1
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Madssen TS, Giskeødegård GF, Smilde AK, Westerhuis JA. Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data. PLoS Comput Biol 2021; 17:e1009585. [PMID: 34752455 PMCID: PMC8604364 DOI: 10.1371/journal.pcbi.1009585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 11/19/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022] Open
Abstract
Longitudinal intervention studies with repeated measurements over time are an important type of experimental design in biomedical research. Due to the advent of "omics"-sciences (genomics, transcriptomics, proteomics, metabolomics), longitudinal studies generate increasingly multivariate outcome data. Analysis of such data must take both the longitudinal intervention structure and multivariate nature of the data into account. The ASCA+-framework combines general linear models with principal component analysis and can be used to separate and visualize the multivariate effect of different experimental factors. However, this methodology has not yet been developed for the more complex designs often found in longitudinal intervention studies, which may be unbalanced, involve randomized interventions, and have substantial missing data. Here we describe a new methodology, repeated measures ASCA+ (RM-ASCA+), and show how it can be used to model metabolic changes over time, and compare metabolic changes between groups, in both randomized and non-randomized intervention studies. Tools for both visualization and model validation are discussed. This approach can facilitate easier interpretation of data from longitudinal clinical trials with multivariate outcomes.
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Affiliation(s)
- Torfinn S. Madssen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Guro F. Giskeødegård
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Age K. Smilde
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Johan A. Westerhuis
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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2
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Bowen TJ, Hall AR, Lloyd GR, Weber RJM, Wilson A, Pointon A, Viant MR. An Extensive Metabolomics Workflow to Discover Cardiotoxin-Induced Molecular Perturbations in Microtissues. Metabolites 2021; 11:644. [PMID: 34564460 PMCID: PMC8470535 DOI: 10.3390/metabo11090644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
Discovering modes of action and predictive biomarkers of drug-induced structural cardiotoxicity offers the potential to improve cardiac safety assessment of lead compounds and enhance preclinical to clinical translation during drug development. Cardiac microtissues are a promising, physiologically relevant, in vitro model, each composed of ca. 500 cells. While untargeted metabolomics is capable of generating hypotheses on toxicological modes of action and discovering metabolic biomarkers, applying this technology to low-biomass microtissues in suspension is experimentally challenging. Thus, we first evaluated a filtration-based approach for harvesting microtissues and assessed the sensitivity and reproducibility of nanoelectrospray direct infusion mass spectrometry (nESI-DIMS) measurements of intracellular extracts, revealing samples consisting of 28 pooled microtissues, harvested by filtration, are suitable for profiling the intracellular metabolome and lipidome. Subsequently, an extensive workflow combining nESI-DIMS untargeted metabolomics and lipidomics of intracellular extracts with ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) analysis of spent culture medium, to profile the metabolic footprint and quantify drug exposure concentrations, was implemented. Using the synthetic drug and model cardiotoxin sunitinib, time-resolved metabolic and lipid perturbations in cardiac microtissues were investigated, providing valuable data for generating hypotheses on toxicological modes of action and identifying putative biomarkers such as disruption of purine metabolism and perturbation of polyunsaturated fatty acid levels.
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Affiliation(s)
- Tara J. Bowen
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
| | - Andrew R. Hall
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (A.R.H.); (A.P.)
| | - Gavin R. Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Ralf J. M. Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Amanda Wilson
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Amy Pointon
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (A.R.H.); (A.P.)
| | - Mark R. Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
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3
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Acute and Delayed Doxorubicin-Induced Myocardiotoxicity Associated with Elevation of Cardiac Biomarkers, Depletion of Cellular Antioxidant Enzymes, and Several Histopathological and Ultrastructural Changes. Life (Basel) 2021; 11:life11090880. [PMID: 34575029 PMCID: PMC8467687 DOI: 10.3390/life11090880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Doxorubicin (DOX; Adricin) is an anthracycline antibiotic, which is an efficient anticancer chemotherapeutic agent that targets many types of adult and pediatric tumors, such as breast cancer, leukemia, and lymphomas. However, use of DOX is limited due to its cardiotoxic effects. This study sequentially investigated the mechanistic pathways of the cardiotoxic process of DOX in rats at different post-treatment periods using cumulative dose, which is used in therapeutic regimes. In this regard, 56 male albino rats were used for the experiment. The experimental animals were divided into seven groups (n = 8/group) based on dose and sacrifice schedule as follows: G1 (2 mg/kg body weight [BW] and sacrificed at day 4), G2 (4 mg/kg BW and sacrificed at day 8), G3 (6 mg/kg BW and sacrificed at day 15), G4 (8 mg/kg BW and sacrificed at day 30), G5 (10 mg/kg BW and sacrificed at day 60), G6 (10 mg/kg BW and sacrificed at day 90), and G7 (10 mg/kg BW and sacrificed at day 120). As expected, G1, G2, and G3-treated groups revealed features of acute toxic myocarditis associated with degenerative and necrotic changes in myocytes, mitochondrial damage, elevation of cardiac biomarkers, and depletion of cellular antioxidant enzymes. However, these changes increased in severity with subsequent treatment with the same dose until reaching a cumulative dose of 10 mg/kg BW for 30 d. Furthermore, after a cumulative dose of 10 mg/kg BW with a withdrawal period of 2–3 months, various predominant changes in chronicity were reported, such as disorganization and atrophy of myocytes, condensation and atrophy of mitochondria, degranulation of mast cells, and fibrosis with occasional focal necrosis, indicating incomplete elimination of DOX and/or its metabolites. Altogether, these data provide interesting observations associated with the cardiotoxic process of DOX in rats that would help understand the accompanying changes underlying the major toxic effects of the drug. Future research is suggested to explore more about the dose-dependent mechanisms of such induced toxicity of DOX that would help determine the proper doses and understand the resulting cardiomyopathy.
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4
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Palmer JA, Smith AM, Gryshkova V, Donley ELR, Valentin JP, Burrier RE. A Targeted Metabolomics-Based Assay Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Identifies Structural and Functional Cardiotoxicity Potential. Toxicol Sci 2021; 174:218-240. [PMID: 32040181 DOI: 10.1093/toxsci/kfaa015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Implementing screening assays that identify functional and structural cardiotoxicity earlier in the drug development pipeline has the potential to improve safety and decrease the cost and time required to bring new drugs to market. In this study, a metabolic biomarker-based assay was developed that predicts the cardiotoxicity potential of a drug based on changes in the metabolism and viability of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). Assay development and testing was conducted in 2 phases: (1) biomarker identification and (2) targeted assay development. In the first phase, metabolomic data from hiPSC-CM spent media following exposure to 66 drugs were used to identify biomarkers that identified both functional and structural cardiotoxicants. Four metabolites that represent different metabolic pathways (arachidonic acid, lactic acid, 2'-deoxycytidine, and thymidine) were identified as indicators of cardiotoxicity. In phase 2, a targeted, exposure-based biomarker assay was developed that measured these metabolites and hiPSC-CM viability across an 8-point concentration curve. Metabolite-specific predictive thresholds for identifying the cardiotoxicity potential of a drug were established and optimized for balanced accuracy or sensitivity. When predictive thresholds were optimized for balanced accuracy, the assay predicted the cardiotoxicity potential of 81 drugs with 86% balanced accuracy, 83% sensitivity, and 90% specificity. Alternatively, optimizing the thresholds for sensitivity yields a balanced accuracy of 85%, 90% sensitivity, and 79% specificity. This new hiPSC-CM-based assay provides a paradigm that can identify structural and functional cardiotoxic drugs that could be used in conjunction with other endpoints to provide a more comprehensive evaluation of a drug's cardiotoxicity potential.
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Affiliation(s)
| | - Alan M Smith
- Stemina Biomarker Discovery, Inc, Madison, Wisconsin
| | - Vitalina Gryshkova
- UCB Biopharma SPRL, Investigative Toxicology, Development Science, B-1420 Braine L'Alleud, Belgium
| | | | - Jean-Pierre Valentin
- UCB Biopharma SPRL, Investigative Toxicology, Development Science, B-1420 Braine L'Alleud, Belgium
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5
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Zhang Y, Zhou Q, Ding X, Wang H, Tan G. HILIC-MS-based metabolomics reveal that Astragalus polysaccharide alleviates doxorubicin-induced cardiomyopathy by regulating sphingolipid and glycerophospholipid homeostasis. J Pharm Biomed Anal 2021; 203:114177. [PMID: 34198197 DOI: 10.1016/j.jpba.2021.114177] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
Doxorubicin (DOX) is widely used against cancer but carries the risk of a progressive cardiomyopathy. Astragalus polysaccharides (ASP) is the main active ingredient of Astragalus membranaceus Bunge. It has been proved to be effective against DOX-induced cardiomyopathy. However, its therapeutic mechanism is not yet well explored. In this study, a metabolomics approach based on hydrophilic interaction liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HILIC-Q-TOFMS) was developed to characterize the metabolic fluctuations associated with DOX cardiomyopathy and elucidate the underlying mechanisms of the protective effects of ASP. By the combination of HILIC-Q-TOFMS and multivariate and univariate data analysis, we identified 22 polar serum metabolites associated with DOX cardiomyopathy, 12 of which were significantly reversed when the animals were co-treated with ASP through two main metabolic pathways, i.e., sphingolipid and glycerophospholipid metabolism. Furthermore, it was found that ASP could alleviate DOX-induced cardiomyopathy by decreasing the levels of acid sphingomyelinase, acid ceramidase and phospholipase A2 and increasing the levels of sphingomyelin synthase to regulate the sphingolipid and glycerophospholipid metabolic disorder. These results revealed that sphingolipid and glycerophospholipid metabolism may be significantly responsible for DOX cardiomyopathy, which is also a major mechanism for the action of ASP against DOX cardiomyopathy.
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Affiliation(s)
- Ya Zhang
- School of Pharmacy, Air Force Medical University, Xi'an, 710032, China.
| | - Qian Zhou
- Department of Traditional Chinese Medicine, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China.
| | - Xin Ding
- School of Pharmacy, Air Force Medical University, Xi'an, 710032, China; School of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, China.
| | - Haibo Wang
- School of Pharmacy, Air Force Medical University, Xi'an, 710032, China.
| | - Guangguo Tan
- School of Pharmacy, Air Force Medical University, Xi'an, 710032, China.
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6
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Olesti E, González-Ruiz V, Wilks MF, Boccard J, Rudaz S. Approaches in metabolomics for regulatory toxicology applications. Analyst 2021; 146:1820-1834. [PMID: 33605958 DOI: 10.1039/d0an02212h] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Innovative methodological approaches are needed to conduct human health and environmental risk assessments on a growing number of marketed chemicals. Metabolomics is progressively proving its value as an efficient strategy to perform toxicological evaluations of new and existing substances, and it will likely become a key tool to accelerate chemical risk assessments. However, additional guidance with widely accepted and harmonized procedures is needed before metabolomics can be routinely incorporated in decision-making for regulatory purposes. The aim of this review is to provide an overview of metabolomic strategies that have been successfully employed in toxicity assessment as well as the most promising workflows in a regulatory context. First, we provide a general view of the different steps of regulatory toxicology-oriented metabolomics. Emphasis is put on three key elements: robustness of experimental design, choice of analytical platform, and use of adapted data treatment tools. Then, examples in which metabolomics supported regulatory toxicology outputs in different scenarios are reviewed, including chemical grouping, elucidation of mechanisms of toxicity, and determination of points of departure. The overall intention is to provide insights into why and how to plan and conduct metabolomic studies for regulatory toxicology purposes.
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Affiliation(s)
- Eulalia Olesti
- School of Pharmaceutical Sciences, University of Geneva, Switzerland.
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7
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Wang M, Lin J, Gong J, Ma M, Tang H, Liu J, Yan F. Rapid and sensitive determination of doxorubicin in human whole blood by vertically-ordered mesoporous silica film modified electrochemically pretreated glassy carbon electrodes. RSC Adv 2021; 11:9021-9028. [PMID: 35423372 PMCID: PMC8695326 DOI: 10.1039/d0ra10000e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Direct and accurate detection of doxorubicin (DOX) in unprocessed human whole blood is of vital importance in medical diagnosis and monitoring. In this work, we demonstrate the utilization of electrochemically pretreated glassy carbon electrodes (p-GCE) modified with vertically-ordered mesoporous silica films (VMSF) for rapid and sensitive electrochemical detection of DOX. The electrochemically pretreated process is a simple, cost-effective and environmentally friendly approach for improving interface catalytic properties and introducing oxygen-containing groups into the GCE surface, which could be suitable for stably growing VMSF without any adhesive layer simultaneously retaining the underlying electrode activity. Benefiting from the highly sensitive electrode substrate of p-GCE and electrostatic preconcentration effect of VMSF, the present VMSF/p-GCE sensor was able to determine DOX with an ultrahigh sensitivity (23.94 μA μM-1) and a relatively low limit of detection (0.2 nM) and a rather wide linear range (0.5 nM to 23 μM). Furthermore, direct and reliable electrochemical detection of DOX in human whole blood without complicated sample pretreatments was achieved owing to the excellent anti-fouling and anti-interference ability of VMSF.
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Affiliation(s)
- Meifang Wang
- Department of Chemistry, Zhejiang Sci-Tech University 928 Second Avenue, Xiasha Higher Education Zone Hangzhou 310018 PR China
| | - Jing Lin
- The First Affiliated Hospital of Guangxi University of Chinese Medicine Nanning 530023 China
| | - Jiawei Gong
- Department of Chemistry, Zhejiang Sci-Tech University 928 Second Avenue, Xiasha Higher Education Zone Hangzhou 310018 PR China
| | - Mingchen Ma
- Guangxi University of Chinese Medicine Nanning 530020 China
| | - Hongliang Tang
- Affiliated Fangchenggang Hospital, Guangxi University of Chinese Medicine Fangchenggang 538001 China
| | - Jiyang Liu
- Department of Chemistry, Zhejiang Sci-Tech University 928 Second Avenue, Xiasha Higher Education Zone Hangzhou 310018 PR China
| | - Fei Yan
- Department of Chemistry, Zhejiang Sci-Tech University 928 Second Avenue, Xiasha Higher Education Zone Hangzhou 310018 PR China
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8
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Geng C, Cui C, Wang C, Lu S, Zhang M, Chen D, Jiang P. Systematic Evaluations of Doxorubicin-Induced Toxicity in Rats Based on Metabolomics. ACS OMEGA 2021; 6:358-366. [PMID: 33458487 PMCID: PMC7807767 DOI: 10.1021/acsomega.0c04677] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Doxorubicin (DOX) is widely used to treat solid tumors, but its use is limited by its severe cardiotoxicity, nephrotoxicity, hepatotoxicity, and neurotoxicity. Metabolomic studies on DOX-induced toxicity are mainly focused on alterations in the heart and kidney, but systematic research on multiple matrices (serum, heart, liver, brain, and kidney) is rare. Thus, in our study, gas chromatography-mass spectrometry analysis of main targeted tissues (serum, heart, liver, brain, and kidney) was used to systemically evaluate the toxicity of DOX. Multivariate analyses, including orthogonal projections to the latent structure and t-test, revealed 21 metabolites in the serum, including cholesterol, d-glucose, d-lactic acid, glycine, l-alanine, l-glutamic acid, l-isoleucine, l-leucine, l-proline, l-serine, l-tryptophan, l-tyrosine, l-valine, MG (0:0/18:0/0:0), MG (16:0/0:0/0:0), N-methylphenylethanolamine, oleamide, palmitic acid, pyroglutamic acid, stearic acid, and urea. In the heart, perturbed metabolites included 3-methyl-1-pentanol, cholesterol, d-glucose, d-lactic acid, glycerol, glycine, l-alanine, l-valine, MG (16:0/0:0/0:0), palmitic acid, phenol, propanoic acid, and stearic acid. For the liver, DOX exposure caused alterations of acetamide, acetic acid, d-glucose, glycerol, l-threonine, palmitic acid, palmitoleic acid, stearic acid, and urea. In the brain, metabolic changes involved 2-butanol, carbamic acid, cholesterol, desmosterol, d-lactic acid, l-valine, MG (16:0/0:0/0:0), palmitic acid, and stearic acid. In the kidney, disturbed metabolites were involved in cholesterol, glycerol, glycine, l-alanine, MG (0:0/18:0/0:0), MG (16:0/0:0/0:0), and squalene. Complementary evidence by multiple matrices revealed disturbed pathways concerning amino acid metabolism, energy metabolism, and lipid metabolism. Our results may help to systematically elucidate the metabolic changes of DOX-induced toxicity and clarify the underlying mechanisms.
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Affiliation(s)
- Chunmei Geng
- Department
of Pharmacy, Jining No 1 People’s Hospital, Jining Medical University, Jining 272000, China
| | - Changmeng Cui
- Department
of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Changshui Wang
- Department
of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining 272000, China
| | - Shuxin Lu
- Department
of Medical Engineering, Jining Medical University, Jining 272000, China
| | - Maokun Zhang
- Department
of Medical Engineering, Jining Medical University, Jining 272000, China
| | - Dan Chen
- Department
of Pharmacy, Jining No 1 People’s Hospital, Jining Medical University, Jining 272000, China
| | - Pei Jiang
- Department
of Pharmacy, Jining No 1 People’s Hospital, Jining Medical University, Jining 272000, China
- . Phone: +86 537 2106208. Fax: +86 537 2106208
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9
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Li A, Zhang W, Zhang L, Liu Y, Li K, Du G, Qin X. Elucidating the time-dependent changes in the urinary metabolome under doxorubicin-induced nephrotoxicity. Toxicol Lett 2020; 319:204-212. [DOI: 10.1016/j.toxlet.2019.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/20/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
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10
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Song J, Xiang S, Yang Y, Sun Z. Assessment of follicular fluid metabolomics of polycystic ovary syndrome in kidney yang deficiency syndrome. Eur J Integr Med 2019. [DOI: 10.1016/j.eujim.2019.100944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Hubbard TD, Liu Q, Murray IA, Dong F, Miller C, Smith PB, Gowda K, Lin JM, Amin S, Patterson AD, Perdew GH. Microbiota Metabolism Promotes Synthesis of the Human Ah Receptor Agonist 2,8-Dihydroxyquinoline. J Proteome Res 2019; 18:1715-1724. [PMID: 30777439 DOI: 10.1021/acs.jproteome.8b00946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a major regulator of immune function within the gastrointestinal tract. Resident microbiota are capable of influencing AHR-dependent signaling pathways via production of an array of bioactive molecules that act as AHR agonists, such as indole or indole-3-aldehyde. Bacteria produce a number of quinoline derivatives, of which some function as quorum-sensing molecules. Thus, we screened relevant hydroxyquinoline derivatives for AHR activity using AHR responsive reporter cell lines. 2,8-Dihydroxyquinoline (2,8-DHQ) was identified as a species-specific AHR agonist that exhibits full AHR agonist activity in human cell lines, but only induces modest AHR activity in mouse cells. Additional dihydroxylated quinolines tested failed to activate the human AHR. Nanomolar concentrations of 2,8-DHQ significantly induced CYP1A1 expression and, upon cotreatment with cytokines, synergistically induced IL6 expression. Ligand binding competition studies subsequently confirmed 2,8-DHQ to be a human AHR ligand. Several dihydroxyquinolines were detected in human fecal samples, with concentrations of 2,8-DHQ ranging between 0 and 3.4 pmol/mg feces. Additionally, in mice the microbiota was necessary for the presence of DHQ in cecal contents. These results suggest that microbiota-derived 2,8-DHQ would contribute to AHR activation in the human gut, and thus participate in the protective and homeostatic effects observed with gastrointestinal AHR activation.
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Affiliation(s)
| | | | | | | | - Charles Miller
- Department of Global Environmental Health Sciences , Tulane University School of Public Health and Tropical Medicine , New Orleans , Louisiana 70112 , United States
| | | | - Krishne Gowda
- Department of Pharmacology , Penn State College of Medicine , Hershey , Pennsylvania 17033 , United States
| | - Jyh Ming Lin
- Department of Biochemistry and Molecular Biology , Penn State College of Medicine , Hershey , Pennsylvania 17033 , United States
| | - Shantu Amin
- Department of Pharmacology , Penn State College of Medicine , Hershey , Pennsylvania 17033 , United States
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12
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Untargeted metabolomic profiling of urine in Wistar rats reveals enhanced bioavailability of soy isoflavones post short-term consumption of noni (Morinda citrifolia) juice. J Funct Foods 2018. [DOI: 10.1016/j.jff.2017.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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13
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Glymenaki M, Barnes A, O'Hagan S, Warhurst G, McBain AJ, Wilson ID, Kell DB, Else KJ, Cruickshank SM. Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation. Sci Rep 2017; 7:8836. [PMID: 28821731 PMCID: PMC5562868 DOI: 10.1038/s41598-017-08732-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/12/2017] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a -/- mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a -/- mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a -/- genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.
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Affiliation(s)
- M Glymenaki
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - A Barnes
- Shimadzu Corporation, Manchester, UK
| | - S O'Hagan
- School of Chemistry, University of Manchester, Manchester, UK; Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - G Warhurst
- Infection, Injury and Inflammation Research Group, Division of Medicine and Neurosciences, University of Manchester and Salford Royal Hospitals NHS Trust, Salford, UK
| | - A J McBain
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - I D Wilson
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, London, UK
| | - D B Kell
- School of Chemistry, University of Manchester, Manchester, UK; Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - K J Else
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - S M Cruickshank
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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14
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Bao Y, Wang S, Yang X, Li T, Xia Y, Meng X. Metabolomic study of the intervention effects of Shuihonghuazi Formula, a Traditional Chinese Medicinal formulae, on hepatocellular carcinoma (HCC) rats using performance HPLC/ESI-TOF-MS. JOURNAL OF ETHNOPHARMACOLOGY 2017; 198:468-478. [PMID: 28108381 DOI: 10.1016/j.jep.2017.01.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/11/2017] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Metabolomics is the comprehensive assessment of endogenous metabolites of a biological system in a holistic context, and its property consists with the global view of Traditional Chinese Medicine (TCM). Shuihonghuazi Formula (SHHZF) has been used for liver cancer early treatment in clinical for more than thirty years, but its mechanism remains unclear completely. This paper was designed to explore the therapeutic effects of SHHZF on liver cancer and its metabolomic characters. MATERIALS AND METHODS All the rats were given diethylnitrosamine (DEN) at the dosage of 70mg/kg for 14 weeks. From the 7th weeks, SHHZF was given to the rats which lasted for 10 weeks. Therapeutic effects of SHHZF was compared with that of cyclophosphamide (CTX). High performance liquid-chromatography/electrospray-ionization time of flight mass spectrometer (HPLC/ESI-TOF-MS) combined with pattern recognition approaches including principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), was integrated to approximate the comprehensive metabolic signature and discover differentiating metabolites by Agilent MPP 12.1. The changes in metabolic profiling in plasma were restored to their baseline values after SHHZF treatment according to the PLS-DA score plots. RESULTS The results indicated that 23 ions as "differentiating metabolites". The alterations in those metabolites were associated with perturbations in fatty acid and bile acid metabolism, in response to liver cancer through immune and nervous system. And SHHZF could increase the uptake and utilization of linoleic acid and oleic acid, increase arachidonic acid-like substance content and enhance organism immunity of liver cancer rats. And it also could increase the translation from phosphatidylethanolamine (PE) to phosphatidylcholine (PC), linoleic acid metabolism and inhibits abnormal metabolism of bile acid. CONCLUSIONS The mechanism of therapeutic effects of SHHZF on liver cancer by adjusting the activities of PE N-methyl transferase (PEMT), Lysophospholipase D, methylenetetrahydrofolate reductase (MTHFR) and lysophospholipase was elucidated by the method of metabonomics for the first time.
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MESH Headings
- Animals
- Bile Acids and Salts/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/pathology
- Chromatography, High Pressure Liquid/methods
- Discriminant Analysis
- Drugs, Chinese Herbal/pharmacology
- Least-Squares Analysis
- Lipid Metabolism/drug effects
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Male
- Medicine, Chinese Traditional
- Metabolomics/methods
- Principal Component Analysis
- Rats
- Rats, Sprague-Dawley
- Spectrometry, Mass, Electrospray Ionization/methods
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Affiliation(s)
- Yongrui Bao
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China; Liaoning University of Traditional Chinese Medicine-Agilent Technologies Modern TCM and Multi-omics Research Collaboration Lab, Dalian 116600, PR China
| | - Shuai Wang
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China; Liaoning University of Traditional Chinese Medicine-Agilent Technologies Modern TCM and Multi-omics Research Collaboration Lab, Dalian 116600, PR China
| | - Xinxin Yang
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China
| | - Tianjiao Li
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China
| | - Yueming Xia
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China
| | - Xiansheng Meng
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, PR China; Liaoning University of Traditional Chinese Medicine-Agilent Technologies Modern TCM and Multi-omics Research Collaboration Lab, Dalian 116600, PR China.
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15
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Metabolomic study on the antihypertensive effect of S-1-propenylcysteine in spontaneously hypertensive rats using liquid chromatography coupled with quadrupole-Orbitrap mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1046:147-155. [PMID: 28183044 DOI: 10.1016/j.jchromb.2017.01.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/19/2022]
Abstract
Aged garlic extract (AGE) has been shown to improve hypertension in both clinical trials and experimental animal models. However, the active ingredient of AGE remains unknown. In the present study, we investigated the antihypertensive effects of AGE and its major constituents including S-1-propenylcysteine (S1PC) and S-allylcysteine (SAC) using spontaneously hypertensive rats (SHR) and found that S1PC is an active substance to lower blood pressure in SHR. In addition, the metabolomics approach was used to investigate the potential mechanism of the antihypertensive action of S1PC in SHR. Treatment with AGE (2g/kg body weight) or S1PC (6.5mg/kg body weight; equivalent to AGE 2g/kg body weight) significantly decreased the systolic blood pressure (SBP) of SHR after the repeated administration for 10 weeks, whereas treatment with SAC (7.9mg/kg body weight; equivalent to AGE 2g/kg body weight) did not decrease the SBP. After the treatment for 10 weeks, the plasma samples obtained from Wistar Kyoto (WKY) rats and SHR were analyzed by means of ultra high performance liquid chromatography coupled with high-resolution quadrupole-Orbitrap mass spectrometry. Multivariate statistical analysis of LC-MS data showed a clear difference in the metabolite profiles between WKY rats and SHR. The results indicated that 30 endogenous metabolites significantly contributed to the difference and 7 of 30 metabolites were changed by the S1PC treatment. Furthermore, regression analysis showed correlation between SBP and the plasma levels of betaine, tryptophan and 3 LysoPCs. This metabolomics approach suggested that S1PC could exert its antihypertensive effect by affecting glycine, serine and threonine metabolism, tryptophan metabolism and glycerophospholipid metabolism.
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16
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Protective Effects of Dexrazoxane against Doxorubicin-Induced Cardiotoxicity: A Metabolomic Study. PLoS One 2017; 12:e0169567. [PMID: 28072830 PMCID: PMC5224977 DOI: 10.1371/journal.pone.0169567] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/19/2016] [Indexed: 12/26/2022] Open
Abstract
Cardioprotection of dexrazoxane (DZR) against doxorubicin (DOX)-induced cardiotoxicity is contentious and the indicator is controversial. A pairwise comparative metabolomics approach was used to delineate the potential metabolic processes in the present study. Ninety-six BALB/c mice were randomly divided into two supergroups: tumor and control groups. Each supergroup was divided into control, DOX, DZR, and DOX plus DZR treatment groups. DOX treatment resulted in a steady increase in 5-hydroxylysine, 2-hydroxybutyrate, 2-oxoglutarate, 3-hydroxybutyrate, and decrease in glucose, glutamate, cysteine, acetone, methionine, asparate, isoleucine, and glycylproline.DZR treatment led to increase in lactate, 3-hydroxybutyrate, glutamate, alanine, and decrease in glucose, trimethylamine N-oxide and carnosine levels. These metabolites represent potential biomarkers for early prediction of cardiotoxicity of DOX and the cardioprotective evaluation of DZR.
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17
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Chen R, Wang J, Liao C, Ma N, Zhang L, Wang X. 1H NMR studies on serum metabonomic changes over time in a kidney-Yang deficiency syndrome model. RSC Adv 2017. [DOI: 10.1039/c7ra04057a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The central aim of this study was to investigate metabolite changes in metabolic pathwaysviametabonomic approaches in rats suffering from Kidney-Yang Deficiency Syndrome (KYDS) induced by hydrocortisone.
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Affiliation(s)
- Ruiqun Chen
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Jia Wang
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Chengbin Liao
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Na Ma
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Lei Zhang
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Xiufeng Wang
- School of Basic Courses
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
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18
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Schnackenberg LK, Pence L, Vijay V, Moland CL, George N, Cao Z, Yu LR, Fuscoe JC, Beger RD, Desai VG. Early metabolomics changes in heart and plasma during chronic doxorubicin treatment in B6C3F1 mice. J Appl Toxicol 2016; 36:1486-95. [PMID: 26934058 DOI: 10.1002/jat.3307] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/13/2016] [Accepted: 01/16/2016] [Indexed: 01/13/2023]
Abstract
The present study aimed to identify molecular markers of early stages of cardiotoxicity induced by a potent chemotherapeutic agent, doxorubicin (DOX). Male B6C3F1 mice were dosed with 3 mg kg(-1) DOX or saline via tail vein weekly for 2, 3, 4, 6 or 8 weeks (cumulative DOX doses of 6, 9, 12, 18 or 24 mg kg(-1) , respectively) and euthanized a week after the last dose. Mass spectrometry-based and nuclear magnetic resonance spectrometry-based metabolic profiling were employed to identify initial biomarkers of cardiotoxicity before myocardial injury and cardiac pathology, which were not noted until after the 18 and 24 mg kg(-1) cumulative doses, respectively. After a cumulative dose of 6 mg kg(-1) , 18 amino acids and four biogenic amines (acetylornithine, kynurenine, putrescine and serotonin) were significantly increased in cardiac tissue; 16 amino acids and two biogenic amines (acetylornithine and hydroxyproline) were significantly altered in plasma. In addition, 16 acylcarnitines were significantly increased in plasma and five were significantly decreased in cardiac tissue compared to saline-treated controls. Plasma lactate and succinate, involved in the Krebs cycle, were significantly altered after a cumulative dose of 6 mg kg(-1) . A few metabolites remained altered at higher cumulative DOX doses, which could partly indicate a transition from injury processes at 2 weeks to repair processes with additional injury happening concurrently before myocardial injury at 8 weeks. These altered metabolic profiles in mouse heart and plasma during the initial stages of injury progression due to DOX treatment may suggest these metabolites as candidate early biomarkers of cardiotoxicity. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA.
| | - Lisa Pence
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Vikrant Vijay
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Carrie L Moland
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Nysia George
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Zhijun Cao
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - James C Fuscoe
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
| | - Varsha G Desai
- Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas, 72079, USA
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19
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Yi L, Dong N, Yun Y, Deng B, Ren D, Liu S, Liang Y. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review. Anal Chim Acta 2016; 914:17-34. [PMID: 26965324 DOI: 10.1016/j.aca.2016.02.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 01/03/2023]
Abstract
This review focuses on recent and potential advances in chemometric methods in relation to data processing in metabolomics, especially for data generated from mass spectrometric techniques. Metabolomics is gradually being regarded a valuable and promising biotechnology rather than an ambitious advancement. Herein, we outline significant developments in metabolomics, especially in the combination with modern chemical analysis techniques, and dedicated statistical, and chemometric data analytical strategies. Advanced skills in the preprocessing of raw data, identification of metabolites, variable selection, and modeling are illustrated. We believe that insights from these developments will help narrow the gap between the original dataset and current biological knowledge. We also discuss the limitations and perspectives of extracting information from high-throughput datasets.
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Affiliation(s)
- Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Naiping Dong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Yonghuan Yun
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Baichuan Deng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dabing Ren
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming, 650500, China
| | - Shao Liu
- Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yizeng Liang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
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20
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Niu QY, Li ZY, Du GH, Qin XM. 1 H NMR based metabolomic profiling revealed doxorubicin-induced systematic alterations in a rat model. J Pharm Biomed Anal 2016; 118:338-348. [DOI: 10.1016/j.jpba.2015.10.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
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21
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Qu T, Wang E, Li A, Du G, Li Z, Qin X. NMR based metabolomic approach revealed cyclophosphamide-induced systematic alterations in a rat model. RSC Adv 2016. [DOI: 10.1039/c6ra18600a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A 1H NMR based metabolomics approach combined with biochemical assay had been employed to study the toxicity of CY.
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Affiliation(s)
- Tingli Qu
- Modern Research Center for Traditional Chinese Medicine of Shanxi University
- Taiyuan 030006
- People's Republic of China
- School of Pharmaceutical Science of Shanxi Medical University
- Taiyuan 030001
| | - Erbing Wang
- Chemical and Biological Engineering College of Taiyuan University of Science and Technology
- Taiyuan 030024
- People's Republic of China
| | - Aiping Li
- Modern Research Center for Traditional Chinese Medicine of Shanxi University
- Taiyuan 030006
- People's Republic of China
| | - GuanHua Du
- Modern Research Center for Traditional Chinese Medicine of Shanxi University
- Taiyuan 030006
- People's Republic of China
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
| | - Zhenyu Li
- Modern Research Center for Traditional Chinese Medicine of Shanxi University
- Taiyuan 030006
- People's Republic of China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine of Shanxi University
- Taiyuan 030006
- People's Republic of China
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22
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Zhao L, Xiong Z, Lu X, Zheng S, Wang F, Ge L, Su G, Yang J, Wu C. Metabonomic Evaluation of Chronic Unpredictable Mild Stress-Induced Changes in Rats by Intervention of Fluoxetine by HILIC-UHPLC/MS. PLoS One 2015; 10:e0129146. [PMID: 26080063 PMCID: PMC4469692 DOI: 10.1371/journal.pone.0129146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 05/05/2015] [Indexed: 01/01/2023] Open
Abstract
Hydrophilic interaction-ultra high performance liquid chromatography (HILIC-UHPLC) allows the analysis of highly polar metabolites, providing complementary information to reversed-phase (RP) chromatography. By optimization of the preparation and analytical conditions in HILIC mode, HILIC-UHPLC/MS was applied for the global metabolic profiling of rat plasma samples generated in an experimental model of chronic unpredictable mild stress (CUMS), and the concomitant investigation of the protective effect of fluoxetine was also evaluated. Identification of plasma metabolic profiles indicated that significant changes in specific metabolites occurred after fluoxetine exposure, including increased phenylalanine, serine, acetyl-L-carnitine, carnitine and decreased creatine, betaine, proline, tryptophan, tyrosine, C16:0 LPC. Some novel biomarkers from this HILIC-UHPLC/MS approach were betaine, proline, tyrosine creatine and serine compared with the results of RP-UHPLC/MS. The complementary nature of this technique is confirmed and is on agreement with previously published studies.
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Affiliation(s)
- Longshan Zhao
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Zhili Xiong
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
- * E-mail: (ZLX); (CFW)
| | - Xiumei Lu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Shuning Zheng
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Fang Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning China
| | - Lin Ge
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning China
| | - Guangyue Su
- Department of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Jingyu Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning China
- * E-mail: (ZLX); (CFW)
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23
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Timmerman ME, Hoefsloot HCJ, Smilde AK, Ceulemans E. Scaling in ANOVA-simultaneous component analysis. Metabolomics 2015; 11:1265-1276. [PMID: 26366136 PMCID: PMC4559107 DOI: 10.1007/s11306-015-0785-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/05/2015] [Indexed: 12/01/2022]
Abstract
In omics research often high-dimensional data is collected according to an experimental design. Typically, the manipulations involved yield differential effects on subsets of variables. An effective approach to identify those effects is ANOVA-simultaneous component analysis (ASCA), which combines analysis of variance with principal component analysis. So far, pre-treatment in ASCA received hardly any attention, whereas its effects can be huge. In this paper, we describe various strategies for scaling, and identify a rational approach. We present the approaches in matrix algebra terms and illustrate them with an insightful simulated example. We show that scaling directly influences which data aspects are stressed in the analysis, and hence become apparent in the solution. Therefore, the cornerstone for proper scaling is to use a scaling factor that is free from the effect of interest. This implies that proper scaling depends on the effect(s) of interest, and that different types of scaling may be proper for the different effect matrices. We illustrate that different scaling approaches can greatly affect the ASCA interpretation with a real-life example from nutritional research. The principle that scaling factors should be free from the effect of interest generalizes to other statistical methods that involve scaling, as classification methods.
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Affiliation(s)
- Marieke E. Timmerman
- University of Groningen, Grote Kruisstraat 2/1, 9712TS Groningen, The Netherlands
| | - Huub C. J. Hoefsloot
- Biosystems Data Analysis, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Age K. Smilde
- Biosystems Data Analysis, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Abstract
Being an emerging field of "omics" research, metabonomics has been increasingly used in toxicological studies mostly because this technology has the ability to provide more detailed information to elucidate mechanism of toxicity. As an interdisciplinary field of science, metabonomics combines analytical chemistry, bioinformatics, statistics, and biochemistry. When applied to toxicology, metabonomics also includes aspects of patho-biochemistry, systems biology, and molecular diagnostics. During a toxicological study, the metabolic changes over time and dose after chemical treatment can be monitored. Therefore, the most important use of this emerging technology is the identification of signatures of toxicity-patterns of metabolic changes predictive of a hazard manifestation. This chapter summarizes the current state of metabonomics technology and its applications in various areas of toxicological studies.
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Affiliation(s)
- Liang Zhao
- Center for Alternatives to Animal Testing, Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
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25
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Yi L, Dong N, Yun Y, Deng B, Liu S, Zhang Y, Liang Y. WITHDRAWN: Recent advances in chemometric methods for plant metabolomics: A review. Biotechnol Adv 2014:S0734-9750(14)00183-9. [PMID: 25461504 DOI: 10.1016/j.biotechadv.2014.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 12/17/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming 650500, China.
| | - Naiping Dong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, Hong Kong, China
| | - Yonghuan Yun
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Baichuan Deng
- Department of Chemistry, University of Bergen, Bergen N-5007, Norway
| | - Shao Liu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yizeng Liang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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26
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Detection of hepatotoxicity potential with metabolite profiling (metabolomics) of rat plasma. Toxicol Lett 2014; 230:467-78. [PMID: 25086301 DOI: 10.1016/j.toxlet.2014.07.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 12/14/2022]
Abstract
While conventional parameters used to detect hepatotoxicity in drug safety assessment studies are generally informative, the need remains for parameters that can detect the potential for hepatotoxicity at lower doses and/or at earlier time points. Previous work has shown that metabolite profiling (metabonomics/metabolomics) can detect signals of potential hepatotoxicity in rats treated with doxorubicin at doses that do not elicit hepatotoxicity as monitored with conventional parameters. The current study extended this observation to the question of whether such signals could be detected in rats treated with compounds that can elicit hepatotoxicity in humans (i.e., drug-induced liver injury, DILI) but have not been reported to do so in rats. Nine compounds were selected on the basis of their known DILI potential, with six other compounds chosen as negative for DILI potential. A database of rat plasma metabolite profiles, MetaMap(®)Tox (developed by metanomics GmbH and BASF SE) was used for both metabolite profiles and mode of action (MoA) metabolite signatures for a number of known toxicities. Eight of the nine compounds with DILI potential elicited metabolite profiles that matched with MoA patterns of various rat liver toxicities, including cholestasis, oxidative stress, acetaminophen-type toxicity and peroxisome proliferation. By contrast, only one of the six non-DILI compounds showed a weak match with rat liver toxicity. These results suggest that metabolite profiling may indeed have promise to detect signals of hepatotoxicity in rats treated with compounds having DILI potential.
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27
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Peng J, Cai S, Wang L, Zhao N, Zhang TJ, Chen ZX, Meng FH. A metabonomic analysis of serum from rats treated with ricinine using ultra performance liquid chromatography coupled with mass spectrometry. PLoS One 2014; 9:e90416. [PMID: 24618672 PMCID: PMC3949718 DOI: 10.1371/journal.pone.0090416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/29/2014] [Indexed: 02/07/2023] Open
Abstract
A metabonomic approach based on ultra performance liquid chromatography coupled with mass spectrometry (UPLC/MS) was used to study the hepatotoxicity of ricinine in rats. Potential biomarkers of ricinine toxicity and toxicological mechanism were analyzed by serum metabonomic method. The significant differences in the metabolic profiling of the control and treated rats were clear by using the principal components analysis (PCA) of the chromatographic data. Significant changes of metabolite biomarkers like phenylalanine, tryptophan, cholic acid, LPC and PC were detected in the serum. These biochemical changes were related to the metabolic disorders in amino acids and phospholipids. This research indicates that UPLC/MS-based metabonomic analysis of serum samples can be used to predict the hepatotoxicity and further understand the toxicological mechanism induced by ricinine. This work shows that metabonomics method is a valuable tool in drug mechanism study.
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Affiliation(s)
- Jing Peng
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Shuang Cai
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
- Department of Pharmacy, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lin Wang
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Nan Zhao
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Ting-jian Zhang
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Zai-xing Chen
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Fan-hao Meng
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
- * E-mail:
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28
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Bouhifd M, Hartung T, Hogberg HT, Kleensang A, Zhao L. Review: toxicometabolomics. J Appl Toxicol 2013; 33:1365-83. [PMID: 23722930 PMCID: PMC3808515 DOI: 10.1002/jat.2874] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 02/10/2013] [Accepted: 02/11/2013] [Indexed: 12/19/2022]
Abstract
Metabolomics use in toxicology is rapidly increasing, particularly owing to advances in mass spectroscopy, which is widely used in the life sciences for phenotyping disease states. Toxicology has the advantage of having the disease agent, the toxicant, available for experimental induction of metabolomics changes monitored over time and dose. This review summarizes the different technologies employed and gives examples of their use in various areas of toxicology. A prominent use of metabolomics is the identification of signatures of toxicity - patterns of metabolite changes predictive of a hazard manifestation. Increasingly, such signatures indicative of a certain hazard manifestation are identified, suggesting that certain modes of action result in specific derangements of the metabolism. This might enable the deduction of underlying pathways of toxicity, which, in their entirety, form the Human Toxome, a key concept for implementing the vision of Toxicity Testing for the 21st century. This review summarizes the current state of metabolomics technologies and principles, their uses in toxicology and gives a thorough overview on metabolomics bioinformatics, pathway identification and quality assurance. In addition, this review lays out the prospects for further metabolomics application also in a regulatory context.
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Affiliation(s)
| | - Thomas Hartung
- Correspondence to: T. Hartung, Johns Hopkins Bloomberg School of Public Health, Environmental Health Sciences, Chair for Evidence-based Toxicology, Center for Alternatives to Animal Testing, 615 N. Wolfe St., Baltimore, MD, 21205, USA.
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van der Greef J, van Wietmarschen H, van Ommen B, Verheij E. Looking back into the future: 30 years of metabolomics at TNO. MASS SPECTROMETRY REVIEWS 2013; 32:399-415. [PMID: 23630115 DOI: 10.1002/mas.21370] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/21/2012] [Accepted: 11/21/2012] [Indexed: 06/02/2023]
Abstract
Metabolites have played an essential role in our understanding of life, health, and disease for thousands of years. This domain became much more important after the concept of metabolism was discovered. In the 1950s, mass spectrometry was coupled to chromatography and made the technique more application-oriented and allowed the development of new profiling technologies. Since 1980, TNO has performed system-based metabolic profiling of body fluids, and combined with pattern recognition has led to many discoveries and contributed to the field known as metabolomics and systems biology. This review describes the development of related concepts and applications at TNO in the biomedical, pharmaceutical, nutritional, and microbiological fields, and provides an outlook for the future.
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Recent advances in metabolomics in neurological disease, and future perspectives. Anal Bioanal Chem 2013; 405:8143-50. [DOI: 10.1007/s00216-013-7061-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/04/2013] [Accepted: 05/10/2013] [Indexed: 12/14/2022]
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Ding W, Qiu P, Liu YH, Feng W. Current Omics Technologies in Biomarker Discovery. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Biomarkers are playing an increasingly important role in drug discovery and development and can be applied for many purposes, including disease mechanism study, diagnosis, prognosis, staging, and treatment selection. Advances in high-throughput “omics” technologies, including genomics, transcriptomics, proteomics and metabolomics, significantly accelerate the pace of biomarker discovery. Comprehensive molecular profiling using these “omics” technology has become a field of intensive research aiming at identifying biomarkers relevant for improved diagnostics and therapeutics. Although each “omics” technology plays important roles in biomarker research, different “omics” platforms have different strengths and limitations. This chapter aims to give an overview of these “omics” technologies and their current application in the biomarker discovery.
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Zhang A, Sun H, Wu X, Wang X. Urine metabolomics. Clin Chim Acta 2012; 414:65-9. [DOI: 10.1016/j.cca.2012.08.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/11/2012] [Accepted: 08/20/2012] [Indexed: 12/14/2022]
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Jiang JW, Ren ZG, Cui GY, Zhang Z, Xie HY, Zhou L. Chronic bile duct hyperplasia is a chronic graft dysfunction following liver transplantation. World J Gastroenterol 2012; 18:1038-47. [PMID: 22416178 PMCID: PMC3296977 DOI: 10.3748/wjg.v18.i10.1038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/11/2012] [Accepted: 02/08/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate pathological types and influential factors of chronic graft dysfunction (CGD) following liver transplantation (LT) in rats.
METHODS: The whole experiment was divided into three groups: (1) normal group (n = 12): normal BN rats without any drug or operation; (2) syngeneic transplant group (SGT of BN-BN, n = 12): both donors and recipients were BN rats; and (3) allogeneic transplant group (AGT of LEW-BN, n = 12): Donors were Lewis and recipients were BN rats. In the AGT group, all recipients were subcutaneously injected by Cyclosporin A after LT. Survival time was observed for 1 year. All the dying rats were sampled, biliary tract tissues were performed bacterial culture and liver tissues for histological study. Twenty-one day after LT, 8 rats were selected randomly in each group for sampling. Blood samples from caudal veins were collected for measurements of plasma endotoxin, cytokines and metabonomic analysis, and faeces were analyzed for intestinal microflora.
RESULTS: During the surgery of LT, no complications of blood vessels or bile duct happened, and all rats in each group were still alive in the next 2 wk. The long term observation revealed that a total of 8 rats in the SGT and AGT groups died of hepatic graft diseases, 5 rats in which died of chronic bile duct hyperplasia. Compared to the SGT and normal groups, survival ratio of rats significantly decreased in the AGT group (P < 0.01). Moreover, liver necrosis, liver infection, and severe chronic bile duct hyperplasia were observed in the AGT group by H and E stain. On 21 d after LT, compared with the normal group (25.38 ± 7.09 ng/L) and SGT group (33.12 ± 10.26 ng/L), plasma endotoxin in the AGT group was remarkably increased (142.86 ± 30.85 ng/L) (both P < 0.01). Plasma tumor necrosis factor-α and interleukin-6 were also significantly elevated in the AGT group (593.6 ± 171.67 pg/mL, 323.8 ± 68.30 pg/mL) vs the normal (225.5 ± 72.07 pg/mL, 114.6 ± 36.67 pg/mL) and SGT groups (321.3 ± 88.47 pg/mL, 205.2 ± 53.06 pg/mL) (P < 0.01). Furthermore, Bacterial cultures of bile duct tissues revealed that the rats close to death from the SGT and AGT groups were strongly positive, while those from the normal group were negative. The analysis of intestinal microflora was performed. Compared to the normal group (7.98 ± 0.92, 8.90 ± 1.44) and SGT group (8.51 ± 0.46, 9.43 ± 0.69), the numbers of Enterococcus and Enterobacteria in the AGT group (8.76 ± 1.93, 10.18 ± 1.64) were significantly increased (both P < 0.01). Meanwhile, compared to the normal group (9.62 ± 1.60, 9.93 ± 1.10) and SGT group (8.95 ± 0.04, 9.02 ± 1.14), the numbers of Bifidobacterium and Lactobacillus in the AGT group (7.83 ± 0.72, 8.87 ± 0.13) were remarkably reduced (both P < 0.01). In addition, metabonomics analysis showed that metabolic profiles of plasma in rats in the AGT group were severe deviated from the normal and SGT groups.
CONCLUSION: Chronic bile duct hyperplasia is a pathological type of CGD following LT in rats. The mechanism of this kind of CGD is associated with the alterations of inflammation, intestinal barrier function and microflora as well as plasma metabolic profiles.
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Recent and potential developments of biofluid analyses in metabolomics. J Proteomics 2012; 75:1079-88. [DOI: 10.1016/j.jprot.2011.10.027] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 10/21/2011] [Accepted: 10/26/2011] [Indexed: 12/14/2022]
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Jiang H, Nie L, Li Y, Xie J. Application of ultra-performance liquid chromatography coupled with mass spectrometry to metabonomic study on spontaneously hypertensive rats and intervention effects of Ping Gan prescription. J Sep Sci 2012; 35:483-9. [DOI: 10.1002/jssc.201100769] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Nieto CI, Ángeles García M, Ángeles Farrán M, Claramunt RM, Carmen Torralba M, Rosario Torres M, Alkorta I, Elguero J. Two polymorphs of 8-hydroxycarbostyril: X-ray crystallography, solid-state NMR and DFT calculations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.11.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mishur RJ, Rea SL. Applications of mass spectrometry to metabolomics and metabonomics: detection of biomarkers of aging and of age-related diseases. MASS SPECTROMETRY REVIEWS 2012; 31:70-95. [PMID: 21538458 DOI: 10.1002/mas.20338] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 05/20/2023]
Abstract
Every 5 years or so new technologies, or new combinations of old ones, seemingly burst onto the science scene and are then sought after until they reach the point of becoming commonplace. Advances in mass spectrometry instrumentation, coupled with the establishment of standardized chemical fragmentation libraries, increased computing power, novel data-analysis algorithms, new scientific applications, and commercial prospects have made mass spectrometry-based metabolomics the latest sought-after technology. This methodology affords the ability to dynamically catalogue and quantify, in parallel, femtomole quantities of cellular metabolites. The study of aging, and the diseases that accompany it, has accelerated significantly in the last decade. Mutant genes that alter the rate of aging have been found that increase lifespan by up to 10-fold in some model organisms, and substantial progress has been made in understanding fundamental alterations that occur at both the mRNA and protein level in tissues of aging organisms. The application of metabolomics to aging research is still relatively new, but has already added significant insight into the aging process. In this review we summarize these findings. We have targeted our manuscript to two audiences: mass spectrometrists interested in applying their technical knowledge to unanswered questions in the aging field, and gerontologists interested in expanding their knowledge of both mass spectrometry and the most recent advances in aging-related metabolomics.
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Affiliation(s)
- Robert J Mishur
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA.
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Castro-Melchor M, Le H, Hu WS. Transcriptome data analysis for cell culture processes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:27-70. [PMID: 22194060 DOI: 10.1007/10_2011_116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the past decade, DNA microarrays have fundamentally changed the way we study complex biological systems. By measuring the expression levels of thousands of transcripts, the paradigm of studying organisms has shifted from focusing on the local phenomena of a few genes to surveying the whole genome. DNA microarrays are used in a variety of ways, from simple comparisons between two samples to more intricate time-series studies. With the large number of genes being studied, the dimensionality of the problem is inevitably high. The analysis of microarray data thus requires specific approaches. In the case of time-series microarray studies, data analysis is further complicated by the correlation between successive time points in a series.In this review, we survey the methodologies used in the analysis of static and time-series microarray data, covering data pre-processing, identification of differentially expressed genes, profile pattern recognition, pathway analysis, and network reconstruction. When available, examples of their use in mammalian cell cultures are presented.
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Smilde AK, Timmerman ME, Hendriks MMWB, Jansen JJ, Hoefsloot HCJ. Generic framework for high-dimensional fixed-effects ANOVA. Brief Bioinform 2011; 13:524-35. [PMID: 22199378 DOI: 10.1093/bib/bbr071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In functional genomics it is more rule than exception that experimental designs are used to generate the data. The samples of the resulting data sets are thus organized according to this design and for each sample many biochemical compounds are measured, e.g. typically thousands of gene-expressions or hundreds of metabolites. This results in high-dimensional data sets with an underlying experimental design. Several methods have recently become available for analyzing such data while utilizing the underlying design. We review these methods by putting them in a unifying and general framework to facilitate understanding the (dis-)similarities between the methods. The biological question dictates which method to use and the framework allows for building new methods to accommodate a range of such biological questions. The framework is built on well known fixed-effect ANOVA models and subsequent dimension reduction. We present the framework both in matrix algebra as well as in more insightful geometrical terms. We show the workings of the different special cases of our framework with a real-life metabolomics example from nutritional research and a gene-expression example from the field of virology.
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Affiliation(s)
- Age K Smilde
- Department of Biosystems Data Analysis, University of Amsterdam, The Netherlands.
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Tan G, Lou Z, Liao W, Zhu Z, Dong X, Zhang W, Li W, Chai Y. Potential biomarkers in mouse myocardium of doxorubicin-induced cardiomyopathy: a metabonomic method and its application. PLoS One 2011; 6:e27683. [PMID: 22110719 PMCID: PMC3218026 DOI: 10.1371/journal.pone.0027683] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/21/2011] [Indexed: 01/21/2023] Open
Abstract
Background Doxorubicin (DOX) is one of the most potent antitumor agents available; however, its clinical use is limited because of the risk of severe cardiotoxicity. Though numerous studies have ascribed DOX cardiomyopathy to specific cellular pathways, the precise mechanism remains obscure. Sini decoction (SND) is a well-known formula of Traditional Chinese Medicine (TCM) and is considered as efficient agents against DOX-induced cardiomyopathy. However, its action mechanisms are not well known due to its complex components. Methodology/Principal Findings A tissue-targeted metabonomic method using gas chromatography–mass spectrometry was developed to characterize the metabolic profile of DOX-induced cardiomyopathy in mice. With Elastic Net for classification and selection of biomarkers, twenty-four metabolites corresponding to DOX-induced cardiomyopathy were screened out, primarily involving glycolysis, lipid metabolism, citrate cycle, and some amino acids metabolism. With these altered metabolic pathways as possible drug targets, we systematically analyzed the protective effect of TCM SND, which showed that SND administration could provide satisfactory effect on DOX-induced cardiomyopathy through partially regulating the perturbed metabolic pathways. Conclusions/Significance The results of the present study not only gave rise to a systematic view of the development of DOX-induced cardiomyopathy but also provided the theoretical basis to prevent or modify expected damage.
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Affiliation(s)
- Guangguo Tan
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Ziyang Lou
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Wenting Liao
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Zhenyu Zhu
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Xin Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Wei Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Wuhong Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
- * E-mail:
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Yu Y, Ma C, Bi K, Yang G, Xie P, Wang J, Chen XH. A metabonomic analysis of urine from rats treated with rhizoma alismatis using ultra-performance liquid chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2633-2640. [PMID: 23657958 DOI: 10.1002/rcm.5163] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 06/02/2023]
Abstract
A metabonomic approach based on ultra-performance liquid chromatography coupled to mass spectrometry (UPLC/MS) was used to study the nephrotoxicity of rhizoma alismatis (RA) in rats. Potential biomarkers of RA toxicity were identified and the toxicological mechanism is discussed. Urine samples were collected from control and treated rats at various stages and analyzed by UPLC/MS in positive ionization mode. Histopathological analysis was used to evaluate renal function. The differences in the metabolic profiles of the control and treated rats were clearly distinguishable with principal components analysis (PCA) of the chromatographic data, and significant changes in 13 metabolite biomarkers were detected in the urine. This metabonomic method combined with PCA could discriminate the treated rats from the control rats on days 60, 120, and 180 after treatment, before serious organic renal damage was apparent on day 180 with histopathology. This research indicates that UPLC/MS-based metabonomic analysis of urine samples can be used to predict the chronic nephrotoxicity induced by rhizoma alismatis.
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Affiliation(s)
- Yue Yu
- Department of Pharmaceutical Analysis, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, PR China
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Analysis of anticancer drugs: a review. Talanta 2011; 85:2265-89. [PMID: 21962644 DOI: 10.1016/j.talanta.2011.08.034] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 01/05/2023]
Abstract
In the last decades, the number of patients receiving chemotherapy has considerably increased. Given the toxicity of cytotoxic agents to humans (not only for patients but also for healthcare professionals), the development of reliable analytical methods to analyse these compounds became necessary. From the discovery of new substances to patient administration, all pharmaceutical fields are concerned with the analysis of cytotoxic drugs. In this review, the use of methods to analyse cytotoxic agents in various matrices, such as pharmaceutical formulations and biological and environmental samples, is discussed. Thus, an overview of reported analytical methods for the determination of the most commonly used anticancer drugs is given.
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Wang X, Sun H, Zhang A, Wang P, Han Y. Ultra-performance liquid chromatography coupled to mass spectrometry as a sensitive and powerful technology for metabolomic studies. J Sep Sci 2011; 34:3451-9. [DOI: 10.1002/jssc.201100333] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 07/01/2011] [Accepted: 07/03/2011] [Indexed: 12/11/2022]
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Cai X, Dong J, Zou L, Xue X, Zhang X, Liang X. Metabonomic Study of Lung Cancer and the Effects of Radiotherapy on Lung Cancer Patients: Analysis of Highly Polar Metabolites by Ultraperformance HILIC Coupled with Q-TOF MS. Chromatographia 2011. [DOI: 10.1007/s10337-011-2077-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Characterization and identification of pradimicin analogs from Actinomadura hibisca using liquid chromatography–tandem mass spectrometry. J Chromatogr A 2011; 1218:2284-91. [DOI: 10.1016/j.chroma.2011.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 11/21/2022]
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Wang X, Sun H, Zhang A, Sun W, Wang P, Wang Z. Potential role of metabolomics apporoaches in the area of traditional Chinese medicine: as pillars of the bridge between Chinese and Western medicine. J Pharm Biomed Anal 2011; 55:859-68. [PMID: 21353755 DOI: 10.1016/j.jpba.2011.01.042] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/27/2011] [Accepted: 01/31/2011] [Indexed: 02/08/2023]
Abstract
Traditional Chinese medicine (TCM) is a holistic approach to health that attempts to bring the body, mind and spirit into harmony. Entering 21st century, TCM is getting more and more popular in the whole world for improving health condition of human beings and preventing or healing diseases, especially shows great advantages in early intervention, combination therapies and personalized medicine, etc. However, like almost all other ethnopharmacology, TCM also faces severe challenges and suffers from insufficient modern research owing to lack of scientific and technologic approaches, restricts the development of TCM in the world. Fortunately, a novel analytical technique, metabolomics (or metabonomics), adopts a 'top-down' strategy to reflect the function of organisms from terminal symptoms of metabolic network and understand metabolic changes of a complete system caused by interventions in holistic context. Its property consists with the holistic thinking of TCM, may beneficially provide an opportunity to scientifically express the meaning of evidence-based Chinese medicine, such as Chinese medicine syndromes (CMS), preventive treatment, action of Chinese medicine, Chinese medical formulae (CMF) and acupuncture efficacy. This review summarizes potential applications of robust metabolomics apporoaches in the area of traditional oriental medicine, and highlights the key role of metabolomics to resolve special TCM issues.
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Affiliation(s)
- Xijun Wang
- National TCM Key Lab of Serum Pharmacochemistry, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China.
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Roux A, Lison D, Junot C, Heilier JF. Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review. Clin Biochem 2011; 44:119-35. [DOI: 10.1016/j.clinbiochem.2010.08.016] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 01/01/2023]
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