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Michalska-Falkowska A, Niklinski J, Juhl H, Sulewska A, Kisluk J, Charkiewicz R, Ciborowski M, Ramlau R, Gryczka R, Piwkowski C, Kozlowski M, Miskiewicz B, Biecek P, Wnorowska K, Dzieciol-Anikiej Z, Sargsyan K, Naumnik W, Mroz R, Reszec-Gielazyn J. Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach. Cancers (Basel) 2023; 15:3742. [PMID: 37509403 PMCID: PMC10378006 DOI: 10.3390/cancers15143742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content. Molecular quality control measures included evaluating the RNA integrity number, assessing cDNA library quality and quantity, and analyzing NGS raw data. Our study yielded the creation of distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples. These workflows offer customization options to suit the capabilities of different biobanking entities. In order to ensure the appropriateness of biospecimens for advanced research applications, we introduced molecular-based quality control methods that align with the demands of high-throughput assays. The novelty of proposed workflows, rooted in innovative molecular techniques, lies in the integration of these QC methods into a comprehensive schema specifically designed for high-throughput research applications.
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Affiliation(s)
- Anna Michalska-Falkowska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Indivumed Services, 20251 Hamburg, Germany
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | | | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Robert Gryczka
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Cezary Piwkowski
- Department of Thoracic Surgery, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Borys Miskiewicz
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Karolina Wnorowska
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Paediatrics and Pediatric Neurology, Jedrzej Sniadecki Independent Public Healthcare Centre Regional Hospital, 15-278 Bialystok, Poland
| | - Zofia Dzieciol-Anikiej
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Rehabilitation, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Karine Sargsyan
- International Biobanking and Education, Medical University of Graz, 8036 Graz, Austria
- Cancer Biobank at Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Joanna Reszec-Gielazyn
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
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De Oro-Carretero P, Sanz-Landaluze J. Miniaturized method for the quantification of persistent organic pollutants and their metabolites in HepG2 cells: assessment of their biotransformation. Anal Bioanal Chem 2023:10.1007/s00216-023-04781-w. [PMID: 37289209 DOI: 10.1007/s00216-023-04781-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Biotransformation can greatly influence the accumulation and, subsequently, toxicity of substances in living beings. Although traditionally these studies to quantify metabolization of a compound have been carried out with in vivo species, currently, in vitro test methods with very different cell lines are being developed for their evaluation. However, this is still a very limited field due to multiple variables of a very diverse nature. So, an increasing number of analytical chemists are working with cells or other similar biological samples of very small size. This makes it necessary to address the development of analytical methods that allow determining their concentration both inside the cells and in their exposure medium. The aim of this study is to develop a set of analytical methodologies for the quantification of polycyclic aromatic hydrocarbons, PAHs (phenanthrene, PHE), and polybrominated diphenyl ethers, PBDEs (2,2',4,4'-tetrabromodiphenyl ether, BDE-47), and their major metabolites in cells and their exposure medium. Analytical methodologies, based on miniaturized ultrasound probe-assisted extraction, gas chromatography-mass spectrometry-microelectron capture detector (GC-MS-µECD), and liquid chromatography-fluorescence detector (LC-FL) determination techniques, have been optimized and then applied to a biotransformation study in HepG2 at 48 h of exposure. Significant concentrations of the major metabolites of PHE (1-OH, 2-OH, 3-OH, 4-OH-, and 9-OH-PHE) and BDE-47 (5-MeO-, 5-OH-, and 3-OH-BDE-47) were detected and quantified inside the cells and in the exposure medium. These results provide a new method for determination and improve information on the metabolization ratios for a better knowledge of the metabolic pathways and their toxicity.
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Affiliation(s)
- Paloma De Oro-Carretero
- Department of Analytical Chemistry, Faculty of Chemical Science, Complutense University of Madrid, Avenida Complutense S/N, 28040, Madrid, Spain.
| | - Jon Sanz-Landaluze
- Department of Analytical Chemistry, Faculty of Chemical Science, Complutense University of Madrid, Avenida Complutense S/N, 28040, Madrid, Spain
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Araújo AM, Carvalho F, Guedes de Pinho P, Carvalho M. Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions. Metabolites 2021; 11:692. [PMID: 34677407 PMCID: PMC8539642 DOI: 10.3390/metabo11100692] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
Given the high biological impact of classical and emerging toxicants, a sensitive and comprehensive assessment of the hazards and risks of these substances to organisms is urgently needed. In this sense, toxicometabolomics emerged as a new and growing field in life sciences, which use metabolomics to provide new sets of susceptibility, exposure, and/or effects biomarkers; and to characterize in detail the metabolic responses and altered biological pathways that various stressful stimuli cause in many organisms. The present review focuses on the analytical platforms and the typical workflow employed in toxicometabolomic studies, and gives an overview of recent exploratory research that applied metabolomics in various areas of toxicology.
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Affiliation(s)
- Ana Margarida Araújo
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Félix Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Márcia Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
- FP-I3ID, FP-ENAS, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004 Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto, Portugal
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Metabolic profiling of organic acids in urine samples of Cri Du Chat syndrome individuals by gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1153:122267. [DOI: 10.1016/j.jchromb.2020.122267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/11/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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Yong-Ping L, Reichetzeder C, Prehn C, Yin LH, Chu C, Elitok S, Krämer BK, Adamski J, Hocher B. Impact of maternal smoking associated lyso-phosphatidylcholine 20:3 on offspring brain development. J Steroid Biochem Mol Biol 2020; 199:105591. [PMID: 31954177 DOI: 10.1016/j.jsbmb.2020.105591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 11/24/2022]
Abstract
Maternal smoking during pregnancy affects fetal neurological development. Metabolomic studies in the general population suggest that smoking is associated with characteristic metabolic alterations. We investigated the association between the maternal smoking status, the fetal metabolome and head circumference at birth, as a surrogate parameter of brain development. 320 mother/newborn pairs of the Berlin Birth Cohort were investigated. Anthropometric parameters, including head circumference, of newborns of smoking mothers, former smoking mothers, and never smoking mothers were compared to assess the impact of maternal smoking behavior. Associations between maternal smoking behavior and 163 cord blood metabolites and associations between newborn head circumference and concentrations of smoking behavior related metabolites were analysed. Male newborns of smoking mothers had a reduced head circumference when compared with newborns from former smoking and never smoking mothers (p < 0.05). Using linear regression models corrected for established confounding factors, maternal smoking during pregnancy showed an independent association with head circumference (95% CI: -0.75~-0.41 cm, p = 2.45×10-11). In a stepwise linear regression model corrected for known confounding factors of brain growth lyso-phosphatidylcholine 20:3 (95% CI: 6.68~39.88 cm, p = 4.62×10-4) was associated with head circumference in male offspring only. None of the metabolites were associated with head circumference of female newborns. In conclusion, maternal smoking during pregnancy impacted on male offspring's development including brain development. The smoking related metabolite lyso-phosphatidylcholine 20:3 was associated with head circumference of male offspring.
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Affiliation(s)
- Lu Yong-Ping
- Department of Nephrology, the First Affiliated Hospital of Jinan University, Guangzhou, China; Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Christoph Reichetzeder
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Potsdam-Rehbrücke, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Liang-Hong Yin
- Department of Nephrology, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Chang Chu
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Saban Elitok
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany; Department of Nephrology, Klinikum Ernst Von Bergmann, Potsdam, Germany
| | - Bernhard K Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Berthold Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
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Mussap M, Loddo C, Fanni C, Fanos V. Metabolomics in pharmacology - a delve into the novel field of pharmacometabolomics. Expert Rev Clin Pharmacol 2020; 13:115-134. [PMID: 31958027 DOI: 10.1080/17512433.2020.1713750] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Pharmacometabolomics is an emerging science pursuing the application of precision medicine. Combining both genetic and environmental factors, the so-called pharmacometabolomic approach guides patient selection and stratification in clinical trials and optimizes personalized drug dosage, improving efficacy and safety.Areas covered: This review illustrates the progressive introduction of pharmacometabolomics as an innovative solution for enhancing the discovery of novel drugs and improving research and development (R&D) productivity of the pharmaceutical industry. An extended analysis on published pharmacometabolomics studies both in animal models and humans includes results obtained in several areas such as hepatology, gastroenterology, nephrology, neuropsychiatry, oncology, drug addiction, embryonic cells, neonatology, and microbiomics.Expert opinion: a tailored, individualized therapy based on the optimization of pharmacokinetics and pharmacodynamics, the improvement of drug efficacy, and the abolition of drug toxicity and adverse drug reactions is a key issue in precision medicine. Genetics alone has become insufficient for deciphring intra- and inter-individual variations in drug-response, since they originate both from genetic and environmental factors, including human microbiota composition. The association between pharmacogenomics and pharmacometabolomics may be considered the new strategy for an in-deep knowledge on changes and alterations in human and microbial metabolic pathways due to the action of a drug.
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Affiliation(s)
- Michele Mussap
- Laboratory Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | | | - Claudia Fanni
- Division of Pediatrics, Rovigo Hospital, Rovigo, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Neonatal Pathology and Neonatal Section, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
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Deng P, Li X, Petriello MC, Wang C, Morris AJ, Hennig B. Application of metabolomics to characterize environmental pollutant toxicity and disease risks. REVIEWS ON ENVIRONMENTAL HEALTH 2019; 34:251-259. [PMID: 31408434 PMCID: PMC6915040 DOI: 10.1515/reveh-2019-0030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/23/2019] [Indexed: 05/08/2023]
Abstract
The increased incidence of non-communicable human diseases may be attributed, at least partially, to exposures to toxic chemicals such as persistent organic pollutants (POPs), air pollutants and heavy metals. Given the high mortality and morbidity of pollutant exposure associated diseases, a better understanding of the related mechanisms of toxicity and impacts on the endogenous host metabolism are needed. The metabolome represents the collection of the intermediates and end products of cellular processes, and is the most proximal reporter of the body's response to environmental exposures and pathological processes. Metabolomics is a powerful tool for studying how organisms interact with their environment and how these interactions shape diseases related to pollutant exposure. This mini review discusses potential biological mechanisms that link pollutant exposure to metabolic disturbances and chronic human diseases, with a focus on recent studies that demonstrate the application of metabolomics as a tool to elucidate biochemical modes of actions of various environmental pollutants. In addition, classes of metabolites that have been shown to be modulated by multiple environmental pollutants will be discussed with an emphasis on their use as potential early biomarkers of disease risks. Taken together, metabolomics is a useful and versatile tool for characterizing the disease risks and mechanisms associated with various environmental pollutants.
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Affiliation(s)
- Pan Deng
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA 40536
| | - Xusheng Li
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou, PR China 510632
| | - Michael C. Petriello
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Division of Cardiovascular Medicine, College of Medicine, University of Kentucky, and Lexington Veterans Affairs Medical Center, Lexington, KY, USA 40536
| | - Chunyan Wang
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA 40536
| | - Andrew J. Morris
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Division of Cardiovascular Medicine, College of Medicine, University of Kentucky, and Lexington Veterans Affairs Medical Center, Lexington, KY, USA 40536
| | - Bernhard Hennig
- Superfund Research Center, University of Kentucky, Lexington, KY, USA 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA 40536
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh Davandra Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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Lin Y, Zeng Q, Lin L, Chen Z. High Resolution Nuclear Magnetic Resonance Spectroscopy on Biological Tissue and Metabolomics. Curr Med Chem 2019; 26:2190-2207. [DOI: 10.2174/0929867326666190312130155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/14/2017] [Accepted: 01/25/2018] [Indexed: 11/22/2022]
Abstract
High-resolution nuclear magnetic resonance (NMR) spectroscopy is a universal
analytical tool. It can provide detailed information on chemical shifts, J coupling constants,
multiplet patterns, and relative peak areas. It plays an important role in the fields of chemistry,
biology, medicine, and pharmacy. A highly homogeneous magnetic field is a prerequisite for
excellent spectral resolution. However, in some cases, such as in vivo and ex vivo biological
tissues, the magnetic field inhomogeneity due to magnetic susceptibility variation in samples
is unavoidable and hard to eliminate by conventional methods. The techniques based on intermolecular
multiple quantum coherences and conventional single quantum coherence can
remove the influence of the field inhomogeneity effects and be applied to obtain highresolution
NMR spectra of biological tissues, including in vivo animal and human tissues.
Broadband 1H homo-decoupled NMR spectroscopy displays J coupled resonances as collapsed
singlets, resulting in highly resolved spectra. It can be used to acquire high-resolution
spectra of some pharmaceuticals. The J-difference edited spectra can be used to detect J coupled
metabolites, such as γ-aminobutyric acid, the detection of which is interfered by intense
neighboring peaks. High-resolution 1H NMR spectroscopy has been widely utilized for the
identification and characterization of biological fluids, constituting an important tool in drug
discovery, drug development, and disease diagnosis.
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Affiliation(s)
- Yanqin Lin
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Qing Zeng
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Liangjie Lin
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Zhong Chen
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
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Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 515] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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Fei Q, Wang D, Jasbi P, Zhang P, Nagana Gowda GA, Raftery D, Gu H. Combining NMR and MS with Chemical Derivatization for Absolute Quantification with Reduced Matrix Effects. Anal Chem 2019; 91:4055-4062. [DOI: 10.1021/acs.analchem.8b05611] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Qiang Fei
- College of Chemistry, Jilin University, Changchun 130021, P. R. China
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Dongfang Wang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- Chongqing Blood Center, Chongqing 400015, P. R. China
| | - Paniz Jasbi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Ping Zhang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - G. A. Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
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Freire RT, Bero J, Beaufay C, Selegato DM, Coqueiro A, Choi YH, Quetin-Leclercq J. Identification of antiplasmodial triterpenes from Keetia species using NMR-based metabolic profiling. Metabolomics 2019; 15:27. [PMID: 30830464 PMCID: PMC6394458 DOI: 10.1007/s11306-019-1487-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The increase in multidrug resistance and lack of efficacy in malaria therapy has propelled the urgent discovery of new antiplasmodial drugs, reviving the screening of secondary metabolites from traditional medicine. In plant metabolomics, NMR-based strategies are considered a golden method providing both a holistic view of the chemical profiles and a correlation between the metabolome and bioactivity, becoming a corner stone of drug development from natural products. OBJECTIVE Create a multivariate model to identify antiplasmodial metabolites from 1H NMR data of two African medicinal plants, Keetia leucantha and K. venosa. METHODS The extracts of twigs and leaves of Keetia species were measured by 1H NMR and the spectra were submitted to orthogonal partial least squares (OPLS) for antiplasmodial correlation. RESULTS Unsupervised 1H NMR analysis showed that the effect of tissues was higher than species and that triterpenoids signals were more associated to Keetia twigs than leaves. OPLS-DA based on Keetia species correlated triterpene signals to K. leucantha, exhibiting a higher concentration of triterpenoids and phenylpropanoid-conjugated triterpenes than K. venosa. In vitro antiplasmodial correlation by OPLS, validated for all Keetia samples, revealed that phenylpropanoid-conjugated triterpenes were highly correlated to the bioactivity, while the acyclic squalene was found as the major metabolite in low bioactivity samples. CONCLUSION NMR-based metabolomics combined with supervised multivariate data analysis is a powerful strategy for the identification of bioactive metabolites in plant extracts. Moreover, combination of statistical total correlation spectroscopy with 2D NMR allowed a detailed analysis of different triterpenes, overcoming the challenge posed by their structure similarity and coalescence in the aliphatic region.
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Affiliation(s)
- Rafael Teixeira Freire
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Joanne Bero
- Pharmacognosy Research Group, Louvain Drug Research Institute, Université catholique de Louvain, UCLouvain, Avenue E. Mounier, 72, B1.72.03, B- 1200, Brussels, Belgium
| | - Claire Beaufay
- Pharmacognosy Research Group, Louvain Drug Research Institute, Université catholique de Louvain, UCLouvain, Avenue E. Mounier, 72, B1.72.03, B- 1200, Brussels, Belgium
| | - Denise Medeiros Selegato
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Aline Coqueiro
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute, Université catholique de Louvain, UCLouvain, Avenue E. Mounier, 72, B1.72.03, B- 1200, Brussels, Belgium.
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15
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Aggarwal D, Arumalla N, Jethwa H, Abraham S. The use of biomarkers as a tool for novel psoriatic disease drug discovery. Expert Opin Drug Discov 2018; 13:875-887. [PMID: 30124339 DOI: 10.1080/17460441.2018.1508206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Psoriatic disease is a relatively new term which encompasses psoriatic arthritis, psoriasis, and associated comorbidities. In this heterogeneous condition, the study of biomarkers is necessary to direct best therapy. Resulting in significant disability and socioeconomic burden, recent recommendations stress the need for tight control in psoriatic disease. Areas covered: The authors outline recent advances in the understanding of psoriatic disease pathogenesis which has highlighted multiple biomarkers that have been pursued as drug targets with varying degrees of success. Current drugs targeting biomarkers and therapies in development are evaluated. The methods of biomarker discovery through genomics, transcriptomics, proteomics, metabolomics, and study of the microbiome are also discussed. Expert opinion: Targeting biomarkers for therapeutic benefit appears to a promising field with multiple success stories, notably those associated with signaling through T-helper-17 cells. The use of genomics, transcriptomics, proteomics, and more recently metabolomics will help individualize targeted biomarker therapies, assist in monitoring therapeutic success, and ultimately yield novel therapeutic targets. Advances in the development of novel biologic molecules targeting more than one cytokine may offer additional gains in therapeutic response.
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Affiliation(s)
- Dinesh Aggarwal
- a Department of Infectious Diseases , Chelsea and Westminster Hospital , London , UK
| | | | - Hannah Jethwa
- c Department of Rheumatology , Ealing Hospital , Southall , UK
| | - Sonya Abraham
- d Department of Rheumatology , Hammersmith Hospital , London , UK.,e Department of Rheumatology , Imperial College Healthcare NHS Trust , London , UK
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16
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van den Brink WJ, Hankemeier T, van der Graaf PH, de Lange ECM. Bundling arrows: improving translational CNS drug development by integrated PK/PD-metabolomics. Expert Opin Drug Discov 2018. [DOI: 10.1080/17460441.2018.1446935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- W. J. van den Brink
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - T. Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - P. H. van der Graaf
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Certara QSP, Canterbury Innovation House, Canterbury, United Kingdom
| | - E. C. M. de Lange
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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Chiu KH, Dong CD, Chen CF, Tsai ML, Ju YR, Chen TM, Chen CW. NMR-based metabolomics for the environmental assessment of Kaohsiung Harbor sediments exemplified by a marine amphipod (Hyalella azteca). MARINE POLLUTION BULLETIN 2017; 124:714-724. [PMID: 28267993 DOI: 10.1016/j.marpolbul.2017.02.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 02/21/2017] [Accepted: 02/24/2017] [Indexed: 05/08/2023]
Abstract
Inflow of wastewater from upstream causes a large flux of pollutants to enter Kaohsiung Harbor in Taiwan daily. To reveal the ecological risk posed by Kaohsiung Harbor sediments, an ecological metabolomic approach was employed to investigate environmental factors pertinent to the physiological regulation of the marine amphipod Hyalella azteca. The amphipods were exposed to sediments collected from different stream inlets of the Love River (LR), Canon River (CR), Jen-Gen River (JR), and Salt River (SR). Harbor entrance 1 (E1) was selected as a reference site. After 10-day exposure, metabolomic analysis of the Hyalella azteca revealed differences between two groups: {E1, LR, CR} and {JR, SR}. The metabolic pathways identified in the two groups of amphipods were significantly different. The results demonstrated that NMR-based metabolomics can be effectively used to characterize metabolic response related to sediment from polluted areas.
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Affiliation(s)
- K H Chiu
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - C D Dong
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan; Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - C F Chen
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - M L Tsai
- Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Y R Ju
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - T M Chen
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - C W Chen
- Department of Marine Environmental Engineering, National Kaohsiung Marine University, Kaohsiung, Taiwan.
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18
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Microdosing, isotopic labeling, radiotracers and metabolomics: relevance in drug discovery, development and safety. Bioanalysis 2017; 9:1913-1933. [PMID: 29171759 DOI: 10.4155/bio-2017-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review discusses the use of stable (13C, 2D) or radioactive isotopes (14C, 11C, 18F, 131I, 64Cu, 68Ga) incorporated into the molecular structure of new drug entities for the purpose of pharmacokinetic or -dynamic studies. Metabolite in safety testing requires the administration of pharmacologically active doses. In such studies, radiotracers find application mainly in preclinical animal investigations, whereby LC-MS/MS is used to identify metabolite structure and drug-related effects. In contrast, first-in-human metabolite studies have to be carried out at nonpharmacological doses not exceeding 100 μg (microdose), which is generally too low for metabolite detection by LC-MS/MS. This short-coming can be overcome by specific radio- or isotopic labeling of the drug of interest and measurements using accelerator mass spectroscopy, single-photon emission computed tomography and positron emission tomography. Such combined radioisotope-based approaches permit Phase 0, first-in-human metabolite study.
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19
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Luies L, du Preez I, Loots DT. The role of metabolomics in tuberculosis treatment research. Biomark Med 2017; 11:1017-1029. [PMID: 29039217 DOI: 10.2217/bmm-2017-0141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Despite the fact that tuberculosis (TB) is a curable disease, it still results in approximately 1.8 million deaths annually. Various inadequacies in the current TB treatment strategies are major contributors to this high disease prevalence, including the long duration of therapy, the severe side effects associated with TB drugs, treatment failure due to drug resistance, post-treatment disease relapse, and HIV co-infection. In this review, we describe how metabolomics has contributed toward better explaining/elucidating the mechanisms of drug action/metabolism, drug toxicity and microbial drug resistance, and how metabolite biomarkers may serve as prognostic indicators for predicting treatment outcome as well as for the development of new TB drugs. We also discuss possible future contributions that metabolomics can make toward more efficient, less toxic TB treatment strategies.
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Affiliation(s)
- Laneke Luies
- Human Metabolomics, School for Physical & Chemical Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Box 269, Potchefstroom 2531, South Africa
| | - Ilse du Preez
- Human Metabolomics, School for Physical & Chemical Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Box 269, Potchefstroom 2531, South Africa
| | - Du Toit Loots
- Human Metabolomics, School for Physical & Chemical Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Box 269, Potchefstroom 2531, South Africa
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20
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Metabolomics: Definitions and Significance in Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:3-17. [DOI: 10.1007/978-3-319-47656-8_1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Issa NT, Wathieu H, Ojo A, Byers SW, Dakshanamurthy S. Drug Metabolism in Preclinical Drug Development: A Survey of the Discovery Process, Toxicology, and Computational Tools. Curr Drug Metab 2017; 18:556-565. [PMID: 28302026 PMCID: PMC5892202 DOI: 10.2174/1389200218666170316093301] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/16/2016] [Accepted: 01/17/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND While establishing efficacy in translational models and humans through clinically-relevant endpoints for disease is of great interest, assessing the potential toxicity of a putative therapeutic drug is critical. Toxicological assessments in the pre-clinical discovery phase help to avoid future failure in the clinical phases of drug development. Many in vitro assays exist to aid in modular toxicological assessment, such as hepatotoxicity and genotoxicity. While these methods have provided tremendous insight into human toxicity by investigational new drugs, they are expensive, require substantial resources, and do not account for pharmacogenomics as well as critical ADME properties. Computational tools can fill this niche in toxicology if in silico models are accurate in relating drug molecular properties to toxicological endpoints as well as reliable in predicting important drug-target interactions that mediate known adverse events or adverse outcome pathways (AOPs). METHODS We undertook an unstructured search of multiple bibliographic databases for peer-reviewed literature regarding computational methods in predictive toxicology for in silico drug discovery. As this review paper is meant to serve as a survey of available methods for the interested reader, no focused criteria were applied. Literature chosen was based on the writers' expertise and intent in communicating important aspects of in silico toxicology to the interested reader. CONCLUSION This review provides a purview of computational methods of pre-clinical toxicologic assessments for novel small molecule drugs that may be of use for novice and experienced investigators as well as academic and commercial drug discovery entities.
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Affiliation(s)
- Naiem T. Issa
- Georgetown-Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington DC, 20057 USA
| | - Henri Wathieu
- Georgetown-Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington DC, 20057 USA
| | - Abiola Ojo
- College of Pharmacy, Howard University, Washington, DC 20059, USA
| | - Stephen W. Byers
- Georgetown-Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington DC, 20057 USA
- Department of Biochemistry & Molecular Biology, Georgetown University, Washington DC, 20057, USA
| | - Sivanesan Dakshanamurthy
- Georgetown-Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington DC, 20057 USA
- Department of Biochemistry & Molecular Biology, Georgetown University, Washington DC, 20057, USA
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22
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Edwards RL, Odom John AR. Muddled mechanisms: recent progress towards antimalarial target identification. F1000Res 2016; 5:2514. [PMID: 27803804 PMCID: PMC5070598 DOI: 10.12688/f1000research.9477.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 01/06/2023] Open
Abstract
In the past decade, malaria rates have plummeted as a result of aggressive infection control measures and the adoption of artemisinin-based combination therapies (ACTs). However, a potential crisis looms ahead. Treatment failures to standard antimalarial regimens have been reported in Southeast Asia, and devastating consequences are expected if resistance spreads to the African continent. To prevent a potential public health emergency, the antimalarial arsenal must contain therapeutics with novel mechanisms of action (MOA). An impressive number of high-throughput screening (HTS) campaigns have since been launched, identifying thousands of compounds with activity against one of the causative agents of malaria,
Plasmodium falciparum. Now begins the difficult task of target identification, for which studies are often tedious, labor intensive, and difficult to interpret. In this review, we highlight approaches that have been instrumental in tackling the challenges of target assignment and elucidation of the MOA for hit compounds. Studies that apply these innovative techniques to antimalarial target identification are described, as well as the impact of the data in the field.
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Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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23
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Chatzimitakos TG, Stalikas CD. Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on (1)H NMR, UHPLC-HRMS, and Metabolic Databases. J Proteome Res 2016; 15:3322-30. [PMID: 27432757 DOI: 10.1021/acs.jproteome.6b00489] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metal nanoparticles (NPs) have proven to be more toxic than bulk analogues of the same chemical composition due to their unique physical properties. The NPs, lately, have drawn the attention of researchers because of their antibacterial and biocidal properties. In an effort to shed light on the mechanism through which the bacteria elimination is achieved and the metabolic changes they undergo, an untargeted metabolomic fingerprint study was carried out on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria species. The (1)H NMR spectroscopy, in conjunction with high resolution mass-spectrometry (HRMS) and an unsophisticated data processing workflow were implemented. The combined NMR/HRMS data, supported by an open-access metabolomic database, proved to be efficacious in the process of assigning a putative annotation to a wide range of metabolite signals and is a useful tool to appraise the metabolome alterations, as a consequence of bacterial response to NPs. Interestingly, not all the NPs diminished the intracellular metabolites; bacteria treated with iron NPs produced metabolites not present in the nonexposed bacteria sample, implying the activation of previously inactive metabolic pathways. In contrast, copper and iron-copper NPs reduced the annotated metabolites, alluding to the conclusion that the metabolic pathways (mainly alanine, aspartate, and glutamate metabolism, beta-alanine metabolism, glutathione metabolism, and arginine and proline metabolism) were hindered by the interactions of NPs with the intracellular metabolites.
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Affiliation(s)
- Theodoros G Chatzimitakos
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Constantine D Stalikas
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
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24
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Deng L, Gu H, Zhu J, Nagana Gowda GA, Djukovic D, Chiorean EG, Raftery D. Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls. Anal Chem 2016; 88:7975-83. [PMID: 27437783 DOI: 10.1021/acs.analchem.6b00885] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical technologies.
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Affiliation(s)
- Lingli Deng
- Department of Information Engineering, East China University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China.,Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - E Gabriela Chiorean
- Department of Medicine, University of Washington , 825 Eastlake Avenue East, Seattle, Washington 98109, United States.,Indiana University Melvin and Bren Simon Cancer Center , 535 Barnhill Drive, Indianapolis, Indiana 46202, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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Abstract
Until recently, the study of mycobacterial diseases was trapped in culture-based technology that is more than a century old. The use of nucleic acid amplification is changing this, and powerful new technologies are on the horizon. Metabolomics, which is the study of sets of metabolites of both the bacteria and host, is being used to clarify mechanisms of disease, and can identify changes leading to better diagnosis, treatment, and prognostication of mycobacterial diseases. Metabolomic profiles are arrays of biochemical products of genes in their environment. These complex patterns are biomarkers that can allow a more complete understanding of cell function, dysfunction, and perturbation than genomics or proteomics. Metabolomics could herald sweeping advances in personalized medicine and clinical trial design, but the challenges in metabolomics are also great. Measured metabolite concentrations vary with the timing within a condition, the intrinsic biology, the instruments, and the sample preparation. Metabolism profoundly changes with age, sex, variations in gut microbial flora, and lifestyle. Validation of biomarkers is complicated by measurement accuracy, selectivity, linearity, reproducibility, robustness, and limits of detection. The statistical challenges include analysis, interpretation, and description of the vast amount of data generated. Despite these drawbacks, metabolomics provides great opportunity and the potential to understand and manage mycobacterial diseases.
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Zhang YX, Yang X, Zou P, Du PF, Wang J, Jin F, Jin MJ, She YX. Nonylphenol Toxicity Evaluation and Discovery of Biomarkers in Rat Urine by a Metabolomics Strategy through HPLC-QTOF-MS. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13050501. [PMID: 27187439 PMCID: PMC4881126 DOI: 10.3390/ijerph13050501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 02/02/2023]
Abstract
Nonylphenol (NP) was quantified using liquid chromatography tandem mass spectrometry (LC-MS/MS) in the urine and plasma of rats treated with 0, 50, and 250 mg/kg/day of NP for four consecutive days. A urinary metabolomic strategy was originally implemented by high performance liquid chromatography time of flight mass spectrometry (HPLC-QTOF-MS) to explore the toxicological effects of NP and determine the overall alterations in the metabolite profiles so as to find potential biomarkers. It is essential to point out that from the observation, the metabolic data were clearly clustered and separated for the three groups. To further identify differentiated metabolites, multivariate analysis, including principal component analysis (PCA), orthogonal partial least-squares discriminant analysis (OPLS-DA), high-resolution MS/MS analysis, as well as searches of Metlin and Massbank databases, were conducted on a series of metabolites between the control and dose groups. Finally, five metabolites, including glycine, glycerophosphocholine, 5-hydroxytryptamine, malonaldehyde (showing an upward trend), and tryptophan (showing a downward trend), were identified as the potential urinary biomarkers of NP-induced toxicity. In order to validate the reliability of these potential biomarkers, an independent validation was performed by using the multiple reaction monitoring (MRM)-based targeted approach. The oxidative stress reflected by urinary 8-oxo-deoxyguanosine (8-oxodG) levels was elevated in individuals highly exposed to NP, supporting the hypothesis that mitochondrial dysfunction was a result of xenoestrogen accumulation. This study reveals a promising approach to find biomarkers to assist researchers in monitoring NP.
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Affiliation(s)
- Yan-Xin Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Xin Yang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Pan Zou
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Peng-Fei Du
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standard & Testing Technology for Agro-Product, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Agro-Product Safety and Quality, Ministry of Agriculture, Beijing 100081, China.
| | - Jing Wang
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standard & Testing Technology for Agro-Product, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Agro-Product Safety and Quality, Ministry of Agriculture, Beijing 100081, China.
| | - Fen Jin
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standard & Testing Technology for Agro-Product, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Agro-Product Safety and Quality, Ministry of Agriculture, Beijing 100081, China.
| | - Mao-Jun Jin
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standard & Testing Technology for Agro-Product, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Agro-Product Safety and Quality, Ministry of Agriculture, Beijing 100081, China.
| | - Yong-Xin She
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standard & Testing Technology for Agro-Product, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Agro-Product Safety and Quality, Ministry of Agriculture, Beijing 100081, China.
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27
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Gu H, Zhang P, Zhu J, Raftery D. Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage. Anal Chem 2015; 87:12355-62. [PMID: 26579731 PMCID: PMC5437843 DOI: 10.1021/acs.analchem.5b03812] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted detection is one of the most important methods in mass spectrometry (MS)-based metabolomics; however, its major limitation is the reduced metabolome coverage that results from the limited set of targeted metabolites typically used in the analysis. In this study we describe a new approach, globally optimized targeted (GOT)-MS, that combines many of the advantages of targeted detection and global profiling in metabolomics analysis, including the capability to detect unknowns, broad metabolite coverage, and excellent quantitation. The key step in GOT-MS is a global search of precursor and product ions using a single liquid chromatography-triple quadrupole (LC-QQQ) mass spectrometer. Here, focused on measuring serum metabolites, we obtained 595 precursor ions and 1 890 multiple reaction monitoring (MRM) transitions, under positive and negative ionization modes in the mass range of 60-600 Da. For many of the MRMs/metabolites under investigation, the analytical performance of GOT-MS is better than or at least comparable to that obtained by global profiling using a quadrupole-time-of-flight (Q-TOF) instrument of similar vintage. Using a study of serum metabolites in colorectal cancer (CRC) as a representative example, GOT-MS significantly outperformed a large targeted MS assay containing ∼160 biologically important metabolites and provided a complementary approach to traditional global profiling using Q-TOF-MS. GOT-MS thus expands and optimizes the detection capabilities for QQQ-MS through a novel approach and should have the potential to significantly advance both basic and clinical metabolic research.
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Affiliation(s)
- Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Ping Zhang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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28
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Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein Cell 2015; 6:628-37. [PMID: 26135925 PMCID: PMC4537470 DOI: 10.1007/s13238-015-0185-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.
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Fillet M, Frédérich M. The emergence of metabolomics as a key discipline in the drug discovery process. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 13:19-24. [PMID: 26190679 DOI: 10.1016/j.ddtec.2015.01.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/21/2015] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Metabolomics is a recent science that could be defined as the comprehensive qualitative and quantitative analysis of all small molecular weight compounds present in a cell, organ (including biofluids) or organism at a specific time point. More and more applications have been found these past years to metabolomics in the pharmaceutical field. Specifically in the drug discovery process, metabolomics open new perspectives, in new targets identification, in toxicological studies and in bioactive natural products discovery. The challenge in metabolomics is to find a technological approach allowing the reproducible identification and quantitation of as much metabolites as possible. In this context, mass spectrometry and NMR are emerging as key and complementary technologies.
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Affiliation(s)
- Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium.
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