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Liu X, Fang Y, Ma H, Zhang N, Li C. Performance comparison of three scaling algorithms in NMR-based metabolomics analysis. Open Life Sci 2023; 18:20220556. [PMID: 36998512 PMCID: PMC10044292 DOI: 10.1515/biol-2022-0556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/15/2022] [Accepted: 01/02/2023] [Indexed: 03/29/2023] Open
Abstract
Unit variance (UV) scaling, mean centering (CTR) scaling, and Pareto (Par) scaling are three commonly used algorithms in the preprocessing of metabolomics data. Based on our NMR-based metabolomics studies, we found that the clustering identification performances of these three scaling methods were dramatically different as tested by the spectra data of 48 young athletes’ urine samples, spleen tissue (from mice), serum (from mice), and cell (from Staphylococcus aureus) samples. Our data suggested that for the extraction of clustering information, UV scaling could serve as a robust approach for NMR metabolomics data for the identification of clustering analysis even with the existence of technical errors. However, for the purpose of discriminative metabolite identification, UV scaling, CTR scaling, and Par scaling could equally extract discriminative metabolites efficiently based on the coefficient values. Based on the data presented in this study, we propose an optimal working pipeline for the selection of scaling algorithms in NMR-based metabolomics analysis, which has the potential to serve as guidance for junior researchers working in the NMR-based metabolomics research field.
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Affiliation(s)
- Xia Liu
- Department of Diving and Hyperbaric Medicine, Navy Medical Center, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Yiqun Fang
- Department of Diving and Hyperbaric Medicine, Navy Medical Center, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Haifeng Ma
- Shanghai University of Sport, Shanghai200438, China
| | - Naixia Zhang
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, P. R. China
| | - Ci Li
- Department of Diving and Hyperbaric Medicine, Navy Medical Center, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
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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: 23] [Impact Index Per Article: 7.7] [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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3
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Lombó M, Ruiz-Díaz S, Gutiérrez-Adán A, Sánchez-Calabuig MJ. Sperm Metabolomics through Nuclear Magnetic Resonance Spectroscopy. Animals (Basel) 2021; 11:ani11061669. [PMID: 34205204 PMCID: PMC8227655 DOI: 10.3390/ani11061669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Proton nuclear magnetic resonance spectroscopy (1 H-NMR) is of special interest for the analysis of metabolites present in seminal plasma and spermatozoa. This metabolomic approach has been used to identify the presence of new biomarkers or their proportions in a non-invasive manner and is, therefore, an interesting tool for male fertility diagnosis. In this paper, we review current knowledge of the use of 1 H-NMR to examine sperm metabolomics in different species with special attention paid to humans and farm animals. We also describe the use of 1 H-NMR to establish a possible relationship between the mammalian diet and the presence of certain hydrophilic and lipophilic metabolites in spermatozoa. Abstract This report reviews current knowledge of sperm metabolomics analysis using proton nuclear magnetic resonance spectroscopy (1 H-NMR) with particular emphasis on human and farm animals. First, we present the benefits of NMR over other techniques to identify sperm metabolites and then describe the specific methodology required for NMR sperm analysis, stressing the importance of analyzing metabolites extracted from both the hydrophilic and lipophilic phases. This is followed by a description of advances produced to date in the use of NMR to diagnose infertility in humans and to identify metabolic differences among the sperm of mammalian herbivore, carnivore, and omnivore species. This last application of NMR mainly seeks to explore the possible use of lipids to fuel sperm physiology, contrary to previous theories that glycolysis and oxidative phosphorylation (OXPHOS) are the only sources of sperm energy. This review describes the use of NMR to identify sperm and seminal plasma metabolites as possible indicators of semen quality, and to examine the metabolites needed to maintain sperm motility, induce their capacitation, and consequently, to predict animal fertility.
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Affiliation(s)
- Marta Lombó
- Department of Animal Reproduction, INIA, Av. Puerta de Hierro, 18, 28040 Madrid, Spain; (M.L.); (S.R.-D.); (A.G.-A.)
| | - Sara Ruiz-Díaz
- Department of Animal Reproduction, INIA, Av. Puerta de Hierro, 18, 28040 Madrid, Spain; (M.L.); (S.R.-D.); (A.G.-A.)
- Mistral Fertility Clinics S.L., Clínica Tambre, 28002 Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- Department of Animal Reproduction, INIA, Av. Puerta de Hierro, 18, 28040 Madrid, Spain; (M.L.); (S.R.-D.); (A.G.-A.)
| | - María-Jesús Sánchez-Calabuig
- Department of Animal Reproduction, INIA, Av. Puerta de Hierro, 18, 28040 Madrid, Spain; (M.L.); (S.R.-D.); (A.G.-A.)
- Department of Animal Medicine and Surgery, Faculty of Veterinary Science, University Complutense of Madrid, 28040 Madrid, Spain
- Correspondence:
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Nizioł J, Copié V, Tripet BP, Nogueira LB, Nogueira KOPC, Ossoliński K, Arendowski A, Ruman T. Metabolomic and elemental profiling of human tissue in kidney cancer. Metabolomics 2021; 17:30. [PMID: 33661419 PMCID: PMC7932981 DOI: 10.1007/s11306-021-01779-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/22/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Kidney cancer is one of the most frequently diagnosed and the most lethal urinary cancer. Despite advances in treatment, no specific biomarker is currently in use to guide therapeutic interventions. OBJECTIVES Major aim of this work was to perform metabolomic and elemental profiling of human kidney cancer and normal tissue and to evaluate cancer biomarkers. METHODS Metabolic and elemental profiling of tumor and adjacent normal human kidney tissue from 50 patients with kidney cancer was undertaken using three different analytical methods. RESULTS Five potential tissue biomarkers of kidney cancer were identified and quantified using with high-resolution nuclear magnetic resonance spectroscopy. The contents of selected chemical elements in tissues was analyzed using inductively coupled plasma optical emission spectrometry. Eleven mass spectral features differentiating between kidney cancer and normal tissues were detected using silver-109 nanoparticle enhanced steel target laser desorption/ionization mass spectrometry. CONCLUSIONS Our results, derived from the combination of ICP-OES, LDI MS and 1H NMR methods, suggest that tissue biomarkers identified herein appeared to have great potential for use in clinical prognosis and/or diagnosis of kidney cancer.
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Affiliation(s)
- Joanna Nizioł
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland.
| | - Valérie Copié
- The Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Brian P Tripet
- The Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Leonardo B Nogueira
- Department of Geology, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Katiane O P C Nogueira
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Krzysztof Ossoliński
- Department of Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Adrian Arendowski
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave., 35-959, Rzeszów, Poland
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Mal TK, Tian Y, Patterson AD. Sample Preparation and Data Analysis for NMR-Based Metabolomics. Methods Mol Biol 2021; 2194:301-313. [PMID: 32926373 DOI: 10.1007/978-1-0716-0849-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
NMR spectroscopy has become one of the preferred analytical techniques for metabolomics studies due to its inherent nondestructive nature, ability to identify and quantify metabolites simultaneously in a complex mixture, minimal sample preparation requirement, and high degree of experimental reproducibility. NMR-based metabolomics studies involve the measurement and multivariate statistical analysis of metabolites present in biological samples such as biofluids, stool/feces, intestinal content, tissue, and cell extracts by high-resolution NMR spectroscopy-the goal then is to identify and quantify metabolites and evaluate changes of metabolite concentrations in response to some perturbation. Here we describe methodologies for NMR sample preparation of biofluids (serum, saliva, and urine) and stool/feces, intestinal content, and tissues for NMR experiments including extraction of polar metabolites and application of NMR in metabolomics studies. One dimensional (1D) 1H NMR experiments with different variations such as pre-saturation, relaxation-edited, and diffusion-edited are routinely acquired for profiling and metabolite identification and quantification. 2D homonuclear 1H-1H TOCSY and COSY, 2D J-resolved, and heteronuclear 1H-13C HSQC and HMBC are also performed to assist with metabolite identification and quantification. The NMR data are then subjected to targeted and/or untargeted multivariate statistical analysis for biomarker discovery, clinical diagnosis, toxicological studies, molecular phenotyping, and functional genomics.
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Affiliation(s)
- Tapas K Mal
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
| | - Yuan Tian
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
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6
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Dospinescu VM, Tiele A, Covington JA. Sniffing Out Urinary Tract Infection-Diagnosis Based on Volatile Organic Compounds and Smell Profile. BIOSENSORS 2020; 10:E83. [PMID: 32717983 PMCID: PMC7460005 DOI: 10.3390/bios10080083] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023]
Abstract
Current available methods for the clinical diagnosis of urinary tract infection (UTI) rely on a urine dipstick test or culturing of pathogens. The dipstick test is rapid (available in 1-2 min), but has a low positive predictive value, while culturing is time-consuming and delays diagnosis (24-72 h between sample collection and pathogen identification). Due to this delay, broad-spectrum antibiotics are often prescribed immediately. The over-prescription of antibiotics should be limited, in order to prevent the development of antimicrobial resistance. As a result, there is a growing need for alternative diagnostic tools. This paper reviews applications of chemical-analysis instruments, such as gas chromatography-mass spectrometry (GC-MS), selected ion flow tube mass spectrometry (SIFT-MS), ion mobility spectrometry (IMS), field asymmetric ion mobility spectrometry (FAIMS) and electronic noses (eNoses) used for the diagnosis of UTI. These methods analyse volatile organic compounds (VOCs) that emanate from the headspace of collected urine samples to identify the bacterial pathogen and even determine the causative agent's resistance to different antibiotics. There is great potential for these technologies to gain wide-spread and routine use in clinical settings, since the analysis can be automated, and test results can be available within minutes after sample collection. This could significantly reduce the necessity to prescribe broad-spectrum antibiotics and allow the faster and more effective use of narrow-spectrum antibiotics.
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Affiliation(s)
| | - Akira Tiele
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK;
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Tayanloo-Beik A, Sarvari M, Payab M, Gilany K, Alavi-Moghadam S, Gholami M, Goodarzi P, Larijani B, Arjmand B. OMICS insights into cancer histology; Metabolomics and proteomics approach. Clin Biochem 2020; 84:13-20. [PMID: 32589887 DOI: 10.1016/j.clinbiochem.2020.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Metabolomics as a post-genomic research area comprising different analytical methods for small molecules analysis. One of the underlying applications of metabolomics technology for better disease diagnosis and prognosis is discovering the metabolic pathway differences between healthy individuals and patients. On the other hand, the other noteworthy applications of metabolomics include its effective role in biomarker screening for cancer detection, monitoring, and prediction. In other words, emerging of the metabolomics field can be hopeful to provide a suitable alternative for the common current cancer diagnostic methods especially histopathological tests. Indeed, cancer as a major global issue places a substantial burden on the health care system. Hence, proper management can be beneficial. In this respect, formalin-fixed paraffin-embedded tissue specimens (in histopathological tests) are considered as a valuable source for metabolomics investigations. Interestingly, formalin-fixed paraffin-embedded tissue specimens can provide informative data for cancer management. In general, using these specimens, determining the cancer stage, individual response to the different therapies, personalized risk prediction are possible and high-quality clinical services are the promise of OMICS technologies for cancer disease. However, considering all of these beneficial characteristics, there are still some limitations in this area that need to be addressed in order to optimize the metabolomics utilizations and advancement.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Masoumeh Sarvari
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Kambiz Gilany
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran; Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahdi Gholami
- Department of Toxicology & Pharmacology, Faculty of Pharmacy; Toxicology and Poisoning Research Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran.
| | - Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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Abstract
The persistent increase in the worldwide burden of type 2 diabetes mellitus (T2D) and the accompanying rise of its complications, including cardiovascular disease, necessitates our understanding of the metabolic disturbances that cause diabetes mellitus. Metabolomics and proteomics, facilitated by recent advances in high-throughput technologies, have given us unprecedented insight into circulating biomarkers of T2D even over a decade before overt disease. These markers may be effective tools for diabetes mellitus screening, diagnosis, and prognosis. As participants of metabolic pathways, metabolite and protein markers may also highlight pathways involved in T2D development. The integration of metabolomics and proteomics with genomics in multiomics strategies provides an analytical method that can begin to decipher causal associations. These methods are not without their limitations; however, with careful study design and sample handling, these methods represent powerful scientific tools that can be leveraged for the study of T2D. In this article, we aim to give a timely overview of circulating metabolomics and proteomics findings with T2D observed in large human population studies to provide the reader with a snapshot into these emerging fields of research.
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Affiliation(s)
- Zsu-Zsu Chen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Cardiovascular Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Robert E. Gerszten
- Cardiovascular Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Cabozantinib for the Management of Metastatic Clear Cell Renal Cell Carcinoma. J Kidney Cancer VHL 2018; 5:1-5. [PMID: 30319937 PMCID: PMC6175852 DOI: 10.15586/jkcvhl.2018.109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/03/2018] [Indexed: 12/18/2022] Open
Abstract
Cabozantinib is a multi-tyrosine kinase inhibitor used for the treatment of various solid-organ tumours. It was recently approved as a first- and second-line therapeutic for the management of advanced/metastatic renal cell carcinoma based on the results of two randomised controlled trials. The phase III METEOR trial compared cabozantinib against everolimus as a second- or greater line therapy and found benefits in progression-free and overall survival, and the phase II CABOSUN trial compared cabozantinib against sunitinib as a first-line therapeutic and found benefits in terms of progression-free survival. This review briefly summarises how cabozantinib fits into current treatment paradigms for the management of advanced renal cell carcinoma.
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10
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Kaushik AK, DeBerardinis RJ. Applications of metabolomics to study cancer metabolism. Biochim Biophys Acta Rev Cancer 2018; 1870:2-14. [PMID: 29702206 PMCID: PMC6193562 DOI: 10.1016/j.bbcan.2018.04.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022]
Abstract
Reprogrammed metabolism supports tumor growth and provides a potential source of therapeutic targets and disease biomarkers. Mass spectrometry-based metabolomics has emerged as a broadly informative technique for profiling metabolic features associated with specific oncogenotypes, disease progression, therapeutic liabilities and other clinically relevant aspects of tumor biology. In this review, we introduce the applications of metabolomics to study deregulated metabolism and metabolic vulnerabilities in cancer. We provide examples of studies that used metabolomics to discover novel metabolic regulatory mechanisms, including processes that link metabolic alterations with gene expression, protein function, and other aspects of systems biology. Finally, we discuss emerging applications of metabolomics for in vivo isotope tracing and metabolite imaging, both of which hold promise to advance our understanding of the role of metabolic reprogramming in cancer.
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Affiliation(s)
- Akash K Kaushik
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-8502, United States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-8502, United States.
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11
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Dietz C, Ehret F, Palmas F, Vandergrift LA, Jiang Y, Schmitt V, Dufner V, Habbel P, Nowak J, Cheng LL. Applications of high-resolution magic angle spinning MRS in biomedical studies II-Human diseases. NMR IN BIOMEDICINE 2017; 30:10.1002/nbm.3784. [PMID: 28915318 PMCID: PMC5690552 DOI: 10.1002/nbm.3784] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 05/06/2023]
Abstract
High-resolution magic angle spinning (HRMAS) MRS is a powerful method for gaining insight into the physiological and pathological processes of cellular metabolism. Given its ability to obtain high-resolution spectra of non-liquid biological samples, while preserving tissue architecture for subsequent histopathological analysis, the technique has become invaluable for biochemical and biomedical studies. Using HRMAS MRS, alterations in measured metabolites, metabolic ratios, and metabolomic profiles present the possibility to improve identification and prognostication of various diseases and decipher the metabolomic impact of drug therapies. In this review, we evaluate HRMAS MRS results on human tissue specimens from malignancies and non-localized diseases reported in the literature since the inception of the technique in 1996. We present the diverse applications of the technique in understanding pathological processes of different anatomical origins, correlations with in vivo imaging, effectiveness of therapies, and progress in the HRMAS methodology.
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Affiliation(s)
- Christopher Dietz
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Felix Ehret
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Francesco Palmas
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Sardinia, 09042 Italy
| | - Lindsey A. Vandergrift
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
| | - Yanni Jiang
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Radiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029 China
| | - Vanessa Schmitt
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Vera Dufner
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Johannes Nowak
- Department of Diagnostic and Interventional Radiology, University Hospital of Würzburg, 97080 Würzburg, Germany
| | - Leo L. Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
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12
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Rodrigues D, Monteiro M, Jerónimo C, Henrique R, Belo L, Bastos MDL, Guedes de Pinho P, Carvalho M. Renal cell carcinoma: a critical analysis of metabolomic biomarkers emerging from current model systems. Transl Res 2017; 180:1-11. [PMID: 27546593 DOI: 10.1016/j.trsl.2016.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/16/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
Abstract
Metabolomics, an emerging field of "omics" sciences, has caught wide scientific attention in the area of biomarker research for cancers in which early diagnostic biomarkers have the potential to greatly improve patient outcome, such as renal cell carcinoma (RCC). Metabolomic approaches have been successfully applied to various human RCC model systems, mostly ex vivo neoplastic renal tissues and biofluids (urine and serum) from patients with RCC. Importantly, in contrast to other cancers, only a few studies have addressed the RCC metabolome using cancer cell culture-based in vitro models. Herein, we first carried out a comprehensive review of current metabolomic data in RCC, with emphasis on metabolite disturbances and dysregulated metabolic pathways identified in each of these experimental models. We then critically analyzed the consistency of evidence in this field and whether metabolites found altered in tumor cell and tissue microenvironment are reflected in biofluids, which constitute the rationale underlying the translation of discovered metabolic biomarkers into noninvasive diagnostic tools. Finally, dominant metabolic pathways and promising metabolites as biomarkers for diagnosis and prognosis of RCC are outlined.
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Affiliation(s)
- Daniela Rodrigues
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Toxicology, Department of Biological Sciences, University of Porto, Porto, Portugal.
| | - Márcia Monteiro
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Toxicology, Department of Biological Sciences, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute-Porto (IPO-Porto), Porto, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute-Porto (IPO-Porto), Porto, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute-Porto (IPO-Porto), Porto, Portugal
| | - Luís Belo
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Biochemistry, Department of Biological Sciences, University of Porto, Porto, Portugal
| | - Maria de Lourdes Bastos
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Toxicology, Department of Biological Sciences, University of Porto, Porto, Portugal
| | - Paula Guedes de Pinho
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Toxicology, Department of Biological Sciences, University of Porto, Porto, Portugal
| | - Márcia Carvalho
- UCIBIO/REQUIMTE, Faculty of Pharmacy, Laboratory of Toxicology, Department of Biological Sciences, University of Porto, Porto, Portugal; FP-ENAS (UFP Energy, Environment and Health Research Unit), CEBIMED (Biomedical Research Centre), Fernando Pessoa University, Porto, Portugal.
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Abstract
This paper reviews the use of NMR metabolomics for the metabolic characterization of renal cancer. The existing challenges in the clinical management of this disease are first presented, followed by a brief introduction to the metabolomics approach, in the context of cancer research. A subsequent review of the literature on NMR metabolic studies of renal cancer reveals that the subject has been clearly underdeveloped, compared with other types of cancer, particularly regarding cultured cells and tissue analysis. NMR analysis of biofluids has focused on blood (plasma or serum) metabolomics, comprising no account of studies on human urine, in spite of its noninvasiveness and physiological proximity to the affected organs. Finally, some areas of potential future development are identified.
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Jain NS, Dürr UH, Ramamoorthy A. Bioanalytical methods for metabolomic profiling: Detection of head and neck cancer, including oral cancer. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Abstract
Hypertension is the most prevalent chronic medical condition and a major risk factor for cardiovascular morbidity and mortality. In the majority of hypertensive cases, the underlying cause of hypertension cannot be easily identified because of the heterogeneous, polygenic and multi-factorial nature of hypertension. Metabolomics is a relatively new field of research that has been used to evaluate metabolic perturbations associated with disease, identify disease biomarkers and to both assess and predict drug safety and efficacy. Metabolomics has been increasingly used to characterize risk factors for cardiovascular disease, including hypertension, and it appears to have significant potential for uncovering mechanisms of this complex disease. This review details the analytical techniques, pre-analytical steps and study designs used in metabolomics studies, as well as the emerging role for metabolomics in gaining mechanistic insights into the development of hypertension. Suggestions as to the future direction for metabolomics research in the field of hypertension are also proposed.
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16
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He XH, Li WT, Gu YJ, Yang BF, Deng HW, Yu YH, Peng WJ. Metabonomic studies of pancreatic cancer response to radiotherapy in a mouse xenograft model using magnetic resonance spectroscopy and principal components analysis. World J Gastroenterol 2013; 19:4200-4208. [PMID: 23864784 PMCID: PMC3710423 DOI: 10.3748/wjg.v19.i26.4200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 04/28/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the metabolic profiles of xenograft pancreatic cancer before and after radiotherapy by high-resolution magic angle spinning proton magnetic resonance spectroscopy (HRMAS 1H NMR) combined with principal components analysis (PCA) and evaluate the radiotherapeutic effect.
METHODS: The nude mouse xenograft model of human pancreatic cancer was established by injecting human pancreatic cancer cell SW1990 subcutaneously into the nude mice. When the tumors volume reached 800 mm3, the mice received various radiation doses. Two weeks later, tumor tissue sections were prepared for running the NMR measurements. 1H NMR and PCA were used to determine the changes in the metabolic profiles of tumor tissues after radiotherapy. Metabolic profiles of normal pancreas, pancreatic tumor tissues, and radiation- treated pancreatic tumor tissues were compared.
RESULTS: Compared with 1H NMR spectra of the normal nude mouse pancreas, the levels of choline, taurine, alanine, isoleucine, leucine, valine, lactate, and glutamic acid of the pancreatic cancer group were increased, whereas an opposite trend for phosphocholine, glycerophosphocholine, and betaine was observed. The ratio of phosphocholine to creatine, and glycerophosphocholine to creatine showed noticeable decrease in the pancreatic cancer group. After further evaluation of the tissue metabolic profile after treatment with three different radiation doses, no significant change in metabolites was observed in the 1H NMR spectra, while the inhibition of tumor growth was in proportion to the radiation doses. However, PCA results showed that the levels of choline and betaine were decreased with the increased radiation dose, and conversely, the level of acetic acid was dramatically increased.
CONCLUSION: The combined methods were demonstrated to have the potential for allowing early diagnosis and assessment of pancreatic cancer response to radiotherapy.
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17
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Forcisi S, Moritz F, Kanawati B, Tziotis D, Lehmann R, Schmitt-Kopplin P. Liquid chromatography–mass spectrometry in metabolomics research: Mass analyzers in ultra high pressure liquid chromatography coupling. J Chromatogr A 2013; 1292:51-65. [DOI: 10.1016/j.chroma.2013.04.017] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 03/29/2013] [Accepted: 04/10/2013] [Indexed: 12/27/2022]
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18
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Anwar M, Shalhoub J, Vorkas P, Lim C, Want E, Nicholson J, Holmes E, Davies A. In-vitro Identification of Distinctive Metabolic Signatures of Intact Varicose Vein Tissue via Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy. Eur J Vasc Endovasc Surg 2012; 44:442-50. [DOI: 10.1016/j.ejvs.2012.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 05/19/2012] [Indexed: 01/13/2023]
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19
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Abstract
The metabolome is a data-rich source of information concerning all the low-molecular-weight metabolites in a biofluid, which can indicate early biological changes to the host due to perturbations in metabolic pathways. Major changes can be seen after minor stimuli, which make it a valuable target for analysis. Due to the diverse and sensitive nature of the metabolome, studies must be designed in a manner to maintain consistency, reduce variation between subjects, and optimize information recovery. Technological advancements in experimental design, mouse models and instrumentation have aided in this effort. Metabolomics has the ultimate potential to be valuable in a clinical setting where it could be used for early diagnosis of a disease and as a predictor of treatment response and survival. During drug treatment, the metabolic status of an individual could be monitored and used to indicate possible toxic effects. Metabolomics therefore has great potential for improving diagnosis, treatment and aftercare of disease.
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Affiliation(s)
- CAROLINE H. JOHNSON
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - FRANK J. GONZALEZ
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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20
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Denkert C, Bucher E, Hilvo M, Salek R, Orešič M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O. Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery. Genome Med 2012; 4:37. [PMID: 22546809 PMCID: PMC3446265 DOI: 10.1186/gm336] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Breast cancer is the most common cancer in women worldwide, and the development of new technologies for better understanding of the molecular changes involved in breast cancer progression is essential. Metabolic changes precede overt phenotypic changes, because cellular regulation ultimately affects the use of small-molecule substrates for cell division, growth or environmental changes such as hypoxia. Differences in metabolism between normal cells and cancer cells have been identified. Because small alterations in enzyme concentrations or activities can cause large changes in overall metabolite levels, the metabolome can be regarded as the amplified output of a biological system. The metabolome coverage in human breast cancer tissues can be maximized by combining different technologies for metabolic profiling. Researchers are investigating alterations in the steady state concentrations of metabolites that reflect amplified changes in genetic control of metabolism. Metabolomic results can be used to classify breast cancer on the basis of tumor biology, to identify new prognostic and predictive markers and to discover new targets for future therapeutic interventions. Here, we examine recent results, including those from the European FP7 project METAcancer consortium, that show that integrated metabolomic analyses can provide information on the stage, subtype and grade of breast tumors and give mechanistic insights. We predict an intensified use of metabolomic screens in clinical and preclinical studies focusing on the onset and progression of tumor development.
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Affiliation(s)
- Carsten Denkert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.
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21
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Udelnow A, Kreyes A, Ellinger S, Landfester K, Walther P, Klapperstueck T, Wohlrab J, Henne-Bruns D, Knippschild U, Würl P. Omeprazole inhibits proliferation and modulates autophagy in pancreatic cancer cells. PLoS One 2011; 6:e20143. [PMID: 21629657 PMCID: PMC3101238 DOI: 10.1371/journal.pone.0020143] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/26/2011] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Omeprazole has recently been described as a modulator of tumour chemoresistance, although its underlying molecular mechanisms remain controversial. Since pancreatic tumours are highly chemoresistant, a logical step would be to investigate the pharmacodynamic, morphological and biochemical effects of omeprazole on pancreatic cancer cell lines. METHODOLOGY/PRINCIPAL FINDINGS Dose-effect curves of omeprazole, pantoprazole, gemcitabine, 5-fluorouracil and the combinations of omeprazole and 5-fluorouracil or gemcitabine were generated for the pancreatic cancer cell lines MiaPaCa-2, ASPC-1, Colo357, PancTu-1, Panc1 and Panc89. They revealed that omeprazole inhibited proliferation at probably non-toxic concentrations and reversed the hormesis phenomena of 5-fluorouracil. Electron microscopy showed that omeprazole led to accumulation of phagophores and early autophagosomes in ASPC-1 and MiaPaCa-2 cells. Signal changes indicating inhibited proliferation and programmed cell death were found by proton NMR spectroscopy of both cell lines when treated with omeprazole which was identified intracellularly. Omeprazole modulates the lysosomal transport pathway as shown by Western blot analysis of the expression of LAMP-1, Cathepsin-D and β-COP in lysosome- and Golgi complex containing cell fractions. Acridine orange staining revealed that the pump function of the vATPase was not specifically inhibited by omeprazole. Gene expression of the autophagy-related LC3 gene as well as of Bad, Mdr-1, Atg12 and the vATPase was analysed after treatment of cells with 5-fluorouracil and omeprazole and confirmed the above mentioned results. CONCLUSIONS We hypothesise that omeprazole interacts with the regulatory functions of the vATPase without inhibiting its pump function. A modulation of the lysosomal transport pathway and autophagy is caused in pancreatic cancer cells leading to programmed cell death. This may circumvent common resistance mechanisms of pancreatic cancer. Since omeprazole use has already been established in clinical practice these results could lead to new clinical applications.
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Affiliation(s)
- Andrej Udelnow
- Department of General, Visceral and Transplantation Surgery, University Hospital of Ulm, Ulm, Germany
| | - Andreas Kreyes
- Institute of Organic Chemistry, Macromolecular Chemistry and Organic Materials, University of Ulm, Ulm, Germany
| | - Stefan Ellinger
- Institute of Organic Chemistry, Macromolecular Chemistry and Organic Materials, University of Ulm, Ulm, Germany
| | | | - Paul Walther
- Department of Electron Microscopy, University of Ulm, Ulm, Germany
| | - Thomas Klapperstueck
- Department of Dermatology and Venereology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Johannes Wohlrab
- Department of Dermatology and Venereology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Doris Henne-Bruns
- Department of General, Visceral and Transplantation Surgery, University Hospital of Ulm, Ulm, Germany
| | - Uwe Knippschild
- Department of General, Visceral and Transplantation Surgery, University Hospital of Ulm, Ulm, Germany
| | - Peter Würl
- Department of General, Visceral and Transplantation Surgery, University Hospital of Ulm, Ulm, Germany
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22
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Ellis JK, Athersuch TJ, Cavill R, Radford R, Slattery C, Jennings P, McMorrow T, Ryan MP, Ebbels TMD, Keun HC. Metabolic response to low-level toxicant exposure in a novel renal tubuleepithelial cell system. ACTA ACUST UNITED AC 2011; 7:247-57. [DOI: 10.1039/c0mb00146e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Mazzei P, Piccolo A, Nugnes L, Mascolo M, De Rosa G, Staibano S. Metabolic profile of intact tissue from uterine leiomyomas using high-resolution magic-angle-spinning ¹H NMR spectroscopy. NMR IN BIOMEDICINE 2010; 23:1137-1145. [PMID: 20623794 DOI: 10.1002/nbm.1540] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
High-resolution magic-angle-spinning (HRMAS) one- and two-dimensional (1)H and (13)C NMR spectroscopy was used to study intact healthy (myometrium) and benign (leiomyoma) uterine tissues of 10 patients. Twenty-eight metabolites were detected and assigned in both types of tissue. Principal component analysis (PCA) was applied to a conventional water-suppressed (1)H HRMAS NMR spectrum, and two NMR spectral editing methods, namely Carr-Purcell- Meiboom-Gill (CPMG) spin-echo and diffusion-edited techniques, were used. Only the PCA of CPMG spectra resulted in a good differentiation between the two tissue types. The CPMG spin-echo spectra were also useful in indicating depleted levels of taurine in uterine leiomyomas, which were well correlated with the histopathological determination. In addition, statistical analysis revealed that most leiomyomas contained elevated concentrations of glutamate and glutamine. Our results suggest that HRMAS represents a valuable adjunct to histopathology to improve the diagnostic accuracy of uterine leiomyomas, whilst concomitantly reducing the diagnosis time.
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Affiliation(s)
- Pierluigi Mazzei
- Pierluigi Mazzei, Alessandro Piccolo Centro Interdipartimentale di Ricerca per la Risonanza Magnetica Nucleare, Università di Napoli Federico II, Portici, Italy
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24
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Novoa-Carballal R, Fernandez-Megia E, Jimenez C, Riguera R. NMR methods for unravelling the spectra of complex mixtures. Nat Prod Rep 2010; 28:78-98. [PMID: 20936238 DOI: 10.1039/c005320c] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main methods for the simplification of the NMR of complex mixtures by selective attenuation/suppression of the signals of certain components are presented. The application of relaxation, diffusion and PSR filters and other techniques to biological samples, pharmaceuticals, foods, living organisms and natural products are illustrated with examples.
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Affiliation(s)
- Ramon Novoa-Carballal
- Department of Organic Chemistry and Centre for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Santiago de Compostela, Spain
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25
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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: 261] [Impact Index Per Article: 17.4] [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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26
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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: 0.4] [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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27
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Lachenmeier DW, Humpfer E, Fang F, Schütz B, Dvortsak P, Sproll C, Spraul M. NMR-spectroscopy for nontargeted screening and simultaneous quantification of health-relevant compounds in foods: the example of melamine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:7194-7199. [PMID: 20349917 PMCID: PMC2725748 DOI: 10.1021/jf902038j] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/16/2009] [Indexed: 05/28/2023]
Abstract
The recent melamine crisis in China has pointed out a serious deficiency in current food control systems, namely, they specifically focus on selected known compounds. This targeted approach allowed the presence of melamine in milk products to be overlooked for a considerable time. To avoid such crises in the future, we propose that nontargeted screening methods need to be developed and applied. To this end, NMR has an extraordinary potential that just started to be recognized and exploited. Our research shows that, from the very same set of spectra, (1)H NMR at 400 MHz can distinguish between melamine-contaminated and melamine-free infant formulas and can provide quantitative information by integration of individual lines after identification. For contaminated Chinese infant formulas or candy, identical results were obtained when comparing NMR with SPE-LC/MS/MS. NMR was found to be suitable for routine nontargeted and targeted analyses of foods, and its use will significantly increase food safety.
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Affiliation(s)
- Dirk W Lachenmeier
- Chemisches und Veterinaruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, Karlsruhe, Germany.
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28
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Borel M, Pastoureau P, Papon J, Madelmont JC, Moins N, Maublant J, Miot-Noirault E. Longitudinal profiling of articular cartilage degradation in osteoarthritis by high-resolution magic angle spinning 1H NMR spectroscopy: experimental study in the meniscectomized guinea pig model. J Proteome Res 2009; 8:2594-600. [PMID: 19323466 DOI: 10.1021/pr8009963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study assessed the 1H HRMAS NMR spectroscopic profile of articular cartilage in both physiological and osteoarthitic situations. One-dimensional and two-dimensional 1H HRMAS NMR spectra were obtained from the tibial plateau cartilage of healthy and operated (unilateral medial meniscectomy and sham surgery) guinea pigs at different stages of disease, over a 6-month period. The major osteoarthritis-induced 1H HRMAS NMR changes were an increase of the N-acetyl peak of proteoglycans (at day 20 after meniscectomy) and a decrease after day 60 as the pathology evolved. These proteoglycan changes revealed by 1H HRMAS NMR analysis were validated by proteoglycan biochemistry assays. 1H HRMAS NMR analysis also evidenced a sharp increase in methylene resonances of chondrocyte membrane lipids from day 90 as a marker of apoptosis. There was an increase of the mobile methyl group of collagen at day 120, which was associated with collagen breakdown. 1H HRMAS NMR analysis provided a multifactorial and sequential picture of cartilage degradation at the extracellular matrix and chondrocyte levels.
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Affiliation(s)
- Michele Borel
- EA 4231, University d'Auvergne, INSERM UMR 484, Clermont-Ferrand, F-63005 France.
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29
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Gowda GAN, Zhang S, Gu H, Asiago V, Shanaiah N, Raftery D. Metabolomics-based methods for early disease diagnostics. Expert Rev Mol Diagn 2009; 8:617-33. [PMID: 18785810 DOI: 10.1586/14737159.8.5.617] [Citation(s) in RCA: 487] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The emerging field of metabolomics, in which a large number of small-molecule metabolites from body fluids or tissues are detected quantitatively in a single step, promises immense potential for early diagnosis, therapy monitoring and for understanding the pathogenesis of many diseases. Metabolomics methods are mostly focused on the information-rich analytical techniques of NMR spectroscopy and mass spectrometry (MS). Analysis of the data from these high-resolution methods using advanced chemometric approaches provides a powerful platform for translational and clinical research and diagnostic applications. In this review, the current trends and recent advances in NMR- and MS-based metabolomics are described with a focus on the development of advanced NMR and MS methods, improved multivariate statistical data analysis and recent applications in the area of cancer, diabetes, inborn errors of metabolism and cardiovascular diseases.
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Affiliation(s)
- G A Nagana Gowda
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
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30
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Swanson MG, Keshari KR, Tabatabai ZL, Simko JP, Shinohara K, Carroll PR, Zektzer AS, Kurhanewicz J. Quantification of choline- and ethanolamine-containing metabolites in human prostate tissues using 1H HR-MAS total correlation spectroscopy. Magn Reson Med 2008; 60:33-40. [PMID: 18581409 DOI: 10.1002/mrm.21647] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A fast and quantitative 2D high-resolution magic angle spinning (HR-MAS) total correlation spectroscopy (TOCSY) experiment was developed to resolve and quantify the choline- and ethanolamine-containing metabolites in human prostate tissues in approximately 1 hr prior to pathologic analysis. At a 40-ms mixing time, magnetization transfer efficiency constants were empirically determined in solution and used to calculate metabolite concentrations in tissue. Phosphocholine (PC) was observed in 11/15 (73%) cancer tissues but only 6/32 (19%) benign tissues. PC was significantly higher (0.39 +/- 0.40 mmol/kg vs. 0.02 +/- 0.07 mmol/kg, z = 3.5), while ethanolamine (Eth) was significantly lower in cancer versus benign prostate tissues (1.0 +/- 0.8 mmol/kg vs. 2.3 +/- 1.9 mmol/kg, z = 3.3). Glycerophosphocholine (GPC) (0.57 +/- 0.87 mmol/kg vs. 0.29 +/- 0.26 mmol/kg, z = 1.2), phosphoethanolamine (PE) (4.4 +/- 2.2 mmol/kg vs. 3.4 +/- 2.6 mmol/kg, z = 1.4), and glycerophosphoethanolamine (GPE) (0.54 +/- 0.82 mmol/kg vs. 0.15 +/- 0.15 mmol/kg, z = 1.8) were higher in cancer versus benign prostate tissues. The ratios of PC/GPC (3.5 +/- 4.5 vs. 0.32 +/- 1.4, z = 2.6), PC/PE (0.08 +/- 0.08 vs. 0.01 +/- 0.03, z = 3.5), PE/Eth (16 +/- 22 vs. 2.2 +/- 2.0, z = 2.4), and GPE/Eth (0.41 +/- 0.51 vs. 0.06 +/- 0.06, z = 2.6) were also significantly higher in cancer versus benign tissues. All samples were pathologically interpretable following HR-MAS analysis; however, degradation experiments showed that PC, GPC, PE, and GPE decreased 7.7 +/- 2.2%, while Cho+mI and Eth increased 18% in 1 hr at 1 degrees C and a 2250 Hz spin rate.
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Affiliation(s)
- Mark G Swanson
- Department of Radiology, University of California-San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
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31
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Opstad KS, Bell BA, Griffiths JR, Howe FA. An assessment of the effects of sample ischaemia and spinning time on the metabolic profile of brain tumour biopsy specimens as determined by high-resolution magic angle spinning (1)H NMR. NMR IN BIOMEDICINE 2008; 21:1138-47. [PMID: 18666093 DOI: 10.1002/nbm.1296] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
High-resolution magic angle spinning (HRMAS) (1)H NMR of biopsy tissue provides a biochemical profile that has potential diagnostic and prognostic value, and can aid interpretation of the lower-resolution (1)H-NMR spectra obtained in vivo. However, the biochemical profile obtained may be affected by experimental factors such as a period of ischaemia before snap-freezing of the biopsy tissue for subsequent analysis and the mechanical stress of the spinning procedure of HRMAS itself. We have used normal rat brain cortex as a 'gold standard', either funnel-frozen or deliberately allowed to become ischaemic for set periods of time before snap-freezing, to quantitatively investigate these two effects. In addition, we have compared biochemical changes that occur in normal rat brain during HRMAS (spun continuously at 5 kHz for 4 h at 4 degrees C as could be required for a two-dimensional acquisition) with those that occur in biopsy samples from low-grade and high-grade adult human astrocytomas, during the same HRMAS procedure. Significant changes due to delayed initial sample freezing were noted in metabolites associated with glycolysis (alanine, glucose and lactate), as expected. However, for the funnel-frozen rat tissue at 4 degrees C, there were even more significant changes, which appear to be the result of extended spinning at 5 kHz. In particular, the 18% total creatine increase observed is unlikely to be de novo synthesis of creatine. More likely, the asymptotic exponential increase in creatine suggests an exponential release of an NMR-invisible bound creatine store as a result of tissue damage from mechanical stress of sample spinning. Overall, it appears that tissue ischaemia during biopsy excision and delays in snap-freezing may have less significant effects on metabolite profile than the prolonged spinning times required for two-dimensional HRMAS, and this must be accounted for when results are being interpreted.
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Affiliation(s)
- Kirstie S Opstad
- Division of Basic Medical Sciences, St George's, University of London, UK.
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Abstract
Since its original description in 1972, apoptosis or programmed cell death has been recognized as the major pathway by which the body precisely regulates the number and type of its cells as part of normal embryogenesis, development, and homeostasis. Later it was found that apoptosis was also involved in the pathogenesis of a number of human diseases, cell immunity, and the action of cytotoxotic drugs and radiation therapy in cancer treatment. As such, the imaging of apoptosis with noninvasive techniques such as with radiotracers, including annexin V and lipid proton magnetic resonance spectroscopy, may have a wide range of clinical utility in both the diagnosis and monitoring therapy of a wide range of human disorders. In this chapter we review the basic biochemical and morphologic features of apoptosis and the methods developed thus far to image this complex process in humans.
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Affiliation(s)
- H William Strauss
- Memorial Sloan Kettering Hospital, 1275 York Ave., Room S-212, Nuclear Medicine, New York, NY 10021, USA.
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Monleón D, Morales JM, Gonzalez-Darder J, Talamantes F, Cortés O, Gil-Benso R, López-Ginés C, Cerdá-Nicolás M, Celda B. Benign and atypical meningioma metabolic signatures by high-resolution magic-angle spinning molecular profiling. J Proteome Res 2008; 7:2882-8. [PMID: 18507434 DOI: 10.1021/pr800110a] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Meningiomas are neoplasms that arise from the leptomeningeal covering of the brain and spinal cord, accounting for 15%-20% of CNS tumors. The WHO classifies meningiomas into three histological grades: benign, atypical, and anaplasic in accordance with the clinical prognosis. Atypical and anaplasic meningiomas tend to recur. Sometimes, meningiomas with histological diagnosis of benign meningioma show clinical characteristics of atypical meningioma. In this context, high-resolution magic-angle spinning (HR-MAS) spectroscopy of intact tissue from brain tumor biopsies has shown great potential as a support diagnostic tool. In this work, we show differences between benign and atypical meningiomas in HR-MAS molecular profiles of meningioma biopsies. Metabolic differences between meningioma grades include changes in the levels of glutathione. Glutathione role in cancer is still unclear, as it may act both as protective and pathogenic factor. Glutamine and glutamate, which are related to glutathione metabolism and have been associated with tumor recurrence, are also increased in atypical meningiomas. Other metabolites associated with tumor malignancy that show statistically significant differences between benign and atypical meningiomas include phosphocholine and phosphoethanolamine. Overall, this work suggests that the additional information obtained by NMR metabolomics applied to biopsies of human meningiomas may be useful for assessing tumor grade and determining optimum treatment strategies.
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Affiliation(s)
- Daniel Monleón
- Fundacion de Investigacion del Hospital Clinico Universitario de Valencia, Valencia, Spain
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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: 1.6] [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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Beckonert O, Keun HC, Ebbels TMD, Bundy J, Holmes E, Lindon JC, Nicholson JK. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2008; 2:2692-703. [PMID: 18007604 DOI: 10.1038/nprot.2007.376] [Citation(s) in RCA: 1536] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metabolic profiling, metabolomic and metabonomic studies mainly involve the multicomponent analysis of biological fluids, tissue and cell extracts using NMR spectroscopy and/or mass spectrometry (MS). We summarize the main NMR spectroscopic applications in modern metabolic research, and provide detailed protocols for biofluid (urine, serum/plasma) and tissue sample collection and preparation, including the extraction of polar and lipophilic metabolites from tissues. 1H NMR spectroscopic techniques such as standard 1D spectroscopy, relaxation-edited, diffusion-edited and 2D J-resolved pulse sequences are widely used at the analysis stage to monitor different groups of metabolites and are described here. They are often followed by more detailed statistical analysis or additional 2D NMR analysis for biomarker discovery. The standard acquisition time per sample is 4-5 min for a simple 1D spectrum, and both preparation and analysis can be automated to allow application to high-throughput screening for clinical diagnostic and toxicological studies, as well as molecular phenotyping and functional genomics.
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Affiliation(s)
- Olaf Beckonert
- Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, UK
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Coen M, Holmes E, Lindon JC, Nicholson JK. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol 2008; 21:9-27. [PMID: 18171018 DOI: 10.1021/tx700335d] [Citation(s) in RCA: 226] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have reviewed the main contributions to the development of NMR-based metabonomic and metabolic profiling approaches for toxicological assessment, biomarker discovery, and studies on toxic mechanisms. The metabonomic approach, (defined as the quantitative measurement of the multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification) was originally developed to assist interpretation in NMR-based toxicological studies. However, in recent years there has been extensive fusion with metabolomic and other metabolic profiling approaches developed in plant biology, and there is much wider coverage of the biomedical and environmental fields. Specifically, metabonomics involves the use of spectroscopic techniques with statistical and mathematical tools to elucidate dominant patterns and trends directly correlated with time-related metabolic fluctuations within spectral data sets usually derived from biofluids or tissue samples. Temporal multivariate metabolic signatures can be used to discover biomarkers of toxic effect, as general toxicity screening aids, or to provide novel mechanistic information. This approach is complementary to proteomics and genomics and is applicable to a wide range of problems, including disease diagnosis, evaluation of xenobiotic toxicity, functional genomics, and nutritional studies. The use of biological fluids as a source of whole organism metabolic information enhances the use of this approach in minimally invasive longitudinal studies.
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Affiliation(s)
- Muireann Coen
- Department of Biomolecular Medicine, Surgery, Oncology, Reproductive Biology and Anesthetics Division, Faculty of Medicine, Imperial College London, London, UK
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Shanaiah N, Zhang S, Desilva MA, Raftery D. NMR-Based Metabolomics for Biomarker Discovery. BIOMARKER METHODS IN DRUG DISCOVERY AND DEVELOPMENT 2008. [DOI: 10.1007/978-1-59745-463-6_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Fang F, He X, Deng H, Chen Q, Lu J, Spraul M, Yu Y. Discrimination of metabolic profiles of pancreatic cancer from chronic pancreatitis by high-resolution magic angle spinning 1H nuclear magnetic resonance and principal components analysis. Cancer Sci 2007; 98:1678-82. [PMID: 17727683 PMCID: PMC11158482 DOI: 10.1111/j.1349-7006.2007.00589.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 07/06/2007] [Indexed: 01/06/2023] Open
Abstract
The metabolic profiles of Sprague-Dawley rat pancreases were investigated by high-resolution magic angle spinning proton magnetic resonance spectroscopy ((1)H NMR) combined with principal components analysis (PCA) to discriminate pancreatic cancer from chronic pancreatitis. Intact pancreatic tissue samples were obtained from Sprague-Dawley rats with histologically proven pancreatic cancer (n = 5), chronic pancreatitis (n = 5), and two matched controls (n = 5 per group). Two (1)H NMR experiments, single-pulse and Carr-Purcell-Meiboom-Gill, were carried out separately. Increases in phosphocholine and glycerophosphocholine levels and decreases in leucine, isoleucine, valine, lactate and alanine levels were observed in chronic pancreatitis, whereas the opposite trends were observed in pancreatic cancer. Increasing taurine and decreasing betaine were found both in chronic pancreatitis and in pancreatic cancer. Additionally, the lipid content in pancreatic cancer was higher than that in chronic pancreatitis. PCA was carried out for the single-pulse and Carr-Purcell-Meiboom-Gill (1)H NMR spectra, respectively, to visualize separation among the samples and to extract characteristic metabolites of pancreatic cancer and chronic pancreatitis. Decreased phosphocholine and glycerophosphocholine were suggested as unique metabolite indicators of pancreatic cancer. Furthermore, even with the disturbance of various quantities of lipid contents pancreatic cancer and chronic pancreatitis could be differentiated well by the combination of high-resolution magic angle spinning (1)H NMR and PCA. Thus this combination was demonstrated to have the potential to improve magnetic resonance spectroscopy for positive early diagnosis of pancreatic cancer in clinical settings.
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Affiliation(s)
- Fang Fang
- Shanghai Key Laboratory of Functional Magnetic Resonance Imaging, Physics Department, East China Normal University, Shanghai 200062, China
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Coen M, Hong YS, Cloarec O, Rhode CM, Reily MD, Robertson DG, Holmes E, Lindon JC, Nicholson JK. Heteronuclear 1H-31P statistical total correlation NMR spectroscopy of intact liver for metabolic biomarker assignment: application to galactosamine-induced hepatotoxicity. Anal Chem 2007; 79:8956-66. [PMID: 17973499 DOI: 10.1021/ac0713961] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of our ongoing development of methods for enhanced biomarker information recovery from spectroscopic data we present the first example of a new hetero-nuclear statistical total correlation spectroscopy (HET-STOCSY) approach applied to intact tissue samples collected as part of a toxicological study. One-dimensional 1H and 31P-{1H} magic angle spinning (MAS) NMR spectra of intact liver samples after galactosamine (galN) treatment to rats and after cotreatment of galN plus uridine were collected at 275 K. Individual samples were also followed by 1H and 31P-{1H} MAS NMR through time generating time dependent modulations in metabolite signatures relating to toxicity. High-resolution 1H NMR spectra of urine and plasma and clinical chemical data were also collected to establish a biological framework in which to place these novel statistical heterospectroscopic data. In HET-STOCSY, calculation of the covariance between the 31P-{1H} and 1H NMR signals of phosphorus containing metabolites allows their molecular connectivities to be established and the construction of virtual two-dimensional heteronuclear correlation spectra that connect all protons on the molecule to the heteroatom. We show how HET-STOCSY applied to MAS NMR spectra of liver samples can be used to augment biomarker detection. This approach is generic and can be applied to correlate the covarying signals for any spin-active nuclei where there is parallel or serial collection of data.
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Affiliation(s)
- Muireann Coen
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, SORA Division, Faculty of Medicine, Imperial College London, SW7 2AZ, U.K
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Gjersing EL, Herberg JL, Horn J, Schaldach CM, Maxwell RS. NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa. Anal Chem 2007; 79:8037-45. [DOI: 10.1021/ac070800t] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erica L. Gjersing
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Julie L. Herberg
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Joanne Horn
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Charlene M. Schaldach
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Robert S. Maxwell
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
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Fris M, Tessem MB, Cejková J, Midelfart A. The effect of single and repeated UVB radiation on rabbit cornea. Graefes Arch Clin Exp Ophthalmol 2007; 244:1680-7. [PMID: 16596404 DOI: 10.1007/s00417-006-0297-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 01/16/2006] [Accepted: 01/27/2006] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cumulative effect of ultraviolet radiation (UVR) is an important aspect of UV corneal damage. The purpose of this study was to apply high resolution magic angle spinning proton nuclear magnetic resonance (HR-MAS 1H NMR) spectroscopy to evaluate the effect of single and repeated UV radiation exposure of the same overall dose on the rabbit cornea. METHODS Corneal surfaces of 24 normal rabbit eyes were examined for the effects of UVB exposure (312 nm). In the first group (UVB1), animals were irradiated with a single dose (3.12 J/cm2; 21 min) of UVB radiation. The animals in the second group (UVB2) were irradiated three times for 7 min every other day (dose of 1.04 J/cm2; days 1, 3, 5) to give the same overall dose (3.12 J/cm2). The third group served as an untreated control group. One day after the last irradiation, the animals were sacrificed, and the corneas were removed and frozen. HR-MAS 1H NMR spectra from intact corneas were obtained. Special grouping patterns among the tissue samples and the relative percentage changes in particular metabolite concentrations were evaluated using modern statistical methods (multivariate analysis, one-way ANOVA). RESULTS The metabolic profile of both groups of UVB-irradiated samples was significantly different from the control corneas. Substantial decreases in taurine, hypo-taurine and choline-derivatives concentrations and substantial elevation in glucose and betaine levels were observed following the UVR exposure. There was no significant difference between the effect of a single and repeated UVB irradiation of the same overall dose. CONCLUSIONS For the first time, the effects of single and repeated UVR doses on the metabolic profile of the rabbit cornea were analysed and compared. The combination of HR-MAS 1H NMR spectroscopy and modern statistical methods (multivariate analysis, one-way ANOVA) proved suitable to assess the overall view of the metabolic alterations in the rabbit corneal tissue following UVB radiation exposure.
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Affiliation(s)
- Miroslav Fris
- Department of Neuroscience, Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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Yang Y, Li C, Nie X, Feng X, Chen W, Yue Y, Tang H, Deng F. Metabonomic studies of human hepatocellular carcinoma using high-resolution magic-angle spinning 1H NMR spectroscopy in conjunction with multivariate data analysis. J Proteome Res 2007; 6:2605-14. [PMID: 17564425 DOI: 10.1021/pr070063h] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
High-resolution magic-angle spinning (MAS) 1H nuclear magnetic resonance spectroscopy has been employed to characterize the metabolite composition (i.e., metabonome) of the human hepatocellular carcinoma (HCC) tumor in combination with principal component analysis (PCA). The results showed that (a) the metabonomes of both low-grade HCC and high-grade HCC tumors differ markedly from that of the adjacent non-involved tissues; and (b) low-grade HCC tumors have clear differences in metabonome from that of the high-grade HCC tumors. Compared with the non-involved adjacent liver tissues, HCC tumors had elevated levels of lactate, glutamate, glutamine, glycine, leucine, alanine, choline metabolites, and phosphorylethanolamine (PE), but declined levels of triglycerides, glucose, and glycogen. The levels of lactate, amino acids including glutamate, glutamine, glycine, leucine and alanine, choline and phosphorylethanolamine (PE) were higher but the levels of PC, GPC, triglycerides, glucose, and glycogen were lower in high-grade HCC than in low-grade HCC tumors. Compared with non-cirrhotic, low-grade HCC tumors, the cirrhotic, low-grade HCC tumors showed statistically significant increases in lactate, phosphocholine (PC), and glycerophosphocholine (GPC). The necrosis in HCC tumors resulted in a drastic increase in the levels of observable triglycerides, signals of which dominated their 1H NMR spectra. These results indicated that HRMAS combined with PCA offers a useful tool for understanding the tumor biochemistry and classification of liver tumor tissues; such tool may also have some potential for liver tumor diagnosis and prognosis even when some other disease processes are present.
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Affiliation(s)
- Yongxia Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, P. R. China
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Rezzi S, Ramadan Z, Fay LB, Kochhar S. Nutritional metabonomics: applications and perspectives. J Proteome Res 2007; 6:513-25. [PMID: 17269708 DOI: 10.1021/pr060522z] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nowadays, nutrition focuses on improving health of individuals through diet. Current nutritional research aims at health promotion, disease prevention, and performance improvement. Modern analytical platforms allow the simultaneous measurement of multiple metabolites providing new insights in the understanding of the functionalities of cells and whole organisms. Metabonomics, "the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modifications", provides a systems approach to understanding global metabolic regulations of organisms. This concept has arisen from various applications of NMR and MS spectroscopies to study the multicomponent metabolic composition of biological fluids, cells, and tissues. The generated metabolic profiles are processed by multivariate statistics to maximize the recovery of information to be correlated with well-determined stimuli such as dietary intervention or with any phenotypic data or diet habits. Metabonomics is thus uniquely suited to assess metabolic responses to deficiencies or excesses of nutrients and bioactive components. Furthermore, metabonomics is used to characterize the metabolic phenotype of individuals integrating genetic polymorphism, metabolic interactions with commensal and symbiotic partners such as gut microflora, as well as environmental and behavioral factors including dietary preferences. This paper reports several experimental key aspects in nutritional metabonomics, reviews its applications employing targeted and holistic approach analysis for the study of the metabolic responses following dietary interventions. It also reports the assessment of intra- and inter-individual variability in animal and human populations. The potentialities of nutritional metabonomics for the discovery of new biomarkers and the characterization of metabolic phenotypes are discussed in a context of their possible utilizations for personalized nutrition to provide health maintenance at the individual level.
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Affiliation(s)
- Serge Rezzi
- BioAnalytical Science, Metabonomics & Biomarkers, Nestlé Research Center, P.O. Box 44, CH-1000 Lausanne 26, Switzerland.
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Abstract
To perform metabonomics investigations, it is necessary to generate comprehensive metabolite profiles for complex samples such as biofluids and tissue/tissue extracts. Analytical technologies that can be used to achieve this aim are constantly evolving, and new developments are changing the way in which such profiles' metabolite profiles can be generated. Here, the utility of various analytical techniques for global metabolite profiling, such as, e.g., 1H NMR, MS, HPLC-MS, and GC-MS, are explored and compared.
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Affiliation(s)
- Eva Maria Lenz
- Department of Drug Metabolism and Pharmacokinetics, AstraZeneca, Mereside, Alderley Park, Cheshire SK10 4TG, United Kingdom
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Duarte IF, Stanley EG, Holmes E, Lindon JC, Gil AM, Tang H, Ferdinand R, McKee CG, Nicholson JK, Vilca-Melendez H, Heaton N, Murphy GM. Metabolic assessment of human liver transplants from biopsy samples at the donor and recipient stages using high-resolution magic angle spinning 1H NMR spectroscopy. Anal Chem 2007; 77:5570-8. [PMID: 16131067 DOI: 10.1021/ac050455c] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work presents the first application of high-resolution magic angle spinning (HR-MAS) 1H NMR spectroscopy to human liver biopsy samples, allowing a determination of their metabolic profiles before removal from donors, during cold perfusion, and after implantation into recipients. The assignment of peaks observed in the 1H HR-MAS NMR spectra was aided by the use of two-dimensional J-resolved, TOCSY and 1H-13C HMQC spectra. The spectra were dominated by resonances from triglycerides, phospholipids, and glycogen and from a variety of small molecules including glycerophosphocholine (GPC), glucose, lactate, creatine, acetate, amino acids, and nucleoside-related compounds such as uridine and adenosine. In agreement with histological data obtained on the same biopsies, two of the six livers were found to contain high amounts of triglycerides by NMR spectroscopy, which also indicated that these tissues contained a higher degree of unsaturated lipids and a lower proportion of phospholipids and low molecular weight compounds. Additionally, proton T2 relaxation times indicated two populations of lipids, a higher mobility triglyceride fraction and a lower mobility phospholipid fraction, the proportions of which changed according to the degree of fat content. GPC was found to decrease from the pretransplant to the posttransplant biopsy of all livers except for one with a histologically confirmed high lipid content, and this might represent a biomarker of liver function posttransplantation. NMR signals produced by the liver preservation solution were clearly detected in the cold perfusion stage biopsies of all livers but remained in the posttransplant spectra of only the two livers with a high lipid content and were prominent mainly in the graft that later developed primary graft dysfunction. This study has shown biochemical differences between livers used for transplants that can be related to the degree and type of lipid composition. This technology might therefore provide a novel screening approach for donor organ quality and a means to assess function in the recipient after transplantation.
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Affiliation(s)
- Iola F Duarte
- Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
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Lucas LH, Wilson SF, Lunte CE, Larive CK. Concentration profiling in rat tissue by high-resolution magic-angle spinning NMR spectroscopy: investigation of a model drug. Anal Chem 2007; 77:2978-84. [PMID: 15859619 PMCID: PMC2519809 DOI: 10.1021/ac0482817] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The utility of high-resolution magic-angle spinning (HR-MAS) NMR for studying drug delivery in whole tissues was explored by dosing female Sprague-Dawley rats with topical or injectable benzoic acid (BA). In principle, HR-MAS NMR permits the detection of both intra- and extracellular compounds. This is an advantage over the previous detection of topically applied BA using microdialysis coupled to HPLC/UV as microdialysis samples only the extracellular space. Skin and muscle samples were analyzed by (1)H HR-MAS NMR, and BA levels were determined using an external standard solution added to the sample rotor. One to two percent of the BA topical dose was detected in the muscle, showing that BA penetrated through the dermal and subcutaneous layers. Since BA was not detected in the muscle in the microdialysis studies, the NMR spectra revealed the intracellular localization of BA. The amount of BA detected in muscle after subcutaneous injection correlated with the distance from the dosing site. Overall, the results suggest that HR-MAS NMR can distinguish differences in the local concentration of BA varying with tissue type, dosage method, and tissue proximity to the dosing site. The results illustrate the potential of this technique for quantitative analysis of drug delivery and distribution and the challenges to be addressed as the method is refined.
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Affiliation(s)
| | | | | | - Cynthia K. Larive
- * Corresponding author. Current address: Department of Chemistry, University of California, Riverside, CA 92521; phone: (951) 827-2990; fax: (951) 827-4713; e-mail:
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Fris M, Tessem MB, Saether O, Midelfart A. Biochemical changes in selenite cataract model measured by high-resolution MAS H NMR spectroscopy. ACTA ACUST UNITED AC 2006; 84:684-92. [PMID: 16965502 DOI: 10.1111/j.1600-0420.2006.00716.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE To correlate certain levels of lens opacification with high-resolution magic-angle spinning proton nuclear magnetic resonance (HR-MAS (1)H NMR) spectroscopy analysis of the biochemical changes in rat lenses in a selenite cataract model. METHODS Selenite cataract was induced by injecting 13-day-old Sprague-Dawley rat pups with a single subcutaneous dose of sodium selenite (3.28 mg/kg in 0.9% sodium chloride solution). Lens opacification was observed using a photographic slit-lamp microscope at selected time-points 3, 6 and 9 days after selenite injection and was then graded (levels 0, 1 and 2). The animals were killed after the slit-lamp microscopy, lenses were removed and HR-MAS (1)H NMR spectra from intact lenses were obtained. Relative changes in metabolite concentrations were determined after comparison with matched lenses from untreated animals. RESULTS Photographic slit-lamp microscopy revealed different stages of cataract in all animals treated with selenite. In the high quality HR-MAS (1)H NMR spectra of the lenses, more than 30 different metabolites were identified in each lens. With the exception of taurine, the concentrations of all amino acids showed a significant increase (p < 0.05) in the second level of cataract. By contrast, glutathione (GSH), succinate and phosphocholine concentrations were significantly reduced. CONCLUSIONS For the first time, this study demonstrates the potential to correlate the level of lens opacification with the biochemical changes obtained with HR-MAS (1)H NMR spectroscopy analysis in a selenite cataract model.
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Affiliation(s)
- Miroslav Fris
- Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
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Abstract
Advances in postgenomic technologies have radically changed the information output from complex biological systems, generating vast amounts of high complexity data that can be interpreted by means of chemometric and bioinformatic methods to achieve disease diagnosis and prognosis. High-resolution nuclear magnetic resonance (NMR) spectroscopy of biofluids such as plasma, cerebrospinal fluid (CSF), and urine can generate robust, interpretable metabolic fingerprints that contain latent information relating to physiological or pathological status. This technology has been successfully applied to both preclinical and clinical studies of neurodegenerative diseases such as Huntington's disease, muscular dystrophy, and cerebellar ataxia. An extension of this technology, (1)H magic-angle-spinning (HRMAS) NMR spectroscopy, can be used to generate metabolic information on small intact tissue samples, providing a metabolic link between metabolic profiling of biofluids and histology. In this review we provide a summary of high-resolution NMR studies in neurodegenerative disease and explore the potential of metabonomics in evaluating disease progression with respect to therapeutic intervention.
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Affiliation(s)
- Elaine Holmes
- Biological Chemistry, Biomedical Sciences Division, Faculty of Natural Science, Imperial College London, South Kensington, UK.
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Lindon JC, Holmes E, Nicholson JK. Metabonomics techniques and applications to pharmaceutical research & development. Pharm Res 2006; 23:1075-88. [PMID: 16715371 DOI: 10.1007/s11095-006-0025-z] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 01/13/2006] [Indexed: 12/14/2022]
Abstract
In this review, the background to the approach known as metabonomics is provided, giving a brief historical perspective and summarizing the analytical and statistical techniques used. Some of the major applications of metabonomics relevant to pharmaceutical Research & Development are then reviewed including the study of various influences on metabolism, such as diet, lifestyle, and other environmental factors. The applications of metabonomics in drug safety studies are explained with special reference to the aims and achievements of the Consortium for Metabonomic Toxicology. Next, the role that metabonomics might have in disease diagnosis and therapy monitoring is provided with some examples, and the concept of pharmacometabonomics as a way of predicting an individual's response to treatment is highlighted. Some discussion is given on the strengths and weaknesses, opportunities of, and threats to metabonomics.
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Affiliation(s)
- John C Lindon
- Biological Chemistry, Biomedical Sciences Division, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, SW7 2AZ, UK.
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