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Zhang X, Su Y, Lane AN, Stromberg AJ, Fan TWM, Wang C. Bayesian kinetic modeling for tracer-based metabolomic data. BMC Bioinformatics 2023; 24:108. [PMID: 36949395 PMCID: PMC10035190 DOI: 10.1186/s12859-023-05211-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/24/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Stable Isotope Resolved Metabolomics (SIRM) is a new biological approach that uses stable isotope tracers such as uniformly [Formula: see text]-enriched glucose ([Formula: see text]-Glc) to trace metabolic pathways or networks at the atomic level in complex biological systems. Non-steady-state kinetic modeling based on SIRM data uses sets of simultaneous ordinary differential equations (ODEs) to quantitatively characterize the dynamic behavior of metabolic networks. It has been increasingly used to understand the regulation of normal metabolism and dysregulation in the development of diseases. However, fitting a kinetic model is challenging because there are usually multiple sets of parameter values that fit the data equally well, especially for large-scale kinetic models. In addition, there is a lack of statistically rigorous methods to compare kinetic model parameters between different experimental groups. RESULTS We propose a new Bayesian statistical framework to enhance parameter estimation and hypothesis testing for non-steady-state kinetic modeling of SIRM data. For estimating kinetic model parameters, we leverage the prior distribution not only to allow incorporation of experts' knowledge but also to provide robust parameter estimation. We also introduce a shrinkage approach for borrowing information across the ensemble of metabolites to stably estimate the variance of an individual isotopomer. In addition, we use a component-wise adaptive Metropolis algorithm with delayed rejection to perform efficient Monte Carlo sampling of the posterior distribution over high-dimensional parameter space. For comparing kinetic model parameters between experimental groups, we propose a new reparameterization method that converts the complex hypothesis testing problem into a more tractable parameter estimation problem. We also propose an inference procedure based on credible interval and credible value. Our method is freely available for academic use at https://github.com/xuzhang0131/MCMCFlux . CONCLUSIONS Our new Bayesian framework provides robust estimation of kinetic model parameters and enables rigorous comparison of model parameters between experimental groups. Simulation studies and application to a lung cancer study demonstrate that our framework performs well for non-steady-state kinetic modeling of SIRM data.
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Affiliation(s)
- Xu Zhang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
| | - Ya Su
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, 23220, USA
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Arnold J Stromberg
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA
| | - Teresa W M Fan
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, 40536, USA
| | - Chi Wang
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, 40536, USA.
- Markey Cancer Center, University of Kentucky, Lexington, 40536, USA.
- Division of Cancer Biostatistics, Department of Internal Medicine, University of Kentucky, Lexington, 40536, USA.
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2
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Capellades J, Junza A, Samino S, Brunner JS, Schabbauer G, Vinaixa M, Yanes O. Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labeling in Metabolomics. Anal Chem 2021; 93:1242-1248. [PMID: 33369389 DOI: 10.1021/acs.analchem.0c02998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Isotopic-labeling experiments have been valuable to monitor the flux of metabolic reactions in biological systems, which is crucial to understand homeostatic alterations with disease. Experimental determination of metabolic fluxes can be inferred from a characteristic rearrangement of stable isotope tracers (e.g., 13C or 15N) that can be detected by mass spectrometry (MS). Metabolites measured are generally members of well-known metabolic pathways, and most of them can be detected using both gas chromatography (GC)-MS and liquid chromatography (LC)-MS. In here, we show that GC methods coupled to chemical ionization (CI) MS have a clear advantage over alternative methodologies due to GC's superior chromatography separation efficiency and the fact that CI is a soft ionization technique that yields identifiable protonated molecular ion peaks. We tested diverse GC-CI-MS setups, including methane and isobutane reagent gases, triple quadrupole (QqQ) MS in SIM mode, or selected ion clusters using optimized narrow windows (∼10 Da) in scan mode, and standard full scan methods using high resolution GC-(q)TOF and GC-Orbitrap systems. Isobutane as a reagent gas in combination with both low-resolution (LR) and high-resolution (HR) MS showed the best performance, enabling precise detection of isotopologues in most metabolic intermediates of central carbon metabolism. Finally, with the aim of overcoming manual operations, we developed an R-based tool called isoSCAN that automatically quantifies all isotopologues of intermediate metabolites of glycolysis, TCA cycle, amino acids, pentose phosphate pathway, and urea cycle, from LRMS and HRMS data.
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Affiliation(s)
- Jordi Capellades
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain
| | - Alexandra Junza
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Samino
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Julia S Brunner
- Institute for Vascular Biology, Centre for Physiology and Pharmacology, Medical University Vienna, 1090 Vienna, Austria.,Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, 1090 Vienna, Austria
| | - Gernot Schabbauer
- Institute for Vascular Biology, Centre for Physiology and Pharmacology, Medical University Vienna, 1090 Vienna, Austria.,Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, 1090 Vienna, Austria
| | - Maria Vinaixa
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain
| | - Oscar Yanes
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain
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3
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Zhang H, Ma J, Tang K, Huang B. Beyond energy storage: roles of glycogen metabolism in health and disease. FEBS J 2020; 288:3772-3783. [PMID: 33249748 DOI: 10.1111/febs.15648] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/19/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
Beyond storing and supplying energy in the liver and muscles, glycogen also plays critical roles in cell differentiation, signaling, redox regulation, and stemness under various physiological and pathophysiological conditions. Such versatile functions have been revealed by various forms of glycogen storage diseases. Here, we outline the source of carbon flux in glycogen metabolism and discuss how glycogen metabolism guides CD8+ T-cell memory formation and maintenance. Likewise, we review how this affects macrophage polarization and inflammatory responses. Furthermore, we dissect how glycogen metabolism supports tumor development by promoting tumor-repopulating cell growth in hypoxic tumor microenvironments. This review highlights the essential role of the gluconeogenesis-glycogenesis-glycogenolysis-PPP metabolic chain in redox homeostasis, thus providing insights into potential therapeutic strategies against major chronic diseases including cancer.
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Affiliation(s)
- Huafeng Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwei Ma
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Huang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing, China.,Clinical Immunology Center, CAMS, Beijing, China
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4
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Volkova S, Matos MRA, Mattanovich M, Marín de Mas I. Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. Metabolites 2020; 10:E303. [PMID: 32722118 PMCID: PMC7465778 DOI: 10.3390/metabo10080303] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
Metabolic networks are regulated to ensure the dynamic adaptation of biochemical reaction fluxes to maintain cell homeostasis and optimal metabolic fitness in response to endogenous and exogenous perturbations. To this end, metabolism is tightly controlled by dynamic and intricate regulatory mechanisms involving allostery, enzyme abundance and post-translational modifications. The study of the molecular entities involved in these complex mechanisms has been boosted by the advent of high-throughput technologies. The so-called omics enable the quantification of the different molecular entities at different system layers, connecting the genotype with the phenotype. Therefore, the study of the overall behavior of a metabolic network and the omics data integration and analysis must be approached from a holistic perspective. Due to the close relationship between metabolism and cellular phenotype, metabolic modelling has emerged as a valuable tool to decipher the underlying mechanisms governing cell phenotype. Constraint-based modelling and kinetic modelling are among the most widely used methods to study cell metabolism at different scales, ranging from cells to tissues and organisms. These approaches enable integrating metabolomic data, among others, to enhance model predictive capabilities. In this review, we describe the current state of the art in metabolic modelling and discuss future perspectives and current challenges in the field.
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Affiliation(s)
| | | | | | - Igor Marín de Mas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (S.V.); (M.R.A.M.); (M.M.)
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5
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Selivanov VA, Marin S, Tarragó-Celada J, Lane AN, Higashi RM, Fan TWM, de Atauri P, Cascante M. Software Supporting a Workflow of Quantitative Dynamic Flux Maps Estimation in Central Metabolism from SIRM Experimental Data. Methods Mol Biol 2020; 2088:271-298. [PMID: 31893378 DOI: 10.1007/978-1-0716-0159-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM), based on the analysis of biological samples from living cells incubated with artificial isotope enriched substrates, enables mapping the rates of biochemical reactions (metabolic fluxes). We developed software supporting a workflow of analysis of SIRM data obtained with mass spectrometry (MS). The evaluation of fluxes starting from raw MS recordings requires at least three steps of computer support: first, extraction of mass spectra of metabolites of interest, then correction of the spectra for natural isotope abundance, and finally, evaluation of fluxes by simulation of the corrected spectra using a corresponding mathematical model. A kinetic model based on ordinary differential equations (ODEs) for isotopomers of metabolites of the corresponding biochemical network supports the final part of the analysis, which provides a dynamic flux map.
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Affiliation(s)
- Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Josep Tarragó-Celada
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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6
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Katzir R, Polat IH, Harel M, Katz S, Foguet C, Selivanov VA, Sabatier P, Cascante M, Geiger T, Ruppin E. The landscape of tiered regulation of breast cancer cell metabolism. Sci Rep 2019; 9:17760. [PMID: 31780802 PMCID: PMC6882817 DOI: 10.1038/s41598-019-54221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 10/21/2019] [Indexed: 01/10/2023] Open
Abstract
Altered metabolism is a hallmark of cancer, but little is still known about its regulation. In this study, we measure transcriptomic, proteomic, phospho-proteomic and fluxomics data in a breast cancer cell-line (MCF7) across three different growth conditions. Integrating these multiomics data within a genome scale human metabolic model in combination with machine learning, we systematically chart the different layers of metabolic regulation in breast cancer cells, predicting which enzymes and pathways are regulated at which level. We distinguish between two types of reactions, directly and indirectly regulated. Directly-regulated reactions include those whose flux is regulated by transcriptomic alterations (~890) or via proteomic or phospho-proteomics alterations (~140) in the enzymes catalyzing them. We term the reactions that currently lack evidence for direct regulation as (putative) indirectly regulated (~930). Many metabolic pathways are predicted to be regulated at different levels, and those may change at different media conditions. Remarkably, we find that the flux of predicted indirectly regulated reactions is strongly coupled to the flux of the predicted directly regulated ones, uncovering a tiered hierarchical organization of breast cancer cell metabolism. Furthermore, the predicted indirectly regulated reactions are predominantly reversible. Taken together, this architecture may facilitate rapid and efficient metabolic reprogramming in response to the varying environmental conditions incurred by the tumor cells. The approach presented lays a conceptual and computational basis for mapping metabolic regulation in additional cancers.
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Affiliation(s)
- Rotem Katzir
- Center for BioInformatics and Computational Biology, Dept. of Computer Science and the University of Maryland Institute of Advanced Computer Studies (UMIACS), University of Maryland, College Park, MD, 20742, USA
| | - Ibrahim H Polat
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.,Equipe environnement et prédiction de la santé des populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, La Tronche, France
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shir Katz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Philippe Sabatier
- Equipe environnement et prédiction de la santé des populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, La Tronche, France
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA.
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7
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DiNuzzo M. How glycogen sustains brain function: A plausible allosteric signaling pathway mediated by glucose phosphates. J Cereb Blood Flow Metab 2019; 39:1452-1459. [PMID: 31208240 PMCID: PMC6681540 DOI: 10.1177/0271678x19856713] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Astrocytic glycogen is the sole glucose reserve of the brain. Both glycogen and glucose are necessary for basic neurophysiology and in turn for higher brain functions. In spite of low concentration, turnover and stimulation-induced degradation, any interference with normal glycogen metabolism in the brain severely affects neuronal excitability and disrupts memory formation. Here, I briefly discuss the glycogenolysis-induced glucose-sparing effect, which involves glucose phosphates as key allosteric effectors in the modulation of astrocytic and neuronal glucose uptake and phosphorylation. I further advance a novel and thus far unexplored effect of glycogenolysis that might be mediated by glucose phosphates.
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8
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Rabbani N, Thornalley PJ. Hexokinase-2 Glycolytic Overload in Diabetes and Ischemia-Reperfusion Injury. Trends Endocrinol Metab 2019; 30:419-431. [PMID: 31221272 DOI: 10.1016/j.tem.2019.04.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/21/2019] [Accepted: 04/25/2019] [Indexed: 01/12/2023]
Abstract
Hexokinase-2 (HK2) was recently found to produce increased metabolic flux through glycolysis in hyperglycemia without concurrent transcriptional or other functional regulation. Rather, stabilization to proteolysis by increased glucose substrate binding produced unscheduled increased glucose metabolism in response to high cytosolic glucose concentration. This produces abnormal increases in glycolytic intermediates or glycolytic overload, driving cell dysfunction and vulnerability to the damaging effects of hyperglycemia in diabetes, explaining tissue-specific pathogenesis. Glycolytic overload is also activated in ischemia-reperfusion injury and cell senescence. A further key feature is HK2 displacement from mitochondria by increased glucose-6-phosphate concentration, inducing mitochondrial dysfunction and oxidative stress. This pathogenic mechanism suggested new targets for therapeutics development that gave promising outcomes in initial clinical evaluation.
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Affiliation(s)
- Naila Rabbani
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, University Hospital, Coventry CV2 2DX, UK
| | - Paul J Thornalley
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar.
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9
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Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E. From correlation to causation: analysis of metabolomics data using systems biology approaches. Metabolomics 2018; 14:37. [PMID: 29503602 PMCID: PMC5829120 DOI: 10.1007/s11306-018-1335-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Metabolomics is a well-established tool in systems biology, especially in the top-down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches. OBJECTIVES This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods. METHODS We review the most recent applications of systems biology tools in the field of metabolomics, such as network inference and analysis, metabolic modelling and pathways analysis. RESULTS We offer an ample overview of systems biology tools that can be applied to address metabolomics problems. The characteristics and application results of these tools are discussed also in a comparative manner. CONCLUSIONS Systems biology-enhanced analysis of metabolomics data can provide insights into the molecular mechanisms originating the observed metabolic profiles and enhance the scientific impact of metabolomics studies.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Cascante
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Ramon De Atauri Carulla
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
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10
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Zhang Y, Beard KFM, Swart C, Bergmann S, Krahnert I, Nikoloski Z, Graf A, Ratcliffe RG, Sweetlove LJ, Fernie AR, Obata T. Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle. Nat Commun 2017; 8:15212. [PMID: 28508886 PMCID: PMC5440813 DOI: 10.1038/ncomms15212] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/09/2017] [Indexed: 11/29/2022] Open
Abstract
Protein complexes of sequential metabolic enzymes, often termed metabolons, may permit direct channelling of metabolites between the enzymes, providing increased control over metabolic pathway fluxes. Experimental evidence supporting their existence in vivo remains fragmentary. In the present study, we test binary interactions of the proteins constituting the plant tricarboxylic acid (TCA) cycle. We integrate (semi-)quantitative results from affinity purification-mass spectrometry, split-luciferase and yeast-two-hybrid assays to generate a single reliability score for assessing protein–protein interactions. By this approach, we identify 158 interactions including those between catalytic subunits of sequential enzymes and between subunits of enzymes mediating non-adjacent reactions. We reveal channelling of citrate and fumarate in isolated potato mitochondria by isotope dilution experiments. These results provide evidence for a functional TCA cycle metabolon in plants, which we discuss in the context of contemporary understanding of this pathway in other kingdoms. A metabolon is a complex of sequential metabolic enzymes that channels substrates directly between enzymes, thus optimizing metabolic flux. Here Zhang et al. provide protein interaction and isotope dilution data that support the existence of a metabolon that channels both citrate and fumarate in the plant TCA cycle.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Corné Swart
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Susan Bergmann
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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11
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Yang Y, Fan TWM, Lane AN, Higashi RM. Chloroformate derivatization for tracing the fate of Amino acids in cells and tissues by multiple stable isotope resolved metabolomics (mSIRM). Anal Chim Acta 2017; 976:63-73. [PMID: 28576319 DOI: 10.1016/j.aca.2017.04.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 12/29/2022]
Abstract
Amino acids have crucial roles in central metabolism, both anabolic and catabolic. To elucidate these roles, steady-state concentrations of amino acids alone are insufficient, as each amino acid participates in multiple pathways and functions in a complex network, which can also be compartmentalized. Stable Isotope-Resolved Metabolomics (SIRM) is an approach that uses atom-resolved tracking of metabolites through biochemical transformations in cells, tissues, or whole organisms. Using different elemental stable isotopes to label multiple metabolite precursors makes it possible to resolve simultaneously the utilization of these precursors in a single experiment. Conversely, a single precursor labeled with two (or more) different elemental isotopes can trace the allocation of e.g. C and N atoms through the network. Such dual-label experiments however challenge the resolution of conventional mass spectrometers, which must distinguish the neutron mass differences among different elemental isotopes. This requires ultrahigh resolution Fourier transform mass spectrometry (UHR-FTMS). When combined with direct infusion nano-electrospray ion source (nano-ESI), UHR-FTMS can provide rapid, global, and quantitative analysis of all possible mass isotopologues of metabolites. Unfortunately, very low mass polar metabolites such as amino acids can be difficult to analyze by current models of UHR-FTMS, plus the high salt content present in typical cell or tissue polar extracts may cause unacceptable ion suppression for sources such as nano-ESI. Here we describe a modified method of ethyl chloroformate (ECF) derivatization of amino acids to enable rapid quantitative analysis of stable isotope labeled amino acids using nano-ESI UHR-FTMS. This method showed excellent linearity with quantifiable limits in the low nanomolar range represented in microgram quantities of biological specimens, which results in extracts with total analyte abundances in the low to sub-femtomole range. We have applied this method to profile amino acids and their labeling patterns in 13C and 2H doubly labeled PC9 cell extracts, cancerous and non-cancerous tissue extracts from a lung cancer patient and their protein hydrolysates as well as plasma extracts from mice fed with a liquid diet containing 13C6-glucose (Glc). The multi-element isotopologue distributions provided key insights into amino acid metabolism and intracellular pools in human lung cancer tissues in high detail. The 13C labeling of Asp and Glu revealed de novo synthesis of these amino acids from 13C6-Glc via the Krebs cycle, specifically the elevated level of 13C3-labeled Asp and Glu in cancerous versus non-cancerous lung tissues was consistent with enhanced pyruvate carboxylation. In addition, tracking the fate of double tracers, (13C6-Glc + 2H2-Gly or 13C6-Glc + 2H3-Ser) in PC9 cells clearly resolved pools of Ser and Gly synthesized de novo from 13C6-Glc (13C3-Ser and 13C2-Gly) versus Ser and Gly derived from external sources (2H3-Ser, 2H2-Gly). Moreover the complex 2H labeling patterns of the latter were results of Ser and Gly exchange through active Ser-Gly one-carbon metabolic pathway in PC9 cells.
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Affiliation(s)
- Ye Yang
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA.
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40539, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40539, USA.
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12
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Marín de Mas I, Marín S, Pachón G, Rodríguez-Prados JC, Vizán P, Centelles JJ, Tauler R, Azqueta A, Selivanov V, López de Ceraín A, Cascante M. Unveiling the Metabolic Changes on Muscle Cell Metabolism Underlying p-Phenylenediamine Toxicity. Front Mol Biosci 2017; 4:8. [PMID: 28321398 PMCID: PMC5338303 DOI: 10.3389/fmolb.2017.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Rhabdomyolysis is a disorder characterized by acute damage of the sarcolemma of the skeletal muscle leading to release of potentially toxic muscle cell components into the circulation, most notably creatine phosphokinase (CK) and myoglobulin, and is frequently accompanied by myoglobinuria. In the present work, we evaluated the toxicity of p-phenylenediamine (PPD), a main component of hair dyes which is reported to induce rhabdomyolysis. We studied the metabolic effect of this compound in vivo with Wistar rats and in vitro with C2C12 muscle cells. To this aim we have combined multi-omic experimental measurements with computational approaches using model-driven methods. The integrative study presented here has unveiled the metabolic disorders associated to PPD exposure that may underlay the aberrant metabolism observed in rhabdomyolys disease. Animals treated with lower doses of PPD (10 and 20 mg/kg) showed depressed activity and myoglobinuria after 10 h of treatment. We measured the serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and creatine kinase (CK) in rats after 24, 48, and 72 h of PPD exposure. At all times, treatment with PPD at higher doses (40 and 60 mg/kg) showed an increase of AST and ALT, and also an increase of lactate dehydrogenase (LDH) and CK after 24 h. Blood packed cell volume and hemoglobin levels, as well as organs weight at 48 and 72 h, were also measured. No significant differences were observed in these parameters under any condition. PPD induce cell cycle arrest in S phase and apoptosis (40% or early apoptotic cells) on mus musculus mouse C2C12 cells after 24 h of treatment. Incubation of mus musculus mouse C2C12 cells with [1,2-13C2]-glucose during 24 h, subsequent quantification of 13C isotopologues distribution in key metabolites of glucose metabolic network and a computational fluxomic analysis using in-house developed software (Isodyn) showed that PPD is inhibiting glycolysis, non-oxidative pentose phosphate pathway, glycogen turnover, and ATPAse reaction leading to a reduction in ATP synthesis. These findings unveil the glucose metabolism collapse, which is consistent with a decrease in cell viability observed in PPD-treated C2C12 cells and with the myoglubinuria and other effects observed in Wistar Rats treated with PPD. These findings shed new light on muscle dysfunction associated to PPD exposure, opening new avenues for cost-effective therapies in Rhabdomyolysis disease.
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Affiliation(s)
- Igor Marín de Mas
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de BarcelonaBarcelona, Spain; Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Silvia Marín
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Gisela Pachón
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Juan C Rodríguez-Prados
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Pedro Vizán
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Josep J Centelles
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Consejo Superior de Investigaciones Científicas Barcelona, Spain
| | - Amaya Azqueta
- Departamento de Farmacología y Toxicología, Facultad de Farmacia y Nutrición, Universidad de Navarra Pamplona, Spain
| | - Vitaly Selivanov
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
| | - Adela López de Ceraín
- Departamento de Farmacología y Toxicología, Facultad de Farmacia y Nutrición, Universidad de Navarra Pamplona, Spain
| | - Marta Cascante
- Departament de Bioquímica i Biologia Molecular, Facultat de Biología, Universitat de Barcelona Barcelona, Spain
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13
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Selivanov VA, Benito A, Miranda A, Aguilar E, Polat IH, Centelles JJ, Jayaraman A, Lee PWN, Marin S, Cascante M. MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. BMC Bioinformatics 2017; 18:88. [PMID: 28158972 PMCID: PMC5291980 DOI: 10.1186/s12859-017-1513-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/31/2017] [Indexed: 12/26/2022] Open
Abstract
Background Tracing stable isotopes, such as 13C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information requires special care, such as a correction for naturally occurring isotopes, or overlapping mass spectra of various components of the cell culture medium. Developing a method for a correction of overlapping peaks is the primary objective of this study. Results Our computer program-MIDcor (free at https://github.com/seliv55/mid_correct) written in the R programming language, corrects the raw MS spectra both for the naturally occurring isotopes and for the overlapping of peaks corresponding to various substances. To this end, the mass spectra of unlabeled metabolites measured in two media are necessary: in a minimal medium containing only derivatized metabolites and chemicals for derivatization, and in a complete cell incubated medium. The MIDcor program calculates the difference (D) between the theoretical and experimentally measured spectra of metabolites containing only the naturally occurring isotopes. The result of comparison of D in the two media determines a way of deciphering the true spectra. (1) If D in the complete medium is greater than that in the minimal medium in at least one peak, then unchanged D is subtracted from the raw spectra of the labeled metabolite. (2) If D does not depend on the medium, then the spectrum probably overlaps with a derivatized fragment of the same metabolite, and D is modified proportionally to the metabolite labeling. The program automatically reaches a decision regarding the way of correction. For some metabolites/fragments in the case (2) D was found to decrease when the tested substance was 13C labeled, and this isotopic effect also can be corrected automatically, if the user provides a measured spectrum of the substance in which the 13C labeling is known a priori. Conclusion Using the developed program improves the reliability of stable isotope tracer data analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1513-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vitaly A Selivanov
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain. .,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain.
| | - Adrián Benito
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Anibal Miranda
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Esther Aguilar
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Ibrahim Halil Polat
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Josep J Centelles
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Anusha Jayaraman
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Paul W N Lee
- Department of Pediatrics, Harbor-UCLA Medical Center, Research and Education Institute, Torrance, CA, 90502, USA
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain. .,Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain.
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14
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Foguet C, Marin S, Selivanov VA, Fanchon E, Lee WNP, Guinovart JJ, de Atauri P, Cascante M. HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data. PLoS Comput Biol 2016; 12:e1004899. [PMID: 27124774 PMCID: PMC4849781 DOI: 10.1371/journal.pcbi.1004899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/05/2016] [Indexed: 11/19/2022] Open
Abstract
The liver performs many essential metabolic functions, which can be studied using computational models of hepatocytes. Here we present HepatoDyn, a highly detailed dynamic model of hepatocyte metabolism. HepatoDyn includes a large metabolic network, highly detailed kinetic laws, and is capable of dynamically simulating the redox and energy metabolism of hepatocytes. Furthermore, the model was coupled to the module for isotopic label propagation of the software package IsoDyn, allowing HepatoDyn to integrate data derived from 13C based experiments. As an example of dynamical simulations applied to hepatocytes, we studied the effects of high fructose concentrations on hepatocyte metabolism by integrating data from experiments in which rat hepatocytes were incubated with 20 mM glucose supplemented with either 3 mM or 20 mM fructose. These experiments showed that glycogen accumulation was significantly lower in hepatocytes incubated with medium supplemented with 20 mM fructose than in hepatocytes incubated with medium supplemented with 3 mM fructose. Through the integration of extracellular fluxes and 13C enrichment measurements, HepatoDyn predicted that this phenomenon can be attributed to a depletion of cytosolic ATP and phosphate induced by high fructose concentrations in the medium.
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Affiliation(s)
- Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Vitaly A. Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
| | - Eric Fanchon
- UGA – CNRS, TIMC-IMAG UMR 5525, Grenoble, France
| | - Wai-Nang Paul Lee
- Department of Pediatrics, Los Angeles Biomedical Research Institute, Torrance, California, United States of America
| | - Joan J. Guinovart
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
- * E-mail: (PdA); (MC)
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain
- * E-mail: (PdA); (MC)
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15
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Abstract
Metabolic processes are altered in cancer cells, which obtain advantages from this metabolic reprogramming in terms of energy production and synthesis of biomolecules that sustain their uncontrolled proliferation. Due to the conceptual progresses in the last decade, metabolic reprogramming was recently included as one of the new hallmarks of cancer. The advent of high-throughput technologies to amass an abundance of omic data, together with the development of new computational methods that allow the integration and analysis of omic data by using genome-scale reconstructions of human metabolism, have increased and accelerated the discovery and development of anticancer drugs and tumor-specific metabolic biomarkers. Here we review and discuss the latest advances in the context of metabolic reprogramming and the future in cancer research.
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16
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Guzmán S, Marin S, Miranda A, Selivanov VA, Centelles JJ, Harmancey R, Smih F, Turkieh A, Durocher Y, Zorzano A, Rouet P, Cascante M. (13)C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes. BMC SYSTEMS BIOLOGY 2014; 8:109. [PMID: 25217974 PMCID: PMC4363945 DOI: 10.1186/s12918-014-0109-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/29/2014] [Indexed: 12/11/2022]
Abstract
Background It has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resistin on the glucose metabolic flux profile and on insulin response in L6E9 myotubes at the metabolic level using a tracer-based metabolomic approach and our in-house developed software, Isodyn. Results Resistin significantly increased glucose uptake and glycolysis, altering pyruvate utilisation by the cell. In the presence of resistin, insulin only slightly increased glucose uptake and glycolysis, and did not alter the flux profile around pyruvate induced by resistin. Resistin prevented the increase in gene expression in pyruvate dehydrogenase-E1 and the sharp decrease in gene expression in cytosolic phosphoenolpyruvate carboxykinase-1 induced by insulin. Conclusions These data suggest that resistin impairs the metabolic activation of insulin. This impairment cannot be explained by the activity of a single enzyme, but instead due to reorganisation of the whole metabolic flux distribution.
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Affiliation(s)
- Shirley Guzmán
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
| | - Anibal Miranda
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
| | - Vitaly A Selivanov
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
| | - Josep J Centelles
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
| | - Romain Harmancey
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Equipe n°7, Toulouse, France.
| | - Fatima Smih
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Equipe n°7, Toulouse, France.
| | - Annie Turkieh
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Equipe n°7, Toulouse, France.
| | - Yves Durocher
- Animal Cell Technology Group, Biotechnology Research Institute, National Research Council Canada, Montreal, QC, Canada.
| | - Antonio Zorzano
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute for Research in Biomedicine (IRB Barcelona) and CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Barcelona, Spain.
| | - Philippe Rouet
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Equipe n°7, Toulouse, France.
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB) and CSIC-Associated Unit, Barcelona, Spain.
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17
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Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Münch R, Eylert E, Eisenreich W, Dandekar T. 'Isotopo' a database application for facile analysis and management of mass isotopomer data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau077. [PMID: 25204646 PMCID: PMC4158277 DOI: 10.1093/database/bau077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application ‘Isotopo’. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of 13C-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. Availability: The ‘Isotopo’ software is available at the following web link (section Download): http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. The package contains three additional files: software executable setup (installer), one data set file (discussed in this article) and one excel file (which can be used to convert data from excel to ‘.iso’ format). The ‘Isotopo’ software is compatible only with the Microsoft Windows operating system. Database URL:http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meye
| | - Saman Zeeshan
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meye
| | - Claudia Huber
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Michael Hensel
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Richard Münch
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Eva Eylert
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Wolfgang Eisenreich
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meye
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Wiechert W, Nöh K. Isotopically non-stationary metabolic flux analysis: complex yet highly informative. Curr Opin Biotechnol 2013; 24:979-86. [DOI: 10.1016/j.copbio.2013.03.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 12/16/2022]
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Sen P, Vial HJ, Radulescu O. Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. BMC SYSTEMS BIOLOGY 2013; 7:123. [PMID: 24209716 PMCID: PMC3829661 DOI: 10.1186/1752-0509-7-123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/01/2013] [Indexed: 12/04/2022]
Abstract
BACKGROUND Plasmodium is the causal parasite of malaria, infectious disease responsible for the death of up to one million people each year. Glycerophospholipid and consequently membrane biosynthesis are essential for the survival of the parasite and are targeted by a new class of antimalarial drugs developed in our lab. In order to understand the highly redundant phospholipid synthethic pathways and eventual mechanism of resistance to various drugs, an organism specific kinetic model of these metabolic pathways need to be developed in Plasmodium species. RESULTS Fluxomic data were used to build a quantitative kinetic model of glycerophospholipid pathways in Plasmodium knowlesi. In vitro incorporation dynamics of phospholipids unravels multiple synthetic pathways. A detailed metabolic network with values of the kinetic parameters (maximum rates and Michaelis constants) has been built. In order to obtain a global search in the parameter space, we have designed a hybrid, discrete and continuous, optimization method. Discrete parameters were used to sample the cone of admissible fluxes, whereas the continuous Michaelis and maximum rates constants were obtained by local minimization of an objective function.The model was used to predict the distribution of fluxes within the network of various metabolic precursors.The quantitative analysis was used to understand eventual links between different pathways. The major source of phosphatidylcholine (PC) is the CDP-choline Kennedy pathway.In silico knock-out experiments showed comparable importance of phosphoethanolamine-N-methyltransferase (PMT) and phosphatidylethanolamine-N-methyltransferase (PEMT) for PC synthesis.The flux values indicate that, major part of serine derived phosphatidylethanolamine (PE) is formed via serine decarboxylation, whereas major part of phosphatidylserine (PS) is formed by base-exchange reactions.Sensitivity analysis of CDP-choline pathway shows that the carrier-mediated choline entry into the parasite and the phosphocholine cytidylyltransferase reaction have the largest sensitivity coefficients in this pathway, but does not distinguish a reaction as an unique rate-limiting step. CONCLUSION We provide a fully parametrized kinetic model for the multiple phospholipid synthetic pathways in P. knowlesi. This model has been used to clarify the relative importance of the various reactions in these metabolic pathways. Future work extensions of this modelling strategy will serve to elucidate the regulatory mechanisms governing the development of Plasmodium during its blood stages, as well as the mechanisms of action of drugs on membrane biosynthetic pathways and eventual mechanisms of resistance.
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Affiliation(s)
- Partho Sen
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235 CNRS, UM1, UM2, CP 107, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Henri J Vial
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235 CNRS, UM1, UM2, CP 107, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Ovidiu Radulescu
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235 CNRS, UM1, UM2, CP 107, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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Mueller D, Heinzle E. Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures. Curr Opin Biotechnol 2012; 24:54-9. [PMID: 23142545 DOI: 10.1016/j.copbio.2012.10.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/08/2012] [Accepted: 10/18/2012] [Indexed: 12/28/2022]
Abstract
The determination of metabolic fluxes provides detailed information of cellular physiology, and the assessment of metabolic flux changes upon a certain perturbation can help to improve biotechnological and pharmaceutical processes. Stable isotope-assisted metabolomics using tracer-labeled substrates is the method of choice to determine the fluxes. Though well-established for microbial cultures, the application to mammalian cells is generally complex and still limited. However, there have been great achievements in recent years and it is now emerging that stable isotope-assisted metabolic flux analysis in mammalian cell cultures will help improving biotechnological production and will also support drug development and discovery.
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Affiliation(s)
- Daniel Mueller
- Biochemical Engineering, Campus A1 5, Saarland University, D-66123 Saarbruecken, Germany.
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