensional 1H and 1H/13C MRS at 600 MHz (14.1 T) was used to analyze 50 cyst aspirates of various US and LM classes. MR parameters and concentrations relative to internal valine were determined for 44 metabolites and four substance classes. The high concentrations of succinate, fumarate, malate, acetate, alanine, and lactate found in earlier studies of viable cysts were confirmed, and additional metabolites such as myo-inositol, sorbitol, 1,5-anhydro-D-glucitol, betaine, and 2-hydroxyisovalerate were identified. Data analysis and cyst classification were performed using univariate (succinate), bivariate (succinate vs fumarate), and multivariate partial least squares discriminant analysis (PSL-DA) methods (with up to 48 metabolite variables). Metabolic classification of 23 viable and 18 nonviable cysts on the basis of succinate alone agreed with LM results. However, for seven samples, LM and MRS gave opposing results. Reclassification of these samples and two unclassified samples by PLS-DA prediction techniques led to a set of 50 samples that could be completely separated into viable and nonviable MRS classes with no overlap, using as few as nine variables: succinate, formate, malate, 2-hydroxyisovalerate, acetate, total protein content, 1,5-anhydro-D-glucitol, alanine, and betaine. Thus, future noninvasive in vivo applications of MRS would appear promising.
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Affiliation(s)
- Waldemar Hosch
- Department of Radiodiagnostics, University Hospital, Heidelberg, Germany
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Technology insight: metabonomics in gastroenterology-basic principles and potential clinical applications. ACTA ACUST UNITED AC 2008; 5:332-43. [PMID: 18431374 DOI: 10.1038/ncpgasthep1125] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 02/19/2008] [Indexed: 01/21/2023]
Abstract
Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function. Metabonomics, especially when based on nuclear magnetic resonance spectroscopy, has the potential to identify biomarkers and prognostic factors, enhance clinical diagnosis, and expand hypothesis generation. As a consequence, the use of metabonomics has been extensively explored in the past decade, and applied successfully to the study of human diseases, toxicology, microbes, nutrition, and plant biology. This Review introduces the basic principles of nuclear magnetic resonance spectroscopy and commonly used tools for multivariate data analysis, before considering the applications and future potential of metabonomics in basic and clinical research, with emphasis on applications in the field of gastroenterology.
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Lindon JC, Nicholson JK. Analytical technologies for metabonomics and metabolomics, and multi-omic information recovery. Trends Analyt Chem 2008. [DOI: 10.1016/j.trac.2007.08.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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