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Ghini V, Meoni G, Vignoli A, Di Cesare F, Tenori L, Turano P, Luchinat C. Fingerprinting and profiling in metabolomics of biosamples. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 138-139:105-135. [PMID: 38065666 DOI: 10.1016/j.pnmrs.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023]
Abstract
This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
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Affiliation(s)
- Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy; Giotto Biotech S.r.l., Sesto Fiorentino, Italy.
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Cheng LL. High-resolution magic angle spinning NMR for intact biological specimen analysis: Initial discovery, recent developments, and future directions. NMR IN BIOMEDICINE 2023; 36:e4684. [PMID: 34962004 DOI: 10.1002/nbm.4684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
High-resolution magic angle spinning (HRMAS) NMR, an approach for intact biological material analysis discovered more than 25 years ago, has been advanced by many technical developments and applied to many biomedical uses. This article provides a history of its discovery, first by explaining the key scientific advances that paved the way for HRMAS NMR's invention, and then by turning to recent developments that have profited from applying and advancing the technique during the last 5 years. Developments aimed at directly impacting healthcare include HRMAS NMR metabolomics applications within studies of human disease states such as cancers, brain diseases, metabolic diseases, transplantation medicine, and adiposity. Here, the discussion describes recent HRMAS NMR metabolomics studies of breast cancer and prostate cancer, as well as of matching tissues with biofluids, multimodality studies, and mechanistic investigations, all conducted to better understand disease metabolic characteristics for diagnosis, opportune windows for treatment, and prognostication. In addition, HRMAS NMR metabolomics studies of plants, foods, and cell structures, along with longitudinal cell studies, are reviewed and discussed. Finally, inspired by the technique's history of discoveries and recent successes, future biomedical arenas that stand to benefit from HRMAS NMR-initiated scientific investigations are presented.
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Affiliation(s)
- Leo L Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Häni A, Diserens G, Oevermann A, Vermathen P, Precht C. Sampling Method Affects HR-MAS NMR Spectra of Healthy Caprine Brain Biopsies. Metabolites 2021; 11:metabo11010038. [PMID: 33419191 PMCID: PMC7825498 DOI: 10.3390/metabo11010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022] Open
Abstract
The metabolic profiling of tissue biopsies using high-resolution–magic angle spinning (HR-MAS) 1H nuclear magnetic resonance (NMR) spectroscopy may be influenced by experimental factors such as the sampling method. Therefore, we compared the effects of two different sampling methods on the metabolome of brain tissue obtained from the brainstem and thalamus of healthy goats by 1H HR-MAS NMR spectroscopy—in vivo-harvested biopsy by a minimally invasive stereotactic approach compared with postmortem-harvested sample by dissection with a scalpel. Lactate and creatine were elevated, and choline-containing compounds were altered in the postmortem compared to the in vivo-harvested samples, demonstrating rapid changes most likely due to sample ischemia. In addition, in the brainstem samples acetate and inositols, and in the thalamus samples ƴ-aminobutyric acid, were relatively increased postmortem, demonstrating regional differences in tissue degradation. In conclusion, in vivo-harvested brain biopsies show different metabolic alterations compared to postmortem-harvested samples, reflecting less tissue degradation. Sampling method and brain region should be taken into account in the analysis of metabolic profiles. To be as close as possible to the actual situation in the living individual, it is desirable to use brain samples obtained by stereotactic biopsy whenever possible.
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Affiliation(s)
- Annakatrin Häni
- Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Länggassstr. 124, 3012 Bern, Switzerland;
| | - Gaëlle Diserens
- Departments of BioMedical Research and Radiology, University and Inselspital Bern, sitem-insel AG, Freiburgstr. 3, 3010 Bern, Switzerland; (G.D.); (P.V.)
| | - Anna Oevermann
- NeuroCenter, Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3012 Bern, Switzerland;
| | - Peter Vermathen
- Departments of BioMedical Research and Radiology, University and Inselspital Bern, sitem-insel AG, Freiburgstr. 3, 3010 Bern, Switzerland; (G.D.); (P.V.)
| | - Christina Precht
- Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Länggassstr. 124, 3012 Bern, Switzerland;
- Correspondence: ; Tel.: +41-31-631-2918
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Hogberg HT, de Cássia da Silveira E Sá R, Kleensang A, Bouhifd M, Cemiloglu Ulker O, Smirnova L, Behl M, Maertens A, Zhao L, Hartung T. Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. Arch Toxicol 2021; 95:207-228. [PMID: 33078273 PMCID: PMC7811506 DOI: 10.1007/s00204-020-02903-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022]
Abstract
Due to regulatory bans and voluntary substitutions, halogenated polybrominated diphenyl ether (PBDE) flame retardants (FR) are increasingly substituted by mainly organophosphorus FR (OPFR). Leveraging a 3D rat primary neural organotypic in vitro model (rat brainsphere), we compare developmental neurotoxic effects of BDE-47-the most abundant PBDE congener-with four OPFR (isopropylated phenyl phosphate-IPP, triphenyl phosphate-TPHP, isodecyl diphenyl phosphate-IDDP, and tricresyl phosphate (also known as trimethyl phenyl phosphate)-TMPP). Employing mass spectroscopy-based metabolomics and transcriptomics, we observe at similar human-relevant non-cytotoxic concentrations (0.1-5 µM) stronger developmental neurotoxic effects by OPFR. This includes toxicity to neurons in the low µM range; all FR decrease the neurotransmitters glutamate and GABA (except BDE-47 and TPHP). Furthermore, n-acetyl aspartate (NAA), considered a neurologic diagnostic molecule, was decreased by all OPFR. At similar concentrations, the FR currently in use decreased plasma membrane dopamine active transporter expression, while BDE-47 did not. Several findings suggest astrogliosis induced by the OPFR, but not BDE-47. At the 5 µM concentrations, the OPFR more than BDE-47 interfered with myelination. An increase of cytokine gene and receptor expressions suggests that exposure to OPFR may induce an inflammatory response. Pathway/category overrepresentation shows disruption in 1) transmission of action potentials, cell-cell signaling, synaptic transmission, receptor signaling, (2) immune response, inflammation, defense response, (3) cell cycle and (4) lipids metabolism and transportation. Taken together, this appears to be a case of regretful substitution with substances not less developmentally neurotoxic in a primary rat 3D model.
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Affiliation(s)
- Helena T Hogberg
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Rita de Cássia da Silveira E Sá
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Physiology and Pathology, Federal University of Paraíba, João Pessoa, Brazil
| | - Andre Kleensang
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mounir Bouhifd
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ozge Cemiloglu Ulker
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Toxicology, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Lena Smirnova
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mamta Behl
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Alexandra Maertens
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Liang Zhao
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas Hartung
- Center for Alternatives To Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- CAAT-Europe, University of Konstanz, Konstanz, Germany
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Diez-Fernandez C, Hertig D, Loup M, Diserens G, Henry H, Vermathen P, Nuoffer JM, Häberle J, Braissant O. Argininosuccinate neurotoxicity and prevention by creatine in argininosuccinate lyase deficiency: An in vitro study in rat three-dimensional organotypic brain cell cultures. J Inherit Metab Dis 2019; 42:1077-1087. [PMID: 30907007 DOI: 10.1002/jimd.12090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/04/2019] [Accepted: 03/22/2019] [Indexed: 12/31/2022]
Abstract
The urea cycle disorder (UCD) argininosuccinate lyase (ASL) deficiency, caused by a defective ASL enzyme, exhibits a wide range of phenotypes, from life-threatening neonatal hyperammonemia to asymptomatic patients, with only the biochemical marker argininosuccinic acid (ASA) elevated in body fluids. Remarkably, even without ever suffering from hyperammonemia, patients often develop severe cognitive impairment and seizures. The goal of this study was to understand the effect on the known toxic metabolite ASA and the assumed toxic metabolite guanidinosuccinic acid (GSA) on developing brain cells, and to evaluate the potential role of creatine (Cr) supplementation, as it was described protective for brain cells exposed to ammonia. We used an in vitro model, in which we exposed three-dimensional (3D) organotypic rat brain cell cultures in aggregates to different combinations of the metabolites of interest at two time points (representing two different developmental stages). After harvest and cryopreservation of the cell cultures, the samples were analyzed mainly by metabolite analysis, immunohistochemistry, and western blotting. ASA and GSA were found toxic for astrocytes and neurons. This toxicity could be reverted in vitro by Cr. As well, an antiapoptotic effect of ASA was revealed, which could contribute to the neurotoxicity in ASL deficiency. Further studies in human ASL deficiency will be required to understand the biochemical situation in the brain of affected patients, and to investigate the impact of high or low arginine doses on brain Cr availability. In addition, clinical trials to evaluate the beneficial effect of Cr supplementation in ASL deficiency would be valuable.
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Affiliation(s)
- Carmen Diez-Fernandez
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Damian Hertig
- Division of Pediatric Endocrinology, Diabetology and Metabolism and University Institute of Clinical Chemistry, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- AMSM, Department of Biomedical Research, University of Bern, Bern, Switzerland
- AMSM, Department of Radiology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marc Loup
- Service of Clinical Chemistry, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Gaelle Diserens
- AMSM, Department of Biomedical Research, University of Bern, Bern, Switzerland
- AMSM, Department of Radiology, University of Bern, Bern, Switzerland
| | - Hugues Henry
- Service of Clinical Chemistry, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Peter Vermathen
- AMSM, Department of Biomedical Research, University of Bern, Bern, Switzerland
- AMSM, Department of Radiology, University of Bern, Bern, Switzerland
| | - Jean-Marc Nuoffer
- Division of Pediatric Endocrinology, Diabetology and Metabolism and University Institute of Clinical Chemistry, Inselspital, University Hospital, University of Bern, Bern, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Olivier Braissant
- Service of Clinical Chemistry, Lausanne University Hospital and University of Lausanne, Switzerland
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