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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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Beber A, Alqabandi M, Prévost C, Viars F, Lévy D, Bassereau P, Bertin A, Mangenot S. Septin‐based readout of PI(4,5)P2 incorporation into membranes of giant unilamellar vesicles. Cytoskeleton (Hoboken) 2018; 76:92-103. [DOI: 10.1002/cm.21480] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/05/2018] [Accepted: 07/10/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Alexandre Beber
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Maryam Alqabandi
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Coline Prévost
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Fanny Viars
- Institut des maladies métaboliques et cardiovasculairesUMR1048, Inserm/Université Paul Sabatier Toulouse France
| | - Daniel Lévy
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Patricia Bassereau
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Aurélie Bertin
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie CurieInstitut Curie, PSL Research University Paris France
- Sorbonne Université Paris France
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Régnier M, Polizzi A, Lippi Y, Fouché E, Michel G, Lukowicz C, Smati S, Marrot A, Lasserre F, Naylies C, Batut A, Viars F, Bertrand-Michel J, Postic C, Loiseau N, Wahli W, Guillou H, Montagner A. Insights into the role of hepatocyte PPARα activity in response to fasting. Mol Cell Endocrinol 2018; 471:75-88. [PMID: 28774777 DOI: 10.1016/j.mce.2017.07.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/04/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022]
Abstract
The liver plays a central role in the regulation of fatty acid metabolism. Hepatocytes are highly sensitive to nutrients and hormones that drive extensive transcriptional responses. Nuclear hormone receptors are key transcription factors involved in this process. Among these factors, PPARα is a critical regulator of hepatic lipid catabolism during fasting. This study aimed to analyse the wide array of hepatic PPARα-dependent transcriptional responses during fasting. We compared gene expression in male mice with a hepatocyte specific deletion of PPARα and their wild-type littermates in the fed (ad libitum) and 24-h fasted states. Liver samples were acquired, and transcriptome and lipidome analyses were performed. Our data extended and confirmed the critical role of hepatocyte PPARα as a central for regulator of gene expression during starvation. Interestingly, we identified novel PPARα-sensitive genes, including Cxcl-10, Rab30, and Krt23. We also found that liver phospholipid remodelling was a novel fasting-sensitive pathway regulated by PPARα. These results may contribute to investigations on transcriptional control in hepatic physiology and underscore the clinical relevance of drugs that target PPARα in liver pathologies, such as non-alcoholic fatty liver disease.
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Affiliation(s)
- Marion Régnier
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Arnaud Polizzi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Yannick Lippi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Edwin Fouché
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Géraldine Michel
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Céline Lukowicz
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Sarra Smati
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Alain Marrot
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Frédéric Lasserre
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Claire Naylies
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Aurélie Batut
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Fanny Viars
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Justine Bertrand-Michel
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Catherine Postic
- Institut National de La Santé et de La Recherche Médicale (INSERM), U1016, Institut Cochin, Paris, France
| | - Nicolas Loiseau
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Walter Wahli
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore; Center for Integrative Genomics, Université de Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Hervé Guillou
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France.
| | - Alexandra Montagner
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France.
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Mujalli A, Chicanne G, Bertrand-Michel J, Viars F, Stephens L, Hawkins P, Viaud J, Gaits-Iacovoni F, Severin S, Gratacap MP, Terrisse AD, Payrastre B. Profiling of phosphoinositide molecular species in human and mouse platelets identifies new species increasing following stimulation. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1121-1131. [PMID: 29902570 DOI: 10.1016/j.bbalip.2018.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/15/2018] [Accepted: 06/10/2018] [Indexed: 12/17/2022]
Abstract
Phosphoinositides are bioactive lipids essential in the regulation of cell signaling as well as cytoskeleton and membrane dynamics. Their metabolism is highly active in blood platelets where they play a critical role during activation, at least through two well identified pathways involving phospholipase C and phosphoinositide 3-kinases (PI3K). Here, using a sensitive high-performance liquid chromatography-mass spectrometry method recently developed, we monitored for the first time the profiling of phosphatidylinositol (PI), PIP, PIP2 and PIP3 molecular species (fatty-acyl profiles) in human and mouse platelets during the course of stimulation by thrombin and collagen-related peptide. Furthermore, using class IA PI3K p110α or p110β deficient mouse platelets and a pharmacological inhibitor, we show the crucial role of p110β and the more subtle role of p110α in the production of PIP3 molecular species following stimulation. This comprehensive platelet phosphoinositides profiling provides important resources for future studies and reveals new information on phosphoinositides biology, similarities and differences in mouse and human platelets and unexpected dramatic increase in low-abundance molecular species of PIP2 during stimulation, opening new perspectives in phosphoinositide signaling in platelets.
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Affiliation(s)
| | - Gaëtan Chicanne
- INSERM U1048, I2MC, Université Paul Sabatier, 31432 Toulouse, France
| | - Justine Bertrand-Michel
- MetaToul-Lipidomic Core Facility, MetaboHUB, INSERM UMR-1048, Université Paul Sabatier, 31432 Toulouse, France
| | - Fanny Viars
- MetaToul-Lipidomic Core Facility, MetaboHUB, INSERM UMR-1048, Université Paul Sabatier, 31432 Toulouse, France
| | - Len Stephens
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Phil Hawkins
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Julien Viaud
- INSERM U1048, I2MC, Université Paul Sabatier, 31432 Toulouse, France
| | | | - Sonia Severin
- INSERM U1048, I2MC, Université Paul Sabatier, 31432 Toulouse, France
| | | | | | - Bernard Payrastre
- INSERM U1048, I2MC, Université Paul Sabatier, 31432 Toulouse, France; CHU de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse Cedex 03, France.
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Tatin F, Renaud-Gabardos E, Godet AC, Hantelys F, Pujol F, Morfoisse F, Calise D, Viars F, Valet P, Masri B, Prats AC, Garmy-Susini B. Apelin modulates pathological remodeling of lymphatic endothelium after myocardial infarction. JCI Insight 2017; 2:93887. [PMID: 28614788 DOI: 10.1172/jci.insight.93887] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
Lymphatic endothelium serves as a barrier to control fluid balance and immune cell trafficking to maintain tissue homeostasis. Long-term alteration of lymphatic vasculature promotes edema and fibrosis, which is an aggravating factor in the onset of cardiovascular diseases such as myocardial infarction. Apelin is a bioactive peptide that plays a central role in angiogenesis and cardiac contractility. Despite an established role of apelin in lymphangiogenesis, little is known about its function in the cardiac lymphatic endothelium. Here, we show that apelin and its receptor APJ were exclusively expressed on newly formed lymphatic vasculature in a pathological model of myocardial infarction. Using an apelin-knockout mouse model, we identified morphological and functional defects in lymphatic vasculature associated with a proinflammatory status. Surprisingly, apelin deficiency increased the expression of lymphangiogenic growth factors VEGF-C and VEGF-D and exacerbated lymphangiogenesis after myocardial infarction. Conversely, the overexpression of apelin in ischemic heart was sufficient to restore a functional lymphatic vasculature and to reduce matrix remodeling and inflammation. In vitro, the expression of apelin prevented the alteration of cellular junctions in lymphatic endothelial cells induced by hypoxia. In addition, we demonstrated that apelin controls the secretion of the lipid mediator sphingosine-1-phosphate in lymphatic endothelial cells by regulating the level of expression of sphingosine kinase 2 and the transporter SPNS2. Taken together, our results show that apelin plays a key role in lymphatic vessel maturation and stability in pathological settings. Thus, apelin may represent a novel candidate to prevent pathological lymphatic remodeling in diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Fanny Viars
- MetaToul-Lipidomique Core Facility, I2MC INSERM 1048, Toulouse, France
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Balas L, Bertrand-Michel J, Viars F, Faugere J, Lefort C, Caspar-Bauguil S, Langin D, Durand T. Regiocontrolled syntheses of FAHFAs and LC-MS/MS differentiation of regioisomers. Org Biomol Chem 2016; 14:9012-20. [DOI: 10.1039/c6ob01597b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A regiospecific synthesis of branched fatty acyl hydroxyl-fatty acids (FAHFA) has been achieved for the development of LC-MS/MS detection.
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Affiliation(s)
- Laurence Balas
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | | | - Fanny Viars
- INSERM
- UMR 1048
- Institute of Metabolic and Cardiovascular Diseases
- Toulouse
- France
| | - Julien Faugere
- INSERM
- UMR 1048
- Institute of Metabolic and Cardiovascular Diseases
- Toulouse
- France
| | - Corinne Lefort
- INSERM
- UMR 1048
- Institute of Metabolic and Cardiovascular Diseases
- Toulouse
- France
| | | | - Dominique Langin
- INSERM
- UMR 1048
- Institute of Metabolic and Cardiovascular Diseases
- Toulouse
- France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
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