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Lejal V, Cerisier N, Rouquié D, Taboureau O. Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis. Chem Res Toxicol 2023; 36:1456-1470. [PMID: 37652439 PMCID: PMC10523580 DOI: 10.1021/acs.chemrestox.2c00381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/30/2022] [Indexed: 09/02/2023]
Abstract
Drug-induced liver injury (DILI) is a significant concern in drug development, often leading to drug withdrawal. Although many studies aim to identify biomarkers and gene/pathway signatures related to liver toxicity and aim to predict DILI compounds, this remains a challenge in drug discovery. With a strong development of high-content screening/imaging (HCS/HCI) for phenotypic screening, we explored the morphological cell perturbations induced by DILI compounds. In the first step, cell morphological signatures were associated with two datasets of DILI chemicals (DILIRank and eTox). The mechanisms of action were then analyzed for chemicals having transcriptomics data and sharing similar morphological perturbations. Signaling pathways associated with liver toxicity (cell cycle, cell growth, apoptosis, ...) were then captured, and a hypothetical relation between cell morphological perturbations and gene deregulation was illustrated within our analysis. Finally, using the cell morphological signatures, machine learning approaches were developed to predict chemicals with a potential risk of DILI. Some models showed relevant performance with validation set balanced accuracies between 0.645 and 0.739. Overall, our findings demonstrate the utility of combining HCI with transcriptomics data to identify the morphological and gene expression signatures related to DILI chemicals. Moreover, our protocol could be extended to other toxicity end points, offering a promising avenue for comprehensive toxicity assessment in drug discovery.
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Affiliation(s)
- Vanille Lejal
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
| | - Natacha Cerisier
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
| | - David Rouquié
- Bayer
SAS, Bayer Crop Science, 355 rue Dostoïevski, CS 90153, 06906 Valbonne, Sophia-Antipolis, France
- Université
Côte d’Azur 3IA Interdisciplinary Institute in Artificial Intelligence, 06103 Nice Cedex, France
| | - Olivier Taboureau
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
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2
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Fassy J, Lacoux C, Leroy S, Noussair L, Hubac S, Degoutte A, Vassaux G, Leclercq V, Rouquié D, Marquette CH, Rottman M, Touron P, Lemoine A, Herrmann JL, Barbry P, Nahon JL, Zaragosi LE, Mari B. Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples. PLoS One 2021; 16:e0243333. [PMID: 33852580 PMCID: PMC8046349 DOI: 10.1371/journal.pone.0243333] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/23/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
The emergence and quick spread of SARS-CoV-2 has pointed at a low capacity response for testing large populations in many countries, in line of material, technical and staff limitations. The traditional RT-qPCR diagnostic test remains the reference method and is by far the most widely used test. These assays are limited to a few probe sets, require large sample PCR reaction volumes, along with an expensive and time-consuming RNA extraction step. Here we describe a quantitative nanofluidic assay that overcomes some of these shortcomings, based on the BiomarkTM instrument from Fluidigm. This system offers the possibility of performing 4608 qPCR end-points in a single run, equivalent to 192 clinical samples combined with 12 pairs of primers/probe sets in duplicate, thus allowing the monitoring of SARS-CoV-2 including the detection of specific SARS-CoV-2 variants, as well as the detection other pathogens and/or host cellular responses (virus receptors, response markers, microRNAs). The 10 nL-range volume of BiomarkTM reactions is compatible with sensitive and reproducible reactions that can be easily and cost-effectively adapted to various RT-qPCR configurations and sets of primers/probe. Finally, we also evaluated the use of inactivating lysis buffers composed of various detergents in the presence or absence of proteinase K to assess the compatibility of these buffers with a direct reverse transcription enzymatic step and we propose several protocols, bypassing the need for RNA purification. We advocate that the combined utilization of an optimized processing buffer and a high-throughput real-time PCR device would contribute to improve the turn-around-time to deliver the test results to patients and increase the SARS-CoV-2 testing capacities.
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Affiliation(s)
- Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Sylvie Leroy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
- Département de Pneumologie, CHU-Nice, FHU-OncoAge, Université Côte d’Azur, Nice, France
| | - Latifa Noussair
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
| | - Sylvain Hubac
- Institut de Recherche Criminelle de la Gendarmerie Nationale (IRCGN), Cergy, France
| | - Aurélien Degoutte
- Département de Pneumologie, CHU-Nice, FHU-OncoAge, Université Côte d’Azur, Nice, France
| | - Georges Vassaux
- Université Côte d’Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | | | | | | | - Martin Rottman
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Patrick Touron
- Institut de Recherche Criminelle de la Gendarmerie Nationale (IRCGN), Cergy, France
| | - Antoinette Lemoine
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
| | - Jean-Louis Herrmann
- Assistance Publique-Hôpitaux de Paris, GHU Paris–Saclay, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Pascal Barbry
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Jean-Louis Nahon
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d’Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
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3
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Pettit SD, Jerome KR, Rouquié D, Mari B, Barbry P, Kanda Y, Matsumoto M, Hester S, Wehmas L, Botten JW, Bruce EA. 'All In': a pragmatic framework for COVID-19 testing and action on a global scale. EMBO Mol Med 2020; 12:e12634. [PMID: 32375201 PMCID: PMC7267598 DOI: 10.15252/emmm.202012634] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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] [Indexed: 11/09/2022] Open
Abstract
Current demand for SARS-CoV-2 testing is straining material resource and labor capacity around the globe. As a result, the public health and clinical community are hindered in their ability to monitor and contain the spread of COVID-19. Despite broad consensus that more testing is needed, pragmatic guidance toward realizing this objective has been limited. This paper addresses this limitation by proposing a novel and geographically agnostic framework (the 4Ps framework) to guide multidisciplinary, scalable, resource-efficient, and achievable efforts toward enhanced testing capacity. The 4Ps (Prioritize, Propagate, Partition, and Provide) are described in terms of specific opportunities to enhance the volume, diversity, characterization, and implementation of SARS-CoV-2 testing to benefit public health. Coordinated deployment of the strategic and tactical recommendations described in this framework has the potential to rapidly expand available testing capacity, improve public health decision-making in response to the COVID-19 pandemic, and/or to be applied in future emergent disease outbreaks.
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Affiliation(s)
- Syril D Pettit
- Health and Environmental Sciences InstituteWashingtonDCUSA
| | - Keith R Jerome
- Virology DivisionDepartment of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
| | | | - Bernard Mari
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)CNRSUniversité Côte d'AzurValbonneFrance
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)CNRSUniversité Côte d'AzurValbonneFrance
| | | | | | - Susan Hester
- Office of Research and DevelopmentEnvironmental Protection AgencyResearch Triangle ParkNCUSA
| | - Leah Wehmas
- Office of Research and DevelopmentEnvironmental Protection AgencyResearch Triangle ParkNCUSA
| | - Jason W Botten
- Division of ImmunobiologyDepartment of MedicineLarner College of MedicineUniversity of VermontBurlingtonVTUSA
| | - Emily A Bruce
- Division of ImmunobiologyDepartment of MedicineLarner College of MedicineUniversity of VermontBurlingtonVTUSA
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4
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Baillif B, Wichard J, Méndez-Lucio O, Rouquié D. Exploring the Use of Compound-Induced Transcriptomic Data Generated From Cell Lines to Predict Compound Activity Toward Molecular Targets. Front Chem 2020; 8:296. [PMID: 32391323 PMCID: PMC7191531 DOI: 10.3389/fchem.2020.00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/02/2019] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
Pharmaceutical or phytopharmaceutical molecules rely on the interaction with one or more specific molecular targets to induce their anticipated biological responses. Nonetheless, these compounds are also prone to interact with many other non-intended biological targets, also known as off-targets. Unfortunately, off-target identification is difficult and expensive. Consequently, QSAR models predicting the activity on a target have gained importance in drug discovery or in the de-risking of chemicals. However, a restricted number of targets are well characterized and hold enough data to build such in silico models. A good alternative to individual target evaluations is to use integrative evaluations such as transcriptomics obtained from compound-induced gene expression measurements derived from cell cultures. The advantage of these particular experiments is to capture the consequences of the interaction of compounds on many possible molecular targets and biological pathways, without having any constraints concerning the chemical space. In this work, we assessed the value of a large public dataset of compound-induced transcriptomic data, to predict compound activity on a selection of 69 molecular targets. We compared such descriptors with other QSAR descriptors, namely the Morgan fingerprints (similar to extended-connectivity fingerprints). Depending on the target, active compounds could show similar signatures in one or multiple cell lines, whether these active compounds shared similar or different chemical structures. Random forest models using gene expression signatures were able to perform similarly or better than counterpart models built with Morgan fingerprints for 25% of the target prediction tasks. These performances occurred mostly using signatures produced in cell lines showing similar signatures for active compounds toward the considered target. We show that compound-induced transcriptomic data could represent a great opportunity for target prediction, allowing to overcome the chemical space limitation of QSAR models.
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Affiliation(s)
| | - Joerg Wichard
- Department of Genetic Toxicology, Bayer AG, Berlin, Germany
| | - Oscar Méndez-Lucio
- Bayer SAS, Bayer CropScience, Sophia Antipolis, France.,Bloomoon, Villeurbanne, France
| | - David Rouquié
- Bayer SAS, Bayer CropScience, Sophia Antipolis, France
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5
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Grenet I, Comet JP, Schorsch F, Ryan N, Wichard J, Rouquié D. Chemical in vitro bioactivity profiles are not informative about the long-term in vivo endocrine mediated toxicity. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2019.100098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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6
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Grenet I, Merlo K, Comet JP, Tertiaux R, Rouquié D, Dayan F. Stacked Generalization with Applicability Domain Outperforms Simple QSAR on in Vitro Toxicological Data. J Chem Inf Model 2019; 59:1486-1496. [PMID: 30735402 DOI: 10.1021/acs.jcim.8b00553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The development of in silico tools able to predict bioactivity and toxicity of chemical substances is a powerful solution envisioned to assess toxicity as early as possible. To enable the development of such tools, the ToxCast program has generated and made publicly available in vitro bioactivity data for thousands of compounds. The goal of the present study is to characterize and explore the data from ToxCast in terms of Machine Learning capability. For this, a large scale analysis on the entire database has been performed to build models to predict bioactivities measured in in vitro assays. Simple classical QSAR algorithms (ANN, SVM, LDA, random forest, and Bayesian) were first applied on the data, and the results of these algorithms suggested that they do not seem to be well-suited for data sets with a high proportion of inactive compounds. The study then showed for the first time that the use of an ensemble method named "Stacked generalization" could improve the model performance on this type of data. Indeed, for 61% of 483 models, the Stacked method led to models with higher performance. Moreover, the combination of this ensemble method with an applicability domain filter allows one to assess the reliability of the predictions for further compound prioritization. In particular we showed that for 50% of the models, the ROC score is better if we do not consider the compounds that are not within the applicability domain.
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Affiliation(s)
- Ingrid Grenet
- University Côte d'Azur, I3S Laboratory , UMR CNRS 7271, CS 40121, 06903 Sophia Antipolis Cedex, France.,Bayer SAS , 06903 Sophia Antipolis Cedex, France
| | - Kevin Merlo
- Dassault Systèmes SE , 06906 Sophia Antipolis, Biot , France
| | - Jean-Paul Comet
- University Côte d'Azur, I3S Laboratory , UMR CNRS 7271, CS 40121, 06903 Sophia Antipolis Cedex, France
| | - Romain Tertiaux
- Dassault Systèmes SE , 06906 Sophia Antipolis, Biot , France
| | | | - Frédéric Dayan
- Dassault Systèmes SE , 06906 Sophia Antipolis, Biot , France
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7
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Satoh R, Teshima R, Kitta K, Lang GH, Schegg K, Blumenthal K, Hicks L, Labory-Carcenac B, Rouquié D, Herman RA, Herouet-Guicheney C, Ladics GS, McClain S, Poulsen LK, Privalle L, Ward JM, Doerrer N, Rascle JB. Inter-laboratory optimization of protein extraction, separation, and fluorescent detection of endogenous rice allergens. Biosci Biotechnol Biochem 2016; 80:2198-2207. [PMID: 27399872 PMCID: PMC5062055 DOI: 10.1080/09168451.2016.1206810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Indexed: 11/02/2022]
Abstract
In rice, several allergens have been identified such as the non-specific lipid transfer protein-1, the α-amylase/trypsin-inhibitors, the α-globulin, the 33 kDa glyoxalase I (Gly I), the 52-63 kDa globulin, and the granule-bound starch synthetase. The goal of the present study was to define optimal rice extraction and detection methods that would allow a sensitive and reproducible measure of several classes of known rice allergens. In a three-laboratory ring-trial experiment, several protein extraction methods were first compared and analyzed by 1D multiplexed SDS-PAGE. In a second phase, an inter-laboratory validation of 2D-DIGE analysis was conducted in five independent laboratories, focusing on three rice allergens (52 kDa globulin, 33 kDa glyoxalase I, and 14-16 kDa α-amylase/trypsin inhibitor family members). The results of the present study indicate that a combination of 1D multiplexed SDS-PAGE and 2D-DIGE methods would be recommended to quantify the various rice allergens.
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Affiliation(s)
- Rie Satoh
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Reiko Teshima
- b Division of Novel Foods and Immunochemistry , National Institute of Health Sciences , Tokyo , Japan
| | - Kazumi Kitta
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Gang-Hua Lang
- a Food Research Institute, National Agriculture and Food Research Organization , Tsukuba , Japan
| | - Kathleen Schegg
- c Nevada Proteomics Center , University of Nevada Reno , Reno , NV , USA
| | - Kenneth Blumenthal
- d Formerly at Department of Biochemistry , State University of New York at Buffalo , Buffalo , NY , USA
| | - Leslie Hicks
- e Formerly at Proteomics & Mass Spectrometry Facility , Donald Danforth Plant Science Center , St. Louis , MI , USA
| | | | - David Rouquié
- f Bayer S.A.S., Bayer CropScience , Sophia Antipolis , France
| | - Rod A Herman
- g Dow AgroSciences LLC , Indianapolis , IN , USA
| | | | - Gregory S Ladics
- i DuPont Haskell Global Centers for Health and Environmental Sciences , Newark , DE , USA
| | - Scott McClain
- j Syngenta Crop Protection, LLC , Research Triangle Park , NC , USA
| | - Lars K Poulsen
- k Allergy Clinic , Copenhagen University Hospital at Gentofte , Copenhagen , Denmark
| | - Laura Privalle
- l Regulatory Science , Formerly at BASF Plant Science , Research Triangle Park , NC , USA
| | - Jason M Ward
- m Regulatory Division, Product Characterization Center , Formerly at Monsanto Co. , St. Louis , MO , USA
| | - Nancy Doerrer
- n Protein Allergenicity Technical Committee , ILSI Health and Environmental Sciences Institute (HESI) , Washington , DC , USA
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8
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Rouquié D, Heneweer M, Botham J, Ketelslegers H, Markell L, Pfister T, Steiling W, Strauss V, Hennes C. Contribution of new technologies to characterization and prediction of adverse effects. Crit Rev Toxicol 2015; 45:172-83. [DOI: 10.3109/10408444.2014.986054] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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9
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Rouquié D, Tinwell H, Blanck O, Schorsch F, Geter D, Wason S, Bars R. Thyroid tumor formation in the male mouse induced by fluopyram is mediated by activation of hepatic CAR/PXR nuclear receptors. Regul Toxicol Pharmacol 2014; 70:673-80. [DOI: 10.1016/j.yrtph.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/03/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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10
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Sarrabay A, Hilmi C, Tinwell H, Schorsch F, Pallardy M, Rouquié D, Bars R. Low dose evaluation of the antiandrogen flutamide following a mode of action approach. Toxicol Lett 2014. [DOI: 10.1016/j.toxlet.2014.06.311] [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: 10/24/2022]
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11
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Ludwig S, Tinwell H, Schorsch F, Cavaillé C, Pallardy M, Rouquié D, Bars R. A molecular and phenotypic integrative approach to identify a no-effect dose level for antiandrogen-induced testicular toxicity. Toxicol Sci 2011; 122:52-63. [PMID: 21525395 DOI: 10.1093/toxsci/kfr099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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
The safety assessment of chemicals for humans relies on identifying no-observed adverse effect levels (NOAELs) in animal toxicity studies using standard methods. With the advent of high information content technologies, especially microarrays, it is pertinent to determine the impact of molecular data on the NOAELs. Consequently, we conducted an integrative study to identify a no-transcriptomic effect dose using microarray analyses coupled with quantitative reverse transcriptase PCR (RT-qPCR) and determined how this correlated with the NOAEL. We assessed the testicular effects of the antiandrogen, flutamide (FM), in a rat 28-day toxicity study using doses of 0.2-30 mg/kg/day. Plasma testosterone levels and testicular histopathology indicated a NOAEL of 1 mg/kg/day. A no-effect dose of 0.2 mg/kg/day was established based on molecular data relevant to the phenotypic changes. We observed differential gene expression starting from 1 mg/kg/day and a deregulation of more than 1500 genes at 30 mg/kg/day. Dose-related changes were identified for the major pathways (e.g., fatty acid metabolism) associated with the testicular lesion (Leydig cell hyperplasia) that were confirmed by RT-qPCR. These data, along with protein accumulation profiles and FM metabolite concentrations in testis, supported the no-effect dose of 0.2 mg/kg/day. Furthermore, the microarray data indicated a dose-dependent change in the fatty acid catabolism pathway, a biological process described for the first time to be affected by FM in testicular tissue. In conclusion, the present data indicate the existence of a transcriptomic threshold, which must be exceeded to progress from a normal state to an adaptative state and subsequently to adverse toxicity.
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Affiliation(s)
- Sophie Ludwig
- Department of Research Toxicology, Université Paris-Sud, INSERM UMR 996, Chatenay-Malabry, France
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12
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Rouquié D, Capt A, Eby WH, Sekar V, Hérouet-Guicheney C. Investigation of endogenous soybean food allergens by using a 2-dimensional gel electrophoresis approach. Regul Toxicol Pharmacol 2010; 58:S47-53. [PMID: 20932868 DOI: 10.1016/j.yrtph.2010.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 09/27/2010] [Accepted: 09/27/2010] [Indexed: 11/28/2022]
Abstract
As part of the safety assessment of genetically modified (GM) soybean, 2-dimensional gel electrophoresis analyses were performed with the isoxaflutole and glyphosate tolerant soybean FG72, its non-GM near-isogenic counterpart (Jack) and three commercial non-GM soybean lines. The objective was to compare the known endogenous human food allergens in seeds in the five different soybean lines in order to evaluate any potential unintended effect(s) of the genetic modification. In total, 37 protein spots representing five well known soybean food allergen groups were quantified in each genotype. Qualitatively, all the allergenic proteins were detected in the different genetic backgrounds. Quantitatively, among 37 protein spots, the levels of accumulation of three allergens were slightly lower in the GM soybean than in the non-GM counterparts. Specifically, while the levels of two of these three allergens fell within the normal range of variation observed in the four non-GM varieties, the level of the third allergen was slightly below the normal range. Overall, there was no significant increase in the level of allergens in FG72 soybean seeds. Therefore, the FG72 soybean can be considered as safe as its non-GM counterpart with regards to endogenous allergenicity. Additional research is needed to evaluate the biological variability in the levels of endogenous soybean allergens and the correlation between level of allergens and allergenic potential in order to improve the interpretation of these data in the safety assessment of GM soybean context.
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13
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Herouet-Guicheney C, Aldemir H, Bars R, de Barbeyrac D, Kennel P, Rouquié D, Stahl BU, Kimber I, Dearman RJ. Inter-laboratory comparisons of assessment of the allergenic potential of proteins in mice. J Appl Toxicol 2009; 29:141-8. [PMID: 18937215 DOI: 10.1002/jat.1391] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Assessment of the potential allergenicity of novel proteins, including those expressed in genetically modified plants, is an important issue. In previous studies, we have shown that the IgE measurement induced by systemic exposure of BALB/c mice to a range of proteins correlates broadly with what is known of their allergenic potential in humans. The approach used a homologous passive cutaneous anaphylaxis (PCA) assay that reflects IgE-dependent biological activity and is of sufficient sensitivity to detect IgE production in the absence of adjuvant. In previous studies, the immunization phase was conducted independently in two separate facilities, and the subsequent analytical work (PCA) conducted in a single facility. The purpose here was to further evaluate the transferability of this approach. To this end, BALB/c mice were exposed to a range of doses of peanut agglutinin or ovalbumin, allergenic proteins of peanut and hen's egg, respectively, in two independent laboratories. Serial doubling dilutions of serum pooled for each treatment group were analyzed for specific IgE. At higher doses of allergen very similar, or identical, IgE titers were achieved in both laboratories, although at lower doses, responses were somewhat more variable. These data demonstrate that, although technically demanding, the measurement of protein allergen-induced IgE antibody production in mice using PCA is relatively robust and is transferable and reproducible between laboratories. This approach may provide a useful tool for the safety assessment of novel proteins and suggests that continued evaluation of the approach with a wider range of protein allergens and non-sensitising proteins is justified.
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Affiliation(s)
- C Herouet-Guicheney
- Bayer CropScience, BP153, 355 rue Dostoïevski, 06130 Sophia Antipolis, France.
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14
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Herouet-Guicheney C, Rouquié D, Freyssinet M, Currier T, Martone A, Zhou J, Bates EEM, Ferullo JM, Hendrickx K, Rouan D. Safety evaluation of the double mutant 5-enol pyruvylshikimate-3-phosphate synthase (2mEPSPS) from maize that confers tolerance to glyphosate herbicide in transgenic plants. Regul Toxicol Pharmacol 2009; 54:143-53. [PMID: 19303906 DOI: 10.1016/j.yrtph.2009.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 03/12/2009] [Accepted: 03/12/2009] [Indexed: 10/21/2022]
Abstract
Glyphosate tolerance can be conferred by decreasing the herbicide's ability to inhibit the enzyme 5-enol pyruvylshikimate-3-phosphate synthase, which is essential for the biosynthesis of aromatic amino acids in all plants, fungi, and bacteria. Glyphosate tolerance is based upon the expression of the double mutant 5-enol pyruvylshikimate-3-phosphate synthase (2mEPSPS) protein. The 2mEPSPS protein, with a lower binding affinity for glyphosate, is highly resistant to the inhibition by glyphosate and thus allows sufficient enzyme activity for the plants to grow in the presence of herbicides that contain glyphosate. Based on both a review of published literature and experimental studies, the potential safety concerns related to the transgenic 2mEPSPS protein were assessed. The safety evaluation supports that the expressed protein is innocuous. The 2mEPSPS enzyme does not possess any of the properties associated with known toxins or allergens, including a lack of amino acid sequence similarity to known toxins and allergens, a rapid degradation in simulated gastric and intestinal fluids, and no adverse effects in mice after intravenous or oral administration (at 10 or 2000 mg/kg body weight, respectively). In conclusion, there is a reasonable certainty of no harm resulting from the inclusion of the 2mEPSPS protein in human food or in animal feed.
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Rouquié D, Friry-Santini C, Schorsch F, Tinwell H, Bars R. Standard and Molecular NOAELs for Rat Testicular Toxicity Induced by Flutamide. Toxicol Sci 2009; 109:59-65. [DOI: 10.1093/toxsci/kfp056] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Tinwell H, Friry-Santini C, Rouquié D, Belluco S, Elies L, Pallen C, Bars R. Evaluation of the Antiandrogenic Effects of Flutamide, DDE, and Linuron in the Weanling Rat Assay Using Organ Weight, Histopathological, and Proteomic Approaches. Toxicol Sci 2007; 100:54-65. [PMID: 17686919 DOI: 10.1093/toxsci/kfm208] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Organization for Economic Cooperation and Development (OECD) is currently funding the validation of the Hershberger assay as a rapid in vivo means of identifying (anti-) androgens. However, as the assay measures weight changes in the androgen-sensitive tissues of castrated rats, the evaluation of the androgen-stimulated intact weanling as a more ethical model to use in the assay has been requested. As part of the OECD validation exercise two weak antiandrogens, 1,1-dichloro-2,2-bis(4 chlorophenyl)ethane (DDE) and linuron (LIN), were investigated in our laboratory at several dose levels in the testosterone propionate (TP)-stimulated weanling using flutamide (FM) as a positive control. In addition to weight measurements (sex accessory tissues [SATs], epididymides, and testes), histopathological assessment of the seminal vesicles, prostate, and testes was conducted for vehicle control, TP-stimulated, and TP-stimulated animals treated with FM or the top dose level of DDE or LIN. The modulation of a novel prostate protein associated with apoptosis, L-amino acid oxidase (LAO), was evaluated in these same treatment groups. Our gravimetric data (supported by the histopathology data) indicated that the weanling assay can detect SAT and epididymal weight changes induced by the antiandrogens evaluated. Inconsistent and variable data were recorded for the testicular weight and histopathological effects, suggesting that the testis is of little value in the identification of antiandrogens using this model. Three isoforms of LAO were identified, and all were regulated by TP. Modulation of LAO by the antiandrogens indicated that this protein could be a biomarker for endocrine disruption in male rodents.
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Affiliation(s)
- Helen Tinwell
- Department of Research Toxicology, Bayer CropScience, 06903 Sophia-Antipolis, France.
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17
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Friry-Santini C, Rouquié D, Kennel P, Tinwell H, Benahmed M, Bars R. Correlation between Protein Accumulation Profiles and Conventional Toxicological Findings Using a Model Antiandrogenic Compound, Flutamide. Toxicol Sci 2007; 97:81-93. [PMID: 17311803 DOI: 10.1093/toxsci/kfm022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In conventional rodent toxicity studies the characterization of the adverse effects of a chemical relies primarily on gravimetric, and histopathological data. The aim of this study was to evaluate if the use of two-dimensional gel electrophoresis could generate protein accumulation profiles, which were in accordance with conventional toxicological findings by investigating a model antiandrogen, flutamide (FM), whose toxic effects, as measured using standard approaches, are well characterized. Male Sprague-Dawley rats were orally exposed to FM (0, 6, 30, and 150 mg/kg/day) for 28 days. The expected inhibition of androgen-dependent tissue stimulation, increased luteinizing hormone and testosterone plasma levels, and Leydig cell hyperplasia were observed. Changes in testicular protein accumulation profiles were evaluated in rats exposed to 150 mg/kg/day FM. Several proteins involved in steroidogenesis (e.g., StAR, ApoE, Hmgcs1, Idi1), cell cycle, and cancer (e.g., Ddx1, Hspd1) were modulated by FM, and these data provided molecular evidence for the hormonal and testicular histopathology changes recorded. Changes in proteins associated with spermatogenesis were also recorded, and these are discussed within the context of the testicular phenotype observed following FM treatment (i.e., normal spermatogenesis but Leydig cell hyperplasia). Overall, our data indicate that the combination of conventional toxicology measurements with omic observations has the potential to improve our global understanding of the toxicity of a compound.
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MESH Headings
- Androgen Antagonists/toxicity
- Animals
- Biomarkers/metabolism
- Dose-Response Relationship, Drug
- Electrophoresis, Gel, Two-Dimensional
- Flutamide/toxicity
- Gene Regulatory Networks/drug effects
- Genitalia, Male/drug effects
- Genitalia, Male/metabolism
- Genitalia, Male/pathology
- Hyperplasia
- Leydig Cells/drug effects
- Leydig Cells/metabolism
- Luteinizing Hormone/blood
- Male
- Organ Size/drug effects
- Proteins/genetics
- Proteins/metabolism
- Proteomics/methods
- Rats
- Rats, Sprague-Dawley
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
- Testis/drug effects
- Testis/metabolism
- Testosterone/blood
- Toxicity Tests/methods
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18
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Bonvalot S, Rouquié D, Vanel D, Domont J, Le Cesne A. Chirurgie des tumeurs stromales gastro-intestinales (GIST) aux stades localisés et métastatiques. ONCOLOGIE 2007. [DOI: 10.1007/s10269-006-0548-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Cayatte C, Pons C, Guigonis JM, Pizzol J, Elies L, Kennel P, Rouquié D, Bars R, Rossi B, Samson M. Protein Profiling of Rat Ventral Prostate following Chronic Finasteride Administration. Mol Cell Proteomics 2006; 5:2031-43. [PMID: 16837577 DOI: 10.1074/mcp.m600165-mcp200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To better understand the effects of antiandrogens on the prostate, we investigated the changes in the proteome of rat ventral prostate (VP) following treatment with a well characterized 5alpha-reductase inhibitor, finasteride. Sprague-Dawley rats were treated daily by gavage with finasteride at 0, 1, 5, 25, and 125 mg/kg/day. Changes in plasma hormone levels as well as the weight and histology of sex accessory tissues were determined after 28 days of treatment and showed a dose-related decrease of VP weights together with a marked atrophy of the tissue visible at the macroscopic and microscopic levels. In addition, significant reductions in seminal vesicle and epididymis weights were noted. VP proteins were analyzed by two-dimensional gel electrophoresis: 37 proteins, mainly involved in protein synthesis, processing, and cellular trafficking and in metabolism, detoxification, and oxidative stress, were identified as modulated by finasteride. The prominent feature of this study is the demonstration of finasteride dose-dependent up-regulation of a protein similar to l-amino-acid oxidase 1 (Lao1). An up-regulation of this protein was also observed with the antiandrogen flutamide. Lao1 expression occurred as early as 48 h after antiandrogen administration and persisted throughout the treatment duration. Immunohistochemistry showed that this protein was only detectable in epithelial cells and secretory vesicles. Altogether these data point to a potential use of Lao1 to reveal antiandrogen-induced prostate injury.
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20
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Dearman RJ, Herouet-Guicheney C, Kennel P, Rouquié D, Kimber I. Assessment of protein allergenic potential in mice: Inter-laboratory comparisons. Toxicology 2006. [DOI: 10.1016/j.tox.2006.05.063] [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: 11/15/2022]
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21
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Friry-Santini C, Katz C, Come MP, Kennel P, Samson M, Benahmed M, Rouquié D, Bars R. Transcriptomic and proteomic analysis of adult rat testes following an acute exposure to the antiandrogen flutamide. Toxicol Lett 2006. [DOI: 10.1016/j.toxlet.2006.07.270] [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: 11/26/2022]
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22
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Nicolaï M, Roncato MA, Canoy AS, Rouquié D, Sarda X, Freyssinet G, Robaglia C. Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 2006; 141:663-673. [PMID: 16632591 DOI: 10.1104/pp.106.079418.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sucrose starvation of Arabidopsis (Arabidopsis thaliana) cell culture was used to identify translationally regulated genes by DNA microarray analysis. Cells were starved by subculture without sucrose, and total and polysomal RNA was extracted between 6 and 48 h. Probes were derived from both RNA populations and used to screen oligonucleotide microarrays. Out of 25,607 screened genes, 224 were found to be differentially accumulated in polysomal RNA following starvation and 21 were found to be invariant in polysomal RNA while their total RNA abundance was modified. Most of the mRNA appears to be translationally repressed (183/245 genes), which is consistent with a general decrease in metabolic activities during starvation. The parallel transcriptional analysis identifies 268 regulated genes. Comparison of transcriptional and translational gene lists highlights the importance of translational regulation (mostly repression) affecting genes involved in cell cycle and cell growth, these being overrepresented in translationally regulated genes, providing a molecular framework for the arrest of cell proliferation following starvation. Starvation-induced translational control also affects chromatin regulation genes, such as the HD1 histone deacetylase, and the level of histone H4 acetylation was found to increase during starvation. This suggests that regulation of the global nuclear transcriptional activity might be linked to cytoplasmic translational regulations.
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Affiliation(s)
- M Nicolaï
- Laboratoire de Génétique et Biophysique des Plantes, Département d'Ecophysiologie Végétale et Microbiologie, Centre National de la Recherche Scientifique, Université Aix-marseille II, 13009 Marseille cedex 9, France
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23
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Nicolaï M, Roncato MA, Canoy AS, Rouquié D, Sarda X, Freyssinet G, Robaglia C. Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 2006; 141:663-73. [PMID: 16632591 PMCID: PMC1475480 DOI: 10.1104/pp.106.079418] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sucrose starvation of Arabidopsis (Arabidopsis thaliana) cell culture was used to identify translationally regulated genes by DNA microarray analysis. Cells were starved by subculture without sucrose, and total and polysomal RNA was extracted between 6 and 48 h. Probes were derived from both RNA populations and used to screen oligonucleotide microarrays. Out of 25,607 screened genes, 224 were found to be differentially accumulated in polysomal RNA following starvation and 21 were found to be invariant in polysomal RNA while their total RNA abundance was modified. Most of the mRNA appears to be translationally repressed (183/245 genes), which is consistent with a general decrease in metabolic activities during starvation. The parallel transcriptional analysis identifies 268 regulated genes. Comparison of transcriptional and translational gene lists highlights the importance of translational regulation (mostly repression) affecting genes involved in cell cycle and cell growth, these being overrepresented in translationally regulated genes, providing a molecular framework for the arrest of cell proliferation following starvation. Starvation-induced translational control also affects chromatin regulation genes, such as the HD1 histone deacetylase, and the level of histone H4 acetylation was found to increase during starvation. This suggests that regulation of the global nuclear transcriptional activity might be linked to cytoplasmic translational regulations.
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Affiliation(s)
- M Nicolaï
- Laboratoire de Génétique et Biophysique des Plantes, Département d'Ecophysiologie Végétale et Microbiologie, Centre National de la Recherche Scientifique, Université Aix-marseille II, 13009 Marseille cedex 9, France
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24
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Wisniewska J, Xu J, Seifertová D, Brewer PB, Ruzicka K, Blilou I, Rouquié D, Benková E, Scheres B, Friml J. Polar PIN localization directs auxin flow in plants. Science 2006; 312:883. [PMID: 16601151 DOI: 10.1126/science.1121356] [Citation(s) in RCA: 579] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Polar flow of the phytohormone auxin requires plasma membrane-associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity.
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Affiliation(s)
- Justyna Wisniewska
- Center for Plant Molecular Biology (ZMBP), Tübingen University, D-72076 Tübingen, Germany
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25
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Abstract
An extensive proteomic approach relies on the possibility to visualize and analyze various types of proteins, including hydrophobic proteins which are rarely detectable on two-dimensional electrophoresis (2-DE) gels. In this study, two methods were employed for the purification of hydrophobic proteins from Arabidopsis thaliana leaf plasma membrane (PM) model plants, prior to analysis on 2-DE immobilized pH gradient (IPG) gels. Solubilization efficiency of two detergents, (3-[(3-cholomidopropyl)-1-propanesulfonic acid (CHAPS) and C8phi, were tested for the recovery of hydrophobic proteins. An immunological approach was used to determine the efficiency of the above methods. Fractionation of proteins by Triton X-114 combined with solubilization with CHAPS resulted in the inability to detect hydrophobic proteins on 2-DE gels. The use of C8phi for protein solubilization did not improve this result. On the contrary, after treatment of membranes with alkaline buffer, the solubilization of PM proteins with detergent C8phi permitted the recovery of such proteins on 2-DE gels. The combination of membrane washing and the use of zwitterionic detergent resulted in the resolution of several integral proteins and the disappearance of peripheral proteins. In the resolution of expressed genome proteins, both large pH gradients in the first dimension and various acrylamide concentrations in the second dimension must be used. Notwithstanding, it is important to combine various sample treatments and different detergents in order to resolve soluble and hydrophobic proteins.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France.
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26
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Abstract
After a brief review of the strategies used to date to identify systematically plasma membrane (PM) proteins, emphasis was given to the proteomic approach of PM proteins from the model plant Arabidopsis thaliana. Comparative analysis of two-dimensional gels from PM and cytosolic fractions was used to assess the cellular origin of proteins found in PM fraction. The classification obtained was confirmed by protein sequencing that showed, in addition, that most analyzed proteins were peripheral proteins. A large proportion of these appeared to correspond to PM-constitutive proteins that were present in the PM from different plant organs, but were not uniquely located at the PM depending on the organ. In addition, the presence of organ-specific sets of PM-specific proteins was also demonstrated. Additional procedures were developed to identify integral PM proteins. The combined use of PM washes with alkaline carbonate buffer or Triton X-100/KBr, and of a new detergent to solubilize protein, resulted in improved recovery of hydrophobic proteins on gels. Results are discussed in terms of construction of comprehensive proteomes for PM and other membranes and organelles.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, Inra/ENSA-M/CNRS URA 2133, Montpellier, France
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27
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Abstract
An extensive proteomic approach relies on the possibility to visualize and analyze various types of proteins, including hydrophobic proteins which are rarely detectable on two-dimensional electrophoresis (2-DE) gels. In this study, two methods were employed for the purification of hydrophobic proteins from Arabidopsis thaliana leaf plasma membrane (PM) model plants, prior to analysis on 2-DE immobilized pH gradient (IPG) gels. Solubilization efficiency of two detergents, (3-[(3-cholomidopropyl)-1-propanesulfonic acid (CHAPS) and C8phi, were tested for the recovery of hydrophobic proteins. An immunological approach was used to determine the efficiency of the above methods. Fractionation of proteins by Triton X-114 combined with solubilization with CHAPS resulted in the inability to detect hydrophobic proteins on 2-DE gels. The use of C8phi for protein solubilization did not improve this result. On the contrary, after treatment of membranes with alkaline buffer, the solubilization of PM proteins with detergent C8phi permitted the recovery of such proteins on 2-DE gels. The combination of membrane washing and the use of zwitterionic detergent resulted in the resolution of several integral proteins and the disappearance of peripheral proteins. In the resolution of expressed genome proteins, both large pH gradients in the first dimension and various acrylamide concentrations in the second dimension must be used. Notwithstanding, it is important to combine various sample treatments and different detergents in order to resolve soluble and hydrophobic proteins.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France.
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28
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Abstract
An extensive proteomic approach relies on the possibility to visualize and analyze various types of proteins, including hydrophobic proteins which are rarely detectable on two-dimensional electrophoresis (2-DE) gels. In this study, two methods were employed for the purification of hydrophobic proteins from Arabidopsis thaliana leaf plasma membrane (PM) model plants, prior to analysis on 2-DE immobilized pH gradient (IPG) gels. Solubilization efficiency of two detergents, (3-[(3-cholomidopropyl)-1-propanesulfonic acid (CHAPS) and C8phi, were tested for the recovery of hydrophobic proteins. An immunological approach was used to determine the efficiency of the above methods. Fractionation of proteins by Triton X-114 combined with solubilization with CHAPS resulted in the inability to detect hydrophobic proteins on 2-DE gels. The use of C8phi for protein solubilization did not improve this result. On the contrary, after treatment of membranes with alkaline buffer, the solubilization of PM proteins with detergent C8phi permitted the recovery of such proteins on 2-DE gels. The combination of membrane washing and the use of zwitterionic detergent resulted in the resolution of several integral proteins and the disappearance of peripheral proteins. In the resolution of expressed genome proteins, both large pH gradients in the first dimension and various acrylamide concentrations in the second dimension must be used. Notwithstanding, it is important to combine various sample treatments and different detergents in order to resolve soluble and hydrophobic proteins.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France.
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29
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Santoni V, Rouquié D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, Bauw G, Posada E, Rouzé P, Dehais P, Sahnoun I, Barlier I, Rossignol M. Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J 1998; 16:633-41. [PMID: 10036779 DOI: 10.1046/j.1365-313x.1998.00335.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A plasma membrane (PM) fraction was purified from Arabidopsis thaliana using a standard procedure and analyzed by two-dimensional (2D) gel electrophoresis. The proteins were classified according to their relative abundance in PM or cell membrane supernatant fractions. Eighty-two of the 700 spots detected on the PM 2D gels were microsequenced. More than half showed sequence similarity to proteins of known function. Of these, all the spots in the PM-specific and PM-enriched fractions, together with half of the spots with similar abundance in PM fraction and supernatant, have previously been found at the PM, supporting the validity of this approach. Extrapolation from this analysis indicates that (i) approximately 550 polypeptides found at the PM could be resolved on 2D gels; (ii) that numerous proteins with multiple locations are found at the PM; and (iii) that approximately 80% of PM-specific spots correspond to proteins with unknown function. Among the later, half are represented by ESTs or cDNAs in databases. In this way, several unknown gene products were potentially localized to the PM. These data are discussed with respect to the efficiency of organelle proteome approaches to link systematically genomic data to genome expression. It is concluded that generalized proteomes can constitute a powerful resource, with future completion of Arabidopsis genome sequencing, for genome-wide exploration of plant function.
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Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France
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30
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Rouquié D, Tournaire-Roux C, Szponarski W, Rossignol M, Doumas P. Cloning of the V-ATPase subunit G in plant: functional expression and sub-cellular localization. FEBS Lett 1998; 437:287-92. [PMID: 9824309 DOI: 10.1016/s0014-5793(98)01252-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A 13-kDa tobacco plasma membrane protein was isolated from two-dimensional electrophoresis gels. After microsequencing, RT-PCR techniques and cDNA library screening allowed for the cloning of two cDNAs. These cDNAs encoded for the subunit G of the vacuolar H+-ATPase, the first one identified in plants. Analysis of mRNA distribution showed a maximum level in the leaves and in the stem of the apical part of the tobacco plant. Heterologous functional complementation of the yeast mutant (deltavma10::URA3) was achieved with the two cDNAs. After fractionation of microsomal membranes on linear sucrose gradient, Western blots were performed using antibodies against recombinant protein and three peaks were identified: one which comigrated with the tonoplast marker and the others at slightly higher density corresponding to endoplasmic reticulum and to plasma membrane fractions.
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Affiliation(s)
- D Rouquié
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France
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31
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Chevallet M, Santoni V, Poinas A, Rouquié D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T. New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 1998; 19:1901-9. [PMID: 9740050 DOI: 10.1002/elps.1150191108] [Citation(s) in RCA: 243] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Severe quantitative loss of protein is often observed in high-resolution two-dimensional electrophoresis of membrane proteins, while the resolution is usually not affected. To improve the solubility of proteins in this technique, we tested denaturing cocktails containing various detergents and chaotropes. Best results were obtained with a denaturing solution containing urea, thiourea, and zwitterionic detergents, synthesized for this purpose. Among the dozen detergents synthesized and tested, amidosulfobetaines with an alkyl tail containing 14-16 carbons proved most efficient, solubilizing previously undetected membrane proteins.
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Affiliation(s)
- M Chevallet
- CEA, Laboratoire de Bioénergétique Cellulaire et Pathologique, Grenoble, France
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32
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Rouquié D, Peltier JB, Marquis-Mansion M, Tournaire C, Doumas P, Rossignol M. Construction of a directory of tobacco plasma membrane proteins by combined two-dimensional gel electrophoresis and protein sequencing. Electrophoresis 1997; 18:654-60. [PMID: 9150956 DOI: 10.1002/elps.1150180352] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The polypeptide pattern of the plasma membrane from tobacco was studied by two-dimensional gel electrophoresis. When using classical carrier ampholyte isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis (IEF/SDS-PAGE) approximately 400 polypeptide spots were detected after silver staining and computer analysis using the QUEST software. This resolution was sufficient to assess physiological effects such as changes in a phytohormone concentration. By using pH 4-8 immobilized pH gradient (IPG)-IEF and 10%T SDS-PAGE gels, approximately 600 polypeptides, corresponding to ca. 80% of the total population expected, were resolved. This cross-section of the plasma membrane polypeptide population was mainly constituted by low or intermediate molecular mass (25 to 45 kDa) and acidic (5.2 < pI < 6.1) polypeptides. After sample application by in-gel rehydration, large amounts of plasma membrane protein (between 5 mg and 10 mg protein) were analyzed using IPG-IEF, and N-terminal protein sequencing was performed for polypeptides collected from one gel. Internal protein sequences were also obtained. Nearly all protein sequences corresponded to unidentified proteins but several of them matched translated sequences from unidentified plant expressed sequence tags (ESTs). It is concluded that the combined use of IPG-IEF gels and in-gel rehydration allows, in the case of plant membrane protein, both analytical and micropreparative separations with an efficiency comparable to that demonstrated for soluble proteins. Finally, it is suggested that a systematic investigation of plant plasma membrane polypeptides is feasible and would constitute a source of new and plant-specific genes.
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Affiliation(s)
- D Rouquié
- INRA/ENSAM/CNRS URA 2133, Montpellier, France
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