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Wong PL, Zolkeflee NKZ, Ramli NS, Tan CP, Azlan A, Tham CL, Shaari K, Abas F. Antidiabetic effect of Ardisia elliptica extract and its mechanisms of action in STZ-NA-induced diabetic rat model via 1H-NMR-based metabolomics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:117015. [PMID: 37572932 DOI: 10.1016/j.jep.2023.117015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ardisia elliptica Thunb. (AE) (Primulaceae) is a medicinal plant found in the Malay Peninsula and has been traditionally used to treat diabetes. However, limited studies to date in providing scientific evidence to support the antidiabetic efficacy of this plant by in-vitro and in-vivo models. AIM OF THE STUDY To investigate the anti-hyperglycemic potential of AE through in-vitro enzymatic activities and streptozotocin-nicotinamide (STZ-NA) induced diabetic rat models using proton-nuclear magnetic resonance (1H-NMR)-based metabolomics approach. MATERIALS AND METHODS Anti-α-amylase and anti-α-glucosidase activities of the hydroethanolic extracts of AE were evaluated. The absolute quantification of bioactive constituents, using ultra-high performance liquid chromatography (UHPLC) was performed for the most active extract. Three different dosage levels of the AE extract were orally administered for 4 weeks consecutively in STZ-NA induced diabetic rats. Physical assessments, biochemical analysis, and an untargeted 1H-NMR-based metabolomics analysis of the urine and serum were carried out on the animal model. RESULTS Type 2 diabetes mellitus (T2DM) rat model was successfully developed based on the clear separation observed between the STZ-NA induced diabetic and normal non-diabetic groups. Discriminating biomarkers included glucose, citrate, succinate, allantoin, hippurate, 2-oxoglutarate, and 3-hydroxybutyrate, as determined through an orthogonal partial least squares-discriminant analysis (OPLS-DA) model. A treatment dosage of 250 mg/kg body weight (BW) of standardized 70% ethanolic AE extract mitigated increase in serum glucose, creatinine, and urea levels, providing treatment levels comparable to that obtained using metformin, with flavonoids primarily contribute to the anti-hyperglycemic activities. Urinary metabolomics disclosed that the following disturbed metabolism pathways: the citrate cycle (TCA cycle), butanoate metabolism, glycolysis and gluconeogenesis, pyruvate metabolism, and synthesis and degradation of ketone bodies, were ameliorated after treatment with the standardized AE extract. CONCLUSIONS This study demonstrated the first attempt at revealing the therapeutic effect of oral treatment with 250 mg/kg BW of standardized AE extract on chemically induced T2DM rats. The present study provides scientific evidence supporting the ethnomedicinal use of Ardisia elliptica and further advances the understanding of the fundamental molecular mechanisms affected by this herbal antidote.
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Affiliation(s)
- Pei Lou Wong
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Nur Khaleeda Zulaikha Zolkeflee
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Nurul Shazini Ramli
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Azrina Azlan
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Khozirah Shaari
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Faridah Abas
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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2
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Loo RL, Chan Q, Nicholson JK, Holmes E. Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine- N-oxide. J Proteome Res 2022; 21:560-589. [PMID: 35142516 DOI: 10.1021/acs.jproteome.1c00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
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Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
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3
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Schugar RC, Gliniak CM, Osborn LJ, Massey W, Sangwan N, Horak A, Banerjee R, Orabi D, Helsley RN, Brown AL, Burrows A, Finney C, Fung KK, Allen FM, Ferguson D, Gromovsky AD, Neumann C, Cook K, McMillan A, Buffa JA, Anderson JT, Mehrabian M, Goudarzi M, Willard B, Mak TD, Armstrong AR, Swanson G, Keshavarzian A, Garcia-Garcia JC, Wang Z, Lusis AJ, Hazen SL, Brown JM. Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms. eLife 2022; 11:63998. [PMID: 35072627 PMCID: PMC8813054 DOI: 10.7554/elife.63998] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here, we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (Lepob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake but is instead associated with alterations in the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that gut microbial CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have potential as anti-obesity therapeutics.
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Affiliation(s)
- Rebecca C Schugar
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - William Massey
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony Horak
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Danny Orabi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Robert N Helsley
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amanda L Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy Burrows
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chelsea Finney
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kevin K Fung
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Frederick M Allen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Daniel Ferguson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Anthony D Gromovsky
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Chase Neumann
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Kendall Cook
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Amy McMillan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Jennifer A Buffa
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - James T Anderson
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | | | - Maryam Goudarzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Belinda Willard
- Research Core Services, Cleveland Clinic Lerner College of Medicine
| | - Tytus D Mak
- Mass Spectromety Data Center, National Institute of Standards and Technology (NIST)
| | | | - Garth Swanson
- Department of Internal Medicine, Rush University Medical Center
| | | | | | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles
| | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner College of Medicine
| | - Jonathan Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine
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Mal TK, Tian Y, Patterson AD. Sample Preparation and Data Analysis for NMR-Based Metabolomics. Methods Mol Biol 2021; 2194:301-313. [PMID: 32926373 DOI: 10.1007/978-1-0716-0849-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
NMR spectroscopy has become one of the preferred analytical techniques for metabolomics studies due to its inherent nondestructive nature, ability to identify and quantify metabolites simultaneously in a complex mixture, minimal sample preparation requirement, and high degree of experimental reproducibility. NMR-based metabolomics studies involve the measurement and multivariate statistical analysis of metabolites present in biological samples such as biofluids, stool/feces, intestinal content, tissue, and cell extracts by high-resolution NMR spectroscopy-the goal then is to identify and quantify metabolites and evaluate changes of metabolite concentrations in response to some perturbation. Here we describe methodologies for NMR sample preparation of biofluids (serum, saliva, and urine) and stool/feces, intestinal content, and tissues for NMR experiments including extraction of polar metabolites and application of NMR in metabolomics studies. One dimensional (1D) 1H NMR experiments with different variations such as pre-saturation, relaxation-edited, and diffusion-edited are routinely acquired for profiling and metabolite identification and quantification. 2D homonuclear 1H-1H TOCSY and COSY, 2D J-resolved, and heteronuclear 1H-13C HSQC and HMBC are also performed to assist with metabolite identification and quantification. The NMR data are then subjected to targeted and/or untargeted multivariate statistical analysis for biomarker discovery, clinical diagnosis, toxicological studies, molecular phenotyping, and functional genomics.
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Affiliation(s)
- Tapas K Mal
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
| | - Yuan Tian
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
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5
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Fujita A, Okuno T, Oda M, Kato K. Urinary volatilome analysis in a mouse model of anxiety and depression. PLoS One 2020; 15:e0229269. [PMID: 32084196 PMCID: PMC7034835 DOI: 10.1371/journal.pone.0229269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 02/03/2020] [Indexed: 11/27/2022] Open
Abstract
Psychiatric disorders including depression and anxiety comprise a broad range of conditions with different symptoms. We have developed a mouse model of depression/anxiety in mice deficient in the St3gal4 gene. In this study, we performed a comparative analysis of urinary volatile organic compounds (VOCs) in St3gal4-deficient (St3gal4-KO) and wild-type mice using gas chromatography-mass spectrometry, and we screened 18 putative VOCs. Principal component analysis (PCA) based on these VOCs identified a major group of 11 VOCs, from which two groups were clarified by hierarchical clustering analysis. One group including six VOCs (pentanoic acid, 4-methyl-, ethyl ester; 3-heptanone, 6-methyl; benzaldehyde; 5,9-undecadien-2-ol, 6,10-dimethyl; and unknown compounds RI1291 and RI1237) was correlated with the startle response (r = 0.620), which is related to an unconscious defensive response. The other group including two VOCs (beta-farnesene and alpha-farnesene) comprised pheromones which increased in KO mice. Next, male mice underwent a social behavior test with female mice in the estrus stage, showing reduced access of KO male mice to female mice. Comparative analysis of urinary VOCs before and after encounters revealed that the six VOCs were not changed by these encounters. However, in WT mice, the two farnesenes increased after the encounters, reaching the level observed in KO mice, which was not altered following the encounter. Taken together, these results indicated that St3gal4 was involved in modulating urinary VOCs. Moreover, VOC clusters discovered by comparison of St3gal4-KO mice with WT mice were correlated with differential emotional behaviors.
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Affiliation(s)
- Akiko Fujita
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Takaya Okuno
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Mika Oda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Keiko Kato
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- * E-mail:
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6
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Pramai P, Abdul Hamid NA, Mediani A, Maulidiani M, Abas F, Jiamyangyuen S. Metabolite profiling, antioxidant, and α-glucosidase inhibitory activities of germinated rice: nuclear-magnetic-resonance-based metabolomics study. J Food Drug Anal 2018; 26:47-57. [PMID: 29389588 PMCID: PMC9332653 DOI: 10.1016/j.jfda.2016.11.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/09/2016] [Accepted: 11/21/2016] [Indexed: 01/03/2023] Open
Abstract
In an attempt to profile the metabolites of three different varieties of germinated rice, specifically black (GBR), red, and white rice, a 1H-nuclear-magnetic-resonance-based metabolomics approach was conducted. Multivariate data analysis was applied to discriminate between the three different varieties using a partial least squares discriminant analysis (PLS-DA) model. The PLS model was used to evaluate the relationship between chemicals and biological activities of germinated rice. The PLS-DA score plot exhibited a noticeable separation between the three rice varieties into three clusters by PC1 and PC2. The PLS model indicated that α-linolenic acid, γ-oryzanol, α-tocopherol, γ-aminobutyric acid, 3-hydroxybutyric acid, fumaric acid, fatty acids, threonine, tryptophan, and vanillic acid were significantly correlated with the higher bioactivities demonstrated by GBR that was extracted in 100% ethanol. Subsequently, the proposed biosynthetic pathway analysis revealed that the increased quantities of secondary metabolites found in GBR may contribute to its nutritional value and health benefits.
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7
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Mioduchowska M, Kaczmarczyk A, Zając K, Zając T, Sell J. Gender-Associated Mitochondrial DNA Heteroplasmy in Somatic Tissues of the Endangered Freshwater Mussel Unio crassus (Bivalvia: Unionidae): Implications for Sex Identification and Phylogeographical Studies. ACTA ACUST UNITED AC 2017; 325:610-625. [PMID: 28102008 DOI: 10.1002/jez.2055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/11/2016] [Accepted: 10/24/2016] [Indexed: 11/11/2022]
Abstract
Some bivalve species possess two independent mitochondrial DNA lineages: maternally (F-type) and paternally (M-type) inherited. This phenomenon is called doubly uniparental inheritance. It is generally agreed that F-type mtDNA is typically present in female somatic and gonadal tissues as well as in male somatic tissues, whereas the M-type mtDNA occurs only in male germ line and gonadal tissue. In the present study, the mtDNA heteroplasmy (for both F and M genomes) in male somatic tissues of Unio crassus (Philipsson, 1788), species threatened with extinction, has been confirmed. Taking advantage from the presence of Mcox1 marker only in male somatic tissues, we developed a new method of sex identification in this endangered species, using nondestructive tissue sampling. Probability of correct sex identification was estimated at 97.5%. The present study is the first report on gender-associated mitochondrial DNA heteroplasmy in male somatic tissues of thick-shelled river mussel and first approach to U. crassus sex identification at molecular level. Our study also confirmed the utility of paternally inherited Mcox1 gene fragment as a complementary molecular tool for resolving phylogeographical relationships among populations of thick-shelled river mussel.
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Affiliation(s)
| | | | - Katarzyna Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland
| | - Jerzy Sell
- Department of Genetics, University of Gdansk, 80-308 Gdansk, Poland
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Zhang C, Wang Z, Zhang D, Zhou J, Lu C, Su X, Ding D. Proteomics and 1H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23704-23713. [PMID: 28864971 DOI: 10.1007/s11356-017-0007-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Vibrio bacteria live in both marine and freshwater habitats and are associated with aquatic animals. Vibrio vulnificus is a pathogenic bacterium that infects people and livestock. It is usually found in offshore waters or within fish and shellfish. This study presents a comparative proteomic analysis of the outer membrane protein (OMP) changes in V. vulnificus proteins after stimulation with sewage from sewage drains. Using two-dimensional electrophoresis followed by MALDI-TOF MS/MS, 32 protein spots with significant differences in abundance were identified and characterized. These identified proteins were found to be involved in various functional categories, including catalysis, transport, membrane proteins progresses, receptor activity, energy metabolism, cytokine activity, and protein metabolism. The mRNA expression levels of 12 differential proteins were further assessed by qRT-PCR. Seven genes including carboxypeptidase, hemoglobin receptor, succinate dehydrogenase iron-sulfur subunit, ATP synthase subunit alpha, thioredoxin, succinyl-CoA synthetase subunit, and alanine dehydrogenase were downregulated upon stimulation, whereas the protein expression levels HupA receptor, type I secretion outer membrane protein, glutamine synthetase, superoxide dismutase, OmpU, and VuuA were upregulated. 1H NMR spectra showed 18 dysregulated metabolites from V. vulnificus after the sewage stimulation and the pathogenicity was enhanced after that.
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Affiliation(s)
- Chundan Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Zhonghua Wang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Dijun Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- School of Marine Science, Ningbo University, Ningbo, China.
| | - Dewen Ding
- School of Marine Science, Ningbo University, Ningbo, China.
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Abstract
AbstractMetabolic diversity leads to differences in nutrient requirements and responses to diet and medication between individuals. Using the concept of metabotyping – that is, grouping metabolically similar individuals – tailored and more efficient recommendations may be achieved. The aim of this study was to review the current literature on metabotyping and to explore its potential for better targeted dietary intervention in subjects with and without metabolic diseases. A comprehensive literature search was performed in PubMed, Google and Google Scholar to find relevant articles on metabotyping in humans including healthy individuals, population-based samples and patients with chronic metabolic diseases. A total of thirty-four research articles on human studies were identified, which established more homogeneous subgroups of individuals using statistical methods for analysing metabolic data. Differences between studies were found with respect to the samples/populations studied, the clustering variables used, the statistical methods applied and the metabotypes defined. According to the number and type of the selected clustering variables, the definitions of metabotypes differed substantially; they ranged between general fasting metabotypes, more specific fasting parameter subgroups like plasma lipoprotein or fatty acid clusters and response groups to defined meal challenges or dietary interventions. This demonstrates that the term ‘metabotype’ has a subjective usage, calling for a formalised definition. In conclusion, this literature review shows that metabotyping can help identify subgroups of individuals responding differently to defined nutritional interventions. Targeted recommendations may be given at such metabotype group levels. Future studies should develop and validate definitions of generally valid metabotypes by exploiting the increasingly available metabolomics data sets.
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Suárez-García S, del Bas JM, Caimari A, Escorihuela RM, Arola L, Suárez M. Impact of a cafeteria diet and daily physical training on the rat serum metabolome. PLoS One 2017; 12:e0171970. [PMID: 28192465 PMCID: PMC5305073 DOI: 10.1371/journal.pone.0171970] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022] Open
Abstract
Regular physical activity and healthy dietary patterns are commonly recommended for the prevention and treatment of metabolic syndrome (MetS), which is diagnosed at an alarmingly increasing rate, especially among adolescents. Nevertheless, little is known regarding the relevance of physical exercise on the modulation of the metabolome in healthy people and those with MetS. We have previously shown that treadmill exercise ameliorated different symptoms of MetS. The aim of this study was to investigate the impact of a MetS-inducing diet and different intensities of aerobic training on the overall serum metabolome of adolescent rats. For 8 weeks, young rats were fed either standard chow (ST) or cafeteria diet (CAF) and were subjected to a daily program of training on a treadmill at different speeds. Non-targeted metabolomics was used to identify changes in circulating metabolites, and a combination of multivariate analysis techniques was implemented to achieve a holistic understanding of the metabolome. Among all the identified circulating metabolites influenced by CAF, lysophosphatidylcholines were the most represented family. Serum sphingolipids, bile acids, acylcarnitines, unsaturated fatty acids and vitamin E and A derivatives also changed significantly in CAF-fed rats. These findings suggest that an enduring systemic inflammatory state is induced by CAF. The impact of physical training on the metabolome was less striking than the impact of diet and mainly altered circulating bile acids and glycerophospholipids. Furthermore, the serum levels of monocyte chemoattractant protein-1 were increased in CAF-fed rats, and C-reactive protein was decreased in trained groups. The leptin/adiponectin ratio, a useful marker of MetS, was increased in CAF groups, but decreased in proportion to training intensity. Multivariate analysis revealed that ST-fed animals were more susceptible to exercise-induced changes in metabolites than animals with MetS, in which moderate-intensity seems more effective than high-intensity training. Our results indicate that CAF has a strong negative impact on the metabolome of animals that is difficult to reverse by daily exercise.
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Affiliation(s)
- Susana Suárez-García
- Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, Universitat Rovira i Virgili, Tarragona, Spain
| | - Josep M. del Bas
- Technological Unit of Nutrition and Health, EURECAT-Technological Center of Catalonia, Reus, Spain
| | - Antoni Caimari
- Technological Unit of Nutrition and Health, EURECAT-Technological Center of Catalonia, Reus, Spain
| | - Rosa M. Escorihuela
- Institut de Neurociències, Departament de Psiquiatria i Medicina Legal, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lluís Arola
- Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, Universitat Rovira i Virgili, Tarragona, Spain
- Technological Unit of Nutrition and Health, EURECAT-Technological Center of Catalonia, Reus, Spain
- * E-mail:
| | - Manuel Suárez
- Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, Universitat Rovira i Virgili, Tarragona, Spain
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Amberg A, Riefke B, Schlotterbeck G, Ross A, Senn H, Dieterle F, Keck M. NMR and MS Methods for Metabolomics. Methods Mol Biol 2017; 1641:229-258. [PMID: 28748468 DOI: 10.1007/978-1-4939-7172-5_13] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabolomics, i.e., NMR, UPLC-MS, and GC-MS, have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabolomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation to determining the measurement details of all analytical platforms, and finally to discussing the corresponding specific steps of data analysis.
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Affiliation(s)
| | - Björn Riefke
- Investigational Toxicology, Metabolic Profiling and Clinical Pathology, Bayer Pharma AG, Muellerstr. 178, Berlin, 13353, Germany.
| | - Götz Schlotterbeck
- School of Life Sciences, Institute for Chemistry and Bioanalytics, University of Applied Sciences, Northwestern Switzerland, Muttenz, Switzerland
| | - Alfred Ross
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Hans Senn
- Heythrop College UCL, Kensington Square, London W85HN, UK
| | - Frank Dieterle
- New Products and Medical, Near Patient Testing, Novartis, Basel, Switzerland
| | - Matthias Keck
- Analytical Development 1, Bayer Pharma AG, Wupperal, 42096, Germany
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12
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Ci Y, Qiao J, Han M. Molecular Mechanisms and Metabolomics of Natural Polyphenols Interfering with Breast Cancer Metastasis. Molecules 2016; 21:E1634. [PMID: 27999314 PMCID: PMC6273039 DOI: 10.3390/molecules21121634] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/10/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023] Open
Abstract
Metastatic cancers are the main cause of cancer-related death. In breast primary cancer, the five-year survival rate is close to 100%; however, for metastatic breast cancer, that rate drops to a mere 25%, due in part to the paucity of effective therapeutic options for treating metastases. Several in vitro and in vivo studies have indicated that consumption of natural polyphenols significantly reduces the risk of cancer metastasis. Therefore, this review summarizes the research findings involving the molecular mechanisms and metabolomics of natural polyphenols and how they may be blocking breast cancer metastasis. Most natural polyphenols are thought to impair breast cancer metastasis through downregulation of MMPs expression, interference with the VEGF signaling pathway, modulation of EMT regulator, inhibition of NF-κB and mTOR expression, and other related mechanisms. Intake of natural polyphenols has been shown to impact endogenous metabolites and complex biological metabolic pathways in vivo. Breast cancer metastasis is a complicated process in which each step is modulated by a complex network of signaling pathways. We hope that by detailing the reported interactions between breast cancer metastasis and natural polyphenols, more attention will be directed to these promising candidates as effective adjunct therapies against metastatic breast cancer in the clinic.
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Affiliation(s)
- Yingqian Ci
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing100875, China.
| | - Jinping Qiao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing100875, China.
| | - Mei Han
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing100875, China.
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Lehman-Mckeeman LD, Car BD. Metabonomics: Application in Predictive and Mechanistic Toxicology. Toxicol Pathol 2016. [DOI: 10.1080/01926230490462084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Bruce D. Car
- Discovery Toxicology, Bristol-Myers Squibb Company,
Princeton, New Jersey 08543, USA
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14
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ZHU C, LIANG QL, WANG YM, LUO GA, Vreeken RJ, Hankmeimer T. Advance in Analysis and Detection Technologies for Phospholipidomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60939-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Metabolite profiles of rats in repeated dose toxicological studies after oral and inhalative exposure. Toxicol Lett 2016; 255:11-23. [PMID: 27153797 DOI: 10.1016/j.toxlet.2016.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 11/24/2022]
Abstract
The MetaMap(®)-Tox database contains plasma-metabolome and toxicity data of rats obtained from oral administration of 550 reference compounds following a standardized adapted OECD 407 protocol. Here, metabolic profiles for aniline (A), chloroform (CL), ethylbenzene (EB), 2-methoxyethanol (ME), N,N-dimethylformamide (DMF) and tetrahydrofurane (THF), dosed inhalatively for six hours/day, five days a week for 4 weeks were compared to oral dosing performed daily for 4 weeks. To investigate if the oral and inhalative metabolome would be comparable statistical analyses were performed. Best correlations for metabolome changes via both routes of exposure were observed for toxicants that induced profound metabolome changes. e.g. CL and ME. Liver and testes were correctly identified as target organs. In contrast, route of exposure dependent differences in metabolic profiles were noted for low profile strength e.g. female rats dosed inhalatively with A or THF. Taken together, the current investigations demonstrate that plasma metabolome changes are generally comparable for systemic effects after oral and inhalation exposure. Differences may result from kinetics and first pass effects. For compounds inducing only weak changes, the differences between both routes of exposure are visible in the metabolome.
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16
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NMR-based metabonomic analysis of normal rat urine and faeces in response to (±)-venlafaxine treatment. J Pharm Biomed Anal 2016; 123:82-92. [DOI: 10.1016/j.jpba.2016.01.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 11/24/2022]
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17
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Abas F, Khatib A, Perumal V, Suppaiah V, Ismail A, Hamid M, Shaari K, Lajis NH. Metabolic alteration in obese diabetes rats upon treatment with Centella asiatica extract. JOURNAL OF ETHNOPHARMACOLOGY 2016; 180:60-69. [PMID: 26775274 DOI: 10.1016/j.jep.2016.01.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 12/08/2015] [Accepted: 01/02/2016] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE 'Pegaga' is a traditional Malay remedy for a wide range of complaints. Among the 'pegaga', Centella asiatica has been used as a remedy for diabetes mellitus. Thus, we decided to validate this claim by evaluating the in vivo antidiabetic property of C. asiatica (CA) on T2DM rat model using the holistic (1)H NMR-based metabolomics approach. METHOD In this study, an obese diabetic (mimic of T2DM condition) animal model was developed using Sprague-Dawley rats fed with a high-fat diet and induced into diabetic condition by the treatment of a low dose of streptozotocin (STZ). The effect of C. asiatica extract on the experimental animals was followed based on the changes observed in the urinary and serum metabolites, measured by (1)H NMR of urine and blood samples collected over the test period. RESULTS A long-term treatment of obese diabetic rats with CA extract could reverse the glucose and lipid levels, as well as the tricarboxylic acid cycle and amino acid metabolic disorders, back towards normal states. Biochemical analysis also showed an increase of insulin production in diabetic rats upon treatment of CA extract. CONCLUSION This study has provided evidence that clearly supported the traditional use of CA as a remedy for diabetes. NMR-based metabolomics was successfully applied to show that CA produced both anti-hyperglycemic and anti-hyperlipidemic effects on a rat model. In addition to increasing the insulin secretion, the CA extract also ameliorates the metabolic pathways affected in the induced diabetic rats. This study further revealed the potential usage of CA extract in managing diabetes mellitus and the results of this work may contribute towards the further understanding of the underlying molecular mechanism of this herbal remedy.
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Affiliation(s)
- F Abas
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia; Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - A Khatib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - V Perumal
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - V Suppaiah
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - A Ismail
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - M Hamid
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - K Shaari
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - N H Lajis
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia; Al-Moalim BinLaden Chair for Scientific Miracles of Prophetic Medicine, Scientific Chairs Unit, Taibah University, P.O. Box 30001, Madinah al Munawarah 41311, Saudi Arabia.
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Ragone R, Sallustio F, Piccinonna S, Rutigliano M, Vanessa G, Palazzo S, Lucarelli G, Ditonno P, Battaglia M, Fanizzi FP, Schena FP. Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics. Diseases 2016; 4:diseases4010007. [PMID: 28933387 PMCID: PMC5456302 DOI: 10.3390/diseases4010007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/15/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is a heterogeneous cancer often showing late symptoms. Until now, some candidate protein markers have been proposed for its diagnosis. Metabolomics approaches have been applied, predominantly using Mass Spectrometry (MS), while Nuclear Magnetic Resonance (NMR)-based studies remain limited. There is no study about RCC integrating NMR-based metabolomics with transcriptomics. In this work, 1H-NMR spectroscopy combined with multivariate statistics was applied on urine samples, collected from 40 patients with clear cell RCC (ccRCC) before nephrectomy and 29 healthy controls; nine out of 40 patients also provided samples one-month after nephrectomy. We observed increases of creatine, alanine, lactate and pyruvate, and decreases of hippurate, citrate, and betaine in all ccRCC patients. A network analysis connected most of these metabolites with glomerular injury, renal inflammation and renal necrosis/cell death. Interestingly, intersecting metabolites with transcriptomic data from CD133+/CD24+ tumoral renal stem cells isolated from ccRCC patients, we found that both genes and metabolites differentially regulated in ccRCC patients belonged to HIF-α signaling, methionine and choline degradation, and acetyl-CoA biosynthesis. Moreover, when comparing urinary metabolome of ccRCC patients after nephrectomy, some processes, such as the glomerular injury, renal hypertrophy, renal necrosis/cell death and renal proliferation, were no more represented.
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Affiliation(s)
- Rosa Ragone
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
| | - Fabio Sallustio
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
| | - Sara Piccinonna
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
| | - Monica Rutigliano
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Galleggiante Vanessa
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Silvano Palazzo
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Pasquale Ditonno
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Michele Battaglia
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Francesco Paolo Fanizzi
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
| | - Francesco Paolo Schena
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
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19
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Trezzi JP, Bulla A, Bellora C, Rose M, Lescuyer P, Kiehntopf M, Hiller K, Betsou F. LacaScore: a novel plasma sample quality control tool based on ascorbic acid and lactic acid levels. Metabolomics 2016; 12:96. [PMID: 27199628 PMCID: PMC4848344 DOI: 10.1007/s11306-016-1038-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Metabolome analysis is complicated by the continuous dynamic changes of metabolites in vivo and ex vivo. One of the main challenges in metabolomics is the robustness and reproducibility of results, partially driven by pre-analytical variations. OBJECTIVES The objective of this study was to analyse the impact of pre-centrifugation time and temperature, and to determine a quality control marker in plasma samples. METHODS Plasma metabolites were measured by gas chromatography-mass spectrometry (GC-MS) and analysed with the MetaboliteDetector software. The metabolites, which were the most labile to pre-analytical variations, were further measured by enzymatic assays. A score was calculated for their use as quality control markers. RESULTS The pre-centrifugation temperature was shown to be critical in the stability of plasma samples and had a significant impact on metabolite concentration profiles. In contrast, pre-centrifugation delay had only a minor impact. Based on the results of this study, whole blood should be kept on wet ice and centrifuged within maximum 3 h as a prerequisite for preparing EDTA plasma samples fit for the purpose of metabolome analysis. CONCLUSIONS We have established a novel blood sample quality control marker, the LacaScore, based on the ascorbic acid to lactic acid ratio in plasma, which can be used as an indicator of the blood pre-centrifugation conditions, and hence the suitability of the sample for metabolome analyses. This method can be applied in research institutes and biobanks, enabling assessment of the quality of their plasma sample collections.
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Affiliation(s)
- Jean-Pierre Trezzi
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
- />Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Alexandre Bulla
- />Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Geneve, 1211 Geneve 14, Switzerland
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
| | - Camille Bellora
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
| | - Michael Rose
- />Institute of Clinical Chemistry and Laboratory Diagnostics and Integrierte BioBank Jena (IBBJ), Jena University Hospital, Erlanger Allee 101, 07740 Jena, Germany
| | - Pierre Lescuyer
- />Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Geneve, 1211 Geneve 14, Switzerland
| | - Michael Kiehntopf
- />Institute of Clinical Chemistry and Laboratory Diagnostics and Integrierte BioBank Jena (IBBJ), Jena University Hospital, Erlanger Allee 101, 07740 Jena, Germany
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
| | - Karsten Hiller
- />Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Fay Betsou
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
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Budde K, Gök ÖN, Pietzner M, Meisinger C, Leitzmann M, Nauck M, Köttgen A, Friedrich N. Quality assurance in the pre-analytical phase of human urine samples by 1H NMR spectroscopy. Arch Biochem Biophys 2016; 589:10-7. [DOI: 10.1016/j.abb.2015.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/06/2015] [Accepted: 07/22/2015] [Indexed: 02/04/2023]
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21
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Griffin JL, Wang X, Stanley E. Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. ACTA ACUST UNITED AC 2015; 8:187-91. [PMID: 25691688 DOI: 10.1161/circgenetics.114.000219] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Millions of microbes are found in the human gut, and are collectively referred as the gut microbiota. Recent studies have estimated that the microbiota genome contains 100-fold more genes than the host genome. These microbiota contribute to digestion by processing energy substrates unutilized by the host, with about half of the total genome of the gut microbiota being related to central carbon and amino acid metabolism as well as the biosynthesis of secondary metabolites. Therefore, the gut microbiome and its interaction with the host influences many aspects of health and disease, including the composition of biofluids such as urine and blood plasma. Metabolomics is uniquely suited to capture these functional host-microbe interactions. This review aims at providing an overview of recent metabolomics evidence of gut microbiota-host metabolic interactions with a specific focus on cardiovascular disease and related aspects of the metabolic syndrome. Furthermore, the emphasis is given on the complexities of translating these metabolite signatures as potential clinical biomarkers, as the composition and activity of gut microbiome change with many factors, particularly with diet, with special reference to trimethylamine-oxide.
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Affiliation(s)
- Julian L Griffin
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom.
| | - Xinzhu Wang
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Stanley
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
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Pelantová H, Bugáňová M, Anýž J, Železná B, Maletínská L, Novák D, Haluzík M, Kuzma M. Strategy for NMR metabolomic analysis of urine in mouse models of obesity--from sample collection to interpretation of acquired data. J Pharm Biomed Anal 2015; 115:225-35. [PMID: 26263053 DOI: 10.1016/j.jpba.2015.06.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 12/11/2022]
Abstract
The mouse model of monosodium glutamate induced obesity was used to examine and consequently optimize the strategy for analysis of urine samples by NMR spectroscopy. A set of nineteen easily detectable metabolites typical in obesity-related studies was selected. The impact of urine collection protocol, choice of (1)H NMR pulse sequence, and finally the impact of the normalization method on the detected concentration of selected metabolites were investigated. We demonstrated the crucial effect of food intake and diurnal rhythms resulting in the choice of a 24-hour fasting collection protocol as the most convenient for tracking obesity-induced increased sensitivity to fasting. It was shown that the Carr-Purcell-Meiboom-Gill (CPMG) experiment is a better alternative to one-dimensional nuclear Overhauser enhancement spectroscopy (1D-NOESY) for NMR analysis of mouse urine due to its ability to filter undesirable signals of proteins naturally present in rodent urine. Normalization to total spectral area provided comparable outcomes as did normalization to creatinine or probabilistic quotient normalization in the CPMG-based model. The optimized approach was found to be beneficial mainly for low abundant metabolites rarely monitored due to their overlap by strong protein signals.
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Affiliation(s)
- Helena Pelantová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic; Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Martina Bugáňová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic; Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Jiří Anýž
- Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Blanka Železná
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Daniel Novák
- Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Martin Haluzík
- 3rd Medical Department, 1st Faculty of Medicine, Charles University and General Faculty Hospital in Prague, U nemocnice 1, 128 08 Prague 2, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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23
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Escalona EE, Leng J, Dona AC, Merrifield CA, Holmes E, Proudman CJ, Swann JR. Dominant components of the Thoroughbred metabolome characterised by (1) H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids. Equine Vet J 2015; 47:721-30. [PMID: 25130591 DOI: 10.1111/evj.12333] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 08/08/2014] [Indexed: 01/11/2023]
Abstract
REASONS FOR PERFORMING STUDY Metabonomics is emerging as a powerful tool for disease screening and investigating mammalian metabolism. This study aims to create a metabolic framework by producing a preliminary reference guide for the normal equine metabolic milieu. OBJECTIVES To metabolically profile plasma, urine and faecal water from healthy racehorses using high resolution (1) H-nuclear magnetic resonance (NMR) spectroscopy and to provide a list of dominant metabolites present in each biofluid for the benefit of future research in this area. STUDY DESIGN This study was performed using 7 Thoroughbreds in race training at a single time point. Urine and faecal samples were collected noninvasively and plasma was obtained from samples taken for routine clinical chemistry purposes. METHODS Biofluids were analysed using (1) H-NMR spectroscopy. Metabolite assignment was achieved via a range of one- and 2-dimensional experiments. RESULTS A total of 102 metabolites were assigned across the 3 biological matrices. A core metabonome of 14 metabolites was ubiquitous across all biofluids. All biological matrices provided a unique window on different aspects of systematic metabolism. Urine was the most populated metabolite matrix with 65 identified metabolites, 39 of which were unique to this biological compartment. A number of these were related to gut microbial host cometabolism. Faecal samples were the most metabolically variable between animals; acetate was responsible for the majority (28%) of this variation. Short-chain fatty acids were the predominant features identified within this biofluid by (1) H-NMR spectroscopy. CONCLUSIONS Metabonomics provides a platform for investigating complex and dynamic interactions between the host and its consortium of gut microbes and has the potential to uncover markers for health and disease in a variety of biofluids. Inherent variation in faecal extracts along with the relative abundance of microbial-mammalian metabolites in urine and invasive nature of plasma sampling, infers that urine is the most appropriate biofluid for the purposes of metabonomic analysis.
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Affiliation(s)
- E E Escalona
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, UK
| | - J Leng
- Department of Food and Nutritional Sciences, University of Reading, Berkshire, UK
| | - A C Dona
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, UK
| | - C A Merrifield
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, UK
| | - E Holmes
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, UK
| | - C J Proudman
- Department of Gastroenterology, School of Veterinary Medicine, University of Liverpool, Neston, UK
| | - J R Swann
- Department of Food and Nutritional Sciences, University of Reading, Berkshire, UK
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Sethi N, Mahar R, Shukla SK, Kumar A, Sinha N. A novel approach for testing the teratogenic potential of chemicals on the platform of metabolomics: studies employing HR-MAS nuclear magnetic resonance spectroscopy. RSC Adv 2015. [DOI: 10.1039/c5ra00671f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The objective is to develop a quick, reliable method for testing the teratogenic potential of a new chemical entity (NCE) on the platform of metabonomics, as an alternative to conventional procedures.
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Affiliation(s)
- Nikunj Sethi
- Division of Toxicology
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Rohit Mahar
- Sophisticated Analytical Instrument Facilities
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
| | - Sanjeev K. Shukla
- Sophisticated Analytical Instrument Facilities
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Akhilesh Kumar
- Division of Toxicology
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Neeraj Sinha
- Division of Toxicology
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
- Academy of Scientific and Innovative Research (AcSIR)
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25
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Yap IKS, Kho MT, Lim SHE, Ismail NH, Yam WK, Chong CW. Acclimatisation-induced stress influenced host metabolic and gut microbial composition change. MOLECULAR BIOSYSTEMS 2015; 11:297-306. [DOI: 10.1039/c4mb00463a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An integrated metabonomics and metagenomics approach utilised here showed that acclimatisation-induced stress leads to host metabolic and gut microbiotal changes.
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Affiliation(s)
- Ivan K. S. Yap
- Life Sciences Department
- School of Pharmacy
- International Medical University
- 57000 Kuala Lumpur
- Malaysia
| | - Mee Teck Kho
- School of Postgraduate Studies and Research
- International Medical University
- 57000 Kuala Lumpur
- Malaysia
| | | | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Products Discovery
- Universiti Teknologi MARA
- 42300 Bandar Puncak Alam
- Malaysia
| | - Wai Keat Yam
- Life Sciences Department
- School of Pharmacy
- International Medical University
- 57000 Kuala Lumpur
- Malaysia
| | - Chun Wie Chong
- Life Sciences Department
- School of Pharmacy
- International Medical University
- 57000 Kuala Lumpur
- Malaysia
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Dona AC, Jiménez B, Schäfer H, Humpfer E, Spraul M, Lewis MR, Pearce JTM, Holmes E, Lindon JC, Nicholson JK. Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping. Anal Chem 2014; 86:9887-94. [PMID: 25180432 DOI: 10.1021/ac5025039] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum samples provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population samples from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including sample preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid samples, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare.
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Affiliation(s)
- Anthony C Dona
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
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27
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Identification of metabolites, clinical chemistry markers and transcripts associated with hepatotoxicity. PLoS One 2014; 9:e97249. [PMID: 24836604 PMCID: PMC4023975 DOI: 10.1371/journal.pone.0097249] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/16/2014] [Indexed: 01/30/2023] Open
Abstract
Early and accurate pre-clinical and clinical biomarkers of hepatotoxicity facilitate the drug development process and the safety monitoring in clinical studies. We selected eight known model compounds to be administered to male Wistar rats to identify biomarkers of drug induced liver injury (DILI) using transcriptomics, metabolite profiling (metabolomics) and conventional endpoints. We specifically explored early biomarkers in serum and liver tissue associated with histopathologically evident acute hepatotoxicity. A tailored data analysis strategy was implemented to better differentiate animals with no treatment-related findings in the liver from animals showing evident hepatotoxicity as assessed by histopathological analysis. From the large number of assessed parameters, our data analysis strategy allowed us to identify five metabolites in serum and five in liver tissue, 58 transcripts in liver tissue and seven clinical chemistry markers in serum that were significantly associated with acute hepatotoxicity. The identified markers comprised metabolites such as taurocholic acid and putrescine (measured as sum parameter together with agmatine), classical clinical chemistry markers like AST (aspartate aminotransferase), ALT (alanine aminotransferase), and bilirubin, as well as gene transcripts like Igfbp1 (insulin-like growth factor-binding protein 1) and Egr1 (early growth response protein 1). The response pattern of the identified biomarkers was concordant across all types of parameters and sample matrices. Our results suggest that a combination of several of these biomarkers could significantly improve the robustness and accuracy of an early diagnosis of hepatotoxicity.
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Kosmides AK, Kamisoglu K, Calvano SE, Corbett SA, Androulakis IP. Metabolomic fingerprinting: challenges and opportunities. Crit Rev Biomed Eng 2014; 41:205-21. [PMID: 24579644 DOI: 10.1615/critrevbiomedeng.2013007736] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Systems biology has primarily focused on studying genomics, transcriptomics, and proteomics and their dynamic interactions. These, however, represent only the potential for a biological outcome since the ultimate phenotype at the level of the eventually produced metabolites is not taken into consideration. The emerging field of metabolomics provides complementary guidance toward an integrated approach to this problem: It allows global profiling of the metabolites of a cell, tissue, or host and presents information on the actual end points of a response. A wide range of data collection methods are currently used and allow the extraction of global or tissue-specific metabolic profiles. The great amount and complexity of data that are collected require multivariate analysis techniques, but the increasing amount of work in this field has made easy-to-use analysis programs readily available. Metabolomics has already shown great potential in drug toxicity studies, disease modeling, and diagnostics and may be integrated with genomic and proteomic data in the future to provide in-depth understanding of systems, pathways, and their functionally dynamic interactions. In this review we discuss the current state of the art of metabolomics, its applications, and future potential.
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Affiliation(s)
- Alyssa K Kosmides
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Kubra Kamisoglu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Steve E Calvano
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Siobhan A Corbett
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Ioannis P Androulakis
- Department of Surgery, Robert Wood Johnson Medical School, Department of Biomedical Engineering, Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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Xue LM, Zhang QY, Han P, Jiang YP, Yan RD, Wang Y, Rahman K, Jia M, Han T, Qin LP. Hepatotoxic constituents and toxicological mechanism of Xanthium strumarium L. fruits. JOURNAL OF ETHNOPHARMACOLOGY 2014; 152:272-82. [PMID: 24447814 DOI: 10.1016/j.jep.2013.12.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/11/2013] [Accepted: 12/11/2013] [Indexed: 05/24/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In the recent years, the international community has attached increasing importance to possible toxicity associated with Traditional Chinese Medicine (TCM). And hepatotoxicity is one of the major concerns, a fundamental pathological process induced by toxicant. This paper is in an attempt to identify the hepatotoxic components in Xanthium strumarium L. fruits (XSF) and interpret the toxicological mechanism induced by XSF. MATERIALS AND METHODS XSF extract was prepared and seven characteristic components were isolated and identified in XSF water extracts. We evaluated their hepatotoxicity effect on cell proliferation and lactate dehydrogenase (LDH) activity in L-02 and BRL liver cell line. An integrated metabonomics study using high-resolution (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy combined with multivariate statistical analysis was undertake to elucidate the hepatotoxicity mechanism induced in rats by XSF. The urine and serum metabolites were measured after treatment of rats with XSF (7.5, 15.0 and 30.0 g/kg/day) for 5 days. RESULTS The results showed that atractyloside, carboxyatractyloside, 4'-desulphate-atractyloside and XSF induced significant cytotoxic effects in both L-02 and BRL liver cell lines, indicating that atractyloside, carboxyatractyloside, and 4'-desulphate-atractyloside were the toxic components of XSF. When rats were treated with XSF at 30.0 g/kg the hepatotoxicity was reflected in the changes observed in serum biochemical profiles and by the histopathological examination of the liver. The levels of VLDL/LDL, 3-HB, lactate, acetate, acetone and glutamate in serum were increased in this group, while d-glucose, choline and valine were decreased. The elevation in the levels of succinate, citrate, 2-oxo-glutamate, glycine, 3-HB, acetate, lactate, hippurate, dimethylglycine, methylamine, dimethylamine, phenylalanine and tryptophan was observed in urine, in contrast a reduction in the intensities of taurine, d-glucose, N-acetyl-glucoprotein and trimethylamine-N-oxide (TMAO) was observed. CONCLUSIONS The results demonstrate that the major hepatotoxicity constituents are atractyloside, carboxyatractyloside and 4'-desulphate-atractyloside, and the hepatotoxicity of XSF involves mitochondrial inability, fatty acid metabolism, and some amino acids metabolism. This integrated (1)H NMR -based metabolic profiling approach has been able to capture and probe the metabolic alterations associated with the onset and progression of hepatotoxicity induced by XSF, and permits a comprehensive understanding of systemic toxicity for phytochemicals and other types of xenobiotic agents.
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Affiliation(s)
- Li-Ming Xue
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China; Health Laboratory, Shanghai Municipal Center for Disease Control and Prevention, 1380 North Zhongshan Road, Shanghai 200336, People's Republic of China
| | - Qiao-Yan Zhang
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China
| | - Ping Han
- Center for Disease Control and Prevention, Jinan Military Region, PLA, 36 East Wenhua Road, Jinan, Shandong 250012, People's Republic of China
| | - Yi-Ping Jiang
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China
| | - Rong-Di Yan
- The Second Affiliated Hospital of Shandong Traditional Chinese Medicine University, 1 Jingba Road, Ji'nan 250001, People's Republic of China
| | - Yang Wang
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China
| | - Khalid Rahman
- Faculty of Science, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Min Jia
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China
| | - Ting Han
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China.
| | - Lu-Ping Qin
- Department of Pharmacognosy, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, People's Republic of China.
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30
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Akira K, Hichiya H, Morita M, Shimizu A, Mitome H. Metabonomic study on the biochemical response of spontaneously hypertensive rats to chronic taurine supplementation using 1H NMR spectroscopic urinalysis. J Pharm Biomed Anal 2013; 85:155-61. [DOI: 10.1016/j.jpba.2013.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 02/02/2023]
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31
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Du Y, Lan W, Ji Z, Zhang X, Jiang B, Zhou X, Li C, Liu M. NMR Spectroscopic Approach Reveals Metabolic Diversity of Human Blood Plasma Associated with Protein–Drug Interaction. Anal Chem 2013; 85:8601-8. [DOI: 10.1021/ac401738z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yuanyuan Du
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Wenxian Lan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
| | - Zhusheng Ji
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Xu Zhang
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Bin Jiang
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Xin Zhou
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Conggang Li
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Maili Liu
- Wuhan
Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
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32
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Kuehnbaum NL, Britz-McKibbin P. New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era. Chem Rev 2013; 113:2437-68. [DOI: 10.1021/cr300484s] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry
and Chemical Biology, McMaster University, Hamilton, Canada
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33
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Liu YM, Hui RR, He CC, Duan JA, Tang YP, Li JX. A Metabonomic Approach to a Unique Detoxification Effect of Co-use of Euphorbia kansui
and Zizyphus jujuba. Phytother Res 2012; 27:1621-8. [DOI: 10.1002/ptr.4914] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/12/2012] [Accepted: 11/25/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Yu-Mei Liu
- State Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210093 P.R. China
- Department of Pharmacy; Tongren Polytechnic College; Tongren Guizhou 554300 P.R. China
| | - Rong-Rong Hui
- State Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210093 P.R. China
| | - Cui-Cui He
- State Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210093 P.R. China
| | - Jin-Ao Duan
- Jiangsu Key Lab of TCM Formulae Research; Nanjing University of Chinese Medicine; Nanjing 210046 P.R. China
| | - Yu-Ping Tang
- Jiangsu Key Lab of TCM Formulae Research; Nanjing University of Chinese Medicine; Nanjing 210046 P.R. China
| | - Jian-Xin Li
- State Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210093 P.R. China
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34
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McRae C, Baskind NE, Orsi NM, Sharma V, Fisher J. Metabolic profiling of follicular fluid and plasma from natural cycle in vitro fertilization patients—a pilot study. Fertil Steril 2012; 98:1449-57.e6. [DOI: 10.1016/j.fertnstert.2012.07.1131] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/20/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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35
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Abstract
Testosterone is the major circulating androgen in men but exhibits an age-related decline in the ageing male. Late-onset hypogonadism or androgen deficiency syndrome (ADS) is a 'syndromic' disorder including both a persistent low testosterone serum concentration and major clinical symptoms, including erectile dysfunction, low libido, decreased muscle mass and strength, increased body fat, decreased vitality or depressed mood. Given its unspecific symptoms, treatment goals and monitoring parameters, this review will outline the various uncertainties concerning the diagnosis, therapy and monitoring of ADS to date. Literature was identified primarily through searches for specific investigators in the PubMed database. No date or language limits were applied in the literature search for the present review. The current state of research, showing that metabolomics is starting to have an impact not only on disease diagnosis and prognosis but also on drug treatment efficacy and safety monitoring, will be presented, and the application of metabolomics to improve the clinical management of ADS will be discussed. Finally, the scientific opportunities presented by metabolomics and other -omics as novel and promising tools for biomarker discovery and individualised testosterone replacement therapy in men will be explored.
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Affiliation(s)
- Robin Haring
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse, D-17475 Greifswald, Germany.
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36
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Hindmarsh JP, Awati A, Edwards PJ, Moughan P. NMR-based metabonomics detection of differences in the metabolism of hydrolysed versus intact protein of similar amino acid profile. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2013-2016. [PMID: 22430354 DOI: 10.1002/jsfa.5636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 12/06/2011] [Accepted: 01/29/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Proton nuclear magnetic resonance (NMR)-based metabonomics has only recently been applied to nutritional research. The limitation of any analytical technique is its sensitivity in detecting the smallest variation. Alterations in nutrition often produce only subtle metabolic modulations. The objective of this study was to determine if NMR-based metabonomics could detect variations in the metabolic profile of urine from pigs digesting either native casein (NC) or the same casein that had been enzymatically hydrolysed (EHC). NMR permits simultaneous detection of a large number of metabolites, thus allowing detection of unanticipated metabolic fluctuations that may otherwise have gone undetected with the use of only targeted analysis. RESULTS Partial least squares discriminant analysis identified significantly (P < 0.05) higher urinary excretions of leucine, valine, taurine and glycine by pigs on the EHC-based diet. CONCLUSION NMR-based metabonomics is a sensitive method that can uncover unanticipated metabolic changes brought about by physicochemical changes to the feedstock (i.e. hydrolysis). The data show a lower efficiency of retention by the kidney of some amino acids following ingestion of a hydrolysed protein.
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Affiliation(s)
- Jason P Hindmarsh
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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37
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Sample preparation method to minimize chemical shift variability for NMR-based urinary metabonomics of genetically hypertensive rats. J Pharm Biomed Anal 2012; 66:339-44. [DOI: 10.1016/j.jpba.2012.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/21/2012] [Accepted: 02/24/2012] [Indexed: 11/21/2022]
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38
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Liu XJ, Li ZY, Li ZF, Gao XX, Zhou YZ, Sun HF, Zhang LZ, Guo XQ, Du GH, Qin XM. Urinary metabonomic study using a CUMS rat model of depression. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:187-192. [PMID: 22367791 DOI: 10.1002/mrc.2865] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/26/2011] [Accepted: 11/08/2011] [Indexed: 05/31/2023]
Abstract
Chronic unpredictable mild stress (CUMS) is a well-validated model of depression. In this study, a urinary metabonomics method based on the NMR spectrometry was used to study the metabolic perturbation in CUMS-induced rat depression model. With pattern recognition analysis, a clear separation of CUMS rats and healthy controls was achieved, and nine endogenous metabolites contributing to the separation were identified. CUMS-treated rats were characterized by the increase of glycine, pyruvate, glutamine, and asparagines, as well as the decrease of 2-oxoglutarate, dimethylglycine, citrate, succinate, and acetate. The urinary biochemical changes related to the metabolic disturbance in CUMS induced depression, and the possible correlations with live qi stagnation in traditional Chinese medicine are discussed. The work shows that CUMS is a reliable model for studying depression, and the noninvasive urinary metabolomic method is a valuable tool to investigate the biochemical pertubations in depression as an early diagnostic means.
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Affiliation(s)
- Xiao-Jie Liu
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan, China
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39
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Heinzmann SS, Merrifield CA, Rezzi S, Kochhar S, Lindon JC, Holmes E, Nicholson JK. Stability and robustness of human metabolic phenotypes in response to sequential food challenges. J Proteome Res 2011; 11:643-55. [PMID: 21999107 DOI: 10.1021/pr2005764] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-resolution spectroscopic profiles of biofluids can define metabolic phenotypes, providing a window onto the impact of diet on health to reflect gene-environment interactions. (1)H NMR spectroscopic profiling was used to characterize the effect of nutritional intervention on the stability of the metabolic phenotype of 7 individuals following a controlled 7 day dietary protocol. Inter-individual metabolic differences influenced proportionally more of the spectrum than dietary modulation, with certain individuals displaying a greater stability of metabolic phenotypes than others. Correlation structures between urinary metabolites were identified and used to map inter-individual pathway differences. Choline degradation was the pathway most affected by the individual, suggesting that the gut microbiota influence host metabolic phenotypes. This influence was further emphasized by the highly correlated excretion of the microbial-mammalian co-metabolites phenylacetylglutamine, 4-cresylsulfate (r = 0.87), and indoxylsulfate (r = 0.67) across all individuals. Above the background of inter-individual differences, clear biochemical effects of single type dietary interventions, animal protein, fruit and wine intake, were observed; for example, the spectral variance introduced by fruit ingestion was attributed to the metabolites tartrate, proline betaine, hippurate, and 4-hydroxyhippurate. This differential metabolic baseline and response to selected dietary challenges highlights the importance of understanding individual differences in metabolism and provides a rationale for evaluating dietary interventions and stratification of individuals with respect to guiding nutrition and health programmes.
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Affiliation(s)
- Silke S Heinzmann
- Biomolecular Medicine, Department of Surgery & Cancer, Imperial College London , Sir Alexander Fleming Building, South Kensington, London, SW7 2AZ, United Kingdom
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40
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A metabonomic study of biochemical changes characteristic of genetically hypertensive rats based on (1)H NMR spectroscopic urinalysis. Hypertens Res 2011; 35:404-12. [PMID: 22089538 DOI: 10.1038/hr.2011.182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Spontaneously hypertensive rats (SHR) provide a simple model for studying essential hypertension. Their genetic and metabolic features are of great interest because they may provide insights into the pathophysiological processes underlying essential hypertension. We have thus investigated the metabolic characteristics of SHR at various ages, covering the prehypertensive stage and the developmental phase of hypertension, using a (1)H nuclear magnetic resonance (NMR)-based metabonomic approach. Twenty-four-hour urine samples from the SHR and their age-matched normotensive control, Wistar-Kyoto rats, were analyzed using (1)H NMR spectroscopy, and the spectral data were subjected to principal components analysis (PCA) to find metabolic differences between the two strains. Consequently, it was possible to separate the urine samples between the two strains at any age ranging from 4 to 20 weeks in the principal component scores plots. The major spectral regions and signals (metabolites) contributing to the separation were picked up based on the loadings. Subsequently, the urinary excreted levels of metabolites highlighted by the PCA were compared based on the signal intensities corrected by urine volume and body weight. These investigations revealed the major metabolic changes characteristic of the SHR, which included differences in citrate, α-ketoglutarate, succinate, hippurate, phenylacetylglycine, p-cresol glucuronide, creatine, taurine, medium-chain dicarboxylates (tentative), unknown (δ 3.11), and the regions at 3.60, 3.64, 3.68 and 3.88 p.p.m. The results supported the occurrence of metabolic acidosis in the SHR in the period of prehypertension as well as rapidly rising blood pressure. In addition, the intestinal microfloral populations in the SHR were suggested to be altered in the developmental phase of hypertension.
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41
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Mellert W, Kapp M, Strauss V, Wiemer J, Kamp H, Walk T, Looser R, Prokoudine A, Fabian E, Krennrich G, Herold M, van Ravenzwaay B. Nutritional impact on the plasma metabolome of rats. Toxicol Lett 2011; 207:173-81. [PMID: 21907771 DOI: 10.1016/j.toxlet.2011.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/16/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022]
Abstract
Metabolite profiling (metabolomics) elucidates changes in biochemical pathways under various conditions, e.g., different nutrition scenarios or compound administration. BASF and metanomics have obtained plasma metabolic profiles of approximately 500 compounds (agrochemicals, chemicals and pharmaceuticals) from 28-day rat studies. With these profiles the establishment of a database (MetaMap(®)Tox) containing specific metabolic patterns associated with many toxicological modes of action was achieved. To evaluate confounding factors influencing metabolome patterns, the effect of fasting vs. non-fasting prior to blood sampling, the influence of high caloric diet and caloric restriction as well as the administration of corn oil and olive oil was studied for its influence on the metabolome. All mentioned treatments had distinct effects: triacylglycerol, phospholipids and their degradation product levels (fatty acids, glycerol, lysophosphatidylcholine) were often altered depending on the nutritional status. Also some amino acid and related compounds were changed. Some metabolites derived from food (e.g. alpha-tocopherol, ascorbic acid, beta-sitosterol, campesterol) were biomarkers related to food consumption, whereas others indicated a changed energy metabolism (e.g. hydroxybutyrate, pyruvate). Strikingly, there was a profound difference in the metabolite responses to diet restriction in male and female rats. Consequently, when evaluating the metabolic profile of a compound, the effect of nutritional status should be taken into account.
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Affiliation(s)
- W Mellert
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
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42
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Zhou Y, Lu L, Li Z, Gao X, Tian J, Zhang L, Wu B, Qin X. Antidepressant-like effects of the fractions of Xiaoyaosan on rat model of chronic unpredictable mild stress. JOURNAL OF ETHNOPHARMACOLOGY 2011; 137:236-244. [PMID: 21640181 DOI: 10.1016/j.jep.2011.05.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/19/2011] [Accepted: 05/11/2011] [Indexed: 05/30/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Xiaoyaosan (XYS), composed of Radix Bupleuri, Radix Angelicae Sinensis, Radix Paeoniae Alba, Rhizoma Atractylodis Macrocephalae, Poria, Herba Menthae, Rhizoma Zingiberis Recens and Radix Glycyrrhizae, is a valuable traditional Chinese medicine (TCM) which is used for the treatment of depression in China. In the formula, Radix Bupleuri usually serves as the principal drug, Radix Angelicae Sinensis and Radix Paeoniae Alba serve as the ministerial drugs, Rhizoma Atractylodis Macrocephalae, Poria, Herba Menthae and Rhizoma Zingiberis Recens serve as adjunctive drugs, Radix Glycyrrhizae serves as messenger drug, they coordinate with each other and enhance the effect of the formula. In our previous experiments, the antidepressant effect of XYS was revealed. However, the antidepressant part (or component) of this prescription was still obscure. We divided the XYS into five different polar fractions, and explored the antidepressant activity of five different polar fractions to identify the active fraction. MATERIALS AND METHODS Behavior research and metabonomics method based on (1)H NMR were used for efficacy study of different fractions in chronic unpredictable mild stress (CUMS) model of depression. Rats were divided into 8 groups and drugs were administered during the 21 days model building period. The urine samples of rats were collected overnight (12h) on 21 day and the metabolic profiling of the urine was measured using NMR. Multivariate analysis was also utilized to evaluate the active fraction of XYS. RESULTS In the behavior research, there were significant difference between the lipophilic fraction group (XY-A) and the model group. In addition, with pattern recognition analysis of urinary metabolites, the results showed a clear separation of the model group and control group, while XY-A group was much closer to the control group in the OSC-PLS score plot. Seven endogenous metabolites contributing to the separation of the model group and control group were detected, while XY-A group regulated the 5 perturbed metabolites showing a tendency of recovering to control group. CONCLUSIONS The present work suggested that petroleum ether fraction was the most effective fraction, implying that lipophilic components contribute to the antidepressant effect of XYS.
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Affiliation(s)
- Yuzhi Zhou
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, No. 92, Wucheng Road, Taiyuan 030006, People's Republic of China.
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Puiggròs F, Solà R, Bladé C, Salvadó MJ, Arola L. Nutritional biomarkers and foodomic methodologies for qualitative and quantitative analysis of bioactive ingredients in dietary intervention studies. J Chromatogr A 2011; 1218:7399-414. [PMID: 21917262 DOI: 10.1016/j.chroma.2011.08.051] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 08/04/2011] [Accepted: 08/09/2011] [Indexed: 01/16/2023]
Abstract
Traditional dietary assessment methods, such as 24-h recalls, weighted food diaries and food frequency questionnaires (FFQs) are highly subjective and impair the assessment of successfully accomplished dietary interventions. Foodomic technologies offer promising methodologies for gathering scientific evidence from clinical trials with sensitive methods (e.g., GC-MS, LC-MS, CE, NMR) to detect and quantify markers of nutrient exposure or subtle changes in dietary patterns. This review provides a summary of recently developed foodomic methodologies for the detection of suggested biomarkers, including the food specificity for each suggested biomarker and a brief description of the key aspects of 24-h recalls that may affect marker detection and stability, such as mixed nutrients and cooking processes. The primary aim of this review is to contribute to the assessment of the metabolic effects of active ingredients and foods using cutting-edge methods to improve approaches to future nutritional programs tailored for health maintenance and disease prevention.
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Affiliation(s)
- Francesc Puiggròs
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, Universitat Rovira i Virgili, Reus, Spain
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Nielsen BL, Jerôme N, Saint-Albin A, Thonat C, Briant C, Boué F, Rampin O, Maurin Y. A mixture of odorant molecules potentially indicating oestrus in mammals elicits penile erections in male rats. Behav Brain Res 2011; 225:584-9. [PMID: 21884731 DOI: 10.1016/j.bbr.2011.08.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
A common set of odorous molecules may indicate female receptiveness across species, as male rats display sexual arousal when exposed to the odour of oestrous faeces from rats, vixens and mares. More than 900 different compounds were identified by GC-MS analyses performed on faeces samples from di-oestrous and oestrous females and from males of the three species. Five carboxylic acids were found in lower concentrations in faeces from all oestrous females. We subjected 12 sexually trained male rats to a 30 min exposure to different dilutions of a mixture of these five molecules in the same proportions as found in female oestrous faeces. The behavioural responses of the rats were compared to those displayed when exposed to water (negative control) and faeces from oestrous female rats (positive control). Frequency of penile erections were found to be significantly dependent on mixture dilution, with two intermediate dilutions eliciting frequencies of penile erections that did not differ from those obtained during exposure to oestrous female rat faeces. Higher and lower dilutions did not elicit more penile erections than observed with water. These results support our hypothesis that a small set of odorous molecules may indicate sexual receptiveness in mammalian females.
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Affiliation(s)
- Birte L Nielsen
- INRA, UR1197 Neurobiologie de l'Olfaction et Modélisation en Imagerie, F-78352 Jouy-en-Josas, France.
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Qiao Q, Li T, Sun J, Liu X, Ren J, Fei J. Metabolomic analysis of normal (C57BL/6J, 129S1/SvImJ) mice by gas chromatography-mass spectrometry: detection of strain and gender differences. Talanta 2011; 85:718-24. [PMID: 21645764 DOI: 10.1016/j.talanta.2011.04.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 11/25/2022]
Abstract
Previous studies have shown that the C57 and 129 strains of mice display marked differences in behavioural performance, neuroanatomy, neurochemistry and synaptic plasticity. However, few metabolomic studies of their biofluids have been performed. As part of a series of metabolic phenotyping, the effects of gender and strain upon serum metabolite composition and variation are examined in this study using gas chromatography-mass spectrometry (GC-MS) in normal C57BL/6J and 129S1/SvImJ strains of mice. The 129S1/SvImJ strain is phenotypically distinct from the C57BL/6J strain and characteristic metabotypes are produced for both male and female mice of each strain. These data demonstrate that the C57BL/6J and 129S1/SvImJ strains of mice show a wide range of metabolic differences across glycine, serine and threonine metabolism; valine, leucine and isoleucine biosynthesis; and tricarboxylic acid cycle pathways. Remarkably, the concentration of glyceric acid in the 129S1/SvImJ strain is significantly increased compared to the C57BL/6J mouse strain, reflecting important considerations for studies that use the 129S1/SvImJ mouse as the human d-glycericaciduria model. We infer that a deficiency of d-glycerate kinase would explain such a glyceric acid accumulation in the 129S1/SvImJ strain. More importantly, this differential metabolite level data provide insight into specific metabolic pathways and lay the groundwork for integrated studies of the mouse models.
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Affiliation(s)
- Qian Qiao
- Department of Chemistry, Tongji University, Shanghai, China
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Shuib NH, Shaari K, Khatib A, Maulidiani, Kneer R, Zareen S, Raof SM, Hj. Lajis N, Neto V. Discrimination of young and mature leaves of Melicope ptelefolia using 1H NMR and multivariate data analysis. Food Chem 2011. [DOI: 10.1016/j.foodchem.2010.10.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fonville JM, Bylesjö M, Coen M, Nicholson JK, Holmes E, Lindon JC, Rantalainen M. Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing. Anal Chim Acta 2011; 705:72-80. [PMID: 21962350 DOI: 10.1016/j.aca.2011.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 03/14/2011] [Accepted: 04/13/2011] [Indexed: 12/25/2022]
Abstract
Linear multivariate projection methods are frequently applied for predictive modeling of spectroscopic data in metabonomic studies. The OPLS method is a commonly used computational procedure for characterizing spectral metabonomic data, largely due to its favorable model interpretation properties providing separate descriptions of predictive variation and response-orthogonal structured noise. However, when the relationship between descriptor variables and the response is non-linear, conventional linear models will perform sub-optimally. In this study we have evaluated to what extent a non-linear model, kernel-based orthogonal projections to latent structures (K-OPLS), can provide enhanced predictive performance compared to the linear OPLS model. Just like its linear counterpart, K-OPLS provides separate model components for predictive variation and response-orthogonal structured noise. The improved model interpretation by this separate modeling is a property unique to K-OPLS in comparison to other kernel-based models. Simulated annealing (SA) was used for effective and automated optimization of the kernel-function parameter in K-OPLS (SA-K-OPLS). Our results reveal that the non-linear K-OPLS model provides improved prediction performance in three separate metabonomic data sets compared to the linear OPLS model. We also demonstrate how response-orthogonal K-OPLS components provide valuable biological interpretation of model and data. The metabonomic data sets were acquired using proton Nuclear Magnetic Resonance (NMR) spectroscopy, and include a study of the liver toxin galactosamine, a study of the nephrotoxin mercuric chloride and a study of Trypanosoma brucei brucei infection. Automated and user-friendly procedures for the kernel-optimization have been incorporated into version 1.1.1 of the freely available K-OPLS software package for both R and Matlab to enable easy application of K-OPLS for non-linear prediction modeling.
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Affiliation(s)
- Judith M Fonville
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK.
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He CC, Dai YQ, Hui RR, Hua J, Chen HJ, Luo QY, Li JX. NMR-based metabonomic approach on the toxicological effects of a Cimicifuga triterpenoid. J Appl Toxicol 2011; 32:88-97. [PMID: 21449050 DOI: 10.1002/jat.1633] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 01/24/2023]
Abstract
Cimicifugae Rhizoma, a well-known botanical dietary supplement, has been the subject of intense interest due to its potential application for alleviating menopausal symptom. Although there are clinic data that the Cimicifuga extract should have hepatotoxicity, no evidence on the main chemical components has been reported. Cimicidol-3-O-β -d-xyloside (CX) is one of the main triterpenoids of the rhizome. This work studies the toxicological effects of CX after oral administration (50 mg kg(-1) per day) over a 7-day period in female SD rats using metabonomic analyses of (1) H NMR spectra of urine, serum and liver tissue extracts. Histopathological studies of liver and analyses of blood biochemical parameter, such as alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, blood urea nitrogen and creatinine revealed that CX had no negative impacts on liver and kidney. However, the metabolic signature of (1) H NMR-based urinalysis of daily samples displayed an increment in the levels of taurine, trimethylamine-N-oxide (TMAO), betaine and acetate. Elevated serum levels of creatinine, glucose, alanine, TMAO and betaine and lower levels of lactate were observed. Metabolic profiling on aqueous soluble extracts of liver showed simultaneously increases in succinate, glycogen, choline, glycerophosphorylcholine, TMAO and betaine levels and reduction in valine, glucose and lactate levels. Nevertheless, no changes in any metabonomic level were found in lipid-soluble extracts of liver. These findings indicate that CX has a slight toxicity in liver and kidney via disturbance of the metabolisms of energy and amino acids. The present study provides a reasonable explanation for the clinical hepatotoxicity of Cimicifuga extract.
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Affiliation(s)
- Cui-Cui He
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, People's Republic of China
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Moroz J, Turner J, Slupsky C, Fallone G, Syme A. Tumour xenograft detection through quantitative analysis of the metabolic profile of urine in mice. Phys Med Biol 2011; 56:535-56. [PMID: 21212470 DOI: 10.1088/0031-9155/56/3/002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The metabolic content of urine from NIH III nude mice (n = 22) was analysed before and after inoculation with human glioblastoma multiforme (GBM) cancer cells. An age- and gender-matched control population (n = 14) was also studied to identify non-tumour-related changes. Urine samples were collected daily for 6 weeks, beginning 1 week before cell injection. Metabolite concentrations were obtained via targeted profiling with Chenomx Suite 5.1, based on nuclear magnetic resonance (NMR) spectra acquired on an Oxford 800 MHz cold probe NMR spectrometer. The Wilcoxon rank sum test was used to evaluate the significance of the change in metabolite concentration between the two time points. Both the metabolite concentrations and the ratios of pairs of metabolites were studied. The complicated inter-relationships between metabolites were assessed through partial least-squares discriminant analysis (PLS-DA). Receiver operating characteristic (ROC) curves were generated for all variables and the area under the curve (AUC) calculated. The data indicate that the number of statistically significant changes in metabolite concentrations was more pronounced in the tumour-bearing population than in the control animals. This was also true of the ratios of pairs of metabolites. ROC analysis suggests that the ratios were better able to differentiate between the pre- and post-injection samples compared to the metabolite concentrations. PLS-DA models produced good separation between the populations and had the best AUC results (all models exceeded 0.937). These results demonstrate that metabolomics may be used as a screening tool for GBM cells grown in xenograft models in mice.
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Affiliation(s)
- Jennifer Moroz
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
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Dieterle F, Riefke B, Schlotterbeck G, Ross A, Senn H, Amberg A. NMR and MS methods for metabonomics. Methods Mol Biol 2011; 691:385-415. [PMID: 20972767 DOI: 10.1007/978-1-60761-849-2_24] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Metabonomics, also often referred to as "metabolomics" or "metabolic profiling," is the systematic profiling of metabolites in bio-fluids or tissues of organisms and their temporal changes. In the last decade, metabonomics has become increasingly popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabonomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabonomics, i.e., NMR, LC-MS, UPLC-MS, and GC-MS have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabonomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation, to determining the measurement details of all analytical platforms, and finally, to discussing the corresponding specific steps of data analysis.
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Affiliation(s)
- Frank Dieterle
- Molecular Diagnostics, Novartis Pharma AG, Basel, Switzerland
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