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Wieder C, Cooke J, Frainay C, Poupin N, Bowler R, Jourdan F, Kechris KJ, Lai RPJ, Ebbels T. PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. PLoS Comput Biol 2024; 20:e1011814. [PMID: 38527092 PMCID: PMC10994553 DOI: 10.1371/journal.pcbi.1011814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. PathIntegrate is available as an open-source Python package.
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Affiliation(s)
- Cecilia Wieder
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Juliette Cooke
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Clement Frainay
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Russell Bowler
- National Jewish Health, Denver, Colorado, United States of America
| | - Fabien Jourdan
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Rachel PJ Lai
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Timothy Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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2
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Cooke J, Delmas M, Wieder C, Rodríguez Mier P, Frainay C, Vinson F, Ebbels T, Poupin N, Jourdan F. Genome scale metabolic network modelling for metabolic profile predictions. PLoS Comput Biol 2024; 20:e1011381. [PMID: 38386685 PMCID: PMC10914266 DOI: 10.1371/journal.pcbi.1011381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/05/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Metabolic profiling (metabolomics) aims at measuring small molecules (metabolites) in complex samples like blood or urine for human health studies. While biomarker-based assessment often relies on a single molecule, metabolic profiling combines several metabolites to create a more complex and more specific fingerprint of the disease. However, in contrast to genomics, there is no unique metabolomics setup able to measure the entire metabolome. This challenge leads to tedious and resource consuming preliminary studies to be able to design the right metabolomics experiment. In that context, computer assisted metabolic profiling can be of strong added value to design metabolomics studies more quickly and efficiently. We propose a constraint-based modelling approach which predicts in silico profiles of metabolites that are more likely to be differentially abundant under a given metabolic perturbation (e.g. due to a genetic disease), using flux simulation. In genome-scale metabolic networks, the fluxes of exchange reactions, also known as the flow of metabolites through their external transport reactions, can be simulated and compared between control and disease conditions in order to calculate changes in metabolite import and export. These import/export flux differences would be expected to induce changes in circulating biofluid levels of those metabolites, which can then be interpreted as potential biomarkers or metabolites of interest. In this study, we present SAMBA (SAMpling Biomarker Analysis), an approach which simulates fluxes in exchange reactions following a metabolic perturbation using random sampling, compares the simulated flux distributions between the baseline and modulated conditions, and ranks predicted differentially exchanged metabolites as potential biomarkers for the perturbation. We show that there is a good fit between simulated metabolic exchange profiles and experimental differential metabolites detected in plasma, such as patient data from the disease database OMIM, and metabolic trait-SNP associations found in mGWAS studies. These biomarker recommendations can provide insight into the underlying mechanism or metabolic pathway perturbation lying behind observed metabolite differential abundances, and suggest new metabolites as potential avenues for further experimental analyses.
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Affiliation(s)
- Juliette Cooke
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Maxime Delmas
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- Idiap Research Institute, Martigny, Switzerland
| | - Cecilia Wieder
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pablo Rodríguez Mier
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Clément Frainay
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Florence Vinson
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Timothy Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
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3
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Witting M, Malik A, Leach A, Bridge A, Aimo L, Conroy MJ, O'Donnell VB, Hoffmann N, Kopczynski D, Giacomoni F, Paulhe N, Gassiot AC, Poupin N, Jourdan F, Bertrand-Michel J. Challenges and perspectives for naming lipids in the context of lipidomics. Metabolomics 2024; 20:15. [PMID: 38267595 PMCID: PMC10808356 DOI: 10.1007/s11306-023-02075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. OBJECTIVES In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. METHODS & RESULTS In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. CONCLUSION Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks.
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Affiliation(s)
- Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354, Freising-Weihenstephan, Germany
| | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Lucila Aimo
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Matthew J Conroy
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Valerie B O'Donnell
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nils Hoffmann
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Dominik Kopczynski
- Institute for Analytical Chemistry, Universität Wien, Währingerstrasse 38, 1090, Vienna, Austria
| | - Franck Giacomoni
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Nils Paulhe
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Amaury Cazenave Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute, and Precision Medicine TRP, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France.
- I2MC, Inserm U1297, Université de Toulouse, Toulouse, France.
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Wieder C, Cooke J, Frainay C, Poupin N, Bowler R, Jourdan F, Kechris KJ, Lai RP, Ebbels T. PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. bioRxiv 2024:2024.01.09.574780. [PMID: 38260498 PMCID: PMC10802464 DOI: 10.1101/2024.01.09.574780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. The PathIntegrate Python package is available at https://github.com/cwieder/PathIntegrate.
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Affiliation(s)
- Cecilia Wieder
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Juliette Cooke
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Clement Frainay
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Russell Bowler
- National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Fabien Jourdan
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Katerina J Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Rachel Pj Lai
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Timothy Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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Stoffels CBA, Angerer TB, Robert H, Poupin N, Lakhal L, Frache G, Mercier-Bonin M, Audinot JN. Lipidomic Profiling of PFOA-Exposed Mouse Liver by Multi-Modal Mass Spectrometry Analysis. Anal Chem 2023; 95:6568-6576. [PMID: 37027489 PMCID: PMC10134131 DOI: 10.1021/acs.analchem.2c05470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Perfluorooctanoic acid (PFOA) is a synthetic perfluorinated chemical classified as a persistent organic pollutant. PFOA has been linked to many toxic effects, including liver injury. Many studies report that PFOA exposure alters serum and hepatic lipid metabolism. However, lipidomic pathways altered by PFOA exposure are largely unknown and only a few lipid classes, mostly triacylglycerol (TG), are usually considered in lipid analysis. Here, we performed a global lipidomic analysis on the liver of PFOA-exposed (high-dose and short-duration) and control mice by combining three mass spectrometry (MS) techniques: liquid chromatography with tandem mass spectrometry (LC-MS/MS), matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI), and time-of-flight secondary ion mass spectrometry (TOF-SIMS). Among all hepatic lipids identified by LC-MS/MS analysis, more than 350 were statistically impacted (increased or decreased levels) after PFOA exposure, as confirmed by multi-variate data analysis. The levels of many lipid species from different lipid classes, most notably phosphatidylethanolamine (PE), phosphatidylcholine (PC), and TG, were significantly altered. Subsequent lipidomic analysis highlights the pathways significantly impacted by PFOA exposure, with the glycerophospholipid metabolism being the most impacted, and the changes in the lipidome network, which connects all the lipid species together. MALDI-MSI displays the heterogeneous distribution of the affected lipids and PFOA, revealing different areas of lipid expression linked to PFOA localization. TOF-SIMS localizes PFOA at the cellular level, supporting MALDI-MSI results. This multi-modal MS analysis unveils the lipidomic impact of PFOA in the mouse liver after high-dose and short-term exposure and opens new opportunities in toxicology.
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Affiliation(s)
- Charlotte B A Stoffels
- Department of Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux 4422, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | - Tina B Angerer
- Department of Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux 4422, Luxembourg
| | - Hervé Robert
- Toxalim, Université de Toulouse, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse 31027, France
| | - Nathalie Poupin
- Toxalim, Université de Toulouse, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse 31027, France
| | - Laila Lakhal
- Toxalim, Université de Toulouse, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse 31027, France
| | - Gilles Frache
- Department of Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux 4422, Luxembourg
| | - Muriel Mercier-Bonin
- Toxalim, Université de Toulouse, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse 31027, France
| | - Jean-Nicolas Audinot
- Department of Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux 4422, Luxembourg
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Lépine G, Huneau JF, Rémond D, Mathé V, David J, Hermier D, Guérin-Deremaux L, Lefranc-Millot C, Poupin N, Mariotti F, Polakof S, Fouillet H. Compared with Milk Protein, a Wheat and Pea Protein Blend Reduces High-Fat, High-Sucrose Induced Metabolic Dysregulations while Similarly Supporting Tissue Protein Anabolism in Rats. J Nutr 2023; 153:645-656. [PMID: 36931747 DOI: 10.1016/j.tjnut.2022.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/02/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Plant proteins (PPs) have been associated with better cardiovascular health than animal proteins (APs) in epidemiological studies. However, the underlying metabolic mechanisms remain mostly unknown. OBJECTIVES Using a combination of cutting-edge isotopic methods, we aimed to better characterize the differences in protein and energy metabolisms induced by dietary protein sources (PP compared with AP) in a prudent or western dietary context. METHODS Male Wistar rats (n = 44, 8 wk old) were fed for 4.5 mo with isoproteic diets differing in their protein isolate sources, either AP (100% milk) or PP (50%:50% pea: wheat) and being normal (NFS) or high (HFS) in sucrose (6% or 15% kcal) and saturated fat (7% or 20% kcal), respectively. We measured body weight and composition, hepatic enzyme activities and lipid content, and plasma metabolites. In the intestine, liver, adipose tissues, and skeletal muscles, we concomitantly assessed the extent of amino acid (AA) trafficking using a 15N natural abundance method, the rates of macronutrient routing to dispensable AA using a 13C natural abundance method, and the metabolic fluxes of protein synthesis (PS) and de novo lipogenesis using a 2H labeling method. Data were analyzed using ANOVA and Mixed models. RESULTS At the whole-body level, PP limited HFS-induced insulin resistance (-27% in HOMA-IR between HFS groups, P < 0.05). In the liver, PP induced lower lipid content (-17%, P < 0.01) and de novo lipogenesis (-24%, P < 0.05). In the different tissues studied, PP induced higher AA transamination accompanied by higher routings of dietary carbohydrates and lipids toward dispensable AA synthesis by glycolysis and β-oxidation, resulting in similar tissue PS and protein mass. CONCLUSIONS In growing rats, compared with AP, a balanced blend of PP similarly supports protein anabolism while better limiting whole-body and tissue metabolic dysregulations through mechanisms related to their less optimal AA profile for direct channeling to PS.
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Affiliation(s)
- Gaïa Lépine
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France; Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France
| | - Jean-François Huneau
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France
| | - Didier Rémond
- Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France
| | - Véronique Mathé
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France
| | - Jérémie David
- Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France
| | - Dominique Hermier
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France
| | | | | | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - François Mariotti
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France
| | - Sergio Polakof
- Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France.
| | - Hélène Fouillet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 91120, Palaiseau, France.
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Wieder C, Bundy JG, Frainay C, Poupin N, Rodríguez-Mier P, Vinson F, Cooke J, Lai RPJ, Jourdan F, Ebbels TMD. Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics. Environ Sci Technol 2022; 56:14219-14222. [PMID: 36162120 PMCID: PMC9583613 DOI: 10.1021/acs.est.2c05588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Cecilia Wieder
- Department
of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Jacob G. Bundy
- Department
of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Clément Frainay
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
| | - Nathalie Poupin
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
| | - Pablo Rodríguez-Mier
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
| | - Florence Vinson
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
| | - Juliette Cooke
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
| | - Rachel P. J. Lai
- Department
of Infectious Disease, Faculty of Medicine, Commonwealth Building, Imperial College London, Du Cane Road, London W12 0NN, U.K.
| | - Fabien Jourdan
- Toxalim
(Research Centre in Food Toxicology), Université
de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 180 chemin de Tournefeuille St-Martin-du-Touch, BP 3, 31931 Toulouse Cedex, France
- MetaToul-MetaboHUB,
National Infrastructure of Metabolomics and Fluxomics, 180 chemin de Tournefeuille St-Martin-du-Touch,
BP 3, 31931 Toulouse Cedex, France
| | - Timothy M. D. Ebbels
- Department
of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
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den Broeder M, Habreaken N, Farnezi H, Massart J, Stingl M, Poupin N, Jourdan F, Legler J, H. Kamstra J. SOC-II-03 Zebrafish as a model for chemical induced adipogenesis and related metabolic diseases. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Chamorro-García R, Poupin N, Tremblay-Franco M, Canlet C, Egusquiza R, Gautier R, Jouanin I, Shoucri BM, Blumberg B, Zalko D. Transgenerational metabolomic fingerprints in mice ancestrally exposed to the obesogen TBT. Environ Int 2021; 157:106822. [PMID: 34455191 PMCID: PMC8919592 DOI: 10.1016/j.envint.2021.106822] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Endocrine disrupting chemicals (EDCs) contribute to the etiology of metabolic disorders such as obesity, insulin resistance and hepatic dysfunction. Concern is growing about the consequences of perinatal EDC exposure on disease predisposition later in life. Metabolomics are promising approaches for studying long-term consequences of early life EDC exposure. These approaches allow for the identification and characterization of biomarkers of direct or ancestral exposures that could be diagnostic for individual susceptibility to disease and help to understand mechanisms through which EDCs act. OBJECTIVES We sought to identify metabolomic fingerprints in mice ancestrally exposed to the model obesogen tributyltin (TBT), to assess whether metabolomics could discriminate potential trans-generational susceptibility to obesity and recognize metabolic pathways modulated by ancestral TBT exposure. METHODS We used non-targeted 1H NMR metabolomic analyses of plasma and liver samples collected from male and female mice ancestrally exposed to TBT in two independent transgenerational experiments in which F3 and F4 males became obese when challenged with increased dietary fat. RESULTS Metabolomics confirmed transgenerational obesogenic effects of environmentally relevant doses of TBT in F3 and F4 males, in two independent studies. Although females never became obese, their specific metabolomic fingerprint evidenced distinct transgenerational effects of TBT in female mice consistent with impaired capacity for liver biotransformation. DISCUSSION This study is the first application of metabolomics to unveil the transgenerational effects of EDC exposure. Very early, significant changes in the plasma metabolome were observed in animals ancestrally exposed to TBT. These changes preceded the onset of obesogenic effects elicited by increased dietary fat in the TBT groups, and which ultimately resulted in significant changes in the liver metabolome. Development of metabolomic fingerprints could facilitate the identification of individuals carrying the signature of ancestral obesogen exposure that might increase their susceptibility to other risk factor such as increased dietary fat.
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Affiliation(s)
- Raquel Chamorro-García
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine 92697-2300, USA
| | - Nathalie Poupin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
| | - Marie Tremblay-Franco
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
| | - Riann Egusquiza
- Department of Pharmaceutical Sciences, University of California, Irvine, USA
| | - Roselyne Gautier
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
| | - Isabelle Jouanin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
| | - Bassem M Shoucri
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine 92697-2300, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine 92697-2300, USA; Department of Pharmaceutical Sciences, University of California, Irvine, USA; Department of Biomedical Engineering, University of California, Irvine, USA.
| | - Daniel Zalko
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France.
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10
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Wieder C, Frainay C, Poupin N, Rodríguez-Mier P, Vinson F, Cooke J, Lai RPJ, Bundy JG, Jourdan F, Ebbels T. Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PLoS Comput Biol 2021; 17:e1009105. [PMID: 34492007 PMCID: PMC8448349 DOI: 10.1371/journal.pcbi.1009105] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/17/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics.
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Affiliation(s)
- Cecilia Wieder
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Clément Frainay
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Pablo Rodríguez-Mier
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Florence Vinson
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Juliette Cooke
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Rachel PJ Lai
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jacob G. Bundy
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Timothy Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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11
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Comte B, Monnerie S, Brandolini-Bunlon M, Canlet C, Castelli F, Chu-Van E, Colsch B, Fenaille F, Joly C, Jourdan F, Lenuzza N, Lyan B, Martin JF, Migné C, Morais JA, Pétéra M, Poupin N, Vinson F, Thevenot E, Junot C, Gaudreau P, Pujos-Guillot E. Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men. EBioMedicine 2021; 69:103440. [PMID: 34161887 PMCID: PMC8237302 DOI: 10.1016/j.ebiom.2021.103440] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MetS), a cluster of factors associated with risks of developing cardiovascular diseases, is a public health concern because of its growing prevalence. Considering the combination of concomitant components, their development and severity, MetS phenotypes are largely heterogeneous, inducing disparity in diagnosis. METHODS A case/control study was designed within the NuAge longitudinal cohort on aging. From a 3-year follow-up of 123 stable individuals, we present a deep phenotyping approach based on a multiplatform metabolomics and lipidomics untargeted strategy to better characterize metabolic perturbations in MetS and define a comprehensive MetS signature stable over time in older men. FINDINGS We characterize significant changes associated with MetS, involving modulations of 476 metabolites and lipids, and representing 16% of the detected serum metabolome/lipidome. These results revealed a systemic alteration of metabolism, involving various metabolic pathways (urea cycle, amino-acid, sphingo- and glycerophospholipid, and sugar metabolisms…) not only intrinsically interrelated, but also reflecting environmental factors (nutrition, microbiota, physical activity…). INTERPRETATION These findings allowed identifying a comprehensive MetS signature, reduced to 26 metabolites for future translation into clinical applications for better diagnosing MetS. FUNDING The NuAge Study was supported by a research grant from the Canadian Institutes of Health Research (CIHR; MOP-62842). The actual NuAge Database and Biobank, containing data and biologic samples of 1,753 NuAge participants (from the initial 1,793 participants), are supported by the Fonds de recherche du Québec (FRQ; 2020-VICO-279753), the Quebec Network for Research on Aging, a thematic network funded by the Fonds de Recherche du Québec - Santé (FRQS) and by the Merck-Frost Chair funded by La Fondation de l'Université de Sherbrooke. All metabolomics and lipidomics analyses were funded and performed within the metaboHUB French infrastructure (ANR-INBS-0010). All authors had full access to the full data in the study and accept responsibility to submit for publication.
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Affiliation(s)
- Blandine Comte
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Stéphanie Monnerie
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Cécile Canlet
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Emeline Chu-Van
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Fabien Jourdan
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Natacha Lenuzza
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Bernard Lyan
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Jean-François Martin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Carole Migné
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - José A Morais
- Division de Gériatrie, McGill University, Center de recherche du Center universitaire de santé McGill, Montreal, Canada
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nathalie Poupin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Vinson
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Etienne Thevenot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Pierrette Gaudreau
- Center de Recherche du Center hospitalier de l'Université de Montréal, Montreal, Canada; Département de médecine, Université de Montréal, Montreal, Canada
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France.
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12
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Lépine G, Mariotti F, Huneau JF, Poupin N, Tremblay-Franco M, Verny MA, Macian N, Courrent M, Guerin-Deremaux L, Lefranc-Millot C, Rémond D, Fouillet H, Polakof S. Study Protocol: A 2-Month Cross-Over Controlled Feeding Trial Investigating the Effect of Animal and Plant Protein Intake on the Metabolome and Cardiometabolic Health. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab057_011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
A dietary shift in favor of plant protein (PP) sources over animal protein (AP) sources has been advocated for both sustainability and health reasons, this dietary transition being noticeably associated to decreased cardiovascular and diabetes risks. The differences in amino acid composition between PP and AP may have several effects on the metabolic pathways, and in turn health impacts, which are still poorly characterized. This project aims at characterizing, with a combination of “omics” approaches, the metabolic reorientations induced by a dietary shift from AP to PP sources and understanding their health effects in a population at cardiometabolic risk.
Methods
We will conduct a cross-over randomized feeding trial (NCT04236518) in 20 healthy overweight males (BMI 25–35), aged 25–55, with an enlarged waist circumference (> 94cm) and high plasma triglycerides (>1.5g/L). Participants will be assigned for 1 month each to 2 diets containing predominantly either AP (65% AP:35% PP) or PP (35% AP:65% PP) in a randomized order, separated by a 2-week wash-out period. Lunch and diner will be directly provided while dietary guidelines will be given for breakfast and snacks. Blood, urine and stool samples will be collected at the fasted state every 2 weeks. At the end of each dietary intervention, blood and urine will be collected following a high fat meal, which challenges metabolism and vascular homeostasis. Plasma and urine non-targeted metabolomics analyses (LC-MS) will be combined with Peripheral Blood Mononuclear Cell (PBMC) transcriptomics and fluxomics analyses (D2O tracer) to get a comprehensive overview of the metabolic phenotype associated with AP or PP intake. Flow-Mediated Dilatation (FMD) and Flow Laser Doppler (FLD) will be used to measure respectively macrovascular endothelial function and microvascular skin blood flow at the fasted state and after the high-fat meal. We will also measure anthropometric parameters and analyze biochemistry and inflammatory markers.
Results
Not applicable (protocols abstract).
Conclusions
We expect the multi-omics fingerprinting to reveal subtle metabolic differences associated to AP or PP intake, with a positive effect of PP intake. Improved inflammatory status and endothelial function are also expected to be associated to PP intake.
Funding Sources
INRAE and Roquette Frères.
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Affiliation(s)
- Gaïa Lépine
- Université Clermont Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, France and Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, France
| | | | | | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, France
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, France; Metatoul-AXIOM platform, MetaboHUB, Toxalim, INRAE, France
| | - Marie-Anne Verny
- Université Clermont Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, France
| | - Nicolas Macian
- University Hospital Clermont-Ferrand, Inserm CIC 1405, Clinical Investigation Center, France
| | - Marion Courrent
- University Hospital Clermont-Ferrand, Inserm CIC 1405, Clinical Investigation Center, France
| | | | | | - Didier Rémond
- Université Clermont Auvergne, INRAE, UMR1019, Unité de Nutrition Humaine, France
| | - Hélène Fouillet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, France
| | - Sergio Polakof
- Université Clermont Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, France
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13
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Stuani L, Sabatier M, Saland E, Cognet G, Poupin N, Bosc C, Castelli FA, Gales L, Turtoi E, Montersino C, Farge T, Boet E, Broin N, Larrue C, Baran N, Cissé MY, Conti M, Loric S, Kaoma T, Hucteau A, Zavoriti A, Sahal A, Mouchel PL, Gotanègre M, Cassan C, Fernando L, Wang F, Hosseini M, Chu-Van E, Le Cam L, Carroll M, Selak MA, Vey N, Castellano R, Fenaille F, Turtoi A, Cazals G, Bories P, Gibon Y, Nicolay B, Ronseaux S, Marszalek JR, Takahashi K, DiNardo CD, Konopleva M, Pancaldi V, Collette Y, Bellvert F, Jourdan F, Linares LK, Récher C, Portais JC, Sarry JE. Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia. J Exp Med 2021; 218:e20200924. [PMID: 33760042 PMCID: PMC7995203 DOI: 10.1084/jem.20200924] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations in IDH induce epigenetic and transcriptional reprogramming, differentiation bias, and susceptibility to mitochondrial inhibitors in cancer cells. Here, we first show that cell lines, PDXs, and patients with acute myeloid leukemia (AML) harboring an IDH mutation displayed an enhanced mitochondrial oxidative metabolism. Along with an increase in TCA cycle intermediates, this AML-specific metabolic behavior mechanistically occurred through the increase in electron transport chain complex I activity, mitochondrial respiration, and methylation-driven CEBPα-induced fatty acid β-oxidation of IDH1 mutant cells. While IDH1 mutant inhibitor reduced 2-HG oncometabolite and CEBPα methylation, it failed to reverse FAO and OxPHOS. These mitochondrial activities were maintained through the inhibition of Akt and enhanced activation of peroxisome proliferator-activated receptor-γ coactivator-1 PGC1α upon IDH1 mutant inhibitor. Accordingly, OxPHOS inhibitors improved anti-AML efficacy of IDH mutant inhibitors in vivo. This work provides a scientific rationale for combinatory mitochondrial-targeted therapies to treat IDH mutant AML patients, especially those unresponsive to or relapsing from IDH mutant inhibitors.
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MESH Headings
- Acute Disease
- Aminopyridines/pharmacology
- Animals
- Cell Line, Tumor
- Doxycycline/pharmacology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enzyme Inhibitors/pharmacology
- Epigenesis, Genetic/drug effects
- Glycine/analogs & derivatives
- Glycine/pharmacology
- HL-60 Cells
- Humans
- Isocitrate Dehydrogenase/antagonists & inhibitors
- Isocitrate Dehydrogenase/genetics
- Isocitrate Dehydrogenase/metabolism
- Isoenzymes/antagonists & inhibitors
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Myeloid/drug therapy
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Mutation
- Oxadiazoles/pharmacology
- Oxidative Phosphorylation/drug effects
- Piperidines/pharmacology
- Pyridines/pharmacology
- Triazines/pharmacology
- Xenograft Model Antitumor Assays/methods
- Mice
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Affiliation(s)
- Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Guillaume Cognet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
| | - Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Florence A. Castelli
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Lara Gales
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Evgenia Turtoi
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
- Montpellier Alliance for Metabolomics and Metabolism Analysis, Platform for Translational Oncometabolomics, Biocampus, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Montpellier, France
| | - Camille Montersino
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nicolas Broin
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Natalia Baran
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Madi Y. Cissé
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Marc Conti
- Institut National de la Santé et de la Recherché Médicale U938, Hôpital St Antoine, Paris, France
- Integracell, Longjumeau, France
| | - Sylvain Loric
- Institut National de la Santé et de la Recherché Médicale U938, Hôpital St Antoine, Paris, France
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Alexis Hucteau
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Aliki Zavoriti
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Ambrine Sahal
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Cédric Cassan
- UMR1332 Biologie du Fruit et Pathologie, Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d'Ornon, France
| | - Laurent Fernando
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
| | - Feng Wang
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Mohsen Hosseini
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Chu-Van
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Laurent Le Cam
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Martin Carroll
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mary A. Selak
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Norbert Vey
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Rémy Castellano
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - François Fenaille
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Andrei Turtoi
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Guillaume Cazals
- Laboratoire de Mesures Physiques, Université de Montpellier, Montpellier, France
| | - Pierre Bories
- Réseau Régional de Cancérologie Onco-Occitanie, Toulouse, France
| | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d'Ornon, France
| | | | | | - Joseph R. Marszalek
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Koichi Takahashi
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Courtney D. DiNardo
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Marina Konopleva
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Véra Pancaldi
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Yves Collette
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Floriant Bellvert
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Fabien Jourdan
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Laetitia K. Linares
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Jean-Charles Portais
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- STROMALab, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
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14
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Rodríguez-Mier P, Poupin N, de Blasio C, Le Cam L, Jourdan F. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PLoS Comput Biol 2021; 17:e1008730. [PMID: 33571201 PMCID: PMC7904180 DOI: 10.1371/journal.pcbi.1008730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/24/2021] [Accepted: 01/21/2021] [Indexed: 11/18/2022] Open
Abstract
The correct identification of metabolic activity in tissues or cells under different conditions can be extremely elusive due to mechanisms such as post-transcriptional modification of enzymes or different rates in protein degradation, making difficult to perform predictions on the basis of gene expression alone. Context-specific metabolic network reconstruction can overcome some of these limitations by leveraging the integration of multi-omics data into genome-scale metabolic networks (GSMN). Using the experimental information, context-specific models are reconstructed by extracting from the generic GSMN the sub-network most consistent with the data, subject to biochemical constraints. One advantage is that these context-specific models have more predictive power since they are tailored to the specific tissue, cell or condition, containing only the reactions predicted to be active in such context. However, an important limitation is that there are usually many different sub-networks that optimally fit the experimental data. This set of optimal networks represent alternative explanations of the possible metabolic state. Ignoring the set of possible solutions reduces the ability to obtain relevant information about the metabolism and may bias the interpretation of the true metabolic states. In this work we formalize the problem of enumerating optimal metabolic networks and we introduce DEXOM, an unified approach for diversity-based enumeration of context-specific metabolic networks. We developed different strategies for this purpose and we performed an exhaustive analysis using simulated and real data. In order to analyze the extent to which these results are biologically meaningful, we used the alternative solutions obtained with the different methods to measure: 1) the improvement of in silico predictions of essential genes in Saccharomyces cerevisiae using ensembles of metabolic network; and 2) the detection of alternative enriched pathways in different human cancer cell lines. We also provide DEXOM as an open-source library compatible with COBRA Toolbox 3.0, available at https://github.com/MetExplore/dexom.
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Affiliation(s)
- Pablo Rodríguez-Mier
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Carlo de Blasio
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
- Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Laurent Le Cam
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
- Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- * E-mail:
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15
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Corral-Jara KF, Cantini L, Poupin N, Ye T, Rigaudière JP, Vincent SDS, Pinel A, Morio B, Capel F. An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. Nutrients 2020; 12:E3864. [PMID: 33348802 PMCID: PMC7765958 DOI: 10.3390/nu12123864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Insulin resistance decreases the ability of insulin to inhibit hepatic gluconeogenesis, a key step in the development of metabolic syndrome. Metabolic alterations, fat accumulation, and fibrosis in the liver are closely related and contribute to the progression of comorbidities, such as hypertension, type 2 diabetes, or cancer. Omega 3 (n-3) polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), were identified as potent positive regulators of insulin sensitivity in vitro and in animal models. In the current study, we explored the effects of a transgenerational supplementation with EPA in mice exposed to an obesogenic diet on the regulation of microRNAs (miRNAs) and gene expression in the liver using high-throughput techniques. We implemented a comprehensive molecular systems biology approach, combining statistical tools, such as MicroRNA Master Regulator Analysis pipeline and Boolean modeling to integrate these biochemical processes. We demonstrated that EPA mediated molecular adaptations, leading to the inhibition of miR-34a-5p, a negative regulator of Irs2 as a master regulatory event leading to the inhibition of gluconeogenesis by insulin during the fasting-feeding transition. Omics data integration provided greater biological insight and a better understanding of the relationships between biological variables. Such an approach may be useful for deriving innovative data-driven hypotheses and for the discovery of molecular-biochemical mechanistic links.
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Affiliation(s)
- Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Laura Cantini
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France;
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France;
| | - Tao Ye
- GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries/BP 10142/, 67404 Illkirch, France;
| | - Jean Paul Rigaudière
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Sarah De Saint Vincent
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Alexandre Pinel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Lyon 1, 69310 Pierre Bénite, France;
| | - Frédéric Capel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
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16
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Villaret-Cazadamont J, Poupin N, Tournadre A, Batut A, Gales L, Zalko D, Cabaton NJ, Bellvert F, Bertrand-Michel J. An Optimized Dual Extraction Method for the Simultaneous and Accurate Analysis of Polar Metabolites and Lipids Carried out on Single Biological Samples. Metabolites 2020; 10:E338. [PMID: 32825089 PMCID: PMC7570216 DOI: 10.3390/metabo10090338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
The functional understanding of metabolic changes requires both a significant investigation into metabolic pathways, as enabled by global metabolomics and lipidomics approaches, and the comprehensive and accurate exploration of specific key pathways. To answer this pivotal challenge, we propose an optimized approach, which combines an efficient sample preparation, aiming to reduce the variability, with a biphasic extraction method, where both the aqueous and organic phases of the same sample are used for mass spectrometry analyses. We demonstrated that this double extraction protocol allows working with one single sample without decreasing the metabolome and lipidome coverage. It enables the targeted analysis of 40 polar metabolites and 82 lipids, together with the absolute quantification of 32 polar metabolites, providing comprehensive coverage and quantitative measurement of the metabolites involved in central carbon energy pathways. With this method, we evidenced modulations of several lipids, amino acids, and energy metabolites in HepaRG cells exposed to fenofibrate, a model hepatic toxicant, and metabolic modulator. This new protocol is particularly relevant for experiments involving limited amounts of biological material and for functional metabolic explorations and is thus of particular interest for studies aiming to decipher the effects and modes of action of metabolic disrupting compounds.
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Affiliation(s)
- Joran Villaret-Cazadamont
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Anthony Tournadre
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
| | - Aurélie Batut
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
| | - Lara Gales
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France
| | - Daniel Zalko
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Nicolas J. Cabaton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (J.V.-C.); (N.P.); (D.Z.); (N.J.C.)
| | - Floriant Bellvert
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 31400 Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul-Lipidomics Core Facility, Inserm U1048, 31432 Toulouse, France; (A.T.); (A.B.)
- MetaboHUB-MetaToul, National Infrastructure for Metabolomics and Fluxomics, 31077 Toulouse, France;
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17
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Tremblay-Franco M, Poupin N, Amiel A, Canlet C, Rémond D, Debrauwer L, Dardevet D, Jourdan F, Savary-Auzeloux I, Polakof S. Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig. Nutrients 2020; 12:nu12082442. [PMID: 32823827 PMCID: PMC7468879 DOI: 10.3390/nu12082442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
The postprandial period represents one of the most challenging phenomena in whole-body metabolism, and it can be used as a unique window to evaluate the phenotypic flexibility of an individual in response to a given meal, which can be done by measuring the resilience of the metabolome. However, this exploration of the metabolism has never been applied to the arteriovenous (AV) exploration of organs metabolism. Here, we applied an AV metabolomics strategy to evaluate the postprandial flexibility across the liver and the intestine of mini-pigs subjected to a high fat–high sucrose (HFHS) diet for 2 months. We identified for the first time a postprandial signature associated to the insulin resistance and obesity outcomes, and we showed that the splanchnic postprandial metabolome was considerably affected by the meal and the obesity condition. Most of the changes induced by obesity were observed in the exchanges across the liver, where the metabolism was reorganized to maintain whole body glucose homeostasis by routing glucose formed de novo from a large variety of substrates into glycogen. Furthermore, metabolites related to lipid handling and energy metabolism showed a blunted postprandial response in the obese animals across organs. Finally, some of our results reflect a loss of flexibility in response to the HFHS meal challenge in unsuspected metabolic pathways that must be further explored as potential new events involved in early obesity and the onset of insulin resistance.
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Affiliation(s)
- Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
- Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31300 Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
| | - Aurélien Amiel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
- Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31300 Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
- Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31300 Toulouse, France
| | - Didier Rémond
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (D.R.); (D.D.); (I.S.-A.)
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
- Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31300 Toulouse, France
| | - Dominique Dardevet
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (D.R.); (D.D.); (I.S.-A.)
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France; (M.T.-F.); (N.P.); (A.A.); (C.C.); (L.D.); (F.J.)
| | - Isabelle Savary-Auzeloux
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (D.R.); (D.D.); (I.S.-A.)
| | - Sergio Polakof
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (D.R.); (D.D.); (I.S.-A.)
- Correspondence: ; Tel.: +33-(0)4-7362-4895; Fax: 33-(0)4-7362-4638
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18
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Poupin N, Vinson F, Moreau A, Batut A, Chazalviel M, Colsch B, Fouillen L, Guez S, Khoury S, Dalloux-Chioccioli J, Tournadre A, Le Faouder P, Pouyet C, Van Delft P, Viars F, Bertrand-Michel J, Jourdan F. Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. Metabolomics 2020; 16:44. [PMID: 32215752 PMCID: PMC7096385 DOI: 10.1007/s11306-020-01663-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/10/2020] [Indexed: 10/28/2022]
Abstract
INTRODUCTION To interpret metabolomic and lipidomic profiles, it is necessary to identify the metabolic reactions that connect the measured molecules. This can be achieved by putting them in the context of genome-scale metabolic network reconstructions. However, mapping experimentally measured molecules onto metabolic networks is challenging due to differences in identifiers and level of annotation between data and metabolic networks, especially for lipids. OBJECTIVES To help linking lipids from lipidomics datasets with lipids in metabolic networks, we developed a new matching method based on the ChEBI ontology. The implementation is freely available as a python library and in MetExplore webserver. METHODS Our matching method is more flexible than an exact identifier-based correspondence since it allows establishing a link between molecules even if a different level of precision is provided in the dataset and in the metabolic network. For instance, it can associate a generic class of lipids present in the network with the molecular species detailed in the lipidomics dataset. This mapping is based on the computation of a distance between molecules in ChEBI ontology. RESULTS We applied our method to a chemical library (968 lipids) and an experimental dataset (32 modulated lipids) and showed that using ontology-based mapping improves and facilitates the link with genome scale metabolic networks. Beyond network mapping, the results provide ways for improvements in terms of network curation and lipidomics data annotation. CONCLUSION This new method being generic, it can be applied to any metabolomics data and therefore improve our comprehension of metabolic modulations.
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Affiliation(s)
- Nathalie Poupin
- UMR1331, Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300, Toulouse, France
| | - Florence Vinson
- UMR1331, Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300, Toulouse, France
| | - Arthur Moreau
- UMR1331, Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300, Toulouse, France
| | - Aurélie Batut
- MetaToul-Lipidomic Core Facility, MetaboHUB, Inserm I2MC, 31000, Toulouse, France
| | | | - Benoit Colsch
- Université Paris Saclay, CEA, INRAE, Médicaments Et Technologies Pour La santé (MTS), 91191, Gif-sur-Yvette, France
| | - Laetitia Fouillen
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, 33140, Villenave d'Ornon, France
| | - Sarah Guez
- MetaToul-Lipidomic Core Facility, MetaboHUB, Inserm I2MC, 31000, Toulouse, France
| | - Spiro Khoury
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France
| | | | - Anthony Tournadre
- MetaToul-Lipidomic Core Facility, MetaboHUB, Inserm I2MC, 31000, Toulouse, France
| | - Pauline Le Faouder
- MetaToul-Lipidomic Core Facility, MetaboHUB, Inserm I2MC, 31000, Toulouse, France
| | - Corinne Pouyet
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France
| | - Pierre Van Delft
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, 33140, Villenave d'Ornon, France
| | - Fanny Viars
- MetaToul-Lipidomic Core Facility, MetaboHUB, Inserm I2MC, 31000, Toulouse, France
| | | | - Fabien Jourdan
- UMR1331, Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300, Toulouse, France.
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19
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Poupin N, Tremblay-Franco M, Amiel A, Canlet C, Rémond D, Debrauwer L, Dardevet D, Thiele I, Aurich MK, Jourdan F, Savary-Auzeloux I, Polakof S. Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig. Sci Rep 2019; 9:12527. [PMID: 31467335 PMCID: PMC6715693 DOI: 10.1038/s41598-019-48997-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Blood circulation mainly aims at distributing the nutrients required for tissue metabolism and collecting safely the by-products of all tissues to be further metabolized or eliminated. The simultaneous study of arterial (A) and venous (V) specific metabolites therefore has appeared to be a more relevant approach to understand and study the metabolism of a given organ. We propose to implement this approach by applying a metabolomics (NMR) strategy on paired AV blood across the intestine and liver on high fat/high sugar (HFHS)-fed minipigs. Our objective was to unravel kinetically and sequentially the metabolic adaptations to early obesity/insulin resistance onset specifically on these two tissues. After two months of HFHS feeding our study of AV ratios of the metabolome highlighted three major features. First, the hepatic metabolism switched from carbohydrate to lipid utilization. Second, the energy demand of the intestine increased, resulting in an enhanced uptake of glutamine, glutamate, and the recruitment of novel energy substrates (choline and creatine). Third, the uptake of methionine and threonine was considered to be driven by an increased intestine turnover to cope with the new high-density diet. Finally, the unique combination of experimental data and modelling predictions suggested that HFHS feeding was associated with changes in tryptophan metabolism and fatty acid β-oxidation, which may play an important role in lipid hepatic accumulation and insulin sensitivity.
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Affiliation(s)
- Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.,Axiom platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Aurélien Amiel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.,Axiom platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.,Axiom platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Didier Rémond
- Université Clermont Auvergne, INRA, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.,Axiom platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Dominique Dardevet
- Université Clermont Auvergne, INRA, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg.,School of Medicine, National University of Ireland, University Road, Galway, Ireland.,Discipline of Microbiology, School of Natural Sciences, National University of Ireland, University Road, Galway, Ireland
| | - Maike K Aurich
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Isabelle Savary-Auzeloux
- Université Clermont Auvergne, INRA, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France
| | - Sergio Polakof
- Université Clermont Auvergne, INRA, Unité de Nutrition Humaine, UMR1019, Clermont-Ferrand, France.
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20
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Cottret L, Frainay C, Chazalviel M, Cabanettes F, Gloaguen Y, Camenen E, Merlet B, Heux S, Portais JC, Poupin N, Vinson F, Jourdan F. MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Res 2019; 46:W495-W502. [PMID: 29718355 PMCID: PMC6030842 DOI: 10.1093/nar/gky301] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
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Affiliation(s)
- Ludovic Cottret
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Maxime Chazalviel
- INRA, UMR1331, Toxalim, F-31000 Toulouse, France.,MedDay Pharmaceuticals, Paris, France
| | | | - Yoann Gloaguen
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | | | - Stéphanie Heux
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
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21
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Poupin N, Corlu A, Cabaton NJ, Dubois-Pot-Schneider H, Canlet C, Person E, Bruel S, Frainay C, Vinson F, Maurier F, Morel F, Robin MA, Fromenty B, Zalko D, Jourdan F. Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation. J Proteome Res 2018; 18:204-216. [PMID: 30394098 DOI: 10.1021/acs.jproteome.8b00524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Being able to explore the metabolism of broad metabolizing cells is of critical importance in many research fields. This article presents an original modeling solution combining metabolic network and omics data to identify modulated metabolic pathways and changes in metabolic functions occurring during differentiation of a human hepatic cell line (HepaRG). Our results confirm the activation of hepato-specific functionalities and newly evidence modulation of other metabolic pathways, which could not be evidenced from transcriptomic data alone. Our method takes advantage of the network structure to detect changes in metabolic pathways that do not have gene annotations and exploits flux analyses techniques to identify activated metabolic functions. Compared to the usual cell-specific metabolic network reconstruction approaches, it limits false predictions by considering several possible network configurations to represent one phenotype rather than one arbitrarily selected network. Our approach significantly enhances the comprehensive and functional assessment of cell metabolism, opening further perspectives to investigate metabolic shifts occurring within various biological contexts.
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Affiliation(s)
- Nathalie Poupin
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Anne Corlu
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Nicolas J Cabaton
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Hélène Dubois-Pot-Schneider
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Cécile Canlet
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Elodie Person
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Sandrine Bruel
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Clément Frainay
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Florence Vinson
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Florence Maurier
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Fabrice Morel
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Marie-Anne Robin
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Bernard Fromenty
- Université Rennes, INSERM, INRA, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_A 1341, UMR_S 1241 , F-35000 Rennes , France
| | - Daniel Zalko
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
| | - Fabien Jourdan
- UMR1331 Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan, UPS , 31027 Toulouse , France
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22
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Cabaton NJ, Poupin N, Canlet C, Tremblay-Franco M, Audebert M, Cravedi JP, Riu A, Jourdan F, Zalko D. An Untargeted Metabolomics Approach to Investigate the Metabolic Modulations of HepG2 Cells Exposed to Low Doses of Bisphenol A and 17β-Estradiol. Front Endocrinol (Lausanne) 2018; 9:571. [PMID: 30319551 PMCID: PMC6167423 DOI: 10.3389/fendo.2018.00571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022] Open
Abstract
The model xeno-estrogen bisphenol A (BPA) has been extensively studied over the past two decades, contributing to major advances in the field of endocrine disrupting chemicals research. Besides its well documented adverse effects on reproduction and development observed in rodents, latest studies strongly suggest that BPA disrupts several endogenous metabolic pathways, with suspected steatogenic and obesogenic effects. BPA's adverse effects on reproduction are attributed to its ability to activate estrogen receptors (ERs), but its effects on metabolism and its mechanism(s) of action at low doses are so far only marginally understood. Metabolomics based approaches are increasingly used in toxicology to investigate the biological changes induced by model toxicants and chemical mixtures, to identify markers of toxicity and biological effects. In this study, we used proton nuclear magnetic resonance (1H-NMR) based untargeted metabolite profiling, followed by multivariate statistics and computational analysis of metabolic networks to examine the metabolic modulation induced in human hepatic cells (HepG2) by an exposure to low and very low doses of BPA (10-6M, 10-9M, and 10-12M), vs. the female reference hormone 17β-estradiol (E2, 10-9M, 10-12M, and 10-15M). Metabolomic analysis combined to metabolic network reconstruction highlighted different mechanisms at lower doses of exposure. At the highest dose, our results evidence that BPA shares with E2 the capability to modulate several major metabolic routes that ensure cellular functions and detoxification processes, although the effects of the model xeno-estrogen and of the natural hormone can still be distinguished.
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Affiliation(s)
- Nicolas J. Cabaton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
- Axiom Platform, MetaToul-MetaboHub, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
- Axiom Platform, MetaToul-MetaboHub, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Marc Audebert
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Jean-Pierre Cravedi
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Anne Riu
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Daniel Zalko
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
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23
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Chazalviel M, Frainay C, Poupin N, Vinson F, Merlet B, Gloaguen Y, Cottret L, Jourdan F. MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics 2017; 34:312-313. [PMID: 28968733 PMCID: PMC5860210 DOI: 10.1093/bioinformatics/btx588] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/04/2017] [Accepted: 09/14/2017] [Indexed: 12/29/2022] Open
Abstract
Summary MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc/
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Affiliation(s)
- Maxime Chazalviel
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France.,MedDay Pharmaceuticals, Paris, France
| | - Clément Frainay
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Nathalie Poupin
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Florence Vinson
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Benjamin Merlet
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Yoann Gloaguen
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Gascube Campus, Bearsden, UK
| | - Ludovic Cottret
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabien Jourdan
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
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24
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Merlet B, Paulhe N, Vinson F, Frainay C, Chazalviel M, Poupin N, Gloaguen Y, Giacomoni F, Jourdan F. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. Front Mol Biosci 2016; 3:2. [PMID: 26909353 PMCID: PMC4754433 DOI: 10.3389/fmolb.2016.00002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.
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Affiliation(s)
- Benjamin Merlet
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
| | - Nils Paulhe
- Nutrition Humaine, Plateforme d'Exploration du Métabolisme, Institut National de la Recherche Agronomique, Centre Clermont-Ferrand-Theix, UMR 1019 Saint-Genès-Champanelle, France
| | - Florence Vinson
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
| | - Clément Frainay
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
| | - Maxime Chazalviel
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
| | - Nathalie Poupin
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
| | - Yoann Gloaguen
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, UK
| | - Franck Giacomoni
- Nutrition Humaine, Plateforme d'Exploration du Métabolisme, Institut National de la Recherche Agronomique, Centre Clermont-Ferrand-Theix, UMR 1019 Saint-Genès-Champanelle, France
| | - Fabien Jourdan
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de Toulouse Toulouse, France
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25
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Poupin N, Mariotti F, Huneau JF, Hermier D, Fouillet H. Natural isotopic signatures of variations in body nitrogen fluxes: a compartmental model analysis. PLoS Comput Biol 2014; 10:e1003865. [PMID: 25275306 PMCID: PMC4183419 DOI: 10.1371/journal.pcbi.1003865] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such natural and interpretable isotopic biomarkers promises interesting applications in nutrition and health. Body proteins ensure vital functions, and their constancy is maintained through the tight coordination of many nitrogen metabolic fluxes, but our understanding of how this flux system is regulated, and sometimes dysregulated, remains fragmentary and incomplete. Besides, body tissues are generally naturally enriched in the heavier stable nitrogen isotope (15N) over the diet: this 15N bioaccumulation (Δ15N) varies depending on tissues and metabolic orientations, likely as the result of isotope effects associated to some metabolic pathways. We used a novel approach, combining multi-tissue Δ15N measurements and their analysis using modeling, to understand how body Δ15N values relate to nitrogen fluxes. The multi-tissue model we have developed provides a clearer understanding of the metabolic processes that generate isotopic fractionation, and of how tissue Δ15N values are modulated in response to changes in the body distribution of specific nitrogen fluxes. We show that Δ15N values tend to rise when the amino acids intake does not optimally fit the metabolic demand, and that Δ15N values constitute natural and interpretable signatures of nutritionally-induced variations in nitrogen fluxes. This approach constitutes a new promising tool to investigate how nitrogen metabolism is nutritionally or physiopathologically reorganized or altered, and promises interesting applications in many areas (nutrition, pathology, ecology, paleontology, etc).
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Affiliation(s)
- Nathalie Poupin
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France; AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - François Mariotti
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France; AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Jean-François Huneau
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France; AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Dominique Hermier
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France; AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Hélène Fouillet
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France; AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
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Poupin N, Huneau JF, Mariotti F, Tomé D, Bos C, Fouillet H. Isotopic and modeling investigation of long-term protein turnover in rat tissues. Am J Physiol Regul Integr Comp Physiol 2012; 304:R218-31. [PMID: 23135789 DOI: 10.1152/ajpregu.00310.2012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fractional synthesis rates (FSR) of tissue proteins (P) are usually measured using labeled amino acid (AA) tracer methods over short periods of time under acute, particular conditions. By combining the long-term and non-steady-state (15)N labeling of AA and P tissue fractions with compartmental modeling, we have developed a new isotopic approach to investigate the degree of compartmentation of P turnover in tissues and to estimate long-term FSR values under sustained and averaged nutritional and physiological conditions. We measured the rise-to-plateau kinetics of nitrogen isotopic enrichments (δ(15)N) in the AA and P fractions of various tissues in rats for 2 mo following a slight increase in diet δ(15)N. Using these δ(15)N kinetics and a numerical method based on a two-compartment model, we determined reliable FSR estimates for tissues in which P turnover is adequately represented by such a simple precursor-product model. This was the case for kidney, liver, plasma, and muscle, where FSR estimates were 103, 101, 58, and 11%/day, respectively. Conversely, we identified tissues, namely, skin and small intestine, where P turnover proved to be too complex to be represented by a simple two-compartment model, evidencing the higher level of subcompartmentation of the P and/or AA metabolism in these tissues. The present results support the value of this new approach in gaining cognitive and practical insights into tissue P turnover and propose new and integrated FSR values over all individual precursor AA and all diurnal variations in P kinetics.
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Affiliation(s)
- Nathalie Poupin
- 1INRA (Institut National de la Recherche Agronomique), CRNH-IdF (Centre de Recherche en Nutrition Humaine d’Ile de France), UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
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Poupin N, Calvez J, Lassale C, Chesneau C, Tomé D. Impact of the diet on net endogenous acid production and acid-base balance. Clin Nutr 2012; 31:313-21. [PMID: 22342140 DOI: 10.1016/j.clnu.2012.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/10/2012] [Accepted: 01/25/2012] [Indexed: 11/26/2022]
Abstract
Net acid production, which is composed of volatile acids (15,000 mEq/day) and metabolic acids (70-100 mEq/day) is relatively small compared to whole-body H⁺ turnover (150,000 mEq/day). Metabolic acids are ingested from the diet or produced as intermediary or end products of endogenous metabolism. The three commonly reported sources of net acid production are the metabolism of sulphur amino acids, the metabolism or ingestion of organic acids, and the metabolism of phosphate esters or dietary phosphoproteins. Net base production occurs mainly as a result of absorption of organic anions from the diet. To maintain acid-base balance, ingested and endogenously produced acids are neutralized within the body by buffer systems or eliminated from the body through the respiratory (excretion of volatile acid in the form of CO₂) and urinary (excretion of fixed acids and remaining H⁺) pathways. Because of the many reactions involved in the acid-base balance, the direct determination of acid production is complex and is usually estimated through direct or indirect measurements of acid excretion. However, indirect approaches, which assess the acid-forming potential of the ingested diet based on its composition, do not take all the acid-producing reactions into account. Direct measurements therefore seem more reliable. Nevertheless, acid excretion does not truly provide information on the way acidity is dealt with in the plasma and this measurement should be interpreted with caution when assessing acid-base imbalance.
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Affiliation(s)
- Nathalie Poupin
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, 16 rue Claude Bernard, F-75005 Paris, France
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Poupin N, Bos C, Mariotti F, Huneau JF, Tomé D, Fouillet H. The nature of the dietary protein impacts the tissue-to-diet 15N discrimination factors in laboratory rats. PLoS One 2011; 6:e28046. [PMID: 22132207 PMCID: PMC3222673 DOI: 10.1371/journal.pone.0028046] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/31/2011] [Indexed: 11/18/2022] Open
Abstract
Due to the existence of isotope effects on some metabolic pathways of amino acid and protein metabolism, animal tissues are 15N-enriched relative to their dietary nitrogen sources and this 15N enrichment varies among different tissues and metabolic pools. The magnitude of the tissue-to-diet discrimination (Δ15N) has also been shown to depend on dietary factors. Since dietary protein sources affect amino acid and protein metabolism, we hypothesized that they would impact this discrimination factor, with selective effects at the tissue level. To test this hypothesis, we investigated in rats the influence of a milk or soy protein-based diet on Δ15N in various nitrogen fractions (urea, protein and non-protein fractions) of blood and tissues, focusing on visceral tissues. Regardless of the diet, the different protein fractions of blood and tissues were generally 15N-enriched relative to their non-protein fraction and to the diet (Δ15N>0), with large variations in the Δ15N between tissue proteins. Δ15N values were markedly lower in tissue proteins of rats fed milk proteins compared to those fed soy proteins, in all sampled tissues except in the intestine, and the amplitude of Δ15N differences between diets differed between tissues. Both between-tissue and between-diet Δ15N differences are probably related to modulations of the relative orientation of dietary and endogenous amino acids in the different metabolic pathways. More specifically, the smaller Δ15N values observed in tissue proteins with milk than soy dietary protein may be due to a slightly more direct channeling of dietary amino acids for tissue protein renewal and to a lower recycling of amino acids through fractionating pathways. In conclusion, the present data indicate that natural Δ15N of tissue are sensitive markers of the specific subtle regional modifications of the protein and amino acid metabolism induced by the protein dietary source.
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Affiliation(s)
- Nathalie Poupin
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Cécile Bos
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - François Mariotti
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Jean-François Huneau
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Daniel Tomé
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
| | - Hélène Fouillet
- INRA, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- AgroParisTech, CRNH-IdF, UMR914 Nutrition Physiology and Ingestive Behavior, Paris, France
- * E-mail:
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29
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Poupin N, Huneau J, Mariotti F, Bos C, Tomé D, Fouillet H. A new method for the multi‐tissue estimation of protein turnover by compartmental analysis of the nitrogen isotope dynamics in rats fed a
15
N‐enriched diet. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.983.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nathalie Poupin
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Jean‐François Huneau
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - François Mariotti
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Cécile Bos
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Daniel Tomé
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Hélène Fouillet
- INRA, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTech, CRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
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West SG, Skulas‐Ray AC, Piotrowski MJ, Crispell MD, Groves LF, Poupin N, Wagner PR. High flavanol cocoa and dark chocolate enhance vasodilation and reduce arterial stiffness. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.722.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | - Paul R Wagner
- Diagnostic Medical SonographySouth Hills School of Business and TechnologyState CollegePA
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Skulas‐Ray AC, Kris‐Etherton PM, Wagner PR, Harris WS, Groves LF, Turbitt WJ, Crispell MD, Poupin N, West SG. Omega‐3 fatty acid concentrates dose‐dependently alter triglycerides and erythrocyte fatty acid composition with no effect on in endothelial function. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.939.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Paul R. Wagner
- Diagnostic Medicial SonographySouth Hills School of Business and TechnologyState CollegePA
| | - William S. Harris
- Cardiovascular Health Research CenterUniversity of South DakotaSioux FallsSD
| | - Lisa F. Groves
- Biobehavioral HealthThe Penn State UniversityUniversity ParkPA
| | | | | | - Nathalie Poupin
- Biobehavioral HealthThe Penn State UniversityUniversity ParkPA
| | - Sheila G. West
- Biobehavioral HealthThe Penn State UniversityUniversity ParkPA
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Poupin N, Fouillet H, Mariotti F, Tomé D, Huneau J, Bos C. Dietary protein quality influences the pattern of natural isotopic composition of nitrogen in rats. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.740.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nathalie Poupin
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Hélène Fouillet
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - François Mariotti
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Daniel Tomé
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Jean‐François Huneau
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
| | - Cécile Bos
- INRACRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
- AgroParisTechCRNH‐IdFUMR914 Nutrition Physiology and Ingestive BehaviorParisFrance
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West S, Hilpert K, Bagshaw D, Lefevre M, Most M, Hinderliter A, Poupin N, Kris‐Etherton P. Effects of dairy foods on angiotensin II and intracellular magnesium. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.112.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sheila West
- Biobehavioral HealthPenn State UniversityUniversity ParkPA
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