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Lind MV, Savolainen OI, Ross AB. The use of mass spectrometry for analysing metabolite biomarkers in epidemiology: methodological and statistical considerations for application to large numbers of biological samples. Eur J Epidemiol 2016; 31:717-33. [PMID: 27230258 DOI: 10.1007/s10654-016-0166-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022]
Abstract
Data quality is critical for epidemiology, and as scientific understanding expands, the range of data available for epidemiological studies and the types of tools used for measurement have also expanded. It is essential for the epidemiologist to have a grasp of the issues involved with different measurement tools. One tool that is increasingly being used for measuring biomarkers in epidemiological cohorts is mass spectrometry (MS), because of the high specificity and sensitivity of MS-based methods and the expanding range of biomarkers that can be measured. Further, the ability of MS to quantify many biomarkers simultaneously is advantageously compared to single biomarker methods. However, as with all methods used to measure biomarkers, there are a number of pitfalls to consider which may have an impact on results when used in epidemiology. In this review we discuss the use of MS for biomarker analyses, focusing on metabolites and their application and potential issues related to large-scale epidemiology studies, the use of MS "omics" approaches for biomarker discovery and how MS-based results can be used for increasing biological knowledge gained from epidemiological studies. Better understanding of the possibilities and possible problems related to MS-based measurements will help the epidemiologist in their discussions with analytical chemists and lead to the use of the most appropriate statistical tools for these data.
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Affiliation(s)
- Mads V Lind
- Food and Nutritional Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 3rd Floor, 1958, Frederiksberg C, Denmark.
| | - Otto I Savolainen
- Food and Nutritional Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alastair B Ross
- Food and Nutritional Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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202
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Millán L, Sampedro MC, Sánchez A, Delporte C, Van Antwerpen P, Goicolea MA, Barrio RJ. Liquid chromatography-quadrupole time of flight tandem mass spectrometry-based targeted metabolomic study for varietal discrimination of grapes according to plant sterols content. J Chromatogr A 2016; 1454:67-77. [PMID: 27268521 DOI: 10.1016/j.chroma.2016.05.081] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/09/2016] [Accepted: 05/24/2016] [Indexed: 01/07/2023]
Abstract
Grapevine and derived products are rich in a wide range of compounds and its quality mainly depends on its metabolites, as a result of viticulture practices. Plant sterols, also called phytosterols (PS), are secondary metabolites regarded as bioactive substance present in grape berries and other plant-based food. The present study deals with a metabolomic approach focusing on phytosterols family in six varieties of Rioja grapes (Cabernet Sauvignon, Tempranillo, Graciano, Garnacha, White Garnacha and Viura), in order to find significant differences among them. Liquid chromatography- mass spectrometry with a quadrupole-time of flight mass analyzer (LC-QTOF) was used to find as many metabolites as possible in the different grape berry fractions, and using statistics to help finding significant clustering of the metabolic profile of pulp, peel and seeds in relation to the variety. The best chromatographic and detection conditions were achieved by gas phase ionization via atmospheric pressure chemical ionization (APCI) in positive mode. Furthermore, analysis with electrospray (ESI) is also needed for phytosterol derivatives confirmation. Putative compounds of interest in the analyzed samples were found by an automated compound extraction algorithm (Molecular Feature Extraction, MFE) and an initial differential expression from the data was created with the aid of commercial software. Once the data were collected, the results were filtered, aligned and normalized, and evaluating applying one-way analysis of variance (ANOVA) with a 95% significance level. For sample class prediction, partial least square-discriminant analysis (PLS-DA) is used as a supervised pattern recognition method and excellent separation among the grape varieties is shown. An overall accuracy of 93.3% (pulp samples), 100.0% (peel) or 96.7% (seeds) in discriminating between grape varieties was achieved when comparing the different fractions. In general, 7 PS derivatives were identified with ID scores higher than 84%.
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Affiliation(s)
- Laura Millán
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - M Carmen Sampedro
- Central Service of Analysis of Alava, SGIker, University of the Basque Country, UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - Alicia Sánchez
- Central Service of Analysis of Alava, SGIker, University of the Basque Country, UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - Cédric Delporte
- Laboratory of Pharmaceutical Chemistry & Analytical Platform, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), B-1050 Brussels, Belgium, Belgium
| | - Pierre Van Antwerpen
- Laboratory of Pharmaceutical Chemistry & Analytical Platform, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), B-1050 Brussels, Belgium, Belgium
| | - M Aranzazu Goicolea
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006 Vitoria-Gasteiz, Spain
| | - Ramón J Barrio
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006 Vitoria-Gasteiz, Spain.
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203
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Sarosiek I, Schicho R, Blandon P, Bashashati M. Urinary metabolites as noninvasive biomarkers of gastrointestinal diseases: A clinical review. World J Gastrointest Oncol 2016; 8:459-465. [PMID: 27190585 PMCID: PMC4865713 DOI: 10.4251/wjgo.v8.i5.459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/12/2016] [Accepted: 03/09/2016] [Indexed: 02/05/2023] Open
Abstract
The diagnosis of gastrointestinal (GI) disorders is usually based on invasive techniques such as endoscopy. A key important factor in GI cancer is early diagnosis which warrants development of non- or less-invasive diagnostic techniques. In addition, monitoring and surveillance are other important parts in the management of GI diseases. Metabolomics studies with nuclear magnetic resonance and mass spectrometry can measure the concentration of more than 3000 chemical compounds in the urine providing possible chemical signature in different diseases and during health. In this review, we discuss the urinary metabolomics signature of different GI diseases including GI cancer and elaborate on how these biomarkers could be used for the classification, early diagnosis and the monitoring of the patients. Moreover, we discuss future directions of this still evolving field of research.
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204
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Kwon HN, Phan HD, Xu WJ, Ko YJ, Park S. Application of a Smartphone Metabolomics Platform to the Authentication of Schisandra sinensis. PHYTOCHEMICAL ANALYSIS : PCA 2016; 27:199-205. [PMID: 27313157 DOI: 10.1002/pca.2617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Herbal medicines have been used for a long time all around the world. Since the quality of herbal preparations depends on the source of herbal materials, there has been a strong need to develop methods to correctly identify the origin of materials. OBJECTIVE To develop a smartphone metabolomics platform as a simpler and low-cost alternative for the identification of herbal material source. METHODOLOGY Schisandra sinensis extracts from Korea and China were prepared. The visible spectra of all samples were measured by a smartphone spectrometer platform. This platform included all the necessary measures built-in for the metabolomics research: data acquisition, processing, chemometric analysis and visualisation of the results. The result of the smartphone metabolomics platform was compared to that of NMR-based metabolomics, suggesting the feasibility of smartphone platform in metabolomics research. RESULTS The smartphone metabolomics platform gave similar results to the NMR method, showing good separation between Korean and Chinese materials and correct predictability for all test samples. CONCLUSION With its accuracy and advantages of affordability, user-friendliness, and portability, the smartphone metabolomics platform could be applied to the authentication of other medicinal plants. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Hyuk Nam Kwon
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Sillim-dong, Gwanak-gu, Seoul, Korea
| | - Hong-Duc Phan
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Sillim-dong, Gwanak-gu, Seoul, Korea
| | - Wen Jun Xu
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Sillim-dong, Gwanak-gu, Seoul, Korea
| | - Yoon-Joo Ko
- National Centre for Inter-University Research Facilities (NCIRF), Seoul National University, Sillim-dong, Gwanak-gu, Seoul, Korea
| | - Sunghyouk Park
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Sillim-dong, Gwanak-gu, Seoul, Korea
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205
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Aretz I, Meierhofer D. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci 2016; 17:ijms17050632. [PMID: 27128910 PMCID: PMC4881458 DOI: 10.3390/ijms17050632] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.
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Affiliation(s)
- Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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206
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Guo W, Feng X. OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism. PLoS One 2016; 11:e0154188. [PMID: 27100883 PMCID: PMC4839607 DOI: 10.1371/journal.pone.0154188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
Constraint-based metabolic modeling such as flux balance analysis (FBA) has been widely used to simulate cell metabolism. Thanks to its simplicity and flexibility, numerous algorithms have been developed based on FBA and successfully predicted the phenotypes of various biological systems. However, their phenotype predictions may not always be accurate in FBA because of using the objective function that is assumed for cell metabolism. To overcome this challenge, we have developed a novel computational framework, namely omFBA, to integrate multi-omics data (e.g. transcriptomics) into FBA to obtain omics-guided objective functions with high accuracy. In general, we first collected transcriptomics data and phenotype data from published database (e.g. GEO database) for different microorganisms such as Saccharomyces cerevisiae. We then developed a “Phenotype Match” algorithm to derive an objective function for FBA that could lead to the most accurate estimation of the known phenotype (e.g. ethanol yield). The derived objective function was next correlated with the transcriptomics data via regression analysis to generate the omics-guided objective function, which was next used to accurately simulate cell metabolism at unknown conditions. We have applied omFBA in studying sugar metabolism of S. cerevisiae and found that the ethanol yield could be accurately predicted in most of the cases tested (>80%) by using transcriptomics data alone, and revealed valuable metabolic insights such as the dynamics of flux ratios. Overall, omFBA presents a novel platform to potentially integrate multi-omics data simultaneously and could be incorporated with other FBA-derived tools by replacing the arbitrary objective function with the omics-guided objective functions.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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207
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Ramesh V, Ganesan K. Integrative functional genomic analysis unveils the differing dysregulated metabolic processes across hepatocellular carcinoma stages. Gene 2016; 588:19-29. [PMID: 27107678 DOI: 10.1016/j.gene.2016.04.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 04/17/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous disease and the development of targeted therapeutics is still at an early stage. The 'omics' based genome-wide profiling comprising the transcriptome, miRNome and proteome are highly useful in identifying the deregulated molecular processes involved in hepatocarcinogenesis. One of the end products and processes of the central dogma being the metabolites and metabolic processes mediate the cellular functions. In recent years, metabolomics based investigations have revealed the major deregulated metabolic processes involved in carcinogenesis. However, the integrative analysis of the holistic metabolic processes with genomics is at an early stage. Since the gene-sets are highly useful in assessing the biological processes and pathways, we made an attempt to infer the deregulated cellular metabolic processes involved in HCC by employing metabolism associated gene-set enrichment analysis. Further, the metabolic process enrichment scores were integrated with the transcriptome profiles of HCC. Integrative analysis shows three distinct metabolic deregulations: i) hepatocyte function related molecular processes involving lipid/fatty acid/bile acid synthesis, ii) inflammatory processes with cytokine, sphingolipid & chondriotin sulphate metabolism and iii) enriched nucleotide metabolic process involving purine/pyrimidine & glucose mediated catabolic process, in hepatocarcinogenesis. The three distinct metabolic processes were found to occur both in tumor and liver cancer cell line profiles. Unsupervised hierarchical clustering of the metabolic processes along with clinical sample information has identified two major clusters based on AFP (alpha-fetoprotein) and metastasis. The study reveals the three major regulatory processes involved in HCC stages.
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Affiliation(s)
- Vignesh Ramesh
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India.
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208
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Biomarkers for nutrient intake with focus on alternative sampling techniques. GENES AND NUTRITION 2016; 11:12. [PMID: 27551313 PMCID: PMC4968438 DOI: 10.1186/s12263-016-0527-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
Abstract
Biomarkers of nutrient intake or nutrient status are important objective measures of foods/nutrients as one of the most important environmental factors people are exposed to. It is very difficult to obtain accurate data on individual food intake, and there is a large variation of nutrient composition of foods consumed in a population. Thus, it is difficult to obtain precise measures of exposure to different nutrients and thereby be able to understand the relationship between diet, health, and disease. This is the background for investing considerable resources in studying biomarkers of nutrients believed to be important in our foods. Modern technology with high sensitivity and specificity concerning many nutrient biomarkers has allowed an interesting development with analyses of very small amounts of blood or tissue material. In combination with non-professional collection of blood by finger-pricking and collection on filters or sticks, this may make collection of samples and analyses of biomarkers much more available for scientists as well as health professionals and even lay people in particular in relation to the marked trend of self-monitoring of body functions linked to mobile phone technology. Assuming standard operating procedures are used for collection, drying, transport, extraction, and analysis of samples, it turns out that many analytes of nutritional interest can be measured like metabolites, drugs, lipids, vitamins, minerals, and many types of peptides and proteins. The advantage of this alternative sampling technology is that non-professionals can collect, dry, and mail the samples; the samples can often be stored under room temperature in a dry atmosphere, requiring small amounts of blood. Another promising area is the potential relation between the microbiome and biomarkers that may be measured in feces as well as in blood.
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209
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Zaitsu K, Hayashi Y, Murata T, Ohara T, Nakagiri K, Kusano M, Nakajima H, Nakajima T, Ishikawa T, Tsuchihashi H, Ishii A. Intact Endogenous Metabolite Analysis of Mice Liver by Probe Electrospray Ionization/Triple Quadrupole Tandem Mass Spectrometry and Its Preliminary Application to in Vivo Real-Time Analysis. Anal Chem 2016; 88:3556-61. [DOI: 10.1021/acs.analchem.5b04046] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kei Zaitsu
- In
Vivo Real-Time Omics Laboratory, Institute for Advanced Research, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya, 464-8601, Japan
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yumi Hayashi
- In
Vivo Real-Time Omics Laboratory, Institute for Advanced Research, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya, 464-8601, Japan
- Department
of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Tasuku Murata
- Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Tomomi Ohara
- Department
of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Kenta Nakagiri
- Department
of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Maiko Kusano
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroki Nakajima
- Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Tamie Nakajima
- College
of Life and Health Sciences, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Tetsuya Ishikawa
- Department
of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Hitoshi Tsuchihashi
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Akira Ishii
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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210
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Schmidt JA, Rinaldi S, Scalbert A, Ferrari P, Achaintre D, Gunter MJ, Appleby PN, Key TJ, Travis RC. Plasma concentrations and intakes of amino acids in male meat-eaters, fish-eaters, vegetarians and vegans: a cross-sectional analysis in the EPIC-Oxford cohort. Eur J Clin Nutr 2016; 70:306-12. [PMID: 26395436 PMCID: PMC4705437 DOI: 10.1038/ejcn.2015.144] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 07/01/2015] [Accepted: 07/21/2015] [Indexed: 01/28/2023]
Abstract
BACKGROUND/OBJECTIVES We aimed to investigate the differences in plasma concentrations and in intakes of amino acids between male meat-eaters, fish-eaters, vegetarians and vegans in the Oxford arm of the European Prospective Investigation into Cancer and Nutrition. SUBJECTS/METHODS This cross-sectional analysis included 392 men, aged 30-49 years. Plasma amino acid concentrations were measured with a targeted metabolomic approach using mass spectrometry, and dietary intake was assessed using a food frequency questionnaire. Differences between diet groups in mean plasma concentrations and intakes of amino acids were examined using analysis of variance, controlling for potential confounding factors and multiple testing. RESULTS In plasma, concentrations of 6 out of 21 amino acids varied significantly by diet group, with differences of -13% to +16% between meat-eaters and vegans. Concentrations of methionine, tryptophan and tyrosine were highest in fish-eaters and vegetarians, followed by meat-eaters, and lowest in vegans. A broadly similar pattern was seen for lysine, whereas alanine concentration was highest in fish-eaters and lowest in meat-eaters. For glycine, vegans had the highest concentration and meat-eaters the lowest. Intakes of all 18 dietary amino acids differed by diet group; for the majority of these, intake was highest in meat-eaters followed by fish-eaters, then vegetarians and lowest in vegans (up to 47% lower than in meat-eaters). CONCLUSIONS Men belonging to different habitual diet groups have significantly different plasma concentrations of lysine, methionine, tryptophan, alanine, glycine and tyrosine. However, the differences in plasma concentrations were less marked than and did not necessarily mirror those seen for amino acid intakes.
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Affiliation(s)
- J A Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - S Rinaldi
- International Agency for Research on Cancer, Lyon, France
| | - A Scalbert
- International Agency for Research on Cancer, Lyon, France
| | - P Ferrari
- International Agency for Research on Cancer, Lyon, France
| | - D Achaintre
- International Agency for Research on Cancer, Lyon, France
| | - M J Gunter
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - P N Appleby
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - T J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - R C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
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211
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Chang HY, Chen CT, Lih TM, Lynn KS, Juo CG, Hsu WL, Sung TY. iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination. PLoS One 2016; 11:e0146112. [PMID: 26784691 PMCID: PMC4718670 DOI: 10.1371/journal.pone.0146112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/14/2015] [Indexed: 11/25/2022] Open
Abstract
Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183) metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤ 0.19) when quantifying the two internal standards and had higher abundance correlation (≥ 0.92) when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html.
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Affiliation(s)
- Hui-Yin Chang
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Tai Chen
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - T. Mamie Lih
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Ke-Shiuan Lynn
- Department of Mathematics, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Chiun-Gung Juo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
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212
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Addis MF, Tanca A, Uzzau S, Oikonomou G, Bicalho RC, Moroni P. The bovine milk microbiota: insights and perspectives from -omics studies. MOLECULAR BIOSYSTEMS 2016; 12:2359-72. [DOI: 10.1039/c6mb00217j] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent findings and future perspectives of -omics studies on the bovine milk microbiota, focusing on its impact on animal health.
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Affiliation(s)
- M. F. Addis
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - A. Tanca
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - S. Uzzau
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
- Università degli Studi di Sassari
| | - G. Oikonomou
- Epidemiology and Population Health
- Institute of Infection and Global Health
- University of Liverpool
- Liverpool
- UK
| | - R. C. Bicalho
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
| | - P. Moroni
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
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213
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Ma P, Zhang Z, Zhou X, Yun Y, Liang Y, Lu H. Feature extraction from resolution perspective for gas chromatography-mass spectrometry datasets. RSC Adv 2016. [DOI: 10.1039/c6ra17864b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Automatic feature extraction from large-scale datasets is one of the major challenges when analyzing complex samples with gas chromatography-mass spectrometry (GC-MS).
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Affiliation(s)
- Pan Ma
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
| | - Xinyi Zhou
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
| | - Yonghuan Yun
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
| | - Yizeng Liang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083
- PR China
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Simmler C, Kulakowski D, Lankin DC, McAlpine JB, Chen SN, Pauli GF. Holistic Analysis Enhances the Description of Metabolic Complexity in Dietary Natural Products. Adv Nutr 2016; 7:179-89. [PMID: 27180381 PMCID: PMC4717887 DOI: 10.3945/an.115.009928] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the field of food and nutrition, complex natural products (NPs) are typically obtained from cells/tissues of diverse organisms such as plants, mushrooms, and animals. Among them, edible fruits, grains, and vegetables represent most of the human diet. Because of an important dietary dependence, the comprehensive metabolomic analysis of dietary NPs, performed holistically via the assessment of as many metabolites as possible, constitutes a fundamental building block for understanding the human diet. Both mass spectrometry (MS) and nuclear magnetic resonance (NMR) are important complementary analytic techniques, covering a wide range of metabolites at different concentrations. Particularly, 1-dimensional 1H-NMR offers an unbiased overview of all metabolites present in a sample without prior knowledge of its composition, thereby leading to an untargeted analysis. In the past decade, NMR-based metabolomics in plant and food analyses has evolved considerably. The scope of the present review, covering literature of the past 5 y, is to address the relevance of 1H-NMR–based metabolomics in food plant studies, including a comparison with MS-based techniques. Major applications of NMR-based metabolomics for the quality control of dietary NPs and assessment of their nutritional values are presented.
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Affiliation(s)
- Charlotte Simmler
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | | | - David C Lankin
- UIC/NIH Center for Botanical Dietary Supplements Research; and
| | - James B McAlpine
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | - Shao-Nong Chen
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | - Guido F Pauli
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
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215
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Wang M, Yang R, Dong J, Zhang T, Wang S, Zhou W, Li H, Zhao H, Zhang L, Wang S, Zhang C, Chen W. Simultaneous quantification of cardiovascular disease related metabolic risk factors using liquid chromatography tandem mass spectrometry in human serum. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:144-51. [DOI: 10.1016/j.jchromb.2015.12.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/08/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
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216
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Gu H, Zhang P, Zhu J, Raftery D. Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage. Anal Chem 2015; 87:12355-62. [PMID: 26579731 PMCID: PMC5437843 DOI: 10.1021/acs.analchem.5b03812] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted detection is one of the most important methods in mass spectrometry (MS)-based metabolomics; however, its major limitation is the reduced metabolome coverage that results from the limited set of targeted metabolites typically used in the analysis. In this study we describe a new approach, globally optimized targeted (GOT)-MS, that combines many of the advantages of targeted detection and global profiling in metabolomics analysis, including the capability to detect unknowns, broad metabolite coverage, and excellent quantitation. The key step in GOT-MS is a global search of precursor and product ions using a single liquid chromatography-triple quadrupole (LC-QQQ) mass spectrometer. Here, focused on measuring serum metabolites, we obtained 595 precursor ions and 1 890 multiple reaction monitoring (MRM) transitions, under positive and negative ionization modes in the mass range of 60-600 Da. For many of the MRMs/metabolites under investigation, the analytical performance of GOT-MS is better than or at least comparable to that obtained by global profiling using a quadrupole-time-of-flight (Q-TOF) instrument of similar vintage. Using a study of serum metabolites in colorectal cancer (CRC) as a representative example, GOT-MS significantly outperformed a large targeted MS assay containing ∼160 biologically important metabolites and provided a complementary approach to traditional global profiling using Q-TOF-MS. GOT-MS thus expands and optimizes the detection capabilities for QQQ-MS through a novel approach and should have the potential to significantly advance both basic and clinical metabolic research.
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Affiliation(s)
- Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Ping Zhang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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217
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Schmidt JA, Rinaldi S, Ferrari P, Carayol M, Achaintre D, Scalbert A, Cross AJ, Gunter MJ, Fensom GK, Appleby PN, Key TJ, Travis RC. Metabolic profiles of male meat eaters, fish eaters, vegetarians, and vegans from the EPIC-Oxford cohort. Am J Clin Nutr 2015; 102:1518-26. [PMID: 26511225 PMCID: PMC4658459 DOI: 10.3945/ajcn.115.111989] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/15/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Human metabolism is influenced by dietary factors and lifestyle, environmental, and genetic factors; thus, men who exclude some or all animal products from their diet might have different metabolic profiles than meat eaters. OBJECTIVE We aimed to investigate differences in concentrations of 118 circulating metabolites, including acylcarnitines, amino acids, biogenic amines, glycerophospholipids, hexose, and sphingolipids related to lipid, protein, and carbohydrate metabolism between male meat eaters, fish eaters, vegetarians, and vegans from the Oxford arm of the European Prospective Investigation into Cancer and Nutrition. DESIGN In this cross-sectional study, concentrations of metabolites were measured by mass spectrometry in plasma from 379 men categorized according to their diet group. Differences in mean metabolite concentrations across diet groups were tested by using ANOVA, and a false discovery rate-controlling procedure was used to account for multiple testing. Principal component analysis was used to investigate patterns in metabolic profiles. RESULTS Concentrations of 79% of metabolites differed significantly by diet group. In the vast majority of these cases, vegans had the lowest concentration, whereas meat eaters most often had the highest concentrations of the acylcarnitines, glycerophospholipids, and sphingolipids, and fish eaters or vegetarians most often had the highest concentrations of the amino acids and a biogenic amine. A clear separation between patterns in the metabolic profiles of the 4 diet groups was seen, with vegans being noticeably different from the other groups because of lower concentrations of some glycerophospholipids and sphingolipids. CONCLUSIONS Metabolic profiles in plasma could effectively differentiate between men from different habitual diet groups, especially vegan men compared with men who consume animal products. The difference in metabolic profiles was mainly explained by the lower concentrations of glycerophospholipids and sphingolipids in vegans.
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Affiliation(s)
- Julie A Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Sabina Rinaldi
- International Agency for Research on Cancer, Lyon, France; and
| | - Pietro Ferrari
- International Agency for Research on Cancer, Lyon, France; and
| | - Marion Carayol
- International Agency for Research on Cancer, Lyon, France; and
| | - David Achaintre
- International Agency for Research on Cancer, Lyon, France; and
| | | | - Amanda J Cross
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Marc J Gunter
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Georgina K Fensom
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Paul N Appleby
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom;
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218
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A Simultaneous Metabolic Profiling and Quantitative Multimetabolite Metabolomic Method for Human Plasma Using Gas-Chromatography Tandem Mass Spectrometry. J Proteome Res 2015; 15:259-65. [PMID: 26615962 DOI: 10.1021/acs.jproteome.5b00790] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
For the first time it is possible to simultaneously collect targeted and nontargeted metabolomics data from plasma based on GC with high scan speed tandem mass spectrometry (GC-MS/MS). To address the challenge of getting broad metabolome coverage while quantifying known biomarker compounds in high-throughput GC-MS metabolomics, we developed a novel GC-MS/MS metabolomics method using a high scan speed (20 000 Da/second) GC-MS/MS that enables simultaneous data acquisition of both nontargeted full scan and targeted quantitative tandem mass spectrometry data. The combination of these two approaches has hitherto not been demonstrated in metabolomics. This method allows reproducible quantification of at least 37 metabolites using multiple reaction monitoring (MRM) and full mass spectral scan-based detection of 601 reproducible metabolic features from human plasma. The method showed good linearity over normal concentrations in plasma (0.06-343 to 0.86-4800 μM depending on the metabolite) and good intra- and interbatch precision (0.9-16.6 and 2.6-29.6% relative standard deviation). Based on the parameters determined for this method, targeted quantification using MRM can be expanded to cover at least 508 metabolites while still collecting full scan data. The new simultaneous targeted and nontargeted metabolomics method enables more sensitive and accurate detection of predetermined metabolites and biomarkers of interest, while still allowing detection and identification of unknown metabolites. This is the first validated GC-MS/MS metabolomics method with simultaneous full scan and MRM data collection, and clearly demonstrates the utility of GC-MS/MS with high scanning rates for complex analyses.
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219
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Zaitsu K, Hayashi Y, Kusano M, Tsuchihashi H, Ishii A. Application of metabolomics to toxicology of drugs of abuse: A mini review of metabolomics approach to acute and chronic toxicity studies. Drug Metab Pharmacokinet 2015; 31:21-26. [PMID: 26613805 DOI: 10.1016/j.dmpk.2015.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 12/24/2022]
Abstract
Metabolomics has been widely applied to toxicological fields, especially to elucidate the mechanism of action of toxicity. In this review, metabolomics application with focus on the studies of chronic and acute toxicities of drugs of abuse like stimulants, opioids and the recently-distributed designer drugs will be presented in addition to an outline of basic analytical techniques used in metabolomics. Limitation of metabolomics studies and future perspectives will be also provided.
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Affiliation(s)
- Kei Zaitsu
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Yumi Hayashi
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya 461-8673, Japan.
| | - Maiko Kusano
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
| | - Hitoshi Tsuchihashi
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
| | - Akira Ishii
- Department of Legal Medicine & Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.
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220
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The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. Methods Mol Biol 2015; 1277:161-93. [PMID: 25677154 DOI: 10.1007/978-1-4939-2377-9_13] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted.
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221
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Palau-Rodriguez M, Tulipani S, Isabel Queipo-Ortuño M, Urpi-Sarda M, Tinahones FJ, Andres-Lacueva C. Metabolomic insights into the intricate gut microbial-host interaction in the development of obesity and type 2 diabetes. Front Microbiol 2015; 6:1151. [PMID: 26579078 PMCID: PMC4621279 DOI: 10.3389/fmicb.2015.01151] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
Gut microbiota has recently been proposed as a crucial environmental factor in the development of metabolic diseases such as obesity and type 2 diabetes, mainly due to its contribution in the modulation of several processes including host energy metabolism, gut epithelial permeability, gut peptide hormone secretion, and host inflammatory state. Since the symbiotic interaction between the gut microbiota and the host is essentially reflected in specific metabolic signatures, much expectation is placed on the application of metabolomic approaches to unveil the key mechanisms linking the gut microbiota composition and activity with disease development. The present review aims to summarize the gut microbial-host co-metabolites identified so far by targeted and untargeted metabolomic studies in humans, in association with impaired glucose homeostasis and/or obesity. An alteration of the co-metabolism of bile acids, branched fatty acids, choline, vitamins (i.e., niacin), purines, and phenolic compounds has been associated so far with the obese or diabese phenotype, in respect to healthy controls. Furthermore, anti-diabetic treatments such as metformin and sulfonylurea have been observed to modulate the gut microbiota or at least their metabolic profiles, thereby potentially affecting insulin resistance through indirect mechanisms still unknown. Despite the scarcity of the metabolomic studies currently available on the microbial-host crosstalk, the data-driven results largely confirmed findings independently obtained from in vitro and animal model studies, putting forward the mechanisms underlying the implication of a dysfunctional gut microbiota in the development of metabolic disorders.
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Affiliation(s)
- Magali Palau-Rodriguez
- Biomarkers and Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona Barcelona, Spain
| | - Sara Tulipani
- Biomarkers and Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona Barcelona, Spain ; Biomedical Research Institute (IBIMA), Service of Endocrinology and Nutrition, Malaga Hospital Complex (Virgen de la Victoria), University of Malaga Malaga, Spain
| | - Maria Isabel Queipo-Ortuño
- Biomedical Research Institute (IBIMA), Service of Endocrinology and Nutrition, Malaga Hospital Complex (Virgen de la Victoria), University of Malaga Malaga, Spain ; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII) Madrid, Spain
| | - Mireia Urpi-Sarda
- Biomarkers and Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona Barcelona, Spain
| | - Francisco J Tinahones
- Biomedical Research Institute (IBIMA), Service of Endocrinology and Nutrition, Malaga Hospital Complex (Virgen de la Victoria), University of Malaga Malaga, Spain ; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII) Madrid, Spain
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona Barcelona, Spain
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222
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Rubert J, Zachariasova M, Hajslova J. Advances in high-resolution mass spectrometry based on metabolomics studies for food – a review. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2015; 32:1685-708. [DOI: 10.1080/19440049.2015.1084539] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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223
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Integrating Multiple Analytical Datasets to Compare Metabolite Profiles of Mouse Colonic-Cecal Contents and Feces. Metabolites 2015; 5:489-501. [PMID: 26378591 PMCID: PMC4588808 DOI: 10.3390/metabo5030489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/25/2015] [Accepted: 09/06/2015] [Indexed: 01/12/2023] Open
Abstract
The pattern of metabolites produced by the gut microbiome comprises a phenotype indicative of the means by which that microbiome affects the gut. We characterized that phenotype in mice by conducting metabolomic analyses of the colonic-cecal contents, comparing that to the metabolite patterns of feces in order to determine the suitability of fecal specimens as proxies for assessing the metabolic impact of the gut microbiome. We detected a total of 270 low molecular weight metabolites in colonic-cecal contents and feces by gas chromatograph, time-of-flight mass spectrometry (GC-TOF) and ultra-high performance liquid chromatography, quadrapole time-of-flight mass spectrometry (UPLC-Q-TOF). Of that number, 251 (93%) were present in both types of specimen, representing almost all known biochemical pathways related to the amino acid, carbohydrate, energy, lipid, membrane transport, nucleotide, genetic information processing, and cancer-related metabolism. A total of 115 metabolites differed significantly in relative abundance between both colonic-cecal contents and feces. These data comprise the first characterization of relationships among metabolites present in the colonic-cecal contents and feces in a healthy mouse model, and shows that feces can be a useful proxy for assessing the pattern of metabolites to which the colonic mucosum is exposed.
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224
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Jeffryes JG, Colastani RL, Elbadawi-Sidhu M, Kind T, Niehaus TD, Broadbelt LJ, Hanson AD, Fiehn O, Tyo KEJ, Henry CS. MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. J Cheminform 2015; 7:44. [PMID: 26322134 PMCID: PMC4550642 DOI: 10.1186/s13321-015-0087-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. DESCRIPTION Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC-MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. CONCLUSIONS MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures. Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.
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Affiliation(s)
- James G Jeffryes
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA ; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
| | - Ricardo L Colastani
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
| | | | - Tobias Kind
- West Coast Metabolomics Center, University of California, Davis, CA USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA USA ; Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
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225
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Carayol M, Licaj I, Achaintre D, Sacerdote C, Vineis P, Key TJ, Onland Moret NC, Scalbert A, Rinaldi S, Ferrari P. Reliability of Serum Metabolites over a Two-Year Period: A Targeted Metabolomic Approach in Fasting and Non-Fasting Samples from EPIC. PLoS One 2015; 10:e0135437. [PMID: 26274920 PMCID: PMC4537119 DOI: 10.1371/journal.pone.0135437] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/23/2015] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE Although metabolic profiles have been associated with chronic disease risk, lack of temporal stability of metabolite levels could limit their use in epidemiological investigations. The present study aims to evaluate the reliability over a two-year period of 158 metabolites and compare reliability over time in fasting and non-fasting serum samples. METHODS Metabolites were measured with the AbsolueIDQp180 kit (Biocrates, Innsbruck, Austria) by mass spectrometry and included acylcarnitines, amino acids, biogenic amines, hexoses, phosphatidylcholines and sphingomyelins. Measurements were performed on repeat serum samples collected two years apart in 27 fasting men from Turin, Italy, and 39 non-fasting women from Utrecht, The Netherlands, all participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Reproducibility was assessed by estimating intraclass correlation coefficients (ICCs) in multivariable mixed models. RESULTS In fasting samples, a median ICC of 0.70 was observed. ICC values were <0.50 for 48% of amino acids, 27% of acylcarnitines, 18% of lysophosphatidylcholines and 4% of phosphatidylcholines. In non-fasting samples, the median ICC was 0.54. ICC values were <0.50 for 71% of acylcarnitines, 48% of amino acids, 44% of biogenic amines, 36% of sphingomyelins, 34% of phosphatidylcholines and 33% of lysophosphatidylcholines. Overall, reproducibility was lower in non-fasting as compared to fasting samples, with a statistically significant difference for 19-36% of acylcarnitines, phosphatidylcholines and sphingomyelins. CONCLUSION A single measurement per individual may be sufficient for the study of 73% and 52% of the metabolites showing ICCs >0.50 in fasting and non-fasting samples, respectively. ICCs were higher in fasting samples that are preferable to non-fasting.
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Affiliation(s)
- Marion Carayol
- International Agency for Research on Cancer, Lyon, France
| | - Idlir Licaj
- International Agency for Research on Cancer, Lyon, France; Institute of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | | | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, AO Citta' della Salute e della Scienza-University of Turin and Center for Cancer Prevention (CPO-Piemonte), Turin, Italy
| | - Paolo Vineis
- Human Genetics Foundation (HuGeF), Turin, Italy; School of Public Health, Imperial College London, London, United Kingdom
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - N Charlotte Onland Moret
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | | | - Sabina Rinaldi
- International Agency for Research on Cancer, Lyon, France
| | - Pietro Ferrari
- International Agency for Research on Cancer, Lyon, France
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226
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Application of CE-MS to a metabonomics study of human urine from cigarette smokers and non-smokers. Bioanalysis 2015; 6:2733-49. [PMID: 25413705 DOI: 10.4155/bio.14.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Novel biomarkers of exposure and early adverse effects are needed for comparative studies of combustible and non-combustible tobacco products for regulatory authority evaluation. Metabolic biomarkers reflect both gene and environmental effects. RESULTS CE-MS has been applied to human urine samples from non-smokers and smokers of cigarettes at two tar levels. Validated chemometric models were able to separate smokers from non-smokers, with discrimination mainly based on the presence of nicotine metabolites. With these removed, it still proved possible to discriminate smokers from non-smokers with models now based on endogenous metabolites. The biochemical relevance of these biomarkers is discussed. CONCLUSION This proof-of-principle metabonomics study illustrates the potential of CE-MS to discover novel biomarkers in urine from tobacco users.
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227
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Edison AS, Clendinen CS, Ajredini R, Beecher C, Ponce FV, Stupp GS. Metabolomics and Natural-Products Strategies to Study Chemical Ecology in Nematodes. Integr Comp Biol 2015; 55:478-85. [PMID: 26141866 PMCID: PMC4543130 DOI: 10.1093/icb/icv077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This review provides an overview of two complementary approaches to identify biologically active compounds for studies in chemical ecology. The first is activity-guided fractionation and the second is metabolomics, particularly focusing on a new liquid chromatography–mass spectrometry-based method called isotopic ratio outlier analysis. To illustrate examples using these approaches, we review recent experiments using Caenorhabditis elegans and related free-living nematodes.
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Affiliation(s)
- Arthur S Edison
- *Department of Biochemistry and Molecular Biology and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32610-0245, USA;
| | - Chaevien S Clendinen
- *Department of Biochemistry and Molecular Biology and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32610-0245, USA
| | - Ramadan Ajredini
- *Department of Biochemistry and Molecular Biology and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32610-0245, USA
| | - Chris Beecher
- *Department of Biochemistry and Molecular Biology and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32610-0245, USA; IROA Technologies, Ann Arbor, MI, USA
| | - Francesca V Ponce
- *Department of Biochemistry and Molecular Biology and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32610-0245, USA
| | - Gregory S Stupp
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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228
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Monteiro JP, Kussmann M, Kaput J. The genomics of micronutrient requirements. GENES & NUTRITION 2015; 10:466. [PMID: 25981693 PMCID: PMC4434349 DOI: 10.1007/s12263-015-0466-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/22/2015] [Indexed: 01/04/2023]
Abstract
Healthy nutrition is accepted as a cornerstone of public health strategies for reducing the risk of noncommunicable conditions such as obesity, cardiovascular disease, and related morbidities. However, many research studies continue to focus on single or at most a few factors that may elicit a metabolic effect. These reductionist approaches resulted in: (1) exaggerated claims for nutrition as a cure or prevention of disease; (2) the wide use of empirically based dietary regimens, as if one fits all; and (3) frequent disappointment of consumers, patients, and healthcare providers about the real impact nutrition can make on medicine and health. Multiple factors including environment, host and microbiome genetics, social context, the chemical form of the nutrient, its (bio)availability, and chemical and metabolic interactions among nutrients all interact to result in nutrient requirement and in health outcomes. Advances in laboratory methodologies, especially in analytical and separation techniques, are making the chemical dissection of foods and their availability in physiological tissues possible in an unprecedented manner. These omics technologies have opened opportunities for extending knowledge of micronutrients and of their metabolic and endocrine roles. While these technologies are crucial, more holistic approaches to the analysis of physiology and environment, novel experimental designs, and more sophisticated computational methods are needed to advance our understanding of how nutrition influences health of individuals.
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Affiliation(s)
- Jacqueline Pontes Monteiro
- />Department of Pediatrics, Faculty of Medicine, Nutrition and Metabolism, University of São Paulo, Bandeirantes Avenue, HCFMRP Campus USP, 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Martin Kussmann
- />Nestlé Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
- />Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - Jim Kaput
- />Nestlé Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
- />Service d’endorcrinologie, diabetologie et metabolosime du CHUV, University of Lausanne, Lausanne, Switzerland
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229
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Wang X, Wei H, Cao J, Li Z, He P. Metabolomics analysis of muscle from piglets fed low protein diets supplemented with branched chain amino acids using HPLC-high-resolution MS. Electrophoresis 2015; 36:2250-2258. [DOI: 10.1002/elps.201500007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/15/2015] [Accepted: 03/15/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Xian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology; China Agricultural University; Beijing P. R. China
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology; Huazhong Agricultural University; Wuhan P. R. China
| | - Jingjing Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences; China Agricultural University; Beijing P. R. China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences; China Agricultural University; Beijing P. R. China
| | - Pingli He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology; China Agricultural University; Beijing P. R. China
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230
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Gowda GAN, Djukovic D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Biol 2015; 1198:3-12. [PMID: 25270919 DOI: 10.1007/978-1-4939-1258-2_1] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The field of metabolomics has witnessed an exponential growth in the last decade driven by important applications spanning a wide range of areas in the basic and life sciences and beyond. Mass spectrometry in combination with chromatography and nuclear magnetic resonance are the two major analytical avenues for the analysis of metabolic species in complex biological mixtures. Owing to its inherent significantly higher sensitivity and fast data acquisition, MS plays an increasingly dominant role in the metabolomics field. Propelled by the need to develop simple methods to diagnose and manage the numerous and widespread human diseases, mass spectrometry has witnessed tremendous growth with advances in instrumentation, experimental methods, software, and databases. In response, the metabolomics field has moved far beyond qualitative methods and simple pattern recognition approaches to a range of global and targeted quantitative approaches that are now routinely used and provide reliable data, which instill greater confidence in the derived inferences. Powerful isotope labeling and tracing methods have become very popular. The newly emerging ambient ionization techniques such as desorption ionization and rapid evaporative ionization have allowed direct MS analysis in real time, as well as new MS imaging approaches. While the MS-based metabolomics has provided insights into metabolic pathways and fluxes, and metabolite biomarkers associated with numerous diseases, the increasing realization of the extremely high complexity of biological mixtures underscores numerous challenges including unknown metabolite identification, biomarker validation, and interlaboratory reproducibility that need to be dealt with for realization of the full potential of MS-based metabolomics. This chapter provides a glimpse at the current status of the mass spectrometry-based metabolomics field highlighting the opportunities and challenges.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA,
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231
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Pathologic metabolism: an exploratory study of the plasma metabolome of critical injury. J Trauma Acute Care Surg 2015; 78:742-51. [PMID: 25807403 DOI: 10.1097/ta.0000000000000589] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Severe trauma is associated with massive alterations in metabolism. Thus far, investigations have relied on traditional bioanalytic approaches including calorimetry or nuclear magnetic resonance. However, recent strides in mass spectrometry (MS)-based metabolomics present enhanced analytic opportunities to characterize a wide range of metabolites in the critical care setting. METHODS MS-based metabolomics analyses were performed on plasma samples from severely injured patients' trauma activation field blood and plasma samples obtained during emergency department thoracotomy. These were compared against the metabolic profiles of healthy controls. RESULTS Few significant alterations were observed between trauma activation field blood and emergency department thoracotomy patients. In contrast, we identified trauma-dependent metabolic signatures, which support a state of hypercatabolism, driven by sugar consumption, lipolysis and fatty acid use, accumulation of ketone bodies, proteolysis and nucleoside breakdown, which provides carbon and nitrogen sources to compensate for trauma-induced energy consumption and negative nitrogen balance. Unexpectedly, metabolites of bacterial origin (including tricarballylate and citramalate) were detected in plasma from trauma patients. CONCLUSION In the future, the correlation between metabolomics adaptation and recovery outcomes could be studied by MS-based approaches, and this work can provide a method for assessing the efficacy of alternative resuscitation strategies.
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232
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Chen C, Deng L, Wei S, Nagana Gowda GA, Gu H, Chiorean EG, Abu Zaid M, Harrison ML, Pekny JF, Loehrer PJ, Zhang D, Zhang M, Raftery D. Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression. J Proteome Res 2015; 14:2492-9. [PMID: 25919433 DOI: 10.1021/acs.jproteome.5b00059] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite the fact that colorectal cancer (CRC) is one of the most prevalent and deadly cancers in the world, the development of improved and robust biomarkers to enable screening, surveillance, and therapy monitoring of CRC continues to be evasive. In particular, patients with colon polyps are at higher risk of developing colon cancer; however, noninvasive methods to identify these patients suffer from poor performance. In consideration of the challenges involved in identifying metabolite biomarkers in individuals with high risk for colon cancer, we have investigated NMR-based metabolite profiling in combination with numerous demographic parameters to investigate the ability of serum metabolites to differentiate polyp patients from healthy subjects. We also investigated the effect of disease risk on different groups of biologically related metabolites. A powerful statistical approach, seemingly unrelated regression (SUR), was used to model the correlated levels of metabolites in the same biological group. The metabolites were found to be significantly affected by demographic covariates such as gender, BMI, BMI(2), and smoking status. After accounting for the effects of the confounding factors, we then investigated potential of metabolites from serum to differentiate patients with polyps and age matched healthy controls. Our results showed that while only valine was slightly associated, individually, with polyp patients, a number of biologically related groups of metabolites were significantly associated with polyps. These results may explain some of the challenges and promise a novel avenue for future metabolite profiling methodologies.
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Affiliation(s)
| | - Lingli Deng
- ‡Department of Electronic Science and Communication Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian Province 361005, China
| | | | - G A Nagana Gowda
- ∥Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Haiwei Gu
- ∥Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Elena G Chiorean
- ⊥Indiana University Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, Indiana 46202, United States.,#Department of Medicine, University of Washington, 825 Eastlake Avenue East, Seattle, Washington 98109, United States
| | - Mohammad Abu Zaid
- ⊥Indiana University Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, Indiana 46202, United States
| | | | | | - Patrick J Loehrer
- ⊥Indiana University Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, Indiana 46202, United States
| | | | | | - Daniel Raftery
- ∥Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States.,△Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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233
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Gu H, Du J, Neto FC, Carroll PA, Turner S, Chiorean EG, Eisenman RN, Raftery D. Metabolomics method to comprehensively analyze amino acids in different domains. Analyst 2015; 140:2726-34. [PMID: 25699545 PMCID: PMC4380628 DOI: 10.1039/c4an02386b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amino acids play essential roles in both metabolism and the proteome. Many studies have profiled free amino acids (FAAs) or proteins; however, few have connected the measurement of FAA with individual amino acids in the proteome. In this study, we developed a metabolomics method to comprehensively analyze amino acids in different domains, using two examples of different sample types and disease models. We first examined the responses of FAAs and insoluble-proteome amino acids (IPAAs) to the Myc oncogene in Tet21N human neuroblastoma cells. The metabolic and proteomic amino acid profiles were quite different, even under the same Myc condition, and their combination provided a better understanding of the biological status. In addition, amino acids were measured in 3 domains (FAAs, free and soluble-proteome amino acids (FSPAAs), and IPAAs) to study changes in serum amino acid profiles related to colon cancer. A penalized logistic regression model based on the amino acids from the three domains had better sensitivity and specificity than that from each individual domain. To the best of our knowledge, this is the first study to perform a combined analysis of amino acids in different domains, and indicates the useful biological information available from a metabolomics analysis of the protein pellet. This study lays the foundation for further quantitative tracking of the distribution of amino acids in different domains, with opportunities for better diagnosis and mechanistic studies of various diseases.
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Affiliation(s)
- Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, 418 Guanglan Ave., Nanchang, Jiangxi Province 330013, China
| | - Jianhai Du
- Department of Biochemistry, University of Washington, 750 Republican St., Seattle, WA 98109, USA
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University, Rua Francisco Degni 55, Araraquara, Sao Paulo 14800-900, Brazil
| | - Patrick Andrew Carroll
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA, 98109, USA
| | - Sally Turner
- Department of Biochemistry, University of Washington, 750 Republican St., Seattle, WA 98109, USA
| | - E. Gabriela Chiorean
- Department of Medicine, University of Washington, 825 Eastlake Ave East, Seattle, WA 98109, USA
- Indiana University Melvin and Bren Simon Cancer Center, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
| | - Robert N. Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA, 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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234
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Huang CH, Hsu FY, Wu YH, Zhong L, Tseng MY, Kuo CJ, Hsu AL, Liang SS, Chiou SH. Analysis of lifespan-promoting effect of garlic extract by an integrated metabolo-proteomics approach. J Nutr Biochem 2015; 26:808-17. [PMID: 25940980 DOI: 10.1016/j.jnutbio.2015.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/16/2015] [Accepted: 02/20/2015] [Indexed: 01/22/2023]
Abstract
The beneficial effects of garlic (Allium sativum) consumption in treating human diseases have been reported worldwide over a long period of human history. The strong antioxidant effect of garlic extract (GE) has also recently been claimed to prevent cancer, thrombus formation, cardiovascular disease and some age-related maladies. Using Caenorhabditis elegans as a model organism, aqueous GE was herein shown to increase the expression of longevity-related FOXO transcription factor daf-16 and extend lifespan by 20%. By employing microarray and proteomics analysis on C. elegans treated with aqueous GE, we have systematically mapped 229 genes and 46 proteins with differential expression profiles, which included many metabolic enzymes and yolky egg vitellogenins. To investigate the garlic components functionally involved in longevity, an integrated metabolo-proteomics approach was employed to identify metabolites and protein components associated with treatment of aqueous GE. Among potential lifespan-promoting substances, mannose-binding lectin and N-acetylcysteine were found to increase daf-16 expression. Our study points to the fact that the lifespan-promoting effect of aqueous GE may entail the DAF-16-mediated signaling pathway. The result also highlights the utility of metabolo-proteomics for unraveling the complexity and intricacy involved in the metabolism of natural products in vivo.
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Affiliation(s)
- Chun-Hao Huang
- Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Fang-Yu Hsu
- Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yuan-Heng Wu
- Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Linda Zhong
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mu-Yun Tseng
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Chao-Jen Kuo
- Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ao-Lin Hsu
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan.
| | - Shih-Shin Liang
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Shyh-Horng Chiou
- Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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235
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Mast C, Lyan B, Joly C, Centeno D, Giacomoni F, Martin JF, Mosoni L, Dardevet D, Pujos-Guillot E, Papet I. Assessment of protein modifications in liver of rats under chronic treatment with paracetamol (acetaminophen) using two complementary mass spectrometry-based metabolomic approaches. J Proteomics 2015; 120:194-203. [DOI: 10.1016/j.jprot.2015.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/27/2015] [Accepted: 03/15/2015] [Indexed: 01/22/2023]
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236
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Mak TD, Laiakis EC, Goudarzi M, Fornace AJ. Selective paired ion contrast analysis: a novel algorithm for analyzing postprocessed LC-MS metabolomics data possessing high experimental noise. Anal Chem 2015; 87:3177-86. [PMID: 25683158 PMCID: PMC4519008 DOI: 10.1021/ac504012a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
One of the consequences in analyzing biological data from noisy sources, such as human subjects, is the sheer variability of experimentally irrelevant factors that cannot be controlled for. This holds true especially in metabolomics, the global study of small molecules in a particular system. While metabolomics can offer deep quantitative insight into the metabolome via easy-to-acquire biofluid samples such as urine and blood, the aforementioned confounding factors can easily overwhelm attempts to extract relevant information. This can mar potentially crucial applications such as biomarker discovery. As such, a new algorithm, called Selective Paired Ion Contrast (SPICA), has been developed with the intent of extracting potentially biologically relevant information from the noisiest of metabolomic data sets. The basic idea of SPICA is built upon redefining the fundamental unit of statistical analysis. Whereas the vast majority of algorithms analyze metabolomics data on a single-ion basis, SPICA relies on analyzing ion-pairs. A standard metabolomic data set is reinterpreted by exhaustively considering all possible ion-pair combinations. Statistical comparisons between sample groups are made only by analyzing the differences in these pairs, which may be crucial in situations where no single metabolite can be used for normalization. With SPICA, human urine data sets from patients undergoing total body irradiation (TBI) and from a colorectal cancer (CRC) relapse study were analyzed in a statistically rigorous manner not possible with conventional methods. In the TBI study, 3530 statistically significant ion-pairs were identified, from which numerous putative radiation specific metabolite-pair biomarkers that mapped to potentially perturbed metabolic pathways were elucidated. In the CRC study, SPICA identified 6461 statistically significant ion-pairs, several of which putatively mapped to folic acid biosynthesis, a key pathway in colorectal cancer. Utilizing support vector machines (SVMs), SPICA was also able to unequivocally outperform binary classifiers built from classical single-ion feature based SVMs.
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Affiliation(s)
| | | | | | - Albert J Fornace
- §Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
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237
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Basak T, Varshney S, Hamid Z, Ghosh S, Seth S, Sengupta S. Identification of metabolic markers in coronary artery disease using an untargeted LC-MS based metabolomic approach. J Proteomics 2015; 127:169-77. [PMID: 25790721 DOI: 10.1016/j.jprot.2015.03.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/04/2015] [Accepted: 03/10/2015] [Indexed: 12/11/2022]
Abstract
UNLABELLED Coronary artery disease (CAD), a complex metabolic disorder, is one of the largest causes of death worldwide. Both environmental and genetic factors contribute to the etiology of this metabolic disease. The gene-environment interaction could lead to modulation of various metabolic pathways resulting in altered levels of various metabolites. Thus, identifying metabolites could aid in deciphering pathways that could be involved in the pathophysiology of the disease. With the advent of high resolution mass spectrometry based methodologies, it is now possible to screen thousands of metabolites in a single snapshot thus, allowing the identification of potential disease metabolite markers. In this work, using an untargeted metabolomic approach, we attempted to identify metabolites that have altered levels in CAD patients. Using reverse phase and HILIC based chromatography followed by mass spectrometry we identified a total of 32 metabolites (2 fold; p<0.05) in plasma whose levels were significantly altered in CAD samples. Further, we have validated the discriminative ability of these metabolites in an independent set of CAD and control samples using multivariate PLS-DA analysis. Interestingly, Lyso PC (18:0), Cortisol, Lyso PC (P-17:0), and glycerophosphocholine were among the top discriminators for CAD which implies involvement of phosphatidylcholine pathway in the pathogenesis of atherosclerosis. BIOLOGICAL SIGNIFICANCE Herein, we report that an unbiased metabolomic study has the potential to identify newer markers which are involved in several important biological pathways like lipid metabolism, phosphatidylcholine pathway etc. which in turn are implicated in CAD. These markers could be of potential clinical importance for screening subjects at risk of CAD. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, SukhdevVihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB Campus, New Delhi, India
| | - Swati Varshney
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, SukhdevVihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB Campus, New Delhi, India
| | - Zeeshan Hamid
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, SukhdevVihar, Mathura Road, New Delhi 110020, India
| | - Sourav Ghosh
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, SukhdevVihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB Campus, New Delhi, India
| | - Sandeep Seth
- Dept. of Cardiology, All India Institute of Medical Sciences, New Delhi, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, SukhdevVihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB Campus, New Delhi, India.
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238
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Panighel A, De Rosso M, Dalla Vedova A, Flamini R. Putative identification of new p-coumaroyl glycoside flavonoids in grape by ultra-high performance liquid chromatography/high-resolution mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:357-366. [PMID: 26406348 DOI: 10.1002/rcm.7115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 06/05/2023]
Abstract
RATIONALE Grape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p-coumaric acid. Until now, only p-coumaroyl anthocyanins have been found in grape. METHODS A method of 'suspect screening analysis' by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures. RESULTS Three putative p-coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide-3-O-p-coumaroylhexoside-like flavanone, isorhamnetin-3-O-p-coumaroylglucoside, and a chrysoeriol-p-coumaroylhexoside-like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound. CONCLUSIONS Compounds were identified by overlapping various analytical methods according to recommendations in the MS-based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties.
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Affiliation(s)
- Annarita Panighel
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Mirko De Rosso
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Antonio Dalla Vedova
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Riccardo Flamini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
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239
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Enhancing metabolomics research through data mining. J Proteomics 2015; 127:275-88. [PMID: 25668325 DOI: 10.1016/j.jprot.2015.01.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 12/11/2022]
Abstract
UNLABELLED Metabolomics research, like other disciplines utilizing high-throughput technologies, generates a large amount of data for every sample. Although handling this data is a challenge and one of the biggest bottlenecks of the metabolomics workflow, it is also the clue to accomplish valuable results. This work has been designed to supply methodological data mining guidelines, describing systematically the steps to be followed in metabolomics data exploration. Instrumental raw data refinement in the pre-processing step and assessment of the statistical assumptions in pre-treatment directly affect the results of subsequent univariate and multivariate analyses. A study of aging in a healthy population was selected to represent this data mining process. Multivariate analysis of variance and linear regression methods were used to analyze the metabolic changes underlying aging. Selection of both multivariate methods aims to illustrate the treatment of age from two rather different perspectives, as a categorical variable and a continuous variable. BIOLOGICAL SIGNIFICANCE Metabolomics is a discipline involving the analysis of a large amount of data to gather relevant information. Researchers in this field have to overcome the challenges of complex data processing and statistical analysis issues. A wide range of tasks has to be executed, from the minimization of batch-to-batch/systematic variations in pre-processing, to the application of common data analysis techniques relying on statistical assumptions. In this work, a real-data metabolic profiling research on aging was used to illustrate the proposed workflow and suggest a set of guidelines for analyzing metabolomics data. This article is part of a Special Issue entitled: HUPO 2014.
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240
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Experimental resistance to drug combinations in Leishmania donovani: metabolic and phenotypic adaptations. Antimicrob Agents Chemother 2015; 59:2242-55. [PMID: 25645828 DOI: 10.1128/aac.04231-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Together with vector control, chemotherapy is an essential tool for the control of visceral leishmaniasis (VL), but its efficacy is jeopardized by growing resistance and treatment failure against first-line drugs. To delay the emergence of resistance, the use of drug combinations of existing antileishmanial agents has been tested systematically in clinical trials for the treatment of visceral leishmaniasis (VL). In vitro, Leishmania donovani promastigotes are able to develop experimental resistance to several combinations of different antileishmanial drugs after 10 weeks of drug pressure. Using an untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics approach, we identified metabolic changes in lines that were experimentally resistant to drug combinations and their respective single-resistant lines. This highlighted both collective metabolic changes (found in all combination therapy-resistant [CTR] lines) and specific ones (found in certain CTR lines). We demonstrated that single-resistant and CTR parasite cell lines show distinct metabolic adaptations, which all converge on the same defensive mechanisms that were experimentally validated: protection against drug-induced and external oxidative stress and changes in membrane fluidity. The membrane fluidity changes were accompanied by changes in drug uptake only in the lines that were resistant against drug combinations with antimonials, and surprisingly, drug accumulation was higher in these lines. Together, these results highlight the importance and the central role of protection against oxidative stress in the different resistant lines. Ultimately, these phenotypic changes might interfere with the mode of action of all drugs that are currently used for the treatment of VL and should be taken into account in drug development.
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Abstract
PURPOSE OF REVIEW Metabolomics is emerging as a powerful tool for studying metabolic processes and in recent years, the applications in the area of nutrition have risen rapidly. The present review gives an overview of the current applications in the field of nutrition and identifies areas in need of advancement. RECENT FINDINGS Applications in nutrition research can in general be divided into three main areas: identification of dietary biomarkers, study of diet-related diseases and identification of biomarkers of disease and application to dietary intervention studies as a tool to identify molecular mechanisms. SUMMARY Metabolomics has made a significant impact on all the areas identified above and is set to have a major impact on the study of diet-health relationships.
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Affiliation(s)
- Helena Gibbons
- aUCD Conway Institute bUCD Institute of Food and Health, Belfield, Dublin, Ireland
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242
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Fujimura Y. Small molecule-sensing strategy and techniques for understanding the functionality of green tea. Biosci Biotechnol Biochem 2015; 79:687-99. [PMID: 25561325 DOI: 10.1080/09168451.2014.996205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Various low-molecular-weight phytochemicals in green tea (Camellia sinensis L.), especially (-)-epigallocatechin-3-O-gallate (EGCG), are known to be involved in health promotion and disease risk reduction. However, the underlying mechanism has remained elusive because of the absence of an analytical technique that can easily detect the precise behavior of such a small molecule. Recently, we have identified a cell-surface EGCG-sensing receptor and the related signaling molecules that control the physiological functions of EGCG. We also developed a novel in situ label-free imaging technique for visualizing spatially resolved biotransformations based on simultaneous mapping of EGCG and its phase II metabolites. Furthermore, we established a chemometric method capable of evaluating the functionality of multicomponent green tea extracts by focusing on their compositional balances. This review highlights our proposed small molecule-sensing techniques for detecting the complex behavior of green tea components and linking such information to an enhanced understanding of green tea functionality.
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Affiliation(s)
- Yoshinori Fujimura
- a Innovation Center for Medical Redox Navigation , Kyushu University , Fukuoka , Japan
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243
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Abu Bakar MH, Sarmidi MR, Cheng KK, Ali Khan A, Suan CL, Zaman Huri H, Yaakob H. Metabolomics – the complementary field in systems biology: a review on obesity and type 2 diabetes. MOLECULAR BIOSYSTEMS 2015; 11:1742-74. [DOI: 10.1039/c5mb00158g] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper highlights the metabolomic roles in systems biology towards the elucidation of metabolic mechanisms in obesity and type 2 diabetes.
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Affiliation(s)
- Mohamad Hafizi Abu Bakar
- Department of Bioprocess Engineering
- Faculty of Chemical Engineering
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Mohamad Roji Sarmidi
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
- Innovation Centre in Agritechnology for Advanced Bioprocessing (ICA)
| | - Kian-Kai Cheng
- Department of Bioprocess Engineering
- Faculty of Chemical Engineering
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Abid Ali Khan
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
- Department of Biosciences
| | - Chua Lee Suan
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Hasniza Zaman Huri
- Department of Pharmacy
- Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Harisun Yaakob
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
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Kaever A, Landesfeind M, Feussner K, Mosblech A, Heilmann I, Morgenstern B, Feussner I, Meinicke P. MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data. Metabolomics 2015; 11:764-777. [PMID: 25972773 PMCID: PMC4419191 DOI: 10.1007/s11306-014-0734-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/23/2014] [Indexed: 11/27/2022]
Abstract
A central aim in the evaluation of non-targeted metabolomics data is the detection of intensity patterns that differ between experimental conditions as well as the identification of the underlying metabolites and their association with metabolic pathways. In this context, the identification of metabolites based on non-targeted mass spectrometry data is a major bottleneck. In many applications, this identification needs to be guided by expert knowledge and interactive tools for exploratory data analysis can significantly support this process. Additionally, the integration of data from other omics platforms, such as DNA microarray-based transcriptomics, can provide valuable hints and thereby facilitate the identification of metabolites via the reconstruction of related metabolic pathways. We here introduce the MarVis-Pathway tool, which allows the user to identify metabolites by annotation of pathways from cross-omics data. The analysis is supported by an extensive framework for pathway enrichment and meta-analysis. The tool allows the mapping of data set features by ID, name, and accurate mass, and can incorporate information from adduct and isotope correction of mass spectrometry data. MarVis-Pathway was integrated in the MarVis-Suite (http://marvis.gobics.de), which features the seamless highly interactive filtering, combination, clustering, and visualization of omics data sets. The functionality of the new software tool is illustrated using combined mass spectrometry and DNA microarray data. This application confirms jasmonate biosynthesis as important metabolic pathway that is upregulated during the wound response of Arabidopsis plants.
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Affiliation(s)
- Alexander Kaever
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Manuel Landesfeind
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Alina Mosblech
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Ingo Heilmann
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Burkhard Morgenstern
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany
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Flamini R, De Rosso M, Bavaresco L. Study of Grape Polyphenols by Liquid Chromatography-High-Resolution Mass Spectrometry (UHPLC/QTOF) and Suspect Screening Analysis. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:350259. [PMID: 25734021 PMCID: PMC4334975 DOI: 10.1155/2015/350259] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/07/2015] [Indexed: 05/04/2023]
Abstract
Suspect screening analysis is a targeted metabolomics method in which the identification of compounds relies on specific available information, such as their molecular formula and isotopic pattern. This method, coupled to liquid chromatography-high-resolution mass spectrometry, is effective in the study of grape metabolomics, in particular for characterization of flavonols, stilbene derivatives, and anthocyanins. For identification of compounds expected in the samples, a new database of putative compounds was expressly constructed by using the molecular information on potential metabolites of grape and wine from the literature and other electronic databases. Currently, this database contains around 1,100 compounds. The method allows identification of several hundred grape metabolites with two analyses (positive and negative ionization modes), and performing of data reprocessing using "untargeted" algorithms also provided the identification of some flavonols and resveratrol trimers and tetramers in grape for the first time. This approach can be potentially used in the study of metabolomics of varieties of other plant species.
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Affiliation(s)
- Riccardo Flamini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Viticoltura (CRA-VIT), Laboratorio Chimico, Viale XXVIII Aprile 26, 31015 Conegliano, Italy
- *Riccardo Flamini:
| | - Mirko De Rosso
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Viticoltura (CRA-VIT), Laboratorio Chimico, Viale XXVIII Aprile 26, 31015 Conegliano, Italy
| | - Luigi Bavaresco
- Istituto di Frutti-Viticoltura, Università Cattolica S.C., Via Emilia Parmense 84, 29122 Piacenza, Italy
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Martin JC, Maillot M, Mazerolles G, Verdu A, Lyan B, Migné C, Defoort C, Canlet C, Junot C, Guillou C, Manach C, Jabob D, Bouveresse DJR, Paris E, Pujos-Guillot E, Jourdan F, Giacomoni F, Courant F, Favé G, Le Gall G, Chassaigne H, Tabet JC, Martin JF, Antignac JP, Shintu L, Defernez M, Philo M, Alexandre-Gouaubau MC, Amiot-Carlin MJ, Bossis M, Triba MN, Stojilkovic N, Banzet N, Molinié R, Bott R, Goulitquer S, Caldarelli S, Rutledge DN. Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study. Metabolomics 2015; 11:807-821. [PMID: 26109925 PMCID: PMC4475541 DOI: 10.1007/s11306-014-0740-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 10/04/2014] [Indexed: 02/03/2023]
Abstract
The metabo-ring initiative brought together five nuclear magnetic resonance instruments (NMR) and 11 different mass spectrometers with the objective of assessing the reliability of untargeted metabolomics approaches in obtaining comparable metabolomics profiles. This was estimated by measuring the proportion of common spectral information extracted from the different LCMS and NMR platforms. Biological samples obtained from 2 different conditions were analysed by the partners using their own in-house protocols. Test #1 examined urine samples from adult volunteers either spiked or not spiked with 32 metabolite standards. Test #2 involved a low biological contrast situation comparing the plasma of rats fed a diet either supplemented or not with vitamin D. The spectral information from each instrument was assembled into separate statistical blocks. Correlations between blocks (e.g., instruments) were examined (RV coefficients) along with the structure of the common spectral information (common components and specific weights analysis). In addition, in Test #1, an outlier individual was blindly introduced, and its identification by the various platforms was evaluated. Despite large differences in the number of spectral features produced after post-processing and the heterogeneity of the analytical conditions and the data treatment, the spectral information both within (NMR and LCMS) and across methods (NMR vs. LCMS) was highly convergent (from 64 to 91 % on average). No effect of the LCMS instrumentation (TOF, QTOF, LTQ-Orbitrap) was noted. The outlier individual was best detected and characterised by LCMS instruments. In conclusion, untargeted metabolomics analyses report consistent information within and across instruments of various technologies, even without prior standardisation.
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Affiliation(s)
- Jean-Charles Martin
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Matthieu Maillot
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Gérard Mazerolles
- INRA, UMR 1083 SPO, INRA Campus SupAgro, Plateforme Polyphénols, 2 Place Viala, 34060 Montpellier Cedex 02, France
| | - Alexandre Verdu
- BRUKER, 4 allée Hendrick Lorentz, 77447 Marne La Vallée Cedex 2, France
| | - Bernard Lyan
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Carole Migné
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Catherine Defoort
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Cecile Canlet
- INRA, UMR 1331 TOXALIM (Research Center in Food Toxicology), Axiom-Metatoul, 31027 Toulouse, France
| | - Christophe Junot
- Laboratoire d’Etude du Métabolisme des Médicaments, DSV/iBiTec-S/SPI, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Claude Guillou
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Claudine Manach
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Daniel Jabob
- INRA, UMR1332 Fruit Biology and Pathology, Centre INRA de Bordeaux, 33140 Villenave d’Ornon, France
| | - Delphine Jouan-Rimbaud Bouveresse
- INRA, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
- AgroParisTech, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
| | - Estelle Paris
- INRA, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
- AgroParisTech, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
| | - Estelle Pujos-Guillot
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Fabien Jourdan
- INRA, UMR 1331 TOXALIM (Research Center in Food Toxicology), Metabolism of Xenobiotics (MeX), 31027 Toulouse, France
| | - Franck Giacomoni
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Frédérique Courant
- LUNAM Université, Oniris, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), USC INRA 1329, BP 50707, 44307 Nantes Cedex 3, France
| | - Gaëlle Favé
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Gwenaëlle Le Gall
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA UK
| | - Hubert Chassaigne
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Jean-Claude Tabet
- UPMC, Institut Parisien de Chimie Moléculaire, UMR-CNRS 7201, 4 Place Jussieu, Paris Cédex 05, France
| | - Jean-Francois Martin
- INRA, UMR 1019, UNH, CRNH Auvergne, 63000 Clermond-Ferrand, France
- INRA, UMR 1019, Plateforme d’Exploration du Métabolisme, UNH, 63000 Clermond-Ferrand, France
| | - Jean-Philippe Antignac
- LUNAM Université, Oniris, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), USC INRA 1329, BP 50707, 44307 Nantes Cedex 3, France
| | - Laetitia Shintu
- Aix-Marseille Université, ISM2, Campus Scientifique Saint Jérôme, 13397 Marseille Cedex 20, France
| | - Marianne Defernez
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA UK
| | - Mark Philo
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA UK
| | | | - Marie-Josephe Amiot-Carlin
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Mathilde Bossis
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Mohamed N. Triba
- Université Paris 13, Sorbonne Paris Cité, Laboratoire CSPBAT, CNRS (UMR 7244), 93017 Bobigny, France
| | - Natali Stojilkovic
- LCH, Laboratoire des Courses Hippiques, 91370 Verrières-le-Buisson, France
| | - Nathalie Banzet
- AP-HM, Hôpital Timone, Laboratoire de Biochimie, 13385 Marseille, France
| | - Roland Molinié
- Université de Picardie Jules Verne, EA 3900 BIOPI Biologie des plantes innovation, UFR de Pharmacie, 1 rue des Louvels, 80000 Amiens, France
| | - Romain Bott
- INRA UMR1260, “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
- Faculté de Médecine, Aix-Marseille Université, 13385 Marseille, France
- INSERM, UMR1062 “Nutrition, Obésité et Risque Thrombotique”, 13385 Marseille, France
| | - Sophie Goulitquer
- MetaboMer, FR2424, CNRS/UPMC, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - Stefano Caldarelli
- Aix-Marseille Université, ISM2, Campus Scientifique Saint Jérôme, 13397 Marseille Cedex 20, France
| | - Douglas N. Rutledge
- INRA, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
- AgroParisTech, UMR 1145 Ingénierie Procédés Aliments, 75005 Paris, France
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Shahbazy M, Zahraei A, Vafaeimanesh J, Kompany-Zareh M. Rapid and non-invasive diagnosis of coronary artery disease via clinical laboratory parameters and1H-NMR spectra of human blood plasma. RSC Adv 2015. [DOI: 10.1039/c5ra17262d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Coronary artery disease (CAD), one of the most common fatal diseases in the world, was examinedviainvestigation of the1H-NMR spectra of human blood plasma and clinical laboratory parameters with the aim of early disease diagnosis.
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Affiliation(s)
- Mohammad Shahbazy
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
| | - Ali Zahraei
- Clinical Research Development Center
- Qom University of Medical Sciences
- Qom
- Iran
| | | | - Mohsen Kompany-Zareh
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45137-66731
- Iran
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Abstract
Being an emerging field of "omics" research, metabonomics has been increasingly used in toxicological studies mostly because this technology has the ability to provide more detailed information to elucidate mechanism of toxicity. As an interdisciplinary field of science, metabonomics combines analytical chemistry, bioinformatics, statistics, and biochemistry. When applied to toxicology, metabonomics also includes aspects of patho-biochemistry, systems biology, and molecular diagnostics. During a toxicological study, the metabolic changes over time and dose after chemical treatment can be monitored. Therefore, the most important use of this emerging technology is the identification of signatures of toxicity-patterns of metabolic changes predictive of a hazard manifestation. This chapter summarizes the current state of metabonomics technology and its applications in various areas of toxicological studies.
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Affiliation(s)
- Liang Zhao
- Center for Alternatives to Animal Testing, Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
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249
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Huan T, Li L. Counting Missing Values in a Metabolite-Intensity Data Set for Measuring the Analytical Performance of a Metabolomics Platform. Anal Chem 2014; 87:1306-13. [DOI: 10.1021/ac5039994] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G2G2, Canada
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250
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Barrajón-Catalán E, Taamalli A, Quirantes-Piné R, Roldan-Segura C, Arráez-Román D, Segura-Carretero A, Micol V, Zarrouk M. Differential metabolomic analysis of the potential antiproliferative mechanism of olive leaf extract on the JIMT-1 breast cancer cell line. J Pharm Biomed Anal 2014; 105:156-162. [PMID: 25560707 DOI: 10.1016/j.jpba.2014.11.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
Abstract
A new differential metabolomic approach has been developed to identify the phenolic cellular metabolites derived from breast cancer cells treated with a supercritical fluid extracted (SFE) olive leaf extract. The SFE extract was previously shown to have significant antiproliferative activity relative to several other olive leaf extracts examined in the same model. Upon SFE extract incubation of JIMT-1 human breast cancer cells, major metabolites were identified by using HPLC coupled to electrospray ionization quadrupole-time-of-flight mass spectrometry (ESI-Q-TOF-MS). After treatment, diosmetin was the most abundant intracellular metabolite, and it was accompanied by minor quantities of apigenin and luteolin. To identify the putative antiproliferative mechanism, the major metabolites and the complete extract were assayed for cell cycle, MAPK and PI3K proliferation pathways modulation. Incubation with only luteolin showed a significant effect in cell survival. Luteolin induced apoptosis, whereas the whole olive leaf extract incubation led to a significant cell cycle arrest at the G1 phase. The antiproliferative activity of both pure luteolin and olive leaf extract was mediated by the inactivation of the MAPK-proliferation pathway at the extracellular signal-related kinase (ERK1/2). However, the flavone concentration of the olive leaf extract did not fully explain the strong antiproliferative activity of the extract. Therefore, the effects of other compounds in the extract, probably at the membrane level, must be considered. The potential synergistic effects of the extract also deserve further attention. Our differential metabolomics approach identified the putative intracellular metabolites from a botanical extract that have antiproliferative effects, and this metabolomics approach can be expanded to other herbal extracts or pharmacological complex mixtures.
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Affiliation(s)
- Enrique Barrajón-Catalán
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. Universidad s/n, 03202 Elche, Spain
| | - Amani Taamalli
- Laboratoire de Biotechnologie de l'Olivier, Centre de Biotechnologie de Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Rosa Quirantes-Piné
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain; Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Cristina Roldan-Segura
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain; Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - David Arráez-Román
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain; Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada 18071, Spain; Research and Development of Functional Food Centre (CIDAF), Health Science Technological Park, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Vicente Micol
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. Universidad s/n, 03202 Elche, Spain.
| | - Mokhtar Zarrouk
- Laboratoire de Biotechnologie de l'Olivier, Centre de Biotechnologie de Borj Cedria, BP 901, 2050 Hammam-Lif, Tunisia
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