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11. List of Authors

Author

Anton, Marc, primary, Arhaliass, Abdellah, additional, Assaf, Ali, additional, Baron, Florence, additional, Coat, Rémy, additional, Courant, Frédérique, additional, Giraudeau, Patrick, additional, Gonçalves, Olivier, additional, Gouilleux, Boris, additional, Jan, Sophie, additional, Lechevalier, Valérie, additional, Legrand, Jack, additional, Martineau, Estelle, additional, Meynier, Anne, additional, Nau, Françoise, additional, Thierry, Anne, additional, and Thouand, Gérald, additional

Published
2018
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14. Preliminary results of a MetaboHUB 2.0 inter-laboratory test on 1D 1H NMR metabolite quantification of a synthetic urine

Author

Deborde, Catherine, Giraudeau, Patrick, Cahoreau, Edern, da Costa, Gregory, Gautier, Roselyne, Jacob, Daniel, Jousse, Cyril, Lacaze, Melia, Le Mao, Inès, Martineau, Estelle, Moing, Annick, Peyriga, Lindsay, Richard, Tristan, Silvestre, Virginie, Traïkia, Mounir, Canlet, Cécile, Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Œnologie [Villenave d'Ornon] (OENO), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ToxAlim (ToxAlim), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Metatoul AXIOM (E20 ), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Institut de Chimie de Clermont-Ferrand (ICCF), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, CAPACITÉS SAS, and Nantes Université (Nantes Univ)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV]Life Sciences [q-bio]
Abstract

International audience

Published
2022

18. Hyperpolarized NMR Metabolomics at Natural 13C Abundance

Author

Dey, Arnab, primary, Charrier, Benoît, additional, Martineau, Estelle, additional, Deborde, Catherine, additional, Gandriau, Elodie, additional, Moing, Annick, additional, Jacob, Daniel, additional, Eshchenko, Dmitry, additional, Schnell, Marc, additional, Melzi, Roberto, additional, Kurzbach, Dennis, additional, Ceillier, Morgan, additional, Chappuis, Quentin, additional, Cousin, Samuel F., additional, Kempf, James G., additional, Jannin, Sami, additional, Dumez, Jean-Nicolas, additional, and Giraudeau, Patrick, additional

Published
2020
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20. Two data pre-processing workflows to facilitate the discovery of biomarkers by 2D NMR metabolomics

Author

UCL - SSH/LIDAM/ISBA - Institut de Statistique, Biostatistique et Sciences Actuarielles, Feraud, Baptiste, Leenders, Justine, Martineau, Estelle, Giraudeau, Patrick, Govaerts, Bernadette, de Tullio, Pascal, UCL - SSH/LIDAM/ISBA - Institut de Statistique, Biostatistique et Sciences Actuarielles, Feraud, Baptiste, Leenders, Justine, Martineau, Estelle, Giraudeau, Patrick, Govaerts, Bernadette, and de Tullio, Pascal

Abstract

Introduction The pre-processing of analytical data in metabolomics must be considered as a whole to allow the construction of a global and unique object for any further simultaneous data analysis or multivariate statistical modelling. For 1D 1H-NMR metabolomics experiments, best practices for data pre-processing are well defined, but not yet for 2D experiments (for instance COSY in this paper). Objective By considering the added value of a second dimension, the objective is to propose two workflows dedicated to 2D NMR data handling and preparation (the Global Peak List and Vectorization approaches) and to compare them (with respect to each other and with 1D standards). This will allow to detect which methodology is the best in terms of amount of metabolomic content and to explore the advantages of the selected workflow in distinguishing among treatment groups and identifying relevant biomarkers. Therefore, this paper explores both the necessity of novel 2D pre-processing workflows, the evaluation of their quality and the evaluation of their performance in the subsequent determination of accurate (2D) biomarkers. Methods To select the more informative data source, MIC (Metabolomic Informative Content) indexes are used, based on clustering and inertia measures of quality. Then, to highlight biomarkers or critical spectral zones, the PLS-DA model is used, along with more advanced sparse algorithms (sPLS and L-sOPLS). Results Results are discussed according to two different experimental designs (one which is unsupervised and based on human urine samples, and the other which is controlled and based on spiked serum media). MIC indexes are shown, leading to the choice of the more relevant workflow to use thereafter. Finally, biomarkers are provided for each case and the predictive power of each candidate model is assessed with cross-validated measures of RMSEP. Conclusion In conclusion, it is shown that no solution can be universally the best in every case, but that 2D exp

Published
2019

24. Microbiological alteration of egg products during their production process : chzracterisation of metabolic pathways and dicovery of early prediction biomarkers

Author

Coat, Rémy, Martineau, Estelle, Giraudeau, Patrick, Arhaliass, Abdellah, Gonçalves, Olivier, Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and Matrices Aliments Procédés Propriétés Structure - Sensoriel (GEPEA-MAPS2)

Subjects
[SPI]Engineering Sciences [physics], [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [CHIM]Chemical Sciences, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

25. Potentiel des systèmes d’analyse en ligne pour le chémotypage de la matrice ovoproduit

Author

Coat, Rémy, Gouilleux, Boris, Arhaliass, Abdellah, Legrand, Jack, Thouand, Gerald, Martineau, Estelle, Assaf, Ali, Giraudeau, Patrick, Gonçalves, Olivier, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Matrices Aliments Procédés Propriétés Structure - Sensoriel (GEPEA-MAPS2), Traitement Eau Air Métrologie (GEPEA-TEAM), Capacités SAS, ISTE Editions, and Legrand, Jack

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.IDA] Life Sciences [q-bio]/Food engineering, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

27. Caractérisation de l’altération des ovoproduits par des approches ciblées et non ciblées

Author

Coat, Rémy, Gouilleux, Boris, Thouand, Gerald, Assaf, Ali, Arhaliass, Abdellah, Legrand, Jack, Thierry, Anne, Martineau, Estelle, Courant, Frédérique, Giraudeau, Patrick, Gonçalves, Olivier, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Traitement Eau Air Métrologie (GEPEA-TEAM), Matrices Aliments Procédés Propriétés Structure - Sensoriel (GEPEA-MAPS2), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Capacités SAS, Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and ISTE Editions

Subjects
[SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

29. Hyperpolarized NMR Metabolomics at Natural 13C Abundance.

Author

Dey, Arnab, Charrier, Benoît, Martineau, Estelle, Deborde, Catherine, Gandriau, Elodie, Moing, Annick, Jacob, Daniel, Eshchenko, Dmitry, Schnell, Marc, Melzi, Roberto, Kurzbach, Dennis, Ceillier, Morgan, Chappuis, Quentin, Cousin, Samuel F., Kempf, James G., Jannin, Sami, Dumez, Jean-Nicolas, and Giraudeau, Patrick

Published
2020
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30. Fast quantitative 2D NMR for metabolomics and lipidomics: A tutorial.

Author

Martineau, Estelle, Dumez, Jean‐Nicolas, and Giraudeau, Patrick

Subjects
*IRREGULAR sampling (Signal processing), *NUCLEAR magnetic resonance
Abstract

Nuclear magnetic resonance (NMR) is a well‐known analytical technique for the analysis of complex mixtures. Its quantitative capability makes it ideally suited to metabolomics or lipidomics studies involving large sample collections of complex biological samples. To overcome the ubiquitous limitation of spectral overcrowding when recording 1D NMR spectra on such samples, the acquisition of 2D NMR spectra allows a better separation between overlapped resonances while yielding accurate quantitative data when appropriate analytical protocols are implemented. Moreover, the experiment duration can be considerably reduced by applying fast acquisition methods. Here, we describe the general workflow to acquire fast quantitative 2D NMR spectra in the "omics" context. It is illustrated on three representative and complementary experiments: UF COSY, ZF‐TOCSY with nonuniform sampling, and HSQC with nonuniform sampling. After giving some details and recommendations on how to apply this protocol, its implementation in the case of targeted and untargeted metabolomics/lipidomics studies is described. [ABSTRACT FROM AUTHOR]

Published
2020
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32. Quantitative in-situ NMR to characterize protein oxidation and its dynamics

Author

Pages, Guilhem, Morisse, Amaël, Gatellier, Philippe, Martineau, Estelle, Giraudeau, Patrick, Bonny, J.-M., Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), and Programme Qualiment Staboxal

Subjects
résonance magnétique nucléaire, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, qualité des aliments, oxydation des protéines
Abstract

International audience; Preserving food quality is critical to limit the oxidation processes. The evolution of meat colour or the development of rancid taste in oils are two examples of oxidative processes degrading the food quality. The reaction of oxygen (or its derivatives) with metal ions naturally present in food ( eg. iron) forms free radical reactive oxygen species (ROS). These ROS are the main factors of food oxidation. The aim of this work is to evaluate the intakes of quantitative in situ NMR to understand and characterize the oxidation mechanisms. Our preliminary work focussed on the evaluation of some amino acid mixtures as models of protein oxidation. Due to NMR signal overlaps, recording 2D NMR spectra is indispensable to isolate NMR signals from targeted amino-acids. However, these experiments are time- consuming and not adapted to chemically evolving media. To address this limitation, we developed tailored hybrid methods based on ultrafast 2D NMR. The spectrum recording time decreased from ~30 min for a classical pulse sequence to a few minutes only with the ultrafast method. This approach allows the real-time monitoring of chemical evolutions in such complex mixtures. Using this quantitative approach, we observed a fast oxidation for the histidine while threonine and lysine oxidization kinetics were significantly slower. Our analytical approach offers a promising tool to monitor oxidation processes in food products.

Published
2016

33. C and 15 N natural isotope abundance reflects breast cancer cell metabolism OPEN

Author

Tea, Illa, Martineau, Estelle, Antheaume, Ingrid, Lalande, Julie, Mauve, Caroline, Gilard, Francoise, Barillé-Nion, Sophie, Blackburn, Anneke, Tcherkez, Guillaume, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Cancer Metabolism and Genetics Group [Canberra, Australia], Australian National University (ANU)-The John Curtin School of Medical Research, Cellule de compétences SPECTROMAITRISE, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - Faculté des Sciences et des Techniques, Plateforme Métabolisme-Métabolome [Orsay], Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Centre de Recherche en Cancérologie / Nantes - Angers (CRCNA), Centre hospitalier universitaire de Nantes (CHU Nantes)-Faculté de Médecine d'Angers-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Centre National de la Recherche Scientifique (CNRS)-Hôpital Laennec-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôtel-Dieu de Nantes, Research School of Biology [Canberra, Australia], and Australian National University (ANU)

Subjects
[SDV.CAN]Life Sciences [q-bio]/Cancer
Abstract

International audience; Breast cancer is the most common cancer in women worldwide. Despite the information provided by anatomopathological assessment and molecular markers (such as receptor expression ER, PR, HER2), breast cancer therapies and prognostics depend on the metabolic properties of tumor cells. However, metabolomics have not provided a robust and congruent biomarker yet, likely because individual metabolite contents are insufficient to encapsulate all of the alterations in metabolic fluxes. Here, we took advantage of natural 13 C and 15 N isotope abundance to show there are isotopic differences between healthy and cancer biopsy tissues or between healthy and malignant cultured cell lines. Isotope mass balance further suggests that these differences are mostly related to lipid metabolism, anaplerosis and urea cycle, three pathways known to be impacted in malignant cells. Our results demonstrate that the isotope signature is a good descriptor of metabolism since it integrates modifications in C partitioning and N excretion altogether. Our present study is thus a starting point to possible clinical applications such as patient screening and biopsy characterization in every cancer that is associated with metabolic changes. Medical applications of stable isotopes are now widespread, like the well-known 13 C-urea breath assay for ulcer detection 1. This takes advantage of 13 C-labelling and thus usually neglects differences in reaction rates between isotopic forms, because the isotopic signal used for diagnosing is far above small natural variations in 13 C. By contrast, the use of isotopes at natural abundance exploits such subtle differences (referred to as isotope effects) to identify bottlenecks in metabolic pathways (rate-limiting steps) or the contribution of multiple elemental sources (mass balance), without the need to introduce expensive isotope tracers into the patient. Isotope effects in metabolism are mostly caused by enzymatic reactions that preferentially consume substrates containing either the light or the heavy isotope (isotopologues) and therefore, the natural isotope abundance in metabolites depends on metabolic fluxes and source substrates 2. For example, the natural 13 C abundance in respired CO 2 has been used to trace diet composition and substrate changes during exercise 3,4. In cancer biology, the use of natural variations in Cu and S stable isotopes in hepatocellular carcinoma has been attempted recently 5. But to our knowledge, no study has looked at alterations of natural isotope abundance in breast cancer. Due to changes in primary C and N metabolism such as increased glycolysis, glutaminolysis and nucleotide synthesis 6 , important changes in 13 C and 15 N natural abundance can be anticipated. To address this question, we examined the isotopic signature of intact breast cancer biopsies (mostly from invasive ductal carcinoma, IDC) and cultured breast cancer cell lines (Supplementary Tables S1 and S2) using elemental analysis coupled to isotope ratio mass spectrometry (EA-IRMS). This technique has been recently shown to be applicable to the biochemical analysis of cancerous cell lines 7 .

Published
2016

35. 13C and 15N natural isotope abundance reflects breast cancer cell metabolism

Author

Tea, Illa, Martineau, Estelle, Antheaume, Ingrid, Lalande, Julie, Mauve, Caroline, Gilard, Francoise, Barillé-Nion, Sophie, Blackburn, Anneke, Tcherkez, Guillaume, Tea, Illa, Martineau, Estelle, Antheaume, Ingrid, Lalande, Julie, Mauve, Caroline, Gilard, Francoise, Barillé-Nion, Sophie, Blackburn, Anneke, and Tcherkez, Guillaume

Abstract

Breast cancer is the most common cancer in women worldwide. Despite the information provided by anatomopathological assessment and molecular markers (such as receptor expression ER, PR, HER2), breast cancer therapies and prognostics depend on the metabolic properties of tumor cells. However, metabolomics have not provided a robust and congruent biomarker yet, likely because individual metabolite contents are insufficient to encapsulate all of the alterations in metabolic fluxes. Here, we took advantage of natural 13C and 15N isotope abundance to show there are isotopic differences between healthy and cancer biopsy tissues or between healthy and malignant cultured cell lines. Isotope mass balance further suggests that these differences are mostly related to lipid metabolism, anaplerosis and urea cycle, three pathways known to be impacted in malignant cells. Our results demonstrate that the isotope signature is a good descriptor of metabolism since it integrates modifications in C partitioning and N excretion altogether. Our present study is thus a starting point to possible clinical applications such as patient screening and biopsy characterization in every cancer that is associated with metabolic changes.

Published
2016

37. Intramolecular isotope profiling: An efficient tool to fight against counterfeiting

Author

Delanoue, Benoit, Silvestre, Virginie, Robins, Richard J., Akoka, Serge, Remaud, Gérald S., Giraudeau, Patrick, Martineau, Estelle, Boisseau, Renaud, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire d'analyse isotopique et électrochimique de metabolismes (LAIEM), Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Cellule de compétences SPECTROMAITRISE, and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST)

Subjects
[CHIM]Chemical Sciences
Abstract

246th National Meeting of the American-Chemical-Society (ACS), Indianapolis, IN, SEP 08-12, 2013

Published
2013

39. Absolute quantification of metabolites in breast cancer cell extracts by quantitative 2D 1H INADEQUATE NMR

Author

Martineau, Estelle, Tea, Illa, Akoka, Serge, Giraudeau, Patrick, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Cellule de compétences SPECTROMAITRISE, and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST)

Subjects
[CHIM]Chemical Sciences
Abstract

Metabolomic studies by NMR spectroscopy are increasingly employed for a variety of biomedical applications. A very standardized 1D proton NMR protocol is generally employed for data acquisition, associated with multivariate statistical tests. Even if targeted approaches have been proposed to quantify metabolites from such experiments, quantification is often made difficult by the high degree of overlap characterizing 1H NMR spectra of biological samples. Two-dimensional spectroscopy presents a high potential for accurately measuring concentrations in complex samples, as it offers a much higher discrimination between metabolite resonances. We have recently proposed an original approach relying on the 1H 2D INADEQUATE pulse sequence, optimized for fast quantitative analysis of complex metabolic mixtures. Here, the first application of the quantitative 1H 2D INADEQUATE experiment to a real metabonomic study is presented. Absolute metabolite concentrations are determined for different breast cancer cell line extracts, by a standard addition procedure. The protocol is characterized by high analytical performances (accuracy better than 1%, excellent linearity), even if it is affected by relatively long acquisition durations (15?min to 1?h per spectrum). It is applied to three different cell lines, expressing different hormonal and tyrosine kinase receptors. The absolute concentrations of 15 metabolites are determined, revealing significant differences between cell lines. The metabolite concentrations measured are in good agreement with previous studies regarding metabolic profile changes of breast cancer. While providing a high degree of discrimination, this methodology offers a powerful tool for the determination of relevant biomarkers. Copyright (c) 2012 John Wiley & Sons, Ltd.

Published
2012

40. Position-Specific Isotope Analysis of Xanthines: A 13C Nuclear Magnetic Resonance Method to Determine the 13C Intramolecular Composition at Natural Abundance

Author

Diomande, Didier G., primary, Martineau, Estelle, additional, Gilbert, Alexis, additional, Nun, Pierrick, additional, Murata, Ariaki, additional, Yamada, Keita, additional, Watanabe, Naoharu, additional, Tea, Illa, additional, Robins, Richard J., additional, Yoshida, Naohiro, additional, and Remaud, Gérald S., additional

Published
2015
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44. Position-Specific Isotope Analysis of Xanthines: A 13C Nuclear Magnetic Resonance Method to Determine the 13C Intramolecular Composition at Natural Abundance.

Author

Diomande, Didier G., Martineau, Estelle, Gilbert, Alexis, Nun, Pierrick, Murata, Ariaki, Yamada, Keita, Watanabe, Naoharu, Illa Tea, Robins, Richard J., Naohiro Yoshida, and Remaud, Gérald S.

Subjects
*ISOTOPES, *XANTHINE, *CAFFEINE, *PROTON magnetic resonance spectroscopy, *THEOBROMINE, *THEOPHYLLINE, *METHYLATION, *COCOA
Abstract

The natural xanthines caffeine, theobromine, and theophylline are of major commercial importance as flavor constituents in coffee, cocoa, tea, and a number of other beverages. However, their exploitation for authenticity, a requirement in these commodities that have a large origin-based price-range, by the standard method of isotope ratio monitoring by mass spectrometry (irm-MS) is limited. We have now developed a methodology that overcomes this deficit that exploits the power of isotopic quantitative 13C nuclear magnetic resonance (NMR) spectrometry combined with chemical modification of the xanthines to enable the determination of positional intramolecular 13C/12C ratios (δ13Ci) with high precision. However, only caffeine is amenable to analysis: theobromine and theophylline present substantial difficulties due to their poor solubility. However, their N-methylation to caffeine makes spectral acquisition feasible. The method is confirmed as robust, with good repeatability of the δ13Ci values in caffeine appropriate for isotope fractionation measurements at natural abundance. It is shown that there is negligible isotope fractionation during the chemical N-methylation procedure. Thus, the method preserves the original positional δ13Ci values. The method has been applied to measure the position-specific variation of the 13C/12C distribution in caffeine. Not only is a clear difference between caffeine isolated from different sources observed, but theobromine from cocoa is found to show a 13C pattern distinct from that of caffeine. [ABSTRACT FROM AUTHOR]

Published
2015
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45. Fast Quantitative 1H-13C Two-Dimensional NMR with Very High Precision.

Author

Martineau, Estelle, Akoka, Serge, Boisseau, Renaud, Delanoue, Benoît, and Giraudeau, Patrick

Subjects
*NUCLEAR magnetic resonance, *QUANTITATIVE chemical analysis, *ISOTOPE separation, *CARBON isotopes, *ISOTOPIC analysis, *HETERONUCLEAR diatomic molecules
Abstract

Quantitative analysis by nuclear magnetic resonance (NMR) requires highly precise measurements to achieve reliable quantification. It is particularly true in 13C site-specific natural isotope fractionation studied by nuclear magnetic resonance, where the range of values of 13C isotopic deviations at natural abundance is highly restricted. Consequently, an NMR method capable of measuring δ13C ‰ values with a very high precision (a few per mil) is indispensable. This high degree of precision has already been achieved by one-dimensional 13C acquisitions; however, this approach is limited by peak overlaps which reduce the precision of the isotope content determination, even for certain small molecules. It is therefore necessary to extend this promising methodology to a higher dimensionality. In this context, this paper aims at determining conditions that allow the achievement of two-dimensional (2D) 1H-13C heteronuclear experiments with a precision of a few per mil in a reasonable time. Our results demonstrate that a high precision (repeatability of 2 per mil) can be reached with the 1H-13C HSQC (Heteronuclear Single Quantum Correlation) experiment, thus satisfying the conditions needed to perform 13C isotope analysis by 2D NMR. We also consider the impact of several approaches which have been proposed to reduce the duration of heteronuclear 2D experiments. Two of these common time-saving strategies, spectral aliasing and linear prediction, are fully compatible with the high-precision requirements of isotopic NMR, while a third one, nonuniform sampling, leads to dramatic precision losses. In conclusion, this study demonstrates the feasibility of very precise 2D NMR measurements and opens a number of application perspectives. [ABSTRACT FROM AUTHOR]

Published
2013
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46. Absolute quantification of metabolites in breast cancer cell extracts by quantitative 2D 1H INADEQUATE NMR.

Author

Martineau, Estelle, Tea, Illa, Akoka, Serge, and Giraudeau, Patrick

Abstract

Metabolomic studies by NMR spectroscopy are increasingly employed for a variety of biomedical applications. A very standardized 1D proton NMR protocol is generally employed for data acquisition, associated with multivariate statistical tests. Even if targeted approaches have been proposed to quantify metabolites from such experiments, quantification is often made difficult by the high degree of overlap characterizing 1H NMR spectra of biological samples. Two-dimensional spectroscopy presents a high potential for accurately measuring concentrations in complex samples, as it offers a much higher discrimination between metabolite resonances. We have recently proposed an original approach relying on the 1H 2D INADEQUATE pulse sequence, optimized for fast quantitative analysis of complex metabolic mixtures. Here, the first application of the quantitative 1H 2D INADEQUATE experiment to a real metabonomic study is presented. Absolute metabolite concentrations are determined for different breast cancer cell line extracts, by a standard addition procedure. The protocol is characterized by high analytical performances (accuracy better than 1%, excellent linearity), even if it is affected by relatively long acquisition durations (15 min to 1 h per spectrum). It is applied to three different cell lines, expressing different hormonal and tyrosine kinase receptors. The absolute concentrations of 15 metabolites are determined, revealing significant differences between cell lines. The metabolite concentrations measured are in good agreement with previous studies regarding metabolic profile changes of breast cancer. While providing a high degree of discrimination, this methodology offers a powerful tool for the determination of relevant biomarkers. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Published
2012
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47. Fast and precise quantitative analysis of metabolic mixtures by 2D 1H INADEQUATE NMR

Author

Martineau, Estelle, Giraudeau, Patrick, Tea, Illa, and Akoka, Serge

Subjects
*QUANTITATIVE chemical analysis, *METABOLITES, *NUCLEAR magnetic resonance spectroscopy, *BIOMARKERS, *CALIBRATION, *MATHEMATICAL optimization
Abstract

Abstract: Quantitative analysis of metabolic mixtures by 1H 1D NMR offers a limited potential for precise quantification of biomarkers, due to strong overlap between the peaks. Two-dimensional spectroscopy is a powerful tool to unambiguously and simultaneously measure a larger number of metabolite contributions. However, it is still rarely used for quantification, first because quantitative analysis by 2D NMR requires a calibration procedure due to the multi-impulsional nature of 2D NMR experiments, and above all because of the prohibitive experiment duration that is necessary to obtain such a calibration curve. In this work, we develop and evaluate a 2D 1H INADEQUATE protocol for a fast determination of metabolite concentrations in complex mixtures. The 2D pulse sequence is carefully optimized and evaluated in terms of precision and linearity. Quantitative 1H INADEQUATE 2D spectra of metabolic mixtures are obtained in 7min with a repeatability better than 2% for metabolite concentrations as small as 100μM and an excellent linearity. The method described in this work allows a fast and precise quantification of metabolic mixtures, and it forms a promising tool for metabonomic studies. [ABSTRACT FROM AUTHOR]

Published
2011
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48. A multidimensional 1H NMR lipidomics workflow to address chemical food safety issues.

Author

Marchand, Jérémy, Martineau, Estelle, Guitton, Yann, Le Bizec, Bruno, Dervilly-Pinel, Gaud, and Giraudeau, Patrick

Subjects
*FOOD safety, *NUCLEAR magnetic resonance, *SERUM, *LIPID metabolism, *FOOD quality
Abstract

Introduction: Although it is still at a very early stage compared to its mass spectrometry (MS) counterpart, proton nuclear magnetic resonance (NMR) lipidomics is worth being investigated as an original and complementary solution for lipidomics. Dedicated sample preparation protocols and adapted data acquisition methods have to be developed to set up an NMR lipidomics workflow; in particular, the considerable overlap observed for lipid signals on 1D spectra may hamper its applicability.Objectives: The study describes the development of a complete proton NMR lipidomics workflow for application to serum fingerprinting. It includes the assessment of fast 2D NMR strategies, which, besides reducing signal overlap by spreading the signals along a second dimension, offer compatibility with the high-throughput requirements of food quality characterization.Method: The robustness of the developed sample preparation protocol is assessed in terms of repeatability and ability to provide informative fingerprints; further, different NMR acquisition schemes—including classical 1D, fast 2D based on non-uniform sampling or ultrafast schemes—are evaluated and compared. Finally, as a proof of concept, the developed workflow is applied to characterize lipid profiles disruption in serum from β-agonists diet fed pigs.Results: Our results show the ability of the workflow to discriminate efficiently sample groups based on their lipidic profile, while using fast 2D NMR methods in an automated acquisition framework.Conclusion: This work demonstrates the potential of fast multidimensional 1H NMR—suited with an appropriate sample preparation—for lipidomics fingerprinting as well as its applicability to address chemical food safety issues. [ABSTRACT FROM AUTHOR]

Published
2018
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50. Hyperpolarized NMR Metabolomics at Natural 13 C Abundance.

Author

Dey A, Charrier B, Martineau E, Deborde C, Gandriau E, Moing A, Jacob D, Eshchenko D, Schnell M, Melzi R, Kurzbach D, Ceillier M, Chappuis Q, Cousin SF, Kempf JG, Jannin S, Dumez JN, and Giraudeau P

Subjects
Carbon Isotopes chemistry, Carbon Isotopes analysis, Magnetic Resonance Spectroscopy, Metabolomics methods
Abstract

Metabolomics plays a pivotal role in systems biology, and NMR is a central tool with high precision and exceptional resolution of chemical information. Most NMR metabolomic studies are based on 1 H 1D spectroscopy, severely limited by peak overlap. 13 C NMR benefits from a larger signal dispersion but is barely used in metabolomics due to ca. 6000-fold lower sensitivity. We introduce a new approach, based on hyperpolarized 13 C NMR at natural abundance, that circumvents this limitation. A new untargeted NMR-based metabolomic workflow based on dissolution dynamic nuclear polarization (d-DNP) for the first time enabled hyperpolarized natural abundance 13 C metabolomics. Statistical analysis of resulting hyperpolarized 13 C data distinguishes two groups of plant (tomato) extracts and highlights biomarkers, in full agreement with previous results on the same biological model. We also optimize parameters of the semiautomated d-DNP system suitable for high-throughput studies.

Published
2020
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