151
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Rivera-Vélez SM, Villarino NF. Feline urine metabolomic signature: characterization of low-molecular-weight substances in urine from domestic cats. J Feline Med Surg 2018; 20:155-163. [PMID: 28367722 PMCID: PMC11129257 DOI: 10.1177/1098612x17701010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Objectives This aim of this study was to characterize the composition and content of the feline urine metabolome. Methods Eight healthy domestic cats were acclimated at least 10 days before starting the study. Urine samples (~2 ml) were collected by ultrasound-guided cystocentesis. Samples were centrifuged at 1000 × g for 8 mins, and the supernatant was analyzed by gas chromatography/time-of-flight mass spectrometery. The urine metabolome was characterized using an untargeted metabolomics approach. Results Three hundred and eighteen metabolites were detected in the urine of the eight cats. These molecules are key components of at least 100 metabolic pathways. Feline urine appears to be dominated by carbohydrates, carbohydrate conjugates, organic acid and derivatives, and amino acids and analogs. The five most abundant molecules were phenaceturic acid, hippuric acid, pseudouridine phosphate and 3-(4-hydroxyphenyl) propionic acid. Conclusions and relevance This study is the first to characterize the feline urine metabolome. The results of this study revealed the presence of multiple low-molecular-weight substances that were not known to be present in feline urine. As expected, the origin of the metabolites detected in urine was diverse, including endogenous compounds and molecules biosynthesized by microbes. Also, the diet seemed to have had a relevant role on the urine metabolome. Further exploration of the urine metabolic phenotype will open a window for discovering unknown, or poorly understood, metabolic pathways. In turn, this will advance our understanding of feline biology and lead to new insights in feline physiology, nutrition and medicine.
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Affiliation(s)
- Sol-Maiam Rivera-Vélez
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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152
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Kang TS, Zhang JT, Vellaisamy K, Ma DL, Leung CH. Recent progress and developments of iridium-based compounds as probes for environmental analytes. Dalton Trans 2018; 47:13314-13317. [DOI: 10.1039/c8dt01167b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Metal complexes based on iridium metal centers have attracted attention as probes due to their tunable biological and chemical characteristics.
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Affiliation(s)
- Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Jia-Tong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | | | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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153
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Ren JL, Zhang AH, Kong L, Wang XJ. Advances in mass spectrometry-based metabolomics for investigation of metabolites. RSC Adv 2018; 8:22335-22350. [PMID: 35539746 PMCID: PMC9081429 DOI: 10.1039/c8ra01574k] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Abstract
Metabolomics is the systematic study of all the metabolites present within a biological system, which consists of a mass of molecules, having a variety of physical and chemical properties and existing over an extensive dynamic range in biological samples. Diverse analytical techniques are needed to achieve higher coverage of metabolites. The application of mass spectrometry (MS) in metabolomics has increased exponentially since the discovery and development of electrospray ionization and matrix-assisted laser desorption ionization techniques. Significant advances have also occurred in separation-based MS techniques (gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, and ion mobility-mass spectrometry), as well as separation-free MS techniques (direct infusion-mass spectrometry, matrix-assisted laser desorption ionization-mass spectrometry, mass spectrometry imaging, and direct analysis in real time mass spectrometry) in the past decades. This review presents a brief overview of the recent advanced MS techniques and their latest applications in metabolomics. The software/websites for MS result analyses are also reviewed. Metabolomics is the systematic study of all the metabolites present within a biological system, supply functional information and has received extensive attention in the field of life sciences.![]()
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Affiliation(s)
- Jun-Ling Ren
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ai-Hua Zhang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ling Kong
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Xi-Jun Wang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
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154
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Tian Y, Yang L, Xu W, Zhang H, Wang Z, Zhang H, Zheng S, Shi Y, Xu P. Predictors for drug effects with brain disease: Shed new light from EEG parameters to brain connectomics. Eur J Pharm Sci 2017; 110:26-36. [PMID: 28456573 DOI: 10.1016/j.ejps.2017.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 01/21/2023]
Abstract
Though researchers spent a lot of effort to develop treatments for neuropsychiatric disorders, the poor translation of drug efficacy data from animals to human hampered the success of these therapeutic approaches in human. Pharmaceutical industry is challenged by low clinical success rates for new drug registration. To maximize the success in drug development, biomarkers are required to act as surrogate end points and predictors of drug effects. The pathology of brain disease could be in part due to synaptic dysfunction. Electroencephalogram (EEG), generating from the result of the postsynaptic potential discharge between cells, could be a potential measure to bridge the gaps between animal and human data. Here we discuss recent progress on using relevant EEG characteristics and brain connectomics as biomarkers to monitor drug effects and measure cognitive changes on animal models and human in real-time. It is expected that the novel approach, i.e. EEG connectomics, will offer a deeper understanding on the drug efficacy at a microcirculatory level, which will be useful to support the development of new treatments for neuropsychiatric disorders.
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Affiliation(s)
- Yin Tian
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China.
| | - Li Yang
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Wei Xu
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Huiling Zhang
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Zhongyan Wang
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Haiyong Zhang
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Shuxing Zheng
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Yupan Shi
- Biomedical Engineering Department, Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, High School Innovation Team of Architecture and Core Technologies of Smart Medical System, ChongQing University of Posts and Telecommunications, ChongQing 400065, China
| | - Peng Xu
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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155
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van den Broek TJ, Bakker GCM, Rubingh CM, Bijlsma S, Stroeve JHM, van Ommen B, van Erk MJ, Wopereis S. Ranges of phenotypic flexibility in healthy subjects. GENES & NUTRITION 2017; 12:32. [PMID: 29225708 PMCID: PMC5718019 DOI: 10.1186/s12263-017-0589-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/20/2017] [Indexed: 11/14/2022]
Abstract
BACKGROUND A key feature of metabolic health is the ability to adapt upon dietary perturbations. A systemic review defined an optimal nutritional challenge test, the "PhenFlex test" (PFT). Recently, it has been shown that the PFT enables the quantification of all relevant metabolic processes involved in maintaining or regaining homeostasis of metabolic health. Furthermore, it was demonstrated that quantification of PFT response was more sensitive as compared to fasting markers in demonstrating reduced phenotypic flexibility in metabolically impaired type 2 diabetes subjects. METHODS This study aims to demonstrate that quantification of PFT response can discriminate between different states of health within the healthy range of the population. Therefore, 100 healthy subjects were enrolled (50 males, 50 females) ranging in age (young, middle, old) and body fat percentage (low, medium, high), assuming variation in phenotypic flexibility. Biomarkers were selected to quantify main processes which characterize phenotypic flexibility in response to PFT: flexibility in glucose, lipid, amino acid and vitamin metabolism, and metabolic stress. Individual phenotypic flexibility was visualized using the "health space" by representing the four processes on the health space axes. By quantifying and presenting the study subjects in this space, individual phenotypic flexibility was visualized. RESULTS Using the "health space" visualization, differences between groups as well as within groups from the healthy range of the population can be easily and intuitively assessed. The health space showed a different adaptation to the metabolic PhenFlex test in the extremes of the recruited population; persons of young age with low to normal fat percentage had a markedly different position in the health space as compared to persons from old age with normal to high fat percentage. CONCLUSION The results of the metabolic PhenFlex test in conjunction with the health space reliably assessed health on an individual basis. This quantification can be used in the future for personalized health quantification and advice.
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Affiliation(s)
| | | | - C. M. Rubingh
- TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - S. Bijlsma
- TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | | | - B. van Ommen
- TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - M. J. van Erk
- TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - S. Wopereis
- TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
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156
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Rodríguez-Pérez C, Segura-Carretero A, Del Mar Contreras M. Phenolic compounds as natural and multifunctional anti-obesity agents: A review. Crit Rev Food Sci Nutr 2017; 59:1212-1229. [PMID: 29156939 DOI: 10.1080/10408398.2017.1399859] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prevalence of obesity worldwide has reached pandemic proportions. Despite the increasing evidence in the implication of phenolic compounds in obesity management, the real effect is not completely understood. The available in vitro and in vivo studies have demonstrated the implication of phenolic compounds in: lowering food intake, decreasing lipogenesis, increasing lipolysis, stimulating fatty acids β-oxidation, inhibiting adipocyte differentiation and growth, attenuating inflammatory responses and suppress oxidative stress. This review encompasses the most recent evidence in the anti-obesity effect of phenolic compounds from plants to different nutraceuticals and functional foods based on the in vitro, in vivo and clinical studies. For that, this review has been focused on popular plant-based products highly consumed today such as cocoa, cinnamon, and olive oil, beverages such as red wine, tea (green, white and black tea) and Hibiscus sabdariffa L. tea, among others.
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Affiliation(s)
- Celia Rodríguez-Pérez
- a Department of Analytical Chemistry , Faculty of Sciences, University of Granada , Avenida Fuentenueva s/n, Granada , Spain
| | - Antonio Segura-Carretero
- a Department of Analytical Chemistry , Faculty of Sciences, University of Granada , Avenida Fuentenueva s/n, Granada , Spain
| | - María Del Mar Contreras
- b Department of Analytical Chemistry , Annex C-3 Building, Campus of Rabanales, University of Córdoba , Córdoba , Spain
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157
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Bazanella M, Maier TV, Clavel T, Lagkouvardos I, Lucio M, Maldonado-Gòmez MX, Autran C, Walter J, Bode L, Schmitt-Kopplin P, Haller D. Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome. Am J Clin Nutr 2017; 106:1274-1286. [PMID: 28877893 DOI: 10.3945/ajcn.117.157529] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/08/2017] [Indexed: 11/14/2022] Open
Abstract
Background: Early-life colonization of the intestinal tract is a dynamic process influenced by numerous factors. The impact of probiotic-supplemented infant formula on the composition and function of the infant gut microbiota is not well defined.Objective: We sought to determine the effects of a bifidobacteria-containing formula on the healthy human intestinal microbiome during the first year of life.Design: A double-blind, randomized, placebo-controlled study of newborn infants assigned to a standard whey-based formula containing a total of 107 colony-forming units (CFU)/g of Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, B. longum subspecies infantis (intervention), or to a control formula without bifidobacteria (placebo). Breastfed controls were included. Diversity and composition of fecal microbiota were determined by 16S ribosomal RNA gene amplicon sequencing, and metabolite profiles were analyzed by ultrahigh-performance liquid chromatography-mass spectrometry over a period of 2 y.Results: Infants (n = 106) were randomly assigned to either the interventional (n = 48) or placebo (n = 49) group; 9 infants were exclusively breastfed throughout the entire intervention period of 12 mo. Infants exposed to bifidobacteria-supplemented formula showed decreased occurrence of Bacteroides and Blautia spp. associated with changes in lipids and unknown metabolites at month 1. Microbiota and metabolite profiles of intervention and placebo groups converged during the study period, and long-term colonization (24 mo) of the supplemented Bifidobacterium strains was not detected. Significant differences in microbiota and metabolites were detected between infants fed breast milk and those fed formula (P < 0.005) and between infants birthed vaginally and those birthed by cesarean delivery (P < 0.005). No significant differences were observed between infant feeding groups regarding growth, antibiotic uptake, or other health variables (P > 0.05).Conclusion: The supplementation of bifidobacteria to infant diet can modulate the occurrence of specific bacteria and metabolites during early life with no detectable long-term effects. This trial was registered at germanctr.de as DRKS00003660.
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Affiliation(s)
| | - Tanja V Maier
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | | | | | - Marianna Lucio
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | | | - Chloe Autran
- Divisions of Neonatology and Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MoMICoRE), University of California, San Diego, La Jolla, CA
| | - Jens Walter
- Chair for Nutrition, Microbes and Gastrointestinal Health, University of Alberta, Edmonton, Alberta, Canada; and
| | - Lars Bode
- Divisions of Neonatology and Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MoMICoRE), University of California, San Diego, La Jolla, CA
| | - Philippe Schmitt-Kopplin
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany.,Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, .,ZIEL - Institute for Food & Health, and
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158
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Brouwer-Brolsma EM, Brennan L, Drevon CA, van Kranen H, Manach C, Dragsted LO, Roche HM, Andres-Lacueva C, Bakker SJL, Bouwman J, Capozzi F, De Saeger S, Gundersen TE, Kolehmainen M, Kulling SE, Landberg R, Linseisen J, Mattivi F, Mensink RP, Scaccini C, Skurk T, Tetens I, Vergeres G, Wishart DS, Scalbert A, Feskens EJM. Combining traditional dietary assessment methods with novel metabolomics techniques: present efforts by the Food Biomarker Alliance. Proc Nutr Soc 2017; 76:619-627. [PMID: 29137687 DOI: 10.1017/s0029665117003949] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
FFQ, food diaries and 24 h recall methods represent the most commonly used dietary assessment tools in human studies on nutrition and health, but food intake biomarkers are assumed to provide a more objective reflection of intake. Unfortunately, very few of these biomarkers are sufficiently validated. This review provides an overview of food intake biomarker research and highlights present research efforts of the Joint Programming Initiative 'A Healthy Diet for a Healthy Life' (JPI-HDHL) Food Biomarkers Alliance (FoodBAll). In order to identify novel food intake biomarkers, the focus is on new food metabolomics techniques that allow the quantification of up to thousands of metabolites simultaneously, which may be applied in intervention and observational studies. As biomarkers are often influenced by various other factors than the food under investigation, FoodBAll developed a food intake biomarker quality and validity score aiming to assist the systematic evaluation of novel biomarkers. Moreover, to evaluate the applicability of nutritional biomarkers, studies are presently also focusing on associations between food intake biomarkers and diet-related disease risk. In order to be successful in these metabolomics studies, knowledge about available electronic metabolomics resources is necessary and further developments of these resources are essential. Ultimately, present efforts in this research area aim to advance quality control of traditional dietary assessment methods, advance compliance evaluation in nutritional intervention studies, and increase the significance of observational studies by investigating associations between nutrition and health.
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Affiliation(s)
- Elske M Brouwer-Brolsma
- Division of Human Nutrition,Wageningen University,PO Box 17,6700 AA Wageningen,The Netherlands
| | | | - Christian A Drevon
- Department of Nutrition,Institute of Basic Medical Sciences,Faculty of Medicine,University of Oslo,Oslo,Norway
| | - Henk van Kranen
- National Institute for Public Health and the Environment,Bilthoven,The Netherlands
| | - Claudine Manach
- INRA,UMR 1019, Human Nutrition Unit,Université Clermont Auvergne,Clermont-Ferrand,France
| | - Lars Ove Dragsted
- Department of Nutrition,Exercise and Sports,University of Copenhagen,Copenhagen,Denmark
| | - Helen M Roche
- Nutrigenomics Research Group,UCD Institute of Food and Health,School of Public Health,Physiotherapy and Sports Science,Belfield,Dublin 4,Ireland
| | - Cristina Andres-Lacueva
- Biomarkers and Nutrimetabolomic Laboratory,Department of Nutrition,Food Sciences and Gastronomy, XaRTA, INSA,Faculty of Pharmacy and Food Sciences,University of Barcelona,Barcelona,Spain
| | - Stephan J L Bakker
- Department of Internal Medicine,University Medical Center Groningen, University of Groningen,Groningen,The Netherlands
| | - Jildau Bouwman
- TNO,Netherlands Organisation for Applied Scientific Research,Zeist,The Netherlands
| | - Francesco Capozzi
- Department of Agricultural and Food Science,University of Bologna,Italy
| | - Sarah De Saeger
- Faculty of Pharmaceutical Sciences, Department of Bioanalysis,Ghent University,Ghent,Belgium
| | | | - Marjukka Kolehmainen
- University of Eastern Finland,Institute of Public Health and Clinical Nutrition,Clinical Nutrition,Kuopio,Finland
| | - Sabine E Kulling
- Max Rubner-Institut, Bundesforschungsinstitut für Ernährung und Lebensmittel,Karlsruhe,Germany
| | - Rikard Landberg
- Department of Biology and Biological Engineering, Food and Nutrition Science,Chalmers University of Technology,Gothenburg,Sweden
| | - Jakob Linseisen
- Institute of Epidemiology II,Helmholtz Centre Munich,Neuherberg,Germany
| | - Fulvio Mattivi
- Fondazione Edmund Mach,Department of Food Quality and Nutrition,Research and Innovation Centre,San Michele all'Adige,Italy
| | - Ronald P Mensink
- Department of Human Biology,NUTRIM School of Nutrition and Translational Research in Metabolism,Maastricht University Medical Center,Maastricht,The Netherlands
| | - Cristina Scaccini
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria - Food and Nutrition Research Center,Roma,Italy
| | - Thomas Skurk
- ZIEL Institute for Food and Health,Core Facility Human Studies,Nutritional Medicine,Technical University of Munich,Freising,Germany
| | - Inge Tetens
- Division of Food,Disease Prevention and Toxicology,National Food Institute,Technical University of Denmark,Kongens Lyngby,Denmark
| | - Guy Vergeres
- Agroscope,Institute for Food Sciences IFS,Bern,Switzerland
| | - David S Wishart
- Departments of Biological Sciences and Computing Science,University of Alberta,Edmonton,Canada
| | - Augustin Scalbert
- International Agency for Research on Cancer,Nutrition and Metabolism Section,Lyon,France
| | - Edith J M Feskens
- Division of Human Nutrition,Wageningen University,PO Box 17,6700 AA Wageningen,The Netherlands
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159
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Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. mBio 2017; 8:mBio.01343-17. [PMID: 29042495 PMCID: PMC5646248 DOI: 10.1128/mbio.01343-17] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of “omics” approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics. This multiomics approach captured changes in the abundance of specific bacterial species, proteins, and metabolites after a diet high in resistant starch (HRS), providing key insights into the influence of dietary interventions on the gut microbiome. The combined data showed that a high-RS diet caused an increase in the ratio of Firmicutes to Bacteroidetes, including increases in relative abundances of some specific members of the Firmicutes and concurrent increases in enzymatic pathways and metabolites involved in lipid metabolism in the gut. This work was undertaken to obtain a mechanistic understanding of the complex interplay between diet and the microorganisms residing in the intestine. Although it is known that gut microbes play a key role in digestion of the food that we consume, the specific contributions of different microorganisms are not well understood. In addition, the metabolic pathways and resultant products of metabolism during digestion are highly complex. To address these knowledge gaps, we used a combination of molecular approaches to determine the identities of the microorganisms in the gut during digestion of dietary starch as well as the metabolic pathways that they carry out. Together, these data provide a more complete picture of the function of the gut microbiome in digestion, including links between an RS diet and lipid metabolism and novel linkages between specific gut microbes and their metabolites and proteins produced in the gut.
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160
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Fujimura Y, Miura D, Tachibana H. A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea. Molecules 2017; 22:molecules22101621. [PMID: 28953237 PMCID: PMC6151411 DOI: 10.3390/molecules22101621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 11/25/2022] Open
Abstract
Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.
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Affiliation(s)
- Yoshinori Fujimura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Daisuke Miura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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161
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Tiwari R, Ahire D, Kumar H, Sinha S, Chauthe SK, Subramanian M, Iyer R, Sarabu R, Bajpai L. Use of Hybrid Capillary Tube Apparatus on 400 MHz NMR for Quantitation of Crucial Low-Quantity Metabolites Using aSICCO Signal. Drug Metab Dispos 2017; 45:1215-1224. [PMID: 28935657 DOI: 10.1124/dmd.117.077073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/13/2017] [Indexed: 11/22/2022] Open
Abstract
Metabolites of new chemical entities can influence safety and efficacy of a molecule and often times need to be quantified in preclinical studies. However, synthetic standards of metabolites are very rarely available in early discovery. Alternate approaches such as biosynthesis need to be explored to generate these metabolites. Assessing the quantity and purity of these small amounts of metabolites with a nondestructive analytical procedure becomes crucial. Quantitative NMR becomes the method of choice for these samples. Recent advances in high-field NMR (>500 MHz) with the use of cryoprobe technology have helped to improve sensitivity for analysis of small microgram quantity of such samples. However, this type of NMR instrumentation is not routinely available in all laboratories. To analyze microgram quantities of metabolites on a routine basis with lower-resolution 400 MHz NMR instrument fitted with a broad band fluorine observe room temperature probe, a novel hybrid capillary tube setup was developed. To quantitate the metabolite in the sample, an artificial signal insertion for calculation of concentration observed (aSICCO) method that introduces an internally calibrated mathematical signal was used after acquiring the NMR spectrum. The linearity of aSICCO signal was established using ibuprofen as a model analyte. The limit of quantification of this procedure was 0.8 mM with 10 K scans that could be improved further with the increase in the number of scans. This procedure was used to quantify three metabolites-phenytoin from fosphenytoin, dextrophan from dextromethorphan, and 4-OH-diclofenac from diclofenac-and is suitable for minibiosynthesis of metabolites from in vitro systems.
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Affiliation(s)
- Ranjeet Tiwari
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Deepak Ahire
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Hemantha Kumar
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Sarmistha Sinha
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Siddheshwar Kisan Chauthe
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Murali Subramanian
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Ramaswamy Iyer
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Ramakanth Sarabu
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Lakshmikant Bajpai
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
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162
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Informatics for Nutritional Genetics and Genomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1005:143-166. [PMID: 28916932 DOI: 10.1007/978-981-10-5717-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While traditional nutrition science is focusing on nourishing population, modern nutrition is aiming at benefiting individual people. The goal of modern nutritional research is to promote health, prevent diseases, and improve performance. With the development of modern technologies like bioinformatics, metabolomics, and molecular genetics, this goal is becoming more attainable. In this chapter, we will discuss the new concepts and technologies especially in informatics and molecular genetics and genomics, and how they have been implemented to change the nutrition science and lead to the emergence of new branches like nutrigenomics, nutrigenetics, and nutritional metabolomics.
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163
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Armitage EG, Ciborowski M. Applications of Metabolomics in Cancer Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:209-234. [PMID: 28132182 DOI: 10.1007/978-3-319-47656-8_9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the start of metabolomics as a field of research, the number of studies related to cancer has grown to such an extent that cancer metabolomics now represents its own discipline. In this chapter, the applications of metabolomics in cancer studies are explored. Different approaches and analytical platforms can be employed for the analysis of samples depending on the goal of the study and the aspects of the cancer metabolome being investigated. Analyses have concerned a range of cancers including lung, colorectal, bladder, breast, gastric, oesophageal and thyroid, amongst others. Developments in these strategies and methodologies that have been applied are discussed, in addition to exemplifying the use of cancer metabolomics in the discovery of biomarkers and in the assessment of therapy (both pharmaceutical and nutraceutical). Finally, the application of cancer metabolomics in personalised medicine is presented.
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Affiliation(s)
- Emily Grace Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad CEU San Pablo, Campus Monteprincipe, Madrid, Spain. .,Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow, UK. .,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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164
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Carayol M, Leitzmann MF, Ferrari P, Zamora-Ros R, Achaintre D, Stepien M, Schmidt JA, Travis RC, Overvad K, Tjønneland A, Hansen L, Kaaks R, Kühn T, Boeing H, Bachlechner U, Trichopoulou A, Bamia C, Palli D, Agnoli C, Tumino R, Vineis P, Panico S, Quirós JR, Sánchez-Cantalejo E, Huerta JM, Ardanaz E, Arriola L, Agudo A, Nilsson J, Melander O, Bueno-de-Mesquita B, Peeters PH, Wareham N, Khaw KT, Jenab M, Key TJ, Scalbert A, Rinaldi S. Blood Metabolic Signatures of Body Mass Index: A Targeted Metabolomics Study in the EPIC Cohort. J Proteome Res 2017; 16:3137-3146. [PMID: 28758405 PMCID: PMC6198936 DOI: 10.1021/acs.jproteome.6b01062] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metabolomics is now widely used to characterize metabolic phenotypes associated with lifestyle risk factors such as obesity. The objective of the present study was to explore the associations of body mass index (BMI) with 145 metabolites measured in blood samples in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Metabolites were measured in blood from 392 men from the Oxford (UK) cohort (EPIC-Oxford) and in 327 control subjects who were part of a nested case-control study on hepatobiliary carcinomas (EPIC-Hepatobiliary). Measured metabolites included amino acids, acylcarnitines, hexoses, biogenic amines, phosphatidylcholines, and sphingomyelins. Linear regression models controlled for potential confounders and multiple testing were run to evaluate the associations of metabolite concentrations with BMI. 40 and 45 individual metabolites showed significant differences according to BMI variations, in the EPIC-Oxford and EPIC-Hepatobiliary subcohorts, respectively. Twenty two individual metabolites (kynurenine, one sphingomyelin, glutamate and 19 phosphatidylcholines) were associated with BMI in both subcohorts. The present findings provide additional knowledge on blood metabolic signatures of BMI in European adults, which may help identify mechanisms mediating the relationship of BMI with obesity-related diseases.
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Affiliation(s)
- Marion Carayol
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Michael F. Leitzmann
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Pietro Ferrari
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Raul Zamora-Ros
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - David Achaintre
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Magdalena Stepien
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Julie A. Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Oxford, OX3 7LF, United Kingdom
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Oxford, OX3 7LF, United Kingdom
| | - Kim Overvad
- Aarhus University, Department of Public Health, Section for Epidemiology, Bartholins Alle 2, DK-8000 Aarhus C, Denmark
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Louise Hansen
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, D-69120 Heidelberg, Germany
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, D-69120 Heidelberg, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Ursula Bachlechner
- Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Alexandroupoleos 23, Athens 11527, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Dept. of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Mikras Asias 75, Goudi GR-11527, Athens, Greece
- Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue. Boston, Massachusetts 02115, USA
| | - Christina Bamia
- Hellenic Health Foundation, Alexandroupoleos 23, Athens 11527, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Dept. of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Mikras Asias 75, Goudi GR-11527, Athens, Greece
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Ponte Nuovo, Via delle Oblate n.4, Padiglione 28-A Mario Fiori, 50141 Florence, Italy
| | - Claudia Agnoli
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 1, 20133 Milan, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, "Civic - M.P. Arezzo" Hospital, Via Dante 109, 97100, ASP Ragusa, Italy
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, St Mary's Campus, Norfolk Place W2 1PG London, UK
- HuGeF Foundation, Via Nizza 52, 10126, Turin, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Medical School of Naples, Federico II University, Via Sergio Pansini, 5, 80131, Naples, Italy
| | - J. Ramón Quirós
- EPIC Asturias, Public Health Directorate, Asturias, Ciriaco Miguel Vigil St, 9 33006 Oviedo, Spain
| | - Emilio Sánchez-Cantalejo
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs. Granada. Hospitales Universitarios de Granada/Universidad de Granada, Cuesta del Observatorio, 4, 18011 Granada, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP). Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - José María Huerta
- CIBER Epidemiología y Salud Pública (CIBERESP). Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca. Ronda de Levante, 11. 30008, Murcia, Spain
| | - Eva Ardanaz
- CIBER Epidemiología y Salud Pública (CIBERESP). Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Navarra Public Health Institute, C/ Leyre, 15, 31003, Pamplona Spain
- IdiSNA, Navarra Institute for Health Research, C/ Irunlarrea, 3, 31008, Pamplona Spain
| | - Larraitz Arriola
- CIBER Epidemiología y Salud Pública (CIBERESP). Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Public Health Division of Gipuzkoa, Instituto BIO-Donostia, Basque Government, Av. Navarra 4, 20013 San Sebastian, Spain
| | - Antonio Agudo
- Unit of Nutrition and Cancer. Cancer Epidemiology Research Program. Catalan Institute of Oncology-IDIBELL. Av. Gran Via de l'Hospitalet 199-203, 08908 L'Hospitalet de Llobregat, Spain
| | - Jan Nilsson
- Department of Clinical Sciences Malmö, Lund University, Jan Waldenströms gata 35, 20502 Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Jan Waldenströms gata 35, 20502 Malmö, Sweden
| | - Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, St Mary's Campus, Norfolk Place W2 1PG London, UK
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), PO Box1, 3720 BA, Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Room number F02.649, Internal mail no F02.618, P.O. Box 85500, 3508 GA UTRECHT, The Netherlands
- Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Pantai Valley, 50603, Kuala Lumpur, Malaysia
| | - Petra H. Peeters
- Department of Epidemiology and Biostatistics, Imperial College London, School of Public Health, St Mary's Campus, Norfolk Place W2 1PG London, UK
- Dept of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, STR 6.131, PO Box 85500, 3508GA Utrecht, the Netherlands
| | - Nick Wareham
- Medical Research Council Epidemiology Unit, MRC Epidemiology Unit, University of Cambridge, School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mazda Jenab
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Oxford, OX3 7LF, United Kingdom
| | - Augustin Scalbert
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Sabina Rinaldi
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
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165
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Targeted metabolome profiling by dual-probe microdialysis sampling and treatment using Gardenia jasminoides for rats with type 2 diabetes. Sci Rep 2017; 7:10105. [PMID: 28860508 PMCID: PMC5579158 DOI: 10.1038/s41598-017-10172-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 08/04/2017] [Indexed: 01/04/2023] Open
Abstract
Diabetes causes a variety of end-stage organ complications, including diabetic nephropathy. Metabolomics offers an approach for characterizing biofluid metabolic changes, but studies focusing on diabetic nephropathy are limited due to the loss of tissue-specific metabolic information. A microdialysis application for the sampling of intact endogenous metabolites has been developed, utilizing two probes simultaneously inserted into the kidney tissues and jugular vein of rats with type 2 diabetes. The comprehensive and quantitative analysis of 20 diagnostic biomarkers closely realated to type 2 diabetes and its complications were performed. Results indicated that amino acid and nucleotide levels were lower in diabetic rats, revealing that the metabolic pathways of amino acid, as well as purine and pyrimidine, were disturbed. Targeted metabolomics using mass spectrometry was performed to find potential therapeutic biomarkers and related metabolic pathways of Gardenia jasminoides (G. jasminoides) for treating diabetes. Results suggested that seven biomarkers in the kidney and five biomarkers in the blood were related to G. jasminoides. In addition, the marked perturbations of pathways were regulated after treatment with G. jasminoides, including amino acid metabolism and purine metabolism. These biomarkers and metabolic pathways provided new understanding for molecular mechanisms of G. jasminoides for treating diabetes and its complications.
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166
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Shokry E, Pereira J, Marques Júnior JG, da Cunha PHJ, Noronha Filho ADF, da Silva JA, Fioravanti MCS, de Oliveira AE, Antoniosi Filho NR. Earwax metabolomics: An innovative pilot metabolic profiling study for assessing metabolic changes in ewes during periparturition period. PLoS One 2017; 12:e0183538. [PMID: 28841695 PMCID: PMC5571955 DOI: 10.1371/journal.pone.0183538] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/07/2017] [Indexed: 01/08/2023] Open
Abstract
Important metabolic changes occur during transition period of late pregnancy and early lactation to meet increasing energy demands of the growing fetus and for milk production. The aim of this investigation is to present an innovative and non-invasive tool using ewe earwax sample analysis to assess the metabolic profile in ewes during late pregnancy and early lactation. In this work, earwax samples were collected from 28 healthy Brazilian Santa Inês ewes divided into 3 sub-groups: 9 non-pregnant ewes, 6 pregnant ewes in the last 30 days of gestation, and 13 lactating ewes ≤ 30 days postpartum. Then, a range of metabolites including volatile organic compounds (VOC), amino acids (AA), and minerals were profiled and quantified in the samples by applying headspace gas chromatography/mass spectrometry, high performance liquid chromatography/tandem mass spectrometry, and inductively coupled plasma-optical emission spectrometry, respectively. As evident in our results, significant changes were observed in the metabolite profile of earwax between the studied groups where a remarkable elevation was detected in the levels of non-esterified fatty acids, alcohols, ketones, and hydroxy urea in the VOC profile of samples obtained from pregnant and lactating ewes. Meanwhile, a significant decrease was detected in the levels of 9 minerals and 14 AA including essential AA (leucine, phenyl alanine, lysine, isoleucine, threonine, valine), conditionally essential AA (arginine, glycine, tyrosine, proline, serine), and a non-essential AA (alanine). Multivariate analysis using robust principal component analysis and hierarchical cluster analysis was successfully applied to discriminate the three study groups using the variations of metabolites in the two stress states (pregnancy and lactation) from the healthy non-stress condition. The innovative developed method was successful in evaluating pre- and post-parturient metabolic changes using earwax and can in the future be applied to recognize markers for diagnosis, prevention, and intervention of pregnancy complications in ewes.
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Affiliation(s)
- Engy Shokry
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
- * E-mail:
| | - Julião Pereira
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
| | - Jair Gonzalez Marques Júnior
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
| | | | | | - Jessica Alves da Silva
- Escola de Veterinária e Zootecnia, Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
| | | | - Anselmo Elcana de Oliveira
- Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
| | - Nelson Roberto Antoniosi Filho
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus Samambaia, Goiânia, Goiás, Brazil
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167
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Myers OD, Sumner SJ, Li S, Barnes S, Du X. One Step Forward for Reducing False Positive and False Negative Compound Identifications from Mass Spectrometry Metabolomics Data: New Algorithms for Constructing Extracted Ion Chromatograms and Detecting Chromatographic Peaks. Anal Chem 2017; 89:8696-8703. [PMID: 28752754 DOI: 10.1021/acs.analchem.7b00947] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
False positive and false negative peaks detected from extracted ion chromatograms (EIC) are an urgent problem with existing software packages that preprocess untargeted liquid or gas chromatography-mass spectrometry metabolomics data because they can translate downstream into spurious or missing compound identifications. We have developed new algorithms that carry out the sequential construction of EICs and detection of EIC peaks. We compare the new algorithms to two popular software packages XCMS and MZmine 2 and present evidence that these new algorithms detect significantly fewer false positives. Regarding the detection of compounds known to be present in the data, the new algorithms perform at least as well as XCMS and MZmine 2. Furthermore, we present evidence that mass tolerance in m/z should be favored rather than mass tolerance in ppm in the process of constructing EICs. The mass tolerance parameter plays a critical role in the EIC construction process and can have immense impact on the detection of EIC peaks.
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Affiliation(s)
- Owen D Myers
- University of North Carolina at Charlotte , Charlotte, North Carolina 28223, United States
| | - Susan J Sumner
- University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27514, United States
| | - Shuzhao Li
- Emory University , Atlanta, Georgia 30322, United States
| | - Stephen Barnes
- University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Xiuxia Du
- University of North Carolina at Charlotte , Charlotte, North Carolina 28223, United States
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168
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Myers OD, Sumner SJ, Li S, Barnes S, Du X. Detailed Investigation and Comparison of the XCMS and MZmine 2 Chromatogram Construction and Chromatographic Peak Detection Methods for Preprocessing Mass Spectrometry Metabolomics Data. Anal Chem 2017; 89:8689-8695. [PMID: 28752757 DOI: 10.1021/acs.analchem.7b01069] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
XCMS and MZmine 2 are two widely used software packages for preprocessing untargeted LC/MS metabolomics data. Both construct extracted ion chromatograms (EICs) and detect peaks from the EICs, the first two steps in the data preprocessing workflow. While both packages have performed admirably in peak picking, they also detect a problematic number of false positive EIC peaks and can also fail to detect real EIC peaks. The former and latter translate downstream into spurious and missing compounds and present significant limitations with most existing software packages that preprocess untargeted mass spectrometry metabolomics data. We seek to understand the specific reasons why XCMS and MZmine 2 find the false positive EIC peaks that they do and in what ways they fail to detect real compounds. We investigate differences of EIC construction methods in XCMS and MZmine 2 and find several problems in the XCMS centWave peak detection algorithm which we show are partly responsible for the false positive and false negative compound identifications. In addition, we find a problem with MZmine 2's use of centWave. We hope that a detailed understanding of the XCMS and MZmine 2 algorithms will allow users to work with them more effectively and will also help with future algorithmic development.
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Affiliation(s)
- Owen D Myers
- University of North Carolina at Charlotte , Charlotte, North Carolina 28223, United States
| | - Susan J Sumner
- University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27514, United States
| | - Shuzhao Li
- Emory University , Atlanta, Georgia 30322, United States
| | - Stephen Barnes
- University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Xiuxia Du
- University of North Carolina at Charlotte , Charlotte, North Carolina 28223, United States
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169
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Shahbazy M, Vasighi M, Kompany-Zareh M, Ballabio D. Oblique rotation of factors: a novel pattern recognition strategy to classify fluorescence excitation-emission matrices of human blood plasma for early diagnosis of colorectal cancer. MOLECULAR BIOSYSTEMS 2017; 12:1963-75. [PMID: 27076033 DOI: 10.1039/c6mb00162a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) ranks high in both men and women, accounting for about 13% of all cancers. In this study, a novel pattern recognition strategy is proposed to improve early diagnosis of CRC through visualizing the relationship between different spectral patterns in a case-control research. Partial least squares-discriminant analysis (PLS-DA) and supervised Kohonen network (SKN) were used to classify the fluorescence excitation-emission matrices (EEMs) from 289 human blood plasma samples containing CRC patients, adenomas tumor, other non-malignant findings and healthy individuals. To obtain optimal factors, oblique rotation (OR) and genetic algorithm (GA) were used to rotate the factors by optimizing transformation matrix elements. Transformed factors were introduced to SKN to build a classification model and the model performance was examined via comparison with a common classifier; PLS-DA. Classification models were built for CRC-healthy and adenomas-healthy samples and the best results were obtained through applying GA-OR on PLS factors and introducing them to the classifiers. Non-error rates for SKN and PLS-DA models assisted with GA (for selecting more informative PLS factors) and OR were equal to 0.97 and 0.95 in cross validation and 0.93 and 0.90 for prediction of the external test set, respectively. Moreover, according to the acceptable results for adenomas-healthy cases using optimal factors, CRC can be diagnosed in early stages. Combining classifiers and optimal factors proved to be efficient for distinguishing healthy and malignant samples, and OR can significantly improve performance of the classification model.
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Affiliation(s)
- Mohammad Shahbazy
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Mahdi Vasighi
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731 Zanjan, Iran.
| | - Davide Ballabio
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126 Milan, Italy
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170
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Schmidt JA, Fensom GK, Rinaldi S, Scalbert A, Appleby PN, Achaintre D, Gicquiau A, Gunter MJ, Ferrari P, Kaaks R, Kühn T, Floegel A, Boeing H, Trichopoulou A, Lagiou P, Anifantis E, Agnoli C, Palli D, Trevisan M, Tumino R, Bueno-de-Mesquita HB, Agudo A, Larrañaga N, Redondo-Sánchez D, Barricarte A, Huerta JM, Quirós JR, Wareham N, Khaw KT, Perez-Cornago A, Johansson M, Cross AJ, Tsilidis KK, Riboli E, Key TJ, Travis RC. Pre-diagnostic metabolite concentrations and prostate cancer risk in 1077 cases and 1077 matched controls in the European Prospective Investigation into Cancer and Nutrition. BMC Med 2017; 15:122. [PMID: 28676103 PMCID: PMC5497352 DOI: 10.1186/s12916-017-0885-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/26/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Little is known about how pre-diagnostic metabolites in blood relate to risk of prostate cancer. We aimed to investigate the prospective association between plasma metabolite concentrations and risk of prostate cancer overall, and by time to diagnosis and tumour characteristics, and risk of death from prostate cancer. METHODS In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition, pre-diagnostic plasma concentrations of 122 metabolites (including acylcarnitines, amino acids, biogenic amines, glycerophospholipids, hexose and sphingolipids) were measured using targeted mass spectrometry (AbsoluteIDQ p180 Kit) and compared between 1077 prostate cancer cases and 1077 matched controls. Risk of prostate cancer associated with metabolite concentrations was estimated by multi-variable conditional logistic regression, and multiple testing was accounted for by using a false discovery rate controlling procedure. RESULTS Seven metabolite concentrations, i.e. acylcarnitine C18:1, amino acids citrulline and trans-4-hydroxyproline, glycerophospholipids PC aa C28:1, PC ae C30:0 and PC ae C30:2, and sphingolipid SM (OH) C14:1, were associated with prostate cancer (p < 0.05), but none of the associations were statistically significant after controlling for multiple testing. Citrulline was associated with a decreased risk of prostate cancer (odds ratio (OR1SD) = 0.73; 95% confidence interval (CI) 0.62-0.86; p trend = 0.0002) in the first 5 years of follow-up after taking multiple testing into account, but not after longer follow-up; results for other metabolites did not vary by time to diagnosis. After controlling for multiple testing, 12 glycerophospholipids were inversely associated with advanced stage disease, with risk reduction up to 46% per standard deviation increase in concentration (OR1SD = 0.54; 95% CI 0.40-0.72; p trend = 0.00004 for PC aa C40:3). Death from prostate cancer was associated with higher concentrations of acylcarnitine C3, amino acids methionine and trans-4-hydroxyproline, biogenic amine ADMA, hexose and sphingolipid SM (OH) C14:1 and lower concentration of glycerophospholipid PC aa C42:4. CONCLUSIONS Several metabolites, i.e. C18:1, citrulline, trans-4-hydroxyproline, three glycerophospholipids and SM (OH) C14:1, might be related to prostate cancer. Analyses by time to diagnosis indicated that citrulline may be a marker of subclinical prostate cancer, while other metabolites might be related to aetiology. Several glycerophospholipids were inversely related to advanced stage disease. More prospective data are needed to confirm these associations.
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Affiliation(s)
- Julie A. Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
| | - Georgina K. Fensom
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
| | - Sabina Rinaldi
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Augustin Scalbert
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Paul N. Appleby
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
| | - David Achaintre
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Audrey Gicquiau
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Marc J. Gunter
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG UK
| | - Pietro Ferrari
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Foundation under Public Law, DE-69120 Heidelberg, Germany
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Foundation under Public Law, DE-69120 Heidelberg, Germany
| | - Anna Floegel
- Department of Epidemiology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, DE-14558 Nuthetal, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, DE-14558 Nuthetal, Germany
| | - Antonia Trichopoulou
- Hellenic Health Foundation, GR-11527 Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
| | - Pagona Lagiou
- Hellenic Health Foundation, GR-11527 Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, 02115 Boston, Massachusetts USA
| | | | - Claudia Agnoli
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 1, 20133 Milano, Italy
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute – ISPO, 50134 Florence, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin, 10126 Turin, Italy
- CPO-Piemonte, 10126 Turin, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, “Civic-M.P.Arezzo” Hospital, ASP 97100 Ragusa, Italy
| | - H. Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG UK
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, 08908 L’Hospitalet de Llobregat Barcelona, Spain
| | - Nerea Larrañaga
- Public Health Division of Gipuzkoa, Regional Government of the Basque Country, 20014 Donostia-San Sebastián, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Daniel Redondo-Sánchez
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, 18012 Granada, Spain
| | - Aurelio Barricarte
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Navarra Public Health Institute, 31003 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA) Pamplona, Pamplona, Spain
| | - José Maria Huerta
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, 30003 Murcia, Spain
| | | | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge, CB2 0SR Cambridge, UK
| | - Kay-Tee Khaw
- School of Clinical Medicine, University of Cambridge, CB2 2QQ Cambridge, UK
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
| | - Mattias Johansson
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08 France
| | - Amanda J. Cross
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG UK
| | - Konstantinos K. Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG UK
- Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG UK
| | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF UK
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171
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Lee MY, Kim HY, Lee DE, Singh D, Yeo SH, Baek SY, Park YK, Lee CH. Construing temporal metabolomes for acetous fermentative production of Rubus coreanus vinegar and its in vivo nutraceutical effects. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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172
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Metabolomics in nutrition research-a powerful window into nutritional metabolism. Essays Biochem 2017; 60:451-458. [PMID: 27980095 DOI: 10.1042/ebc20160029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 01/22/2023]
Abstract
Metabolomics is the study of small molecules present in biological samples. In recent years it has become evident that such small molecules, called metabolites, play a key role in the development of disease states. Furthermore, metabolomic applications can reveal information about alterations in certain metabolic pathways under different conditions. Data acquisition in metabolomics is usually performed using nuclear magnetic resonance (NMR)-based approaches or mass spectrometry (MS)-based approaches with a more recent trend including the application of multiple platforms in order to maximise the coverage in terms of metabolites measured. The application of metabolomics is rapidly increasing and the present review will highlight applications in nutrition research.
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173
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Uchiyama K, Yagi N, Mizushima K, Higashimura Y, Hirai Y, Okayama T, Yoshida N, Katada K, Kamada K, Handa O, Ishikawa T, Takagi T, Konishi H, Kuriu Y, Nakanishi M, Otsuji E, Itoh Y, Naito Y. Serum metabolomics analysis for early detection of colorectal cancer. J Gastroenterol 2017; 52:677-694. [PMID: 27650200 DOI: 10.1007/s00535-016-1261-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 09/01/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although colorectal cancer (CRC) is one of the most common causes of cancer mortality, early-stage detection improves survival rates dramatically. Because cancer impacts important metabolic pathways, the alteration of metabolite levels as a potential biomarker of early-stage cancer has been the focus of many studies. Here, we used CE-TOFMS, a novel and promising method with small injection volume and high resolution, to separate and detect ionic compounds based on the different migration rates of charged metabolites in order to detect metabolic biomarkers in patients with CRC. METHODS A total of 56 patients with CRC (n = 14 each of Stages I-IV), 60 healthy controls, and 59 patients with colonic adenoma were included in this study. Metabolome analysis was conducted by CE-TOFMS on serum samples of patients and controls using the Advanced Scan package (Human Metabolome Technologies). RESULTS We obtained 334 metabolites in the serum, of which 139 were identified as known substances. Among these 139 known metabolites, 16 were correlated with CRC stage by upregulation and 44 by downregulation, with benzoic acid (r = -0.649, t = 11.653, p = 6.07599E-24), octanoic acid (r = 0.557, t = 9.183, p = 7.9557E-17), decanoic acid (r = 0.539, t = 8.749, p = 1.24352E-15), and histidine (r = -0.513, t = 8.194, p = 3.90224E-14) exhibiting significant correlation. CONCLUSIONS To the best of our knowledge, this is the first report to determine the correlation between serum metabolites and CRC stage using CE-TOFMS. Our results show that benzoic acid exhibited excellent diagnostic power and could potentially serve as a novel disease biomarker for CRC diagnosis.
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Affiliation(s)
- Kazuhiko Uchiyama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Nobuaki Yagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan.,Department of Gastroenterology, Murakami Memorial Hospital, Asahi University, 3-23 Hashimotocho Gifu-city, Gifu, 500-8523, Japan
| | - Katsura Mizushima
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuki Higashimura
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuko Hirai
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tetsuya Okayama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Naohisa Yoshida
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiro Katada
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiro Kamada
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Osamu Handa
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Takeshi Ishikawa
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hideyuki Konishi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshiaki Kuriu
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Masayoshi Nakanishi
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Eigo Otsuji
- Department of Surgery, Division of Digestive Surgery, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshito Itoh
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuji Naito
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan. .,Department of Endoscopy and Ultrasound Medicine, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan.
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174
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Gao J, Louie KB, Steinke P, Bowen BP, Raad MD, Zuckermann RN, Siuzdak G, Northen TR. Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry. Anal Chem 2017; 89:6521-6526. [PMID: 28520405 DOI: 10.1021/acs.analchem.7b00599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Nanostructure-initiator mass spectrometry (NIMS) is a laser desorption/ionization analysis technique based on the vaporization of a nanostructure-trapped liquid "initiator" phase. Here we report an intriguing relationship between NIMS surface morphology and analyte selectivity. Scanning electron microscopy and spectroscopic ellipsometry were used to characterize the surface morphologies of a series of NIMS substrates generated by anodic electrochemical etching. Mass spectrometry imaging was applied to compare NIMS sensitivity of these various surfaces toward the analysis of diverse analytes. The porosity of NIMS surfaces was found to increase linearly with etching time where the pore size ranged from 4 to 12 nm with corresponding porosities estimated to be 7-70%. Surface morphology was found to significantly and selectively alter NIMS sensitivity. The small molecule (<2k Da) sensitivity was found to increase with increased porosity, whereas low porosity had the highest sensitivity for the largest molecules examined. Estimation of molecular sizes showed that this transition occurs when the pore size is <3× the maximum of molecular dimensions. While the origins of selectivity are unclear, increased signal from small molecules with increased surface area is consistent with a surface area restructuring-driven desorption/ionization process where signal intensity increases with porosity. In contrast, large molecules show highest signal for the low-porosity and small-pore-size surfaces. We attribute this to strong interactions between the initiator-coated pore structures and large molecules that hinder desorption/ionization by trapping large molecules. This finding may enable us to design NIMS surfaces with increased specificity to molecules of interest.
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Affiliation(s)
- Jian Gao
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Katherine B Louie
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Philipp Steinke
- Fraunhofer Institute for Photonic Microsystems IPMS - Center Nanoelectronic Technologies (CNT), Königsbrücker Strasse 178, 01099 Dresden, Germany
| | - Benjamin P Bowen
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Markus de Raad
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | | | - Gary Siuzdak
- Scripps Center for Metabolomics & Departments of Chemistry, Molecular and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Trent R Northen
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
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175
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Zhang Y, Dai X, Yang S, Zhang C, Han M, Huang HF, Fan J. Maternal low thyroxin levels are associated with adverse pregnancy outcomes in a Chinese population. PLoS One 2017; 12:e0178100. [PMID: 28542464 PMCID: PMC5441606 DOI: 10.1371/journal.pone.0178100] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/06/2017] [Indexed: 12/21/2022] Open
Abstract
Although thyroid dysfunction in early pregnancy may have adverse effects on pregnancy outcomes, few studies have examined the relationship between maternal low free thyroxin (FT4) levels in both first and third trimesters of pregnancy and the incidence of adverse pregnancy outcomes. We hypothesized that low FT4 levels in either first or third trimesters of pregnancy may have different effects on pregnancy outcomes. The study included 6,031 mothers who provided both first and third pregnancy serum samples for analyses of thyroid function. Adverse pregnancy outcomes, such as gestational diabetes mellitus (GDM), pregnancy-induced hypertension and preeclampsia, were diagnosed using the oral glucose tolerance test, blood pressure and urine protein test. Serum metabolites like adenosine and its analogues were identified using hydrophilic interaction liquid chromatography (HILIC)-tandem mass spectrometry (MS/MS). The incidence of hypothyroidism in pregnant women tended to increase with age and pre-pregnancy body mass index (BMI). The incidence of GDM was negatively correlated with maternal FT4 levels during early pregnancy while the incidence of preeclampsia was negatively correlated with maternal FT4 levels during late pregnancy. The incidence of pregnancy-induced hypertension was not significantly correlated with maternal FT4 levels. The women who had isolated maternal hypothyroxemia (IMH) in the third trimester of pregnancy had an increased risk of developing preeclampsia. Some metabolites like adenosine and its analogues in the serum were significantly changed in pregnant mothers with IMH. In conclusion, low FT4 levels during pregnancy are a risk factor for GDM and preeclampsia. Adenosine and its analogues may be important bridges between IMH and preeclampsia.
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Affiliation(s)
- Yong Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobei Dai
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuai Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mi Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxia Fan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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176
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Yoshitomi T, Oshima N, Goto Y, Nakamori S, Wakana D, Anjiki N, Sugimura K, Kawano N, Fuchino H, Iida O, Kagawa T, Jinno H, Kawahara N, Kobayashi Y, Maruyama T. Construction of Prediction Models for the Transient Receptor Potential Vanilloid Subtype 1 (TRPV1)-Stimulating Activity of Ginger and Processed Ginger Based on LC-HRMS Data and PLS Regression Analyses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3581-3588. [PMID: 28398734 DOI: 10.1021/acs.jafc.7b00577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To construct a model formula to evaluate the thermogenetic effect of ginger (Zingiber officinale Roscoe) from the ingredient information, we established transient receptor potential vanilloid subtype 1 (TRPV1)-stimulating activity prediction models by using a partial least-squares projections to latent structures (PLS) regression analysis in which the ingredient data from liquid chromatography-high-resolution mass spectrometry (LC-HRMS) and the stimulating activity values for TRPV1 receptor were used as explanatory and objective variables, respectively. By optimizing the peak extraction condition of the LC-HRMS data and the data preprocessing parameters of the PLS regression analysis, we succeeded in the construction of a TRPV1-stimulating activity prediction model with high precision ability. We then searched for the components responsible for the TRPV1-stimulating activity by analyzing the loading plot and s-plot of the model, and we identified [6]-gingerol (1) and hexahydrocurcumin (3) as TRPV1-stimulating activity components.
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Affiliation(s)
- Taichi Yoshitomi
- Division of Pharmacognosy, Phytochemistry and Narcotics, National Institute of Health Sciences , 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Naohiro Oshima
- Faculty of Pharmaceutical Sciences, Tokyo University of Science , 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuto Goto
- Division of Pharmacognosy, Phytochemistry and Narcotics, National Institute of Health Sciences , 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Shunsuke Nakamori
- School of Pharmacy Sciences, Kitasato University , 5-9-1 Shirogane, Minato-ku, Tokyo 108-8641, Japan
| | - Daigo Wakana
- Faculty of Pharmaceutical Sciences, Hoshi University , 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Naoko Anjiki
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Koji Sugimura
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Noriaki Kawano
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Hiroyuki Fuchino
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Osamu Iida
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Toshiko Kagawa
- Department of Clinical Pharmacy, Yokohama University of Pharmacy , 601 Matano-cho, Totsuka-ku, Yokohama, Kanagawa 245-0066, Japan
| | - Hideto Jinno
- Faculty of Pharmacy, Meijo University , 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Nobuo Kawahara
- National Institutes of Biomedical Innovation, Health and Nutrition , 1-2 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Yoshinori Kobayashi
- School of Pharmacy Sciences, Kitasato University , 5-9-1 Shirogane, Minato-ku, Tokyo 108-8641, Japan
| | - Takuro Maruyama
- Division of Pharmacognosy, Phytochemistry and Narcotics, National Institute of Health Sciences , 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
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177
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Cho YU, Lee D, Lee JE, Kim KH, Lee DY, Jung YC. Exploratory metabolomics of biomarker identification for the internet gaming disorder in young Korean males. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1057:24-31. [PMID: 28482325 DOI: 10.1016/j.jchromb.2017.04.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/19/2017] [Accepted: 04/28/2017] [Indexed: 01/22/2023]
Abstract
The main aim of the current research is to characterize the molecular dynamics related to internet gaming disorder (IGD) using non-targeted plasma metabolite profiling based on gas-chromatography time-of-flight mass spectrometry (GC-TOF MS). IGD is a psychiatric disorder instigated by excessive and prolonged internet gaming, which shared many pathological symptoms with attention deficit hyperactivity disorder (ADHD). The prevalence of the disorder has been rapidly increased particularly in East Asia countries (5.9% in South Korea) compared to Europe or North America (0.3-1.0% in United States and 1.16% in Germany). Thus we comparably explored the correlation between plasma metabolites and internet addiction severity in IGD patients, and potential biomarker composite in combination with clinical parameters. The systematic metabolite profiling of 54 blood samples (normal user, N=28 and IGD, N=24) identified a total of 104 metabolites out of 1212 metabolic feature, and revealed unique relation of co-linearly regressed set of plasma metabolites (arabitol, myo-inositol, methionine, pyrrole-2-carboxylic acid, and aspartic acid) with internet addiction severity scale (R=0.795). In addition, orthogonal partial least squared discriminant analysis (OPLS-DA) and receiver operating characteristic (ROC) analysis identified the potential biomarker cluster that simultaneously discriminated the different types of the psychiatric status. The potential biomarker re-composite was comprehensively evaluated by a receiver operating characteristic (ROC) analysis where the AUCs were 0.890, 0.880, 1.000, and 0.935 for control, IGD, AD and IGD+AD, respectively (N=18, 19, 5, and 10) against the others. This exploratory method may provide robustness of predictive diagnosis in population screening of IGD. The identified metabolic features, the relatedness with clinical parameters, and the putative biochemical linkage will hopefully aid future pathological studies in IGD.
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Affiliation(s)
- Yeo Ul Cho
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul 02707, Republic of Korea
| | - Deokjong Lee
- The Department of Psychiatry, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung-Eun Lee
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul 02707, Republic of Korea
| | - Kyoung Heon Kim
- The Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Do Yup Lee
- The Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul 02707, Republic of Korea.
| | - Young-Chul Jung
- The Department of Psychiatry, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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178
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Koistinen VM, Hanhineva K. Mass spectrometry-based analysis of whole-grain phytochemicals. Crit Rev Food Sci Nutr 2017; 57:1688-1709. [PMID: 26167744 DOI: 10.1080/10408398.2015.1016477] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Whole grains are a rich source of several classes of phytochemicals, such as alkylresorcinols, benzoxazinoids, flavonoids, lignans, and phytosterols. A high intake of whole grains has been linked to a reduced risk of some major noncommunicable diseases, and it has been postulated that a complex mixture of phytochemicals works in synergy to generate beneficial health effects. Mass spectrometry, especially when coupled with liquid chromatography, is a widely used method for the analysis of phytochemicals owing to its high sensitivity and dynamic range. In this review, the current knowledge of the mass spectral properties of the most important classes of phytochemicals found in cereals of common wheat, barley, oats, and rye is discussed.
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Affiliation(s)
- Ville Mikael Koistinen
- a Institute of Public Health and Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
| | - Kati Hanhineva
- a Institute of Public Health and Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
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179
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Lim DK, Mo C, Long NP, Kim G, Kwon SW. Simultaneous Profiling of Lysoglycerophospholipids in Rice (Oryza sativa L.) Using Direct Infusion-Tandem Mass Spectrometry with Multiple Reaction Monitoring. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2628-2634. [PMID: 28245645 DOI: 10.1021/acs.jafc.7b00148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
White rice is the final product after the hull and bran layers have been removed during the milling process. Although lysoglycerophospholipids (lysoGPLs) only occupy a small proportion in white rice, they are essential for evaluating rice authenticity and quality. In this study, we developed a high-throughput and targeted lipidomics approach that involved direct infusion-tandem mass spectrometry with multiple reaction monitoring to simultaneously profile lysoGPLs in white rice. The method is capable of characterizing 17 lysoGPLs within 1 min. In addition, unsupervised and supervised analyses exhibited a considerably large diversity of lysoGPL concentrations in white rice from different origins. In particular, a classification model was built using identified lysoGPLs that can differentiate white rice from Korea, China, and Japan. Among the discriminatory lysoGPLs, for the lysoPE(16:0) and lysoPE(18:2) compositions, there were relatively small within-group variations, and they were considerably different among the three countries. In conclusion, our proposed method provides a rapid, high-throughput, and comprehensive format for profiling lysoGPLs in rice samples.
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Affiliation(s)
- Dong Kyu Lim
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
| | - Changyeun Mo
- National Institute of Agricultural Sciences, Rural Development Administration , Jeonju 54875, Republic of Korea
| | - Nguyen Phuoc Long
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
| | - Giyoung Kim
- National Institute of Agricultural Sciences, Rural Development Administration , Jeonju 54875, Republic of Korea
| | - Sung Won Kwon
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University , Seoul 08826, Republic of Korea
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180
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Li Y, Jin Y, Yang S, Zhang W, Zhang J, Zhao W, Chen L, Wen Y, Zhang Y, Lu K, Zhang Y, Zhou J, Yang S. Strategy for comparative untargeted metabolomics reveals honey markers of different floral and geographic origins using ultrahigh-performance liquid chromatography-hybrid quadrupole-orbitrap mass spectrometry. J Chromatogr A 2017; 1499:78-89. [PMID: 28390668 DOI: 10.1016/j.chroma.2017.03.071] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Accepted: 03/25/2017] [Indexed: 01/13/2023]
Abstract
Honey discrimination based on floral and geographic origins is limited by the ability to determine reliable markers because developing hypothetical substances in advance considerably limits the throughput of metabolomics studies. Here, we present a novel approach to screen and elucidate honey markers based on comparative untargeted metabolomics using ultrahigh-performance liquid chromatography-hybrid quadrupole-orbitrap mass spectrometry (UHPLC-Q-Orbitrap). To reduce metabolite information losses during sample preparation, the honey samples were dissolved in water and centrifuged to remove insoluble particles prior to UHPLC-Q-Orbitrap analysis in positive and negative electrospray ionization modes. The data were pretreated using background subtraction, chromatographic peak extraction, normalization, transformation and scaling to remove interferences from unwanted biases and variance in the experimental data. The pretreated data were further processed using principal component analysis (PCA) and a three-stage approach (t-test, volcano plot and variable importance in projection (VIP) plot) to ensure marker authenticity. A correlation between the molecular and fragment ions with a mass accuracy of less than 1.0ppm was used to annotate and elucidate the marker structures, and the marker responses in real samples were used to confirm the effectiveness of the honey discrimination. Moreover, we evaluated the data quality using blank and quality control (QC) samples based on PCA clustering, retention times, normalized levels and peak areas. This strategy will help guide standardized, comparative untargeted metabolomics studies of honey and other agro-products from different floral and geographic origins.
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Affiliation(s)
- Yi Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China; Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yue Jin
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China
| | - Shupeng Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China; Key Laboratory of Bee Products for Quality and Safety Control, Ministry of Agriculture, Beijing 100093, PR China
| | - Wenwen Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Jinzhen Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China; Bee Product Quality Supervision and Testing Centre, Ministry of Agriculture, Beijing 100093, PR China
| | - Wen Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China; Bee Product Quality Supervision and Testing Centre, Ministry of Agriculture, Beijing 100093, PR China
| | - Lanzhen Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China
| | - Yaqin Wen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Yongxin Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Kaizhi Lu
- Thermo Fisher Scientific Co., Ltd., Shanghai 201206, PR China
| | - Yaping Zhang
- Thermo Fisher Scientific Co., Ltd., Shanghai 201206, PR China
| | - Jinhui Zhou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China; Laboratory of Risk Assessment for Quality and Safety of Bee Products, Ministry of Agriculture, Beijing 100093, PR China; Key Laboratory of Bee Products for Quality and Safety Control, Ministry of Agriculture, Beijing 100093, PR China; Bee Product Quality Supervision and Testing Centre, Ministry of Agriculture, Beijing 100093, PR China.
| | - Shuming Yang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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181
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Amin AM, Sheau Chin L, Azri Mohamed Noor D, SK Abdul Kader MA, Kah Hay Y, Ibrahim B. The Personalization of Clopidogrel Antiplatelet Therapy: The Role of Integrative Pharmacogenetics and Pharmacometabolomics. Cardiol Res Pract 2017; 2017:8062796. [PMID: 28421156 PMCID: PMC5379098 DOI: 10.1155/2017/8062796] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
Dual antiplatelet therapy of aspirin and clopidogrel is pivotal for patients undergoing percutaneous coronary intervention. However, the variable platelets reactivity response to clopidogrel may lead to outcome failure and recurrence of cardiovascular events. Although many genetic and nongenetic factors are known, great portion of clopidogrel variable platelets reactivity remain unexplained which challenges the personalization of clopidogrel therapy. Current methods for clopidogrel personalization include CYP2C19 genotyping, pharmacokinetics, and platelets function testing. However, these methods lack precise prediction of clopidogrel outcome, often leading to insufficient prediction. Pharmacometabolomics which is an approach to identify novel biomarkers of drug response or toxicity in biofluids has been investigated to predict drug response. The advantage of pharmacometabolomics is that it does not only predict the response but also provide extensive information on the metabolic pathways implicated with the response. Integrating pharmacogenetics with pharmacometabolomics can give insight on unknown genetic and nongenetic factors associated with the response. This review aimed to review the literature on factors associated with the variable platelets reactivity response to clopidogrel, as well as appraising current methods for the personalization of clopidogrel therapy. We also aimed to review the literature on using pharmacometabolomics approach to predict drug response, as well as discussing the plausibility of using it to predict clopidogrel outcome.
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Affiliation(s)
- Arwa M. Amin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Lim Sheau Chin
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | | | - Yuen Kah Hay
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Baharudin Ibrahim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
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182
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Lane AN, Fan TWM. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry. Arch Biochem Biophys 2017; 628:123-131. [PMID: 28263717 DOI: 10.1016/j.abb.2017.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 01/23/2023]
Abstract
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA.
| | - Teresa W-M Fan
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA
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183
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Elmsjö A, Haglöf J, Engskog MK, Nestor M, Arvidsson T, Pettersson C. The co-feature ratio, a novel method for the measurement of chromatographic and signal selectivity in LC-MS-based metabolomics. Anal Chim Acta 2017; 956:40-47. [DOI: 10.1016/j.aca.2016.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 01/17/2023]
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184
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Khamis MM, Adamko DJ, El-Aneed A. Mass spectrometric based approaches in urine metabolomics and biomarker discovery. MASS SPECTROMETRY REVIEWS 2017; 36:115-134. [PMID: 25881008 DOI: 10.1002/mas.21455] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 05/25/2023]
Abstract
Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.
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Affiliation(s)
- Mona M Khamis
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
- Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Darryl J Adamko
- Department of Pediatrics, College of Medicine, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
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185
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Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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186
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Uppal K, Walker DI, Jones DP. xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data. Anal Chem 2017; 89:1063-1067. [PMID: 27977166 DOI: 10.1021/acs.analchem.6b01214] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Improved analytical technologies and data extraction algorithms enable detection of >10 000 reproducible signals by liquid chromatography-high-resolution mass spectrometry, creating a bottleneck in chemical identification. In principle, measurement of more than one million chemicals would be possible if algorithms were available to facilitate utilization of the raw mass spectrometry data, especially low-abundance metabolites. Here we describe an automated computational framework to annotate ions for possible chemical identity using a multistage clustering algorithm in which metabolic pathway associations are used along with intensity profiles, retention time characteristics, mass defect, and isotope/adduct patterns. The algorithm uses high-resolution mass spectrometry data for a series of samples with common properties and publicly available chemical, metabolic, and environmental databases to assign confidence levels to annotation results. Evaluation results show that the algorithm achieves an F1-measure of 0.8 for a data set with known targets and is more robust than previously reported results for cases when database size is much greater than the actual number of metabolites. MS/MS evaluation of a set of randomly selected 210 metabolites annotated using xMSannotator in an untargeted metabolomics human data set shows that 80% of features with high or medium confidence scores have ion dissociation patterns consistent with the xMSannotator annotation. The algorithm has been incorporated into an R package, xMSannotator, which includes utilities for querying local or online databases such as ChemSpider, KEGG, HMDB, T3DB, and LipidMaps.
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Affiliation(s)
- Karan Uppal
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30308, United States
| | - Douglas I Walker
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30308, United States.,Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02153, United States
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30308, United States
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187
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Collection and Preparation of Clinical Samples for Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:19-44. [DOI: 10.1007/978-3-319-47656-8_2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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188
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Rangel-Huerta OD, Gil A. Nutrimetabolomics: An Update on Analytical Approaches to Investigate the Role of Plant-Based Foods and Their Bioactive Compounds in Non-Communicable Chronic Diseases. Int J Mol Sci 2016; 17:ijms17122072. [PMID: 27941699 PMCID: PMC5187872 DOI: 10.3390/ijms17122072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/28/2016] [Accepted: 12/03/2016] [Indexed: 12/17/2022] Open
Abstract
Metabolomics is the study of low-weight molecules present in biological samples such as biofluids, tissue/cellular extracts, and culture media. Metabolomics research is increasing, and at the moment, it has several applications in the food science and nutrition fields. In the present review, we provide an update about the most frequently used methodologies and metabolomic platforms in these areas. Also, we discuss different metabolomic strategies regarding the discovery of new bioactive compounds (BACs) in plant-based foods. Furthermore, we review the existing literature related to the use of metabolomics to investigate the potential protective role of BACs in the prevention and treatment of non-communicable chronic diseases, namely cardiovascular disease, diabetes, and cancer.
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Affiliation(s)
- Oscar Daniel Rangel-Huerta
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology "José Mataix", Center for Biomedical Research, University of Granada, 18100 Granada, Spain.
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology "José Mataix", Center for Biomedical Research, University of Granada, 18100 Granada, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Ciberobn, 28029 Madrid, Spain.
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189
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Kapoore RV, Vaidyanathan S. Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0363. [PMID: 27644979 PMCID: PMC5031630 DOI: 10.1098/rsta.2015.0363] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 05/03/2023]
Abstract
Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo Typically, the analysis is carried out in vitro, by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Rahul Vijay Kapoore
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Seetharaman Vaidyanathan
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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190
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Serum Metabolomic Response to Long-Term Supplementation with all-rac- α-Tocopheryl Acetate in a Randomized Controlled Trial. J Nutr Metab 2016; 2016:6158436. [PMID: 27840740 PMCID: PMC5093288 DOI: 10.1155/2016/6158436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/28/2016] [Indexed: 12/14/2022] Open
Abstract
Background. The Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study, a randomized controlled cancer prevention trial, showed a 32% reduction in prostate cancer incidence in response to vitamin E supplementation. Two other trials were not confirmatory, however. Objective. We compared the change in serum metabolome of the ATBC Study participants randomized to receive vitamin E to those who were not by randomly selecting 50 men from each of the intervention groups (50 mg/day all-rac-α-tocopheryl acetate (ATA), 20 mg/day β-carotene, both, placebo). Methods. Metabolomic profiling was conducted on baseline and follow-up fasting serum (Metabolon, Inc.). Results. After correction for multiple comparisons, five metabolites were statistically significantly altered (β is the change in metabolite level expressed as number of standard deviations on the log scale): α-CEHC sulfate (β = 1.51, p = 1.45 × 10−38), α-CEHC glucuronide (β = 1.41, p = 1.02 × 10−31), α-tocopherol (β = 0.97, p = 2.22 × 10−13), γ-tocopherol (β = −0.90, p = 1.76 × 10−11), and β-tocopherol (β = −0.73, p = 9.40 × 10−8). Glutarylcarnitine, beta-alanine, ornithine, and N6-acetyllysine were also decreased by ATA supplementation (β range 0.40 to −0.36), but not statistically significantly. Conclusions. Comparison of the observed metabolite alterations resulting from ATA supplementation to those in other vitamin E trials of different populations, dosages, or formulations may shed light on the apparently discordant vitamin E-prostate cancer risk findings.
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191
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Uppal K, Walker DI, Liu K, Li S, Go YM, Jones DP. Computational Metabolomics: A Framework for the Million Metabolome. Chem Res Toxicol 2016; 29:1956-1975. [PMID: 27629808 DOI: 10.1021/acs.chemrestox.6b00179] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"Sola dosis facit venenum." These words of Paracelsus, "the dose makes the poison", can lead to a cavalier attitude concerning potential toxicities of the vast array of low abundance environmental chemicals to which humans are exposed. Exposome research teaches that 80-85% of human disease is linked to environmental exposures. The human exposome is estimated to include >400,000 environmental chemicals, most of which are uncharacterized with regard to human health. In fact, mass spectrometry measures >200,000 m/z features (ions) in microliter volumes derived from human samples; most are unidentified. This crystallizes a grand challenge for chemical research in toxicology: to develop reliable and affordable analytical methods to understand health impacts of the extensive human chemical experience. To this end, there appears to be no choice but to abandon the limitations of measuring one chemical at a time. The present review looks at progress in computational metabolomics to provide probability-based annotation linking ions to known chemicals and serve as a foundation for unambiguous designation of unidentified ions for toxicologic study. We review methods to characterize ions in terms of accurate mass m/z, chromatographic retention time, correlation of adduct, isotopic and fragment forms, association with metabolic pathways and measurement of collision-induced dissociation products, collision cross section, and chirality. Such information can support a largely unambiguous system for documenting unidentified ions in environmental surveillance and human biomonitoring. Assembly of this data would provide a resource to characterize and understand health risks of the array of low-abundance chemicals to which humans are exposed.
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Affiliation(s)
- Karan Uppal
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States
| | - Douglas I Walker
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States.,Hercules Exposome Research Center, Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia 30322, United States.,Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02155, United States
| | - Ken Liu
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States
| | - Shuzhao Li
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States.,Hercules Exposome Research Center, Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia 30322, United States
| | - Young-Mi Go
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University , Atlanta, Georgia 30322, United States.,Hercules Exposome Research Center, Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia 30322, United States
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192
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Birjandi AP, Bojko B, Ning Z, Figeys D, Pawliszyn J. High throughput solid phase microextraction: A new alternative for analysis of cellular lipidome? J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1043:12-19. [PMID: 27720680 DOI: 10.1016/j.jchromb.2016.09.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/19/2016] [Accepted: 09/24/2016] [Indexed: 11/30/2022]
Abstract
A new SPME method for untargeted lipidomic study of cell line cultures was proposed for the first time. In this study the feasibility to monitor changes in lipid profile after external stimuli was demonstrated and compared to the conventional Bligh & Dyer method. The human hepatocellular carcinoma (HCC) cell line was used as a model. The obtained results provided a list of up-regulated and down-regulated lipids through a comparison between control (non-stimulated) cells versus the group of cells treated with polyunsaturated fatty acid (20:5). Use of the SPME technique yielded a list of 77 lipid species whose concentrations were recognized to be significantly different between control and treated cells, from which 63 lipids were up-regulated in treated cells. In general, the list was comparable to the peer list obtained by the Bligh & Dyer method. However, more diversity of lipid classes and subclasses such as LPC, sphingomyelins, ceramides, and prenol lipids were observed with the application of the SPME method. Method precision for the SPME approach was within the acceptable analytical range (5-18% RSD) for all detected lipids, which was advantageous over solvent extraction applied. The evaluation of ionization efficiency indicated no matrix effect for the SPME technique, while Bligh & Dyer presented significant ionization suppression for low abundant species such as LysoPC, PG, ceramides, and sphingomyelins, and ionization enhancement for high abundant phospholipids such as PE.
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Affiliation(s)
- Afsoon Pajand Birjandi
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Barbara Bojko
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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193
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Zhou Z. Non-target impurity profiling of marketplace Cetirizine using high-resolution mass spectrometry and multivariate data analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1941-1950. [PMID: 27384394 DOI: 10.1002/rcm.7675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE As always, drug impurity is the first concern of medication safety. The quality of pre- and post-marketed drugs is estimated through systematic analysis of potential hazardous substances by impurity profiling. Impurity profile is the general name of all unwanted materials which may affect the purity of an active pharmaceutical ingredient (API). The safety of original drugs is guaranteed by an enormous amount of animal experiments and clinical research while the safety of generic drugs should also be ensured by comparative analysis for consistency evaluation. The significantly differential impurities between them should be focused on and the toxicity should be further estimated if necessary. Herein, we take a marketplace drug named Cetirizine as an example to investigate if there was a method which could effectively discover the potential markers among Cetirizine tablets with different brands and describe specific impurity profiling which makes the unknown brand of Cetirizine tablets predictable. METHODS Liquid chromatography coupled with high-resolution mass spectrometry (LC/HRMS) was applied to capture the characteristic features of the impurity profile for three brands of marketplace Cetirizine tablets using full scan data-dependent MS/MS scan mode (FS-ddMS(2) ). RESULTS Unsupervised learning: principal component analysis (PCA) and supervised learning: consensus orthogonal partial least squares discriminant analysis (OPLS-DA) were utilized to reveal the essential character of Cetirizine impurity profile; 16 differential impurities were finally found, their structures were speculated by HRMS(2) data. CONCLUSIONS The cause of formation was further elucidated which gave a suggestion for production process optimization. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Zhe Zhou
- Thermo Fisher Scientific (China) Co., Ltd, No 6 Building, 27 Xinjinqiao Road, Shanghai, 201206, China
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194
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Beger RD, Dunn W, Schmidt MA, Gross SS, Kirwan JA, Cascante M, Brennan L, Wishart DS, Oresic M, Hankemeier T, Broadhurst DI, Lane AN, Suhre K, Kastenmüller G, Sumner SJ, Thiele I, Fiehn O, Kaddurah-Daouk R. Metabolomics enables precision medicine: "A White Paper, Community Perspective". Metabolomics 2016; 12:149. [PMID: 27642271 PMCID: PMC5009152 DOI: 10.1007/s11306-016-1094-6] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/08/2016] [Indexed: 01/12/2023]
Abstract
INTRODUCTION BACKGROUND TO METABOLOMICS Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates. OBJECTIVES OF WHITE PAPER—EXPECTED TREATMENT OUTCOMES AND METABOLOMICS ENABLING TOOL FOR PRECISION MEDICINE We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject's response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient's metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine. CONCLUSIONS KEY SCIENTIFIC CONCEPTS AND RECOMMENDATIONS FOR PRECISION MEDICINE Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
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Affiliation(s)
- Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079 USA
| | - Warwick Dunn
- School of Biosciences, Phenome Centre Birmingham and Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Michael A. Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO 80521 USA
| | - Steven S. Gross
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10021 USA
| | - Jennifer A. Kirwan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
| | | | - David S. Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Thomas Hankemeier
- Division of Analytical Biosciences and Cluster Systems Pharmacology, Leiden Academic Centre for Drug Research, Leiden University & Netherlands Metabolomics Centre, Leiden, The Netherlands
| | | | - Andrew N. Lane
- Center for Environmental Systems Biochemistry, Department Toxicology and Cancer Biology, Markey Cancer Center, Lexington, KY USA
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Susan J. Sumner
- Discovery Sciences, RTI International, Research Triangle Park, Durham, NC USA
| | - Ines Thiele
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis, Davis, CA USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rima Kaddurah-Daouk
- Psychiatry and Behavioral Sciences, Duke Internal Medicine and Duke Institute for Brain Sciences and Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Box 3903, Durham, NC 27710 USA
| | - for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079 USA
- School of Biosciences, Phenome Centre Birmingham and Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO 80521 USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10021 USA
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain
- UCD Institute of Food and Health, UCD, Belfield, Dublin Ireland
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB Canada
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
- Division of Analytical Biosciences and Cluster Systems Pharmacology, Leiden Academic Centre for Drug Research, Leiden University & Netherlands Metabolomics Centre, Leiden, The Netherlands
- School of Science, Edith Cowan University, Perth, Australia
- Center for Environmental Systems Biochemistry, Department Toxicology and Cancer Biology, Markey Cancer Center, Lexington, KY USA
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Oberschleißheim, Germany
- Discovery Sciences, RTI International, Research Triangle Park, Durham, NC USA
- University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Campus Belval, Esch-Sur-Alzette, Luxembourg
- West Coast Metabolomics Center, UC Davis, Davis, CA USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
- Psychiatry and Behavioral Sciences, Duke Internal Medicine and Duke Institute for Brain Sciences and Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Box 3903, Durham, NC 27710 USA
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Sarais G, D'Urso G, Lai C, Pirisi FM, Pizza C, Montoro P. Targeted and untargeted mass spectrometric approaches in discrimination between Myrtus communis cultivars from Sardinia region. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:704-715. [PMID: 27416492 DOI: 10.1002/jms.3811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/10/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
In the present study, the discrimination of phytochemical content of Myrtus communis berries from different geographical origin and cultivars was explored by Liquid Chromatography-Electrospray Ionization-Fourier Transform-Mass Spectrometry (LC-ESI-FT-MS) metabolic profiling and quantitative analysis. Experiments were carried on myrtle plants grown in an experimental area of Sardinia region, obtained by the germination of seeds taken from berries collected in each part of the region. A preliminary untargeted approach on fruit's extracts was realized by collecting LC-ESI-FT-(Orbitrap)-MS data obtained by operating in negative ion mode and performing principal component analysis with the result of differentiation of samples. In a second step, targeted analysis with a reduced number of variables was realized. A data matrix was obtained by the data fusion of positive and negative ionization LC-ESI-MS results, by using as variables the peak areas of each known compounds. By the observation of principal component analysis, results found that anthocyanins, and mainly derivatives of cyanidin, are the principal marker compounds responsive for the discrimination of samples based on the geographical origin of the seeds. Based on this finding, finally, an LC-diode array detector method was developed, validated and applied for the quantitative analysis of berries' extracts based on 11 commercial standard compounds corresponding to the identified markers. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- G Sarais
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale, 72, 09124, Cagliari, Italy.
| | - G D'Urso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 84084, Fisciano, SA, Italy
| | - C Lai
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale, 72, 09124, Cagliari, Italy
| | - F M Pirisi
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale, 72, 09124, Cagliari, Italy
| | - C Pizza
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 84084, Fisciano, SA, Italy
| | - P Montoro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 84084, Fisciano, SA, Italy.
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196
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GC-TOF/MS-based metabolomics approach to study the cellular immunotoxicity of deoxynivalenol on murine macrophage ANA-1 cells. Chem Biol Interact 2016; 256:94-101. [DOI: 10.1016/j.cbi.2016.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/22/2022]
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197
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Tang C, Tan J, Fan R, Zhao B, Tang C, Ou W, Jin J, Peng X. Quasi-targeted analysis of hydroxylation-related metabolites of polycyclic aromatic hydrocarbons in human urine by liquid chromatography–mass spectrometry. J Chromatogr A 2016; 1461:59-69. [DOI: 10.1016/j.chroma.2016.07.051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 01/09/2023]
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van Duynhoven JPM, Jacobs DM. Assessment of dietary exposure and effect in humans: The role of NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:58-72. [PMID: 27573181 DOI: 10.1016/j.pnmrs.2016.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/19/2016] [Accepted: 03/19/2016] [Indexed: 06/06/2023]
Abstract
In human nutritional science progress has always depended strongly on analytical measurements for establishing relationships between diet and health. This field has undergone significant changes as a result of the development of NMR and mass spectrometry methods for large scale detection, identification and quantification of metabolites in body fluids. This has allowed systematic studies of the metabolic fingerprints that biological processes leave behind, and has become the research field of metabolomics. As a metabolic profiling technique, NMR is at its best when its unbiased nature, linearity and reproducibility are exploited in well-controlled nutritional intervention and cross-sectional population screening studies. Although its sensitivity is less good than that of mass spectrometry, NMR has maintained a strong position in metabolomics through implementation of standardisation protocols, hyphenation with mass spectrometry and chromatographic techniques, accurate quantification and spectral deconvolution approaches, and high-throughput automation. Thus, NMR-based metabolomics has contributed uniquely to new insights into dietary exposure, in particular by unravelling the metabolic fates of phytochemicals and the discovery of dietary intake markers. NMR profiling has also contributed to the understanding of the subtle effects of diet on central metabolism and lipoprotein metabolism. In order to hold its ground in nutritional metabolomics, NMR will need to step up its performance in sensitivity and resolution; the most promising routes forward are the analytical use of dynamic nuclear polarisation and developments in microcoil construction and automated fractionation.
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Affiliation(s)
- John P M van Duynhoven
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3130AC Vlaardingen, The Netherlands; Laboratory of Biophysics and Wageningen NMR Centre, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, The Netherlands.
| | - Doris M Jacobs
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3130AC Vlaardingen, The Netherlands
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199
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Deng L, Gu H, Zhu J, Nagana Gowda GA, Djukovic D, Chiorean EG, Raftery D. Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls. Anal Chem 2016; 88:7975-83. [PMID: 27437783 DOI: 10.1021/acs.analchem.6b00885] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical technologies.
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Affiliation(s)
- Lingli Deng
- Department of Information Engineering, East China University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China.,Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - 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 University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - E Gabriela Chiorean
- Department of Medicine, University of Washington , 825 Eastlake Avenue East, Seattle, Washington 98109, United States.,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 , 850 Republican Street, Seattle, Washington 98109, United States.,Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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200
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Noninvasive metabolic profiling for painless diagnosis of human diseases and disorders. Future Sci OA 2016; 2:FSO106. [PMID: 28031956 PMCID: PMC5137983 DOI: 10.4155/fsoa-2015-0014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/29/2016] [Indexed: 12/16/2022] Open
Abstract
Metabolic profiling provides a powerful diagnostic tool complementary to genomics and proteomics. The pain, discomfort and probable iatrogenic injury associated with invasive or minimally invasive diagnostic methods, render them unsuitable in terms of patient compliance and participation. Metabolic profiling of biomatrices like urine, breath, saliva, sweat and feces, which can be collected in a painless manner, could be used for noninvasive diagnosis. This review article covers the noninvasive metabolic profiling studies that have exhibited diagnostic potential for diseases and disorders. Their potential applications are evident in different forms of cancer, metabolic disorders, infectious diseases, neurodegenerative disorders, rheumatic diseases and pulmonary diseases. Large scale clinical validation of such diagnostic methods is necessary in future.
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