1
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Vecchio F, Carré A, Korenkov D, Zhou Z, Apaolaza P, Tuomela S, Burgos-Morales O, Snowhite I, Perez-Hernandez J, Brandao B, Afonso G, Halliez C, Kaddis J, Kent SC, Nakayama M, Richardson SJ, Vinh J, Verdier Y, Laiho J, Scharfmann R, Solimena M, Marinicova Z, Bismuth E, Lucidarme N, Sanchez J, Bustamante C, Gomez P, Buus S, You S, Pugliese A, Hyoty H, Rodriguez-Calvo T, Flodstrom-Tullberg M, Mallone R. Coxsackievirus infection induces direct pancreatic β cell killing but poor antiviral CD8 + T cell responses. Sci Adv 2024; 10:eadl1122. [PMID: 38446892 PMCID: PMC10917340 DOI: 10.1126/sciadv.adl1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β cell autoimmunity and type 1 diabetes. We investigated how CVB affects human β cells and anti-CVB T cell responses. β cells were efficiently infected by CVB in vitro, down-regulated human leukocyte antigen (HLA) class I, and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized a fraction of these peptides; only another subfraction was targeted by effector/memory T cells that expressed exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with β cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Our in vitro and ex vivo data highlight limited CD8+ T cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and nonstructural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.
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Affiliation(s)
- Federica Vecchio
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Daniil Korenkov
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Paola Apaolaza
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Soile Tuomela
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | - Isaac Snowhite
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | | | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Clémentine Halliez
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | - John Kaddis
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical Chan School, Worcester, MA, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sarah J. Richardson
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Jutta Laiho
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Michele Solimena
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Zuzana Marinicova
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Elise Bismuth
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
| | - Nadine Lucidarme
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
| | - Janine Sanchez
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Carmen Bustamante
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Patricia Gomez
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Soren Buus
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - the nPOD-Virus Working Group
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical Chan School, Worcester, MA, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Fimlab Laboratories, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Heikki Hyoty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Malin Flodstrom-Tullberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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2
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Ravi Kumar R, Ndiaye MM, Haddad I, Vinh J, Verdier Y. ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia. J Proteome Res 2024; 23:869-880. [PMID: 38353246 PMCID: PMC10913871 DOI: 10.1021/acs.jproteome.3c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.
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Affiliation(s)
- Ranjith
Kumar Ravi Kumar
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Massamba Mbacke Ndiaye
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Iman Haddad
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Joelle Vinh
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Yann Verdier
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
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3
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Vecchio F, Carré A, Korenkov D, Zhou Z, Apaolaza P, Tuomela S, Burgos-Morales O, Snowhite I, Perez-Hernandez J, Brandao B, Afonso G, Halliez C, Kaddis J, Kent SC, Nakayama M, Richardson SJ, Vinh J, Verdier Y, Laiho J, Scharfmann R, Solimena M, Marinicova Z, Bismuth E, Lucidarme N, Sanchez J, Bustamante C, Gomez P, Buus S, You S, Pugliese A, Hyoty H, Rodriguez-Calvo T, Flodstrom-Tullberg M, Mallone R. Coxsackievirus infection induces direct pancreatic β-cell killing but poor anti-viral CD8+ T-cell responses. bioRxiv 2023:2023.08.19.553954. [PMID: 37662376 PMCID: PMC10473604 DOI: 10.1101/2023.08.19.553954] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β-cell autoimmunity. We investigated how CVB impacts human β cells and anti-CVB T-cell responses. β cells were efficiently infected by CVB in vitro, downregulated HLA Class I and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized only a fraction of these peptides, and only another sub-fraction was targeted by effector/memory T cells that expressed the exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with the β-cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Thus, our in-vitro and ex-vivo data highlight limited T-cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and non-structural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.
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Affiliation(s)
- Federica Vecchio
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Daniil Korenkov
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Paola Apaolaza
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Soile Tuomela
- Center for Infectious Medicine, Department of medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | - Isaac Snowhite
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | | | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | | | - John Kaddis
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sally C. Kent
- University of Massachusetts Medical Chan School, Diabetes Center of Excellence, Department of Medicine, Worcester, MA, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sarah J. Richardson
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Jutta Laiho
- Tampere University, Faculty of Medicine and Health Technology and Fimlab Laboratories, Tampere, Finland
| | | | - Michele Solimena
- Paul Langerhans Institute, Technical University Dresden, Germany
| | | | - Elise Bismuth
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
| | - Nadine Lucidarme
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
| | - Janine Sanchez
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Carmen Bustamante
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Patricia Gomez
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Soren Buus
- Panum Institute, Department of International Health, Immunology and Microbiology, Copenhagen, Denmark
| | | | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Heikki Hyoty
- Tampere University, Faculty of Medicine and Health Technology and Fimlab Laboratories, Tampere, Finland
| | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Malin Flodstrom-Tullberg
- Center for Infectious Medicine, Department of medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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4
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Wang Y, Chiappetta G, Guérois R, Liu Y, Romero S, Boesch DJ, Krause M, Dessalles CA, Babataheri A, Barakat AI, Chen B, Vinh J, Polesskaya A, Gautreau AM. PPP2R1A regulates migration persistence through the NHSL1-containing WAVE Shell Complex. Nat Commun 2023; 14:3541. [PMID: 37322026 PMCID: PMC10272187 DOI: 10.1038/s41467-023-39276-w] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
The RAC1-WAVE-Arp2/3 signaling pathway generates branched actin networks that power lamellipodium protrusion of migrating cells. Feedback is thought to control protrusion lifetime and migration persistence, but its molecular circuitry remains elusive. Here, we identify PPP2R1A by proteomics as a protein differentially associated with the WAVE complex subunit ABI1 when RAC1 is activated and downstream generation of branched actin is blocked. PPP2R1A is found to associate at the lamellipodial edge with an alternative form of WAVE complex, the WAVE Shell Complex, that contains NHSL1 instead of the Arp2/3 activating subunit WAVE, as in the canonical WAVE Regulatory Complex. PPP2R1A is required for persistence in random and directed migration assays and for RAC1-dependent actin polymerization in cell extracts. PPP2R1A requirement is abolished by NHSL1 depletion. PPP2R1A mutations found in tumors impair WAVE Shell Complex binding and migration regulation, suggesting that the coupling of PPP2R1A to the WAVE Shell Complex is essential to its function.
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Affiliation(s)
- Yanan Wang
- Laboratory of Structural Biology of the Cell (BIOC), CNRS UMR7654, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Giovanni Chiappetta
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, LPC CNRS UMR8249, 75005, Paris, France
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Yijun Liu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Stéphane Romero
- Laboratory of Structural Biology of the Cell (BIOC), CNRS UMR7654, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Daniel J Boesch
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthias Krause
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Claire A Dessalles
- LadHyX, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Avin Babataheri
- LadHyX, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Abdul I Barakat
- LadHyX, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Joelle Vinh
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, LPC CNRS UMR8249, 75005, Paris, France
| | - Anna Polesskaya
- Laboratory of Structural Biology of the Cell (BIOC), CNRS UMR7654, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
| | - Alexis M Gautreau
- Laboratory of Structural Biology of the Cell (BIOC), CNRS UMR7654, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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5
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Zoumpoulaki M, Schanne G, Delsuc N, Preud'homme H, Quévrain E, Eskenazi N, Gazzah G, Guillot R, Seksik P, Vinh J, Lobinski R, Policar C. Deciphering the Metal Speciation in Low‐Molecular‐Weight Complexes by IMS‐MS: Application to the Detection of Manganese Superoxide Dismutase Mimics in Cell Lysates. Angew Chem Int Ed Engl 2022; 61:e202203066. [DOI: 10.1002/anie.202203066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Martha Zoumpoulaki
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
| | - Gabrielle Schanne
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
| | - Nicolas Delsuc
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Elodie Quévrain
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Géraldine Gazzah
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | - Regis Guillot
- ICMMO UMR CNRS 8182 Université Paris-Saclay 91405 Orsay France
| | - Philippe Seksik
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
- Gastroenterology Department Saint-Antoine Hospital Sorbonne Université, APHP Paris France
| | - Joelle Vinh
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
| | - Ryszard Lobinski
- Universite de Pau, CNRS, E2S, IPREM-UMR5254, Hélioparc 64053 Pau France
- Chair of Analytical Chemistry Warsaw University of Technology, Noakowskiego 3 00-664 Warsaw Poland
| | - Clotilde Policar
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
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6
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Zoumpoulaki M, Schanne G, Delsuc N, Preud'homme H, Quévrain E, Eskenazi N, Gazzah G, Guillot R, Seksik P, Vinh J, Lobinski R, Policar C. Inside Cover: Deciphering the Metal Speciation in Low‐Molecular‐Weight Complexes by IMS‐MS: Application to the Detection of Manganese Superoxide Dismutase Mimics in Cell Lysates (Angew. Chem. Int. Ed. 38/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202210260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martha Zoumpoulaki
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
| | - Gabrielle Schanne
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
| | - Nicolas Delsuc
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Elodie Quévrain
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Géraldine Gazzah
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | - Regis Guillot
- ICMMO UMR CNRS 8182 Université Paris-Saclay 91405 Orsay France
| | - Philippe Seksik
- Centre de Recherche de Saint-Antoine, INSERM, UMRS 938 Sorbonne University, INSERM 75012 Paris France
- Gastroenterology Department Saint-Antoine Hospital Sorbonne Université, APHP Paris France
| | - Joelle Vinh
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
| | - Ryszard Lobinski
- Universite de Pau, CNRS, E2S, IPREM-UMR5254, Hélioparc 64053 Pau France
- Chair of Analytical Chemistry Warsaw University of Technology, Noakowskiego 3 00-664 Warsaw Poland
| | - Clotilde Policar
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
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Zoumpoulaki M, Schanne G, Delsuc N, Preud'homme H, Quévrain E, Eskenazi N, Gazzah G, Guillot R, Seksik P, Vinh J, Lobinski R, Policar C. Deciphering the Metal Speciation in Low‐Molecular‐Weight Complexes by IMS‐MS: Application to the Detection of Manganese Superoxide Dismutase Mimics in Cell Lysates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Martha Zoumpoulaki
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
- Centre de Recherche de Saint-Antoine Sorbonne University, INSERM 75012 Paris France
| | - Gabrielle Schanne
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
- Centre de Recherche de Saint-Antoine Sorbonne University, INSERM 75012 Paris France
| | - Nicolas Delsuc
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | - Hugues Preud'homme
- IPREM-UMR5254, E2S UPPA, CNRS Technopôle Helioparc 64053 Pau Cedex 9 France
| | - Elodie Quévrain
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Géraldine Gazzah
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
| | | | - Philippe Seksik
- Centre de Recherche de Saint-Antoine Sorbonne University, INSERM 75012 Paris France
| | - Joelle Vinh
- SMBP ESPCI Paris PSL University, UMR 8249 CNRS France
| | - Ryszard Lobinski
- IPREM-UMR5254, E2S UPPA, CNRS Technopôle Helioparc 64053 Pau Cedex 9 France
| | - Clotilde Policar
- Laboratoire des biomolécules (LBM) Département de chimie École normale supérieure PSL University, Sorbonne Université, CNRS 75005 Paris France
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8
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Chiappetta G, Gamberi T, Faienza F, Limaj X, Rizza S, Messori L, Filomeni G, Modesti A, Vinh J. Redox proteome analysis of auranofin exposed ovarian cancer cells (A2780). Redox Biol 2022; 52:102294. [PMID: 35358852 PMCID: PMC8966199 DOI: 10.1016/j.redox.2022.102294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/03/2023] Open
Abstract
The effects of Auranofin (AF) on protein expression and protein oxidation in A2780 cancer cells were investigated through a strategy based on simultaneous expression proteomics and redox proteomics determinations. Bioinformatics analysis of the proteomics data supports the view that the most critical cellular changes elicited by AF treatment consist of thioredoxin reductase inhibition, alteration of the cell redox state, impairment of the mitochondrial functions, metabolic changes associated with conversion to a glycolytic phenotype, induction of ER stress. The occurrence of the above cellular changes was extensively validated by performing direct biochemical assays. Our data are consistent with the concept that AF produces its effects through a multitarget mechanism that mainly affects the redox metabolism and the mitochondrial functions and results into severe ER stress. Results are discussed in the context of the current mechanistic knowledge existing on AF. Redox proteomics allows to underline cell adaptation mechanisms in response to Auranofin treatment in ovarian cancer cells. BRCA1 is one of the major candidates of the ovarian cancer cell adaptation to Auranofin treatment. Auranofin alters the oxidative phosphorylation and mitochondrial protein import machinery. TRAP1 C501 modulates Auranofin toxicity. Auranofin induces severe stress of the endoplasmic reticulum.
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Affiliation(s)
- Giovanni Chiappetta
- Biological Mass Spectrometry and Proteomics Group, SMBP, PDC CNRS UMR, 8249, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005, Paris, France.
| | - Tania Gamberi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134, Florence, Italy.
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Xhesika Limaj
- Biological Mass Spectrometry and Proteomics Group, SMBP, PDC CNRS UMR, 8249, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005, Paris, France
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Luigi Messori
- Metmed Lab, Department of Chemistry, University of Florence, via della lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giuseppe Filomeni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy; Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, Copenhagen, Denmark; Center for Healthy Aging, University of Copenhagen, Denmark
| | - Alessandra Modesti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134, Florence, Italy
| | - Joelle Vinh
- Biological Mass Spectrometry and Proteomics Group, SMBP, PDC CNRS UMR, 8249, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005, Paris, France
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9
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Azoury ME, Samassa F, Buitinga M, Nigi L, Brusco N, Callebaut A, Giraud M, Irla M, Lalanne AI, Carré A, Afonso G, Zhou Z, Brandao B, Colli ML, Sebastiani G, Dotta F, Nakayama M, Eizirik DL, You S, Pinto S, Mamula MJ, Verdier Y, Vinh J, Buus S, Mathieu C, Overbergh L, Mallone R. CD8 + T Cells Variably Recognize Native Versus Citrullinated GRP78 Epitopes in Type 1 Diabetes. Diabetes 2021; 70:2879-2891. [PMID: 34561224 PMCID: PMC8660990 DOI: 10.2337/db21-0259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022]
Abstract
In type 1 diabetes, autoimmune β-cell destruction may be favored by neoantigens harboring posttranslational modifications (PTMs) such as citrullination. We studied the recognition of native and citrullinated glucose-regulated protein (GRP)78 peptides by CD8+ T cells. Citrullination modulated T-cell recognition and, to a lesser extent, HLA-A2 binding. GRP78-reactive CD8+ T cells circulated at similar frequencies in healthy donors and donors with type 1 diabetes and preferentially recognized either native or citrullinated versions, without cross-reactivity. Rather, the preference for native GRP78 epitopes was associated with CD8+ T cells cross-reactive with bacterial mimotopes. In the pancreas, a dominant GRP78 peptide was instead preferentially recognized when citrullinated. To further clarify these recognition patterns, we considered the possibility of citrullination in the thymus. Citrullinating peptidylarginine deiminase (Padi) enzymes were expressed in murine and human medullary epithelial cells (mTECs), with citrullinated proteins detected in murine mTECs. However, Padi2 and Padi4 expression was diminished in mature mTECs from NOD mice versus C57BL/6 mice. We conclude that, on one hand, the CD8+ T cell preference for native GRP78 peptides may be shaped by cross-reactivity with bacterial mimotopes. On the other hand, PTMs may not invariably favor loss of tolerance because thymic citrullination, although impaired in NOD mice, may drive deletion of citrulline-reactive T cells.
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Affiliation(s)
| | | | - Mijke Buitinga
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Laura Nigi
- Toscana Life Sciences, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Noemi Brusco
- Toscana Life Sciences, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Aïsha Callebaut
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Matthieu Giraud
- Centre de Recherche en Transplantation et Immunologie, INSERM UMR1064, Université de Nantes, Nantes, France
| | - Magali Irla
- Centre d'Immunologie de Marseille-Luminy, INSERM, CNRS, Aix-Marseille University, Marseille, France
| | - Ana Ines Lalanne
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Alexia Carré
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Barbara Brandao
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Maikel L Colli
- Medical Faculty, Center for Diabetes Research and Welbio, Université Libre de Bruxelles, Brussels, Belgium
| | - Guido Sebastiani
- Toscana Life Sciences, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Francesco Dotta
- Toscana Life Sciences, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Decio L Eizirik
- Medical Faculty, Center for Diabetes Research and Welbio, Université Libre de Bruxelles, Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN
| | - Sylvaine You
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Sheena Pinto
- Division of Developmental Immunology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Soren Buus
- Department of International Health, Immunology and Microbiology, Panum Institute, Copenhagen, Denmark
| | - Chantal Mathieu
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lut Overbergh
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Roberto Mallone
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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10
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Barraud N, Létoffé S, Beloin C, Vinh J, Chiappetta G, Ghigo JM. Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress. NPJ Biofilms Microbiomes 2021; 7:34. [PMID: 33850153 PMCID: PMC8044216 DOI: 10.1038/s41522-021-00203-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/18/2021] [Indexed: 02/03/2023] Open
Abstract
Communities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen, and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG, and GltD altered important biofilm properties, including motility, biofilm maturation, or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.
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Affiliation(s)
- Nicolas Barraud
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Sylvie Létoffé
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Joelle Vinh
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, CNRS FRE2032, 75005, Paris, France
| | - Giovanni Chiappetta
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, CNRS FRE2032, 75005, Paris, France.
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France.
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11
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Azoury ME, Tarayrah M, Afonso G, Pais A, Colli ML, Maillard C, Lavaud C, Alexandre-Heymann L, Gonzalez-Duque S, Verdier Y, Vinh J, Pinto S, Buus S, Dubois-Laforgue D, Larger E, Beressi JP, Bruno G, Eizirik DL, You S, Mallone R. Peptides Derived From Insulin Granule Proteins Are Targeted by CD8 + T Cells Across MHC Class I Restrictions in Humans and NOD Mice. Diabetes 2020; 69:2678-2690. [PMID: 32928873 DOI: 10.2337/db20-0013] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022]
Abstract
The antigenic peptides processed by β-cells and presented through surface HLA class I molecules are poorly characterized. Each HLA variant (e.g., the most common being HLA-A2 and HLA-A3) carries some peptide-binding specificity. Hence, features that, despite these specificities, remain shared across variants may reveal factors favoring β-cell immunogenicity. Building on our previous description of the HLA-A2/A3 peptidome of β-cells, we analyzed the HLA-A3-restricted peptides targeted by circulating CD8+ T cells. Several peptides were recognized by CD8+ T cells within a narrow frequency (1-50/106), which was similar in donors with and without type 1 diabetes and harbored variable effector/memory fractions. These epitopes could be classified as conventional peptides or neoepitopes, generated either via peptide cis-splicing or mRNA splicing (e.g., secretogranin-5 [SCG5]-009). As reported for HLA-A2-restricted peptides, several epitopes originated from β-cell granule proteins (e.g., SCG3, SCG5, and urocortin-3). Similarly, H-2Kd-restricted CD8+ T cells recognizing the murine orthologs of SCG5, urocortin-3, and proconvertase-2 infiltrated the islets of NOD mice and transferred diabetes into NOD/scid recipients. The finding of granule proteins targeted in both humans and NOD mice supports their disease relevance and identifies the insulin granule as a rich source of epitopes, possibly reflecting its impaired processing in type 1 diabetes.
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Affiliation(s)
| | - Mahmoud Tarayrah
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Aurore Pais
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Maikel L Colli
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Claire Maillard
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Cassandra Lavaud
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Laure Alexandre-Heymann
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires de Paris Centre-Université de Paris, Cochin Hospital, Service de Diabétologie et Immunologie Clinique, Paris, France
| | - Sergio Gonzalez-Duque
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- École Supérieure de Physique et de Chimie Industrielles Paris, Université Paris Sciences et Lettres, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, Paris, France
| | - Yann Verdier
- École Supérieure de Physique et de Chimie Industrielles Paris, Université Paris Sciences et Lettres, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, Paris, France
| | - Joelle Vinh
- École Supérieure de Physique et de Chimie Industrielles Paris, Université Paris Sciences et Lettres, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, Paris, France
| | - Sheena Pinto
- Division of Developmental Immunology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Soren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Danièle Dubois-Laforgue
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires de Paris Centre-Université de Paris, Cochin Hospital, Service de Diabétologie et Immunologie Clinique, Paris, France
| | - Etienne Larger
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires de Paris Centre-Université de Paris, Cochin Hospital, Service de Diabétologie et Immunologie Clinique, Paris, France
| | - Jean-Paul Beressi
- Service de Diabétologie, Centre Hospitalier de Versailles André Mignot, Le Chesnay, France
| | - Graziella Bruno
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Decio L Eizirik
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Sylvaine You
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Roberto Mallone
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires de Paris Centre-Université de Paris, Cochin Hospital, Service de Diabétologie et Immunologie Clinique, Paris, France
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12
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Duval R, Bui LC, Mathieu C, Nian Q, Berthelet J, Xu X, Haddad I, Vinh J, Dupret JM, Busi F, Guidez F, Chomienne C, Rodrigues-Lima F. Benzoquinone, a leukemogenic metabolite of benzene, catalytically inhibits the protein tyrosine phosphatase PTPN2 and alters STAT1 signaling. J Biol Chem 2019; 294:12483-12494. [PMID: 31248982 DOI: 10.1074/jbc.ra119.008666] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Protein tyrosine phosphatase, nonreceptor type 2 (PTPN2) is mainly expressed in hematopoietic cells, where it negatively regulates growth factor and cytokine signaling. PTPN2 is an important regulator of hematopoiesis and immune/inflammatory responses, as evidenced by loss-of-function mutations of PTPN2 in leukemia and lymphoma and knockout mice studies. Benzene is an environmental chemical that causes hematological malignancies, and its hematotoxicity arises from its bioactivation in the bone marrow to electrophilic metabolites, notably 1,4-benzoquinone, a major hematotoxic benzene metabolite. Although the molecular bases for benzene-induced leukemia are not well-understood, it has been suggested that benzene metabolites alter topoisomerases II function and thereby significantly contribute to leukemogenesis. However, several studies indicate that benzene and its hematotoxic metabolites may also promote the leukemogenic process by reacting with other targets and pathways. Interestingly, alterations of cell-signaling pathways, such as Janus kinase (JAK)/signal transducer and activator of transcription (STAT), have been proposed to contribute to benzene-induced malignant blood diseases. We show here that 1,4-benzoquinone directly impairs PTPN2 activity. Mechanistic and kinetic experiments with purified human PTPN2 indicated that this impairment results from the irreversible formation (k inact = 645 m-1·s-1) of a covalent 1,4-benzoquinone adduct at the catalytic cysteine residue of the enzyme. Accordingly, cell experiments revealed that 1,4-benzoquinone exposure irreversibly inhibits cellular PTPN2 and concomitantly increases tyrosine phosphorylation of STAT1 and expression of STAT1-regulated genes. Our results provide molecular and cellular evidence that 1,4-benzoquinone covalently modifies key signaling enzymes, implicating it in benzene-induced malignant blood diseases.
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Affiliation(s)
- Romain Duval
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Linh-Chi Bui
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Cécile Mathieu
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Qing Nian
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | | | - Ximing Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Iman Haddad
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | | | - Florent Busi
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Fabien Guidez
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France
| | - Christine Chomienne
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France; Service de Biologie Cellulaire, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint Louis, F-75010 Paris, France
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13
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Gonzalez-Duque S, Azoury ME, Colli ML, Afonso G, Turatsinze JV, Nigi L, Lalanne AI, Sebastiani G, Carré A, Pinto S, Culina S, Corcos N, Bugliani M, Marchetti P, Armanet M, Diedisheim M, Kyewski B, Steinmetz LM, Buus S, You S, Dubois-Laforgue D, Larger E, Beressi JP, Bruno G, Dotta F, Scharfmann R, Eizirik DL, Verdier Y, Vinh J, Mallone R. Conventional and Neo-antigenic Peptides Presented by β Cells Are Targeted by Circulating Naïve CD8+ T Cells in Type 1 Diabetic and Healthy Donors. Cell Metab 2018; 28:946-960.e6. [PMID: 30078552 DOI: 10.1016/j.cmet.2018.07.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/20/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
Abstract
Although CD8+ T-cell-mediated autoimmune β cell destruction occurs in type 1 diabetes (T1D), the target epitopes processed and presented by β cells are unknown. To identify them, we combined peptidomics and transcriptomics strategies. Inflammatory cytokines increased peptide presentation in vitro, paralleling upregulation of human leukocyte antigen (HLA) class I expression. Peptide sources featured several insulin granule proteins and all known β cell antigens, barring islet-specific glucose-6-phosphatase catalytic subunit-related protein. Preproinsulin yielded HLA-A2-restricted epitopes previously described. Secretogranin V and its mRNA splice isoform SCG5-009, proconvertase-2, urocortin-3, the insulin gene enhancer protein ISL-1, and an islet amyloid polypeptide transpeptidation product emerged as antigens processed into HLA-A2-restricted epitopes, which, as those already described, were recognized by circulating naive CD8+ T cells in T1D and healthy donors and by pancreas-infiltrating cells in T1D donors. This peptidome opens new avenues to understand antigen processing by β cells and for the development of T cell biomarkers and tolerogenic vaccination strategies.
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Affiliation(s)
- Sergio Gonzalez-Duque
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Marie Eliane Azoury
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Maikel L Colli
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Georgia Afonso
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Jean-Valery Turatsinze
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Laura Nigi
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Ana Ines Lalanne
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Guido Sebastiani
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Alexia Carré
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Sheena Pinto
- DKFZ, Division of Developmental Immunology, 69120 Heidelberg, Germany
| | - Slobodan Culina
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Noémie Corcos
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Marco Bugliani
- University of Pisa, Department of Clinical and Experimental Medicine, 56124 Pisa, Italy
| | - Piero Marchetti
- University of Pisa, Department of Clinical and Experimental Medicine, 56124 Pisa, Italy
| | - Mathieu Armanet
- Assistance Publique Hôpitaux de Paris, Cell Therapy Unit, Saint Louis Hospital, 75010 Paris, France
| | - Marc Diedisheim
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Bruno Kyewski
- DKFZ, Division of Developmental Immunology, 69120 Heidelberg, Germany
| | - Lars M Steinmetz
- Stanford University, School of Medicine, Department of Genetics and Stanford Genome Technology Center, Stanford, CA 94305, USA; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Søren Buus
- Panum Institute, Department of International Health, Immunology and Microbiology, 2200 Copenhagen, Denmark
| | - Sylvaine You
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Daniele Dubois-Laforgue
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Etienne Larger
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Jean-Paul Beressi
- Centre Hospitalier de Versailles André Mignot, Service de Diabétologie, 78150 Le Chesnay, France
| | - Graziella Bruno
- University of Turin, Department of Medical Sciences, 10126 Turin, Italy
| | - Francesco Dotta
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Raphael Scharfmann
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Decio L Eizirik
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Roberto Mallone
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France.
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14
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Le Manach S, Sotton B, Huet H, Duval C, Paris A, Marie A, Yépremian C, Catherine A, Mathéron L, Vinh J, Edery M, Marie B. Physiological effects caused by microcystin-producing and non-microcystin producing Microcystis aeruginosa on medaka fish: A proteomic and metabolomic study on liver. Environ Pollut 2018; 234:523-537. [PMID: 29220784 DOI: 10.1016/j.envpol.2017.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/10/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Cyanobacterial blooms have become a common phenomenon in eutrophic freshwater ecosystems worldwide. Microcystis is an important bloom-forming and toxin-producing genus in continental aquatic ecosystems, which poses a potential risk to Human populations as well as on aquatic organisms. Microcystis is known to produce along with various bioactive peptides, the microcystins (MCs) that have attracted more attention notably due to their high hepatotoxicity. To better understand the effects of cyanobacterial blooms on fish, medaka fish (Oryzias latipes) were sub-chronically exposed to either non-MC-producing or MC-producing living strains and, for this latter, to its subsequent MC-extract of Microcystis aeruginosa. Toxicological effects on liver have been evaluated through the combined approach of histopathology and 'omics' (i.e. proteomics and metabolomics). All treatments induce sex-dependent effects at both cellular and molecular levels. Moreover, the modalities of exposure appear to induce differential responses as the direct exposure to the cyanobacterial strains induce more acute effects than the MC-extract treatment. Our histopathological observations indicate that both non-MC-producing and MC-producing strains induce cellular impairments. Both proteomic and metabolomic analyses exhibit various biological disruptions in the liver of females and males exposed to strain and extract treatments. These results support the hypothesis that M. aeruginosa is able to produce bioactive peptides, other than MCs, which can induce toxicological effects in fish liver. Moreover, they highlight the importance of considering cyanobacterial cells as a whole to assess the realistic environmental risk of cyanobacteria on fish.
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Affiliation(s)
- Séverine Le Manach
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France.
| | - Benoit Sotton
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Hélène Huet
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France; Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, BioPôle Alfort, F-94704 Maisons-Alfort Cedex, France
| | - Charlotte Duval
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Alain Paris
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Claude Yépremian
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Arnaud Catherine
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Joelle Vinh
- USR 3149 ESPCI/CNRS SMPB, Laboratory of Biological Mass Spectrometry and Proteomics, ESPCI Paris, PSL Research University, Paris, France
| | - Marc Edery
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de communication et adaptation des microorganismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, 12 rue Buffon, F-75231 Paris Cedex 05, France.
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15
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Shahali Y, Sutra J, Hilger C, Swiontek K, Haddad I, Vinh J, Guilloux L, Charpin D, Sénéchal H, Poncet P. Identification of a polygalacturonase (Cup s 2) as the major CCD-bearing allergen in Cupressus sempervirens pollen. Allergy 2017; 72:1806-1810. [PMID: 28439939 DOI: 10.1111/all.13191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 11/28/2022]
Abstract
As IgE glyco-epitopes, also referred to as cross-reactive carbohydrate determinants (CCDs), can share significant structural homologies between different plants, they are prone to extensive cross-reactivity among allergen pollen extracts. Here, cypress pollen allergens, especially a polygalacturonase (PG), were further characterized using double one-dimensional electrophoresis (D1-DE). The presence of specific IgE directed against CCDs was investigated by bromelain IgE inhibition and concanavalin A binding assays using sera of cypress pollen-sensitized patients. Our results showed that IgE reactivity to CCDs in Cupressus sempervirens pollen extracts is mainly related to bromelain-type epitopes of a newly identified cypress PG. This glycoprotein has been further characterized through an immunoproteomic approach and officially indexed as Cup s 2 by the WHO/IUIS allergen nomenclature. Cup s 2 could thus be associated with the increased prevalence of IgE reactivity to cypress pollen extracts because of CCD interference.
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Affiliation(s)
- Y. Shahali
- Department of Biochemistry, Allergy & Environment Team Armand Trousseau Children Hospital, AP‐HP Paris France
- Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
| | - J.‐P. Sutra
- Department of Biochemistry, Allergy & Environment Team Armand Trousseau Children Hospital, AP‐HP Paris France
| | - C. Hilger
- Department of Infection and Immunity Luxembourg Institute of Health Esch‐sur‐Alzette Luxembourg
| | - K. Swiontek
- Department of Infection and Immunity Luxembourg Institute of Health Esch‐sur‐Alzette Luxembourg
| | - I. Haddad
- ESPCI ParisTech SMBP USR CNRS 3149 Paris France
| | - J. Vinh
- ESPCI ParisTech SMBP USR CNRS 3149 Paris France
| | - L. Guilloux
- Eurofins‐Biomnis Bio‐medical analysis laboratory Lyon France
| | - D. Charpin
- Department of Pneumology and Allergy AP‐HM and Inserm, U1067 CNRS UMR 7333, Aix‐Marseille University Marseille France
| | - H. Sénéchal
- Department of Biochemistry, Allergy & Environment Team Armand Trousseau Children Hospital, AP‐HP Paris France
| | - P. Poncet
- Department of Biochemistry, Allergy & Environment Team Armand Trousseau Children Hospital, AP‐HP Paris France
- Center for Innovation and Technological Research Pasteur Institute Paris France
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16
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Shakir S, Vinh J, Chiappetta G. Quantitative analysis of the cysteine redoxome by iodoacetyl tandem mass tags. Anal Bioanal Chem 2017; 409:3821-3830. [PMID: 28389918 PMCID: PMC5427158 DOI: 10.1007/s00216-017-0326-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/04/2022]
Abstract
The redox conditions that reign inside a cell have a determining effect on a number of biological processes. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are key redox players and have been linked to a number of pathologies. They have also been shown to play an important regulating role in cell signaling events. On the proteome level, thiol groups of cysteinyl side chains constitute the major targets of ROS and RNS. A number of analytical techniques based on mass spectrometry have been developed to characterize the cysteine redoxome, often facing a number of technical challenges, mostly related to the lability, heterogeneity, and low abundance of the oxidized forms. Furthermore, any posttranslational modification (PTM) quantification method needs to take the parent protein’s expression level into account. While taking all these limitations into consideration, we have developed a quantitative analytical strategy named OxiTMT, based on chemical labeling with iodoacetyl isobaric tandem mass tags (iodoTMT). OxiTMT allowed the generation of quantitative redox data that could be normalized by the protein’s expression profile in up to three different conditions. The method was tested on Escherichia coli with or without an oxidative treatment. Results showed the method to be adequate for the analysis of cysteine PTMs with a good coverage of the cysteine redoxome, especially for the low abundant oxidized species. Some of the challenges that face reporter ion quantification of PTMs by mass spectrometry were also assessed. This study serves as a proof of concept of the established protocol and consequent data treatment step. The use of tandem mass tags opens the ways towards the application of the method to the study of tissues and sera. OxiTMT workflow ![]()
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Affiliation(s)
- Shakir Shakir
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France
| | - Joelle Vinh
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France
| | - Giovanni Chiappetta
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France.
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17
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Mathieu C, Bui LC, Petit E, Haddad I, Agbulut O, Vinh J, Dupret JM, Rodrigues-Lima F. Molecular Mechanisms of Allosteric Inhibition of Brain Glycogen Phosphorylase by Neurotoxic Dithiocarbamate Chemicals. J Biol Chem 2016; 292:1603-1612. [PMID: 27965358 DOI: 10.1074/jbc.m116.766725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/08/2016] [Indexed: 12/19/2022] Open
Abstract
Dithiocarbamates (DTCs) are important industrial chemicals used extensively as pesticides and in a variety of therapeutic applications. However, they have also been associated with neurotoxic effects and in particular with the development of Parkinson-like neuropathy. Although different pathways and enzymes (such as ubiquitin ligases or the proteasome) have been identified as potential targets of DTCs in the brain, the molecular mechanisms underlying their neurotoxicity remain poorly understood. There is increasing evidence that alteration of glycogen metabolism in the brain contributes to neurodegenerative processes. Interestingly, recent studies with N,N-diethyldithiocarbamate suggest that brain glycogen phosphorylase (bGP) and glycogen metabolism could be altered by DTCs. Here, we provide molecular and mechanistic evidence that bGP is a target of DTCs. To examine this system, we first tested thiram, a DTC pesticide known to display neurotoxic effects, observing that it can react rapidly with bGP and readily inhibits its glycogenolytic activity (kinact = 1.4 × 105 m-1 s-1). Using cysteine chemical labeling, mass spectrometry, and site-directed mutagenesis approaches, we show that thiram (and certain of its metabolites) alters the activity of bGP through the formation of an intramolecular disulfide bond (Cys318-Cys326), known to act as a redox switch that precludes the allosteric activation of bGP by AMP. Given the key role of glycogen metabolism in brain functions and neurodegeneration, impairment of the glycogenolytic activity of bGP by DTCs such as thiram may be a new mechanism by which certain DTCs exert their neurotoxic effects.
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Affiliation(s)
- Cécile Mathieu
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, France
| | - Linh-Chi Bui
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, France
| | - Emile Petit
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, France
| | - Iman Haddad
- ESPCI ParisTech, Université Paris Sciences et Lettres, Laboratoire de Spectrométrie de Masse Biologique et Protéomique, CNRS USR, 3149 Paris, France
| | - Onnik Agbulut
- the Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine, UMR CNRS 8256, Biological Adaptation and Ageing, 75005 Paris, France
| | - Joelle Vinh
- ESPCI ParisTech, Université Paris Sciences et Lettres, Laboratoire de Spectrométrie de Masse Biologique et Protéomique, CNRS USR, 3149 Paris, France
| | - Jean-Marie Dupret
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, France; UFR Sciences du Vivant, Université Paris Diderot, 75013 Paris, France
| | - Fernando Rodrigues-Lima
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, France; UFR Sciences du Vivant, Université Paris Diderot, 75013 Paris, France.
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18
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Mathieu C, Duval R, Cocaign A, Petit E, Bui LC, Haddad I, Vinh J, Etchebest C, Dupret JM, Rodrigues-Lima F. An Isozyme-specific Redox Switch in Human Brain Glycogen Phosphorylase Modulates Its Allosteric Activation by AMP. J Biol Chem 2016; 291:23842-23853. [PMID: 27660393 DOI: 10.1074/jbc.m116.757062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Brain glycogen and its metabolism are increasingly recognized as major players in brain functions. Moreover, alteration of glycogen metabolism in the brain contributes to neurodegenerative processes. In the brain, both muscle and brain glycogen phosphorylase isozymes regulate glycogen mobilization. However, given their distinct regulatory features, these two isozymes could confer distinct metabolic functions of glycogen in brain. Interestingly, recent proteomics studies have identified isozyme-specific reactive cysteine residues in brain glycogen phosphorylase (bGP). In this study, we show that the activity of human bGP is redox-regulated through the formation of a disulfide bond involving a highly reactive cysteine unique to the bGP isozyme. We found that this disulfide bond acts as a redox switch that precludes the allosteric activation of the enzyme by AMP without affecting its activation by phosphorylation. This unique regulatory feature of bGP sheds new light on the isoform-specific regulation of glycogen phosphorylase and glycogen metabolism.
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Affiliation(s)
- Cécile Mathieu
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris
| | - Romain Duval
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris
| | - Angélique Cocaign
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris
| | - Emile Petit
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris
| | - Linh-Chi Bui
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris
| | - Iman Haddad
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, F75231 Paris cedex 05, France
| | - Joelle Vinh
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, F75231 Paris cedex 05, France
| | - Catherine Etchebest
- INSERM, UMR S1134, Université Paris Diderot, F-75015 Paris.,Université Paris Diderot, Sorbonne Paris Cité, F-75013 Paris.,Institut National de la Transfusion Sanguine (INTS), 75015 Paris.,GR-Ex, Laboratoire d'excellence, 75015 Paris, and.,UFR Sciences du Vivant, Université Paris Diderot, 75013 Paris, France
| | - Jean-Marie Dupret
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris.,UFR Sciences du Vivant, Université Paris Diderot, 75013 Paris, France
| | - Fernando Rodrigues-Lima
- From the Université Paris Diderot, Sorbonne Paris Cité, Unité BFA, CNRS UMR 8251, 75013 Paris, .,UFR Sciences du Vivant, Université Paris Diderot, 75013 Paris, France
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19
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Qiao Q, Le Manach S, Sotton B, Huet H, Duvernois-Berthet E, Paris A, Duval C, Ponger L, Marie A, Blond A, Mathéron L, Vinh J, Bolbach G, Djediat C, Bernard C, Edery M, Marie B. Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach. Sci Rep 2016; 6:32459. [PMID: 27561897 PMCID: PMC5000296 DOI: 10.1038/srep32459] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/09/2016] [Indexed: 02/05/2023] Open
Abstract
Sexual dimorphism describes the features that discriminate between the two sexes at various biological levels. Especially, during the reproductive phase, the liver is one of the most sexually dimorphic organs, because of different metabolic demands between the two sexes. The liver is a key organ that plays fundamental roles in various physiological processes, including digestion, energetic metabolism, xenobiotic detoxification, biosynthesis of serum proteins, and also in endocrine or immune response. The sex-dimorphism of the liver is particularly obvious in oviparous animals, as the female liver is the main organ for the synthesis of oocyte constituents. In this work, we are interested in identifying molecular sexual dimorphism in the liver of adult medaka fish and their sex-variation in response to hepatotoxic exposures. By developing an integrative approach combining histology and different high-throughput omic investigations (metabolomics, proteomics and transcriptomics), we were able to globally depict the strong sexual dimorphism that concerns various cellular and molecular processes of hepatocytes comprising protein synthesis, amino acid, lipid and polysaccharide metabolism, along with steroidogenesis and detoxification. The results of this work imply noticeable repercussions on the biology of oviparous organisms environmentally exposed to chemical or toxin issues.
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Affiliation(s)
- Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benoit Sotton
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, BioPôle Alfort, Maisons-Alfort, France
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN, Évolution des Régulations Endocriniennes, Sorbonne Universités, Muséum Nationale d'Histoire Naturelle, Paris, France
| | - Alain Paris
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Loïc Ponger
- UMR 7196 MNHN/CNRS, INSERM U1154, Sorbonne Universités, Museum National d'Histoire Naturelle, Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Alain Blond
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Joelle Vinh
- USR 3149 ESPCI/CNRS SMPB, Laboratory of Biological Mass Spectrometry and Proteomics, ESPCI Paris, PSL Research University, Paris, France
| | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
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20
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Franza T, Delavenne E, Derré-Bobillot A, Juillard V, Boulay M, Demey E, Vinh J, Lamberet G, Gaudu P. A partial metabolic pathway enables group b streptococcus to overcome quinone deficiency in a host bacterial community. Mol Microbiol 2016; 102:81-91. [PMID: 27328751 DOI: 10.1111/mmi.13447] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 11/28/2022]
Abstract
Aerobic respiration metabolism in Group B Streptococcus (GBS) is activated by exogenous heme and menaquinone. This capacity enhances resistance of GBS to acid and oxidative stress and improves its survival. In this work, we discovered that GBS is able to respire in the presence of heme and 1,4-dihydroxy-2-naphthoic acid (DHNA). DHNA is a biosynthetic precursor of demethylmenaquinone (DMK) in many bacterial species. A GBS gene (gbs1789) encodes a homolog of the MenA 1,4-dihydroxy-2-naphthoate prenyltransferase enzyme, involved in the synthesis of demethylmenaquinone. In this study, we showed that gbs1789 is involved in the biosynthesis of long-chain demethylmenaquinones (DMK-10). The Δgbs1789 mutant cannot respire in the presence of heme and DHNA, indicating that endogenously synthesized DMKs are cofactors of the GBS respiratory chain. We also found that isoprenoid side chains from GBS DMKs are produced by the protein encoded by the gbs1783 gene, since this gene can complement an Escherichia coli ispB mutant defective for isoprenoids chain synthesis. In the gut or vaginal microbiote, where interspecies metabolite exchanges occur, this partial DMK biosynthetic pathway can be important for GBS respiration and survival in different niches.
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Affiliation(s)
- Thierry Franza
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France.
| | - Emilie Delavenne
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Aurélie Derré-Bobillot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Vincent Juillard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Mylène Boulay
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | | | - Joelle Vinh
- ESPCI Paris, SMBP USR3149 CNRS, Paris, F-75005, France
| | - Gilles Lamberet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Philippe Gaudu
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
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Chaze T, Hornez L, Chambon C, Haddad I, Vinh J, Peyrat JP, Benderitter M, Guipaud O. Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation. Proteomes 2013; 1:40-69. [PMID: 28250398 PMCID: PMC5302747 DOI: 10.3390/proteomes1020040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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: 05/23/2013] [Revised: 06/28/2013] [Accepted: 07/02/2013] [Indexed: 02/05/2023] Open
Abstract
The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes.
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Affiliation(s)
- Thibault Chaze
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-HOM, SRBE, LRTE, 31 avenue de la Division Leclerc, Fontenay-aux-Roses 92260, France.
| | - Louis Hornez
- Laboratoire d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, 3 rue Frédéric Combemale, BP 307, Lille 59020, France.
| | - Christophe Chambon
- PFEM, Composante Protéomique, UR370, INRA, Saint-Genès Champanelle 63322, France.
| | - Iman Haddad
- Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, ESPCI, 10 rue Vauquelin, Paris 75005, France.
| | - Joelle Vinh
- Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, ESPCI, 10 rue Vauquelin, Paris 75005, France.
| | - Jean-Philippe Peyrat
- Laboratoire d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, 3 rue Frédéric Combemale, BP 307, Lille 59020, France.
| | - Marc Benderitter
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-HOM, SRBE, LRTE, 31 avenue de la Division Leclerc, Fontenay-aux-Roses 92260, France.
| | - Olivier Guipaud
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-HOM, SRBE, LRTE, 31 avenue de la Division Leclerc, Fontenay-aux-Roses 92260, France.
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Monet-Leprêtre M, Haddad I, Baron-Menguy C, Fouillot-Panchal M, Riani M, Domenga-Denier V, Dussaule C, Cognat E, Vinh J, Joutel A. Abnormal recruitment of extracellular matrix proteins by excess Notch3 ECD: a new pathomechanism in CADASIL. ACTA ACUST UNITED AC 2013; 136:1830-45. [PMID: 23649698 DOI: 10.1093/brain/awt092] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, or CADASIL, one of the most common inherited small vessel diseases of the brain, is characterized by a progressive loss of vascular smooth muscle cells and extracellular matrix accumulation. The disease is caused by highly stereotyped mutations within the extracellular domain of the NOTCH3 receptor (Notch3(ECD)) that result in an odd number of cysteine residues. While CADASIL-associated NOTCH3 mutations differentially affect NOTCH3 receptor function and activity, they all are associated with early accumulation of Notch3(ECD)-containing aggregates in small vessels. We still lack mechanistic explanation to link NOTCH3 mutations with small vessel pathology. Herein, we hypothesized that excess Notch3(ECD) could recruit and sequester functionally important proteins within small vessels of the brain. We performed biochemical, nano-liquid chromatography-tandem mass spectrometry and immunohistochemical analyses, using cerebral and arterial tissue derived from patients with CADASIL and mouse models of CADASIL that exhibit vascular lesions in the end- and early-stage of the disease, respectively. Biochemical fractionation of brain and artery samples demonstrated that mutant Notch3(ECD) accumulates in disulphide cross-linked detergent-insoluble aggregates in mice and patients with CADASIL. Further proteomic and immunohistochemical analyses identified two functionally important extracellular matrix proteins, tissue inhibitor of metalloproteinases 3 (TIMP3) and vitronectin (VTN) that are sequestered into Notch3(ECD)-containing aggregates. Using cultured cells, we show that increased levels or aggregation of Notch3 enhances the formation of Notch3(ECD)-TIMP3 complex, promoting TIMP3 recruitment and accumulation. In turn, TIMP3 promotes complex formation including NOTCH3 and VTN. In vivo, brain vessels from mice and patients with CADASIL exhibit elevated levels of both insoluble cross-linked and soluble TIMP3 species. Moreover, reverse zymography assays show a significant elevation of TIMP3 activity in the brain vessels from mice and patients with CADASIL. Collectively, our findings lend support to a Notch3(ECD) cascade hypothesis in CADASIL disease pathology, which posits that aggregation/accumulation of Notch3(ECD) in the brain vessels is a central event, promoting the abnormal recruitment of functionally important extracellular matrix proteins that may ultimately cause multifactorial toxicity. Specifically, our results suggest a dysregulation of TIMP3 activity, which could contribute to mutant Notch3(ECD) toxicity by impairing extracellular matrix homeostasis in small vessels.
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Brezar V, Culina S, Østerbye T, Guillonneau F, Chiappetta G, Verdier Y, Vinh J, Wong FS, Buus S, Mallone R. T cells recognizing a peptide contaminant undetectable by mass spectrometry. PLoS One 2011; 6:e28866. [PMID: 22194932 PMCID: PMC3237501 DOI: 10.1371/journal.pone.0028866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/16/2011] [Indexed: 12/18/2022] Open
Abstract
Synthetic peptides are widely used in immunological research as epitopes to stimulate their cognate T cells. These preparations are never completely pure, but trace contaminants are commonly revealed by mass spectrometry quality controls. In an effort to characterize novel major histocompatibility complex (MHC) Class I-restricted β-cell epitopes in non-obese diabetic (NOD) mice, we identified islet-infiltrating CD8+ T cells recognizing a contaminating peptide. The amount of this contaminant was so small to be undetectable by direct mass spectrometry. Only after concentration by liquid chromatography, we observed a mass peak corresponding to an immunodominant islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)206-214 epitope described in the literature. Generation of CD8+ T-cell clones recognizing IGRP206-214 using a novel method confirmed the identity of the contaminant, further underlining the immunodominance of IGRP206-214. If left undetected, minute impurities in synthetic peptide preparations may thus give spurious results.
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Affiliation(s)
- Vedran Brezar
- INSERM, U986, DeAR Lab Avenir, Saint Vincent de Paul Hospital, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Slobodan Culina
- INSERM, U986, DeAR Lab Avenir, Saint Vincent de Paul Hospital, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Thomas Østerbye
- Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - François Guillonneau
- Université Paris Descartes, Sorbonne Paris Cité, 3P5 Proteomics Facility, Paris, France
| | - Giovanni Chiappetta
- Ecole Supérieure de Physique et de Chimie Industrielles de Paris, USR 3149 CNRS/ESPCI ParisTech, Paris, France
| | - Yann Verdier
- Ecole Supérieure de Physique et de Chimie Industrielles de Paris, USR 3149 CNRS/ESPCI ParisTech, Paris, France
| | - Joelle Vinh
- Ecole Supérieure de Physique et de Chimie Industrielles de Paris, USR 3149 CNRS/ESPCI ParisTech, Paris, France
| | - F. Susan Wong
- Centre for Endocrine and Diabetes Sciences, Cardiff University, Cardiff, United Kingdom
| | - Søren Buus
- Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roberto Mallone
- INSERM, U986, DeAR Lab Avenir, Saint Vincent de Paul Hospital, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Assistance Publique – Hopitaux de Paris, Hôpital Cochin et Hôtel Dieu, Service de Diabétologie, Paris, France
- * E-mail:
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Hesse AM, Ndiaye S, Vinh J. Reversed-phase HPLC and hyphenated analytical strategies for peptidomics. Methods Mol Biol 2011; 789:203-221. [PMID: 21922410 DOI: 10.1007/978-1-61779-310-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Peptide study and analysis widely involve liquid chromatography. Among the different strategies available, reversed-phase liquid chromatography (RP-HPLC) is one of the methods of choice to separate species in a nontargeted approach. The compounds are sorted according to their hydrophobicity, even though the experimental order of elution could change according to the nature of the mobile phase and the stationary phase. In our work, we have developed protocols to resolve hundred of peptidic species. To overcome the limitations of peak capacity of RP-HPLC alone, it has been coupled downstream to tandem mass spectrometry using two different ionization modes. To overcome the limitations of peak capacity of RP-HPLC MS/MS, it has been coupled upstream to strong cation exchange liquid chromatography. Multidimensional analysis allows for a deeper description of a sample because the limit of detection is often due to a lack of dynamic range of the detection itself rather than due to a lack of sensitivity. In this chapter, different protocols are presented. They should be considered as examples that could be used as starting point for new protocols optimization. Even if RP-HPLC is a universal peptide separation method, it should be optimized according to the specific characteristics of the peptide(s) of interest.
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Affiliation(s)
- Anne-Marie Hesse
- Laboratory of Biological Mass Spectrometry and Proteomics (SMBP), CNRS USR3149, ESPCI ParisTech, Paris, France
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25
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Abstract
The oxidation of the cysteine (Cys) residue to sulfenic (-S-OH), disulfide (-S-S-), or S-nitroso (S-NO) forms are thought to be a posttranslational modifications that regulate protein function. However, despite a few solid examples of its occurrence, thiol-redox regulation of protein function is still debated and often seen as an exotic phenomenon. A systematic and exhaustive characterization of all oxidized Cys residues, an experimental approach called redox proteomics or redoxome analysis, should help establish the physiological scope of Cys residue oxidation and give clues to its mechanisms. Redox proteomics still remains a technical challenge, mainly because of the labile nature of thiol-redox reactions and the lack of tools to directly detect the modified residues. Here we consider recent technical advances in redox proteomics, focusing on a gel-based fluorescent method and on the shotgun OxICAT technique.
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Affiliation(s)
- Giovanni Chiappetta
- Laboratoire Stress Oxydants et Cancer, DSV, IBITECS, CEA-Saclay, Gif-sur-Yvette, France
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26
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Hesse AM, Marcelo P, Rossier J, Vinh J. Simple and universal tool to remove on-line impurities in mono- or two-dimensional liquid chromatography–mass spectrometry analysis. J Chromatogr A 2008; 1189:175-82. [DOI: 10.1016/j.chroma.2007.12.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 12/11/2007] [Accepted: 12/19/2007] [Indexed: 11/15/2022]
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Huguet S, Vinh J, Johanet C, Samuel D, Gigou M, Zamfir O, Duclos-Vallée JC, Ballot E. Identification by proteomic tool of atypical anti-liver/kidney microsome autoantibodies targets in de novo autoimmune hepatitis after liver transplantation. Ann N Y Acad Sci 2007; 1109:345-57. [PMID: 17785324 DOI: 10.1196/annals.1398.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
De novo autoimmune hepatitis (AIH) occurs after liver transplantation for nonautoimmune disorders. Autoantibodies so-called atypical anti-liver/kidney microsome antibodies (LKMA) with an unusual liver/kidney cytoplasmic staining as judged by indirect immunofluorescence, can be detected in some patients' sera. Few studies investigated their molecular targets, and the aim of this work was to identify the atypical anti-LKMA targets by proteomic tool. This proteomic approach consisted of (a) two-dimensional gel electrophoresis of cytosolic and microsomal proteins obtained by differential centrifugations of rat liver and rat kidney, followed by (b) two-dimensional immunoblotting with sera of patients with de novo AIH (n = 8, including 2 with anti-LKMA antibodies) and then (c) identifications of interest spots performed by ion trap mass spectrometry. By this way several proteins at 25 kDa were unambiguously identified: isoforms of carbonic anhydrase III, members of different glutathione S-transferase (GST) families, and subunit beta1 of proteasome. This is the first report of proteasome and carbonic anhydrase III as autoantigens in de novo AIH. These results could lead to a better diagnosis of this disease using identified autoantigens in diagnostic tests, and strengthen proteomic approach as a new way of autoantigens investigation.
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Joanny G, Derout JL, Bréchemier-Baey D, Labas V, Vinh J, Régnier P, Hajnsdorf E. Polyadenylation of a functional mRNA controls gene expression in Escherichia coli. Nucleic Acids Res 2007; 35:2494-502. [PMID: 17395638 PMCID: PMC1885654 DOI: 10.1093/nar/gkm120] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although usually implicated in the stabilization of mRNAs in eukaryotes, polyadenylation was initially shown to destabilize RNA in bacteria. All the data are consistent with polyadenylation being part of a quality control process targeting folded RNA fragments and non-functional RNA molecules to degradation. We report here an example in Escherichia coli, where polyadenylation directly controls the level of expression of a gene by modulating the stability of a functional transcript. Inactivation of poly(A)polymerase I causes overexpression of glucosamine–6-phosphate synthase (GlmS) and both the accumulation and stabilization of the glmS transcript. Moreover, we show that the glmS mRNA results from the processing of the glmU-glmS cotranscript by RNase E. Interestingly, the glmU-glmS cotranscript and the mRNA fragment encoding GlmU only slightly accumulated in the absence of poly(A)polymerase, suggesting that the endonucleolytically generated glmS mRNA harbouring a 5′ monophosphate and a 3′ stable hairpin is highly susceptible to poly(A)-dependent degradation.
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Affiliation(s)
- Géraldine Joanny
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Jacques Le Derout
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Dominique Bréchemier-Baey
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Valérie Labas
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Joelle Vinh
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Philippe Régnier
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
| | - Eliane Hajnsdorf
- Régulation de l’Expression Génétique chez les Microorganismes, UPR CNRS n° 9073, conventionnée avec l’Université Paris 7—Denis Diderot, Paris, France and Neurobiologie et Diversité Cellulaire, UMR CNRS n° 7637, Paris, France
- *To whom correspondence should be addressed +33 1 58 41 51 26+33 1 58 41 50 20
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Abstract
A microfluidic poly(dimethylsiloxane) (PDMS) microdevice was realized, combining on-line protein electrophoretic separation, selection, and digestion of a protein of interest for identification by mass spectrometry. The system includes eight integrated valves and one micropump dedicated to control the flow operations. Myoglobin was successfully isolated from bovine serum albumin (BSA), then selected using integrated valves and digested in a rotary micromixer. Proteolytic peptides were recovered from the micromixer for protein identification. Total analysis from sample injection to protein identification is performed under 30 minutes, with samples of tens of nanolitres. The paper shows that PDMS technology can be successfully used for integrating complex preparation protocols of proteic samples prior to MS analysis.
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Affiliation(s)
- Arash Dodge
- Microfluidics, MEMS and Nanostructures Laboratory, ESPCI, 10 rue Vauquelin, 75231, Paris, France
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Even S, Pellegrini O, Zig L, Labas V, Vinh J, Bréchemmier-Baey D, Putzer H. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res 2005; 33:2141-52. [PMID: 15831787 PMCID: PMC1079966 DOI: 10.1093/nar/gki505] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many prokaryotic organisms lack an equivalent of RNase E, which plays a key role in mRNA degradation in Escherichia coli. In this paper, we report the purification and identification by mass spectrometry in Bacillus subtilis of two paralogous endoribonucleases, here named RNases J1 and J2, which share functional homologies with RNase E but no sequence similarity. Both enzymes are able to cleave the B.subtilis thrS leader at a site that can also be cleaved by E.coli RNase E. We have previously shown that cleavage at this site increases the stability of the downstream messenger. Moreover, RNases J1/J2 are sensitive to the 5′ phosphorylation state of the substrate in a site-specific manner. Orthologues of RNases J1/J2, which belong to the metallo-β-lactamase family, are evolutionarily conserved in many prokaryotic organisms, representing a new family of endoribonucleases. RNases J1/J2 appear to be implicated in regulatory processing/maturation of specific mRNAs, such as the T-box family members thrS and thrZ, but may also contribute to global mRNA degradation.
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Affiliation(s)
| | | | | | - Valerie Labas
- CNRS UMR7637, ESPCI10 rue Vauquelin 75005 Paris, France
| | - Joelle Vinh
- CNRS UMR7637, ESPCI10 rue Vauquelin 75005 Paris, France
| | | | - Harald Putzer
- To whom correspondence should be addressed. Tel: +33 1 58 41 51 27; Fax: +33 1 58 41 50 20;
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31
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Ballot E, Marcelo P, Labas V, Doan S, Zamfir O, Chaumeil C, Vinh J, Batellier L. Apport de l’analyse protéomique associant électrophorèse bi-dimensionnelle et spectrométrie de masse en lacrymologie. J Fr Ophtalmol 2004; 27:1141-5. [PMID: 15687924 DOI: 10.1016/s0181-5512(04)96283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE Identification of a lacrimal protein by proteomic analysis, i.e., two-dimensional electrophoresis and mass spectrometry. MATERIAL AND METHODS We studied the tears of a 25-year-old female with adrenal gland hyperplasia and hyperandrogenism complaining of chronic dryness and mild bilateral papillary hypertrophy. An allergologic workup was negative. Agarose electrophoresis of the tears showed a bilateral high level of rapid migrated proteins. RESULTS Dodecyl sulfate polyacrylamide gel electrophoresis of the tears from both eyes showed a highly stained 15-kDa band after Coomassie colloidal blue coloration compared to controls. On two-dimensional electrophoresis, this band focused on a single spot at pI 7.0. After tryptic digestion in gel, peptide mass fingerprint analysis by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry provided clear identification of cystatin SN. It is known that mRNA regulated by androgens and encoding glycoproteins homologous to human cystatin exists in the rat lacrimal gland. CONCLUSION We conclude that the hyperandrogenism of the patient may be cause for the hypersecretion of this cystatin SN, giving an explanation for the high level of rapid migrated proteins (lipocalins). This result provides a concrete example of the proteomic tool used to identify lacrimal proteins, still largely unknown.
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Affiliation(s)
- E Ballot
- Laboratoire de Biologie, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, 28, rue de Charenton, 75571 Paris cedex 12, France
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Abstract
The endothelium is a single layer of cells lining the inside face of all blood vessels. It constitutes a major metabolic organ which is critically involved in the generation and the regulation of multiple physiological and pathological processes such as coagulation, hemostasis, inflammation, atherosclerosis, angiogenesis and cancerous metastasis dissemination. In order to increase our knowledge about the protein content and the main biological pathways of human vascular endothelial cells, we have undertaken the proteomic analysis of the most explored present endothelial cell model, i.e. primocultures of human umbilical vein endothelial cells (HUVECs). Using low levels of protein loads (~ 30 nug), the association of two-dimensional electrophoresis with matrix-assisted laser desorption/ionization-time of flight mass spectrometry, liquid chromatography-tandem mass spectrometry and database interrogations allowed us to identify 53 proteins of suspected endothelial origin in quiescent HUVECs. Beside cytoskeletal proteins such as actin, tubulin, tropomyosin and vimentin, we identified various proteins more especially implicated in cellular motility and plasticity (e.g. cofilin, F-actin capping protein and prefoldin), in regulation of apoptosis and senescence (protease inhibitor 9, glucose related proteins, heat shock proteins, thioredoxin peroxidase, nucleophosmin) as well as other proteins implicated in coagulation (annexin V, high mobility group protein), antigen presentation (valosin containing protein and ubiquitin carboxyl terminal hydrolase isozyme L1) and enzymatic capabilities (glutathione-S-transferase, protein disulfide isomerases, lactate deshydrogenase). The presented annotated 2-D maps of HUVECs will be soon available on the web at http://www. huvec.com.
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Affiliation(s)
- Arnaud Bruneel
- Service de Biochimie A, Hôpital Saint-Antoine, AP-HP, Paris, France.
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Abstract
The Yap1 transcription factor regulates hydroperoxide homeostasis in S. cerevisiae. Yap1 is activated by oxidation when hydroperoxide levels increase. We show that Yap1 is not directly oxidized by hydroperoxide. We identified the glutathione peroxidase (GPx)-like enzyme Gpx3 as a second component of the pathway, serving the role of sensor and transducer of the hydroperoxide signal to Yap1. When oxidized by H2O2, Gpx3 Cys36 bridges Yap1 Cys598 by a disulfide bond. This intermolecular disulfide bond is then resolved into a Yap1 intramolecular disulfide bond, the activated form of the regulator. Thioredoxin turns off the pathway by reducing both sensor and regulator. These data reveal a redox-signaling function for a GPx-like enzyme and elucidate a eukaryotic hydroperoxide-sensing mechanism. Gpx3 is thus a hydroperoxide receptor and redox-transducer.
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Affiliation(s)
- Agnès Delaunay
- Laboratoire Stress Oxydants et Cancers, SBGM, DBJC, CEA-Saclay, 91191 Gif-sur-Yvette, Cedex, France
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Zito F, Vinh J, Popot JL, Finazzi G. Chimeric fusions of subunit IV and PetL in the b6f complex of Chlamydomonas reinhardtii: structural implications and consequences on state transitions. J Biol Chem 2002; 277:12446-55. [PMID: 11796719 DOI: 10.1074/jbc.m110914200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [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: 12/15/2022] Open
Abstract
The cytochrome b(6)f complex of Chlamydomonas reinhardtii contains four large subunits and at least three small ones, PetG, PetL, and PetM, whose role and location are unknown. Chimeric proteins have been constructed, in which the C terminus of subunit IV is fused to either one or the other of the two putative N termini of PetL. Biochemical and functional analysis of the chimeras together with mass spectrometry analysis of the wild-type (WT) complex led to the following conclusions: (i) neither a free subunit IV C terminus nor a free PetL N terminus is required for assembly of the b(6)f complex; (ii) the first AUG codon in the sequence of the gene petL is used for initiation; (iii) the N terminus of WT PetL lies in the lumen; (iv) in the WT complex, the N terminus of PetL and the C terminus of subunit IV are within reach of each other; (v) the purified b(6)f complex from C. reinhardtii contains an eighth, hitherto unrecognized subunit, PetN; and (vi) the ability to perform state transitions is lost in the chimeric mutants, although (vii) the Q-cycle is unaffected. A structural hypothesis is presented to account for this peculiar phenotype.
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Affiliation(s)
- Francesca Zito
- UMR 7099, CNRS and Université Paris-7, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris F-75005, France.
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Raveh S, Vinh J, Rossier J, Agou F, Véron M. Peptidic determinants and structural model of human NDP kinase B (Nm23-H2) bound to single-stranded DNA. Biochemistry 2001; 40:5882-93. [PMID: 11352723 DOI: 10.1021/bi001085j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [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: 11/30/2022]
Abstract
Isoform B of human NDP kinase (NDPK-B) was previously identified as a transcription factor stimulating in vitro and ex vivo the transcription of the c-myc oncogene, which involves this enzyme in carcinogenesis. We have studied the enzymatic properties of NDPK-B in the presence of several single-stranded oligonucleotides. We show that the oligonucleotides are competitive inhibitors of the catalytic activity, indicating that the active site acts as a binding template for the anchorage of the oligonucleotide. Furthermore, the presence of a guanine at the 3'-end of several different aptamers increases its affinity 10-fold. To define the surface of the protein contacting the DNA within the nucleoprotein complex, we used single nanosecond laser pulses as the cross-linking reagent and MALDI-TOF mass spectrometry to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Using 11-mer and 30-mer single-stranded oligonucleotides, the same three different nucleopeptides were identified after irradiation of the complexes, indicating a common binding mode for these two aptamers. Taken together, these results allowed us to propose a structural model of NDPK-B bound to single-stranded DNA.
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Affiliation(s)
- S Raveh
- Unité de Régulation Enzymatique des Activités Cellulaires, Institut Pasteur, CNRS-FRE 2364, 25-28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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Vinh J, Langridge JI, Bré MH, Levilliers N, Redeker V, Loyaux D, Rossier J. Structural characterization by tandem mass spectrometry of the posttranslational polyglycylation of tubulin. Biochemistry 1999; 38:3133-9. [PMID: 10074368 DOI: 10.1021/bi982304s] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [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: 02/01/2023]
Abstract
Polyglycylation is a posttranslational modification specific to tubulin. This modification was originally identified in highly stable microtubules from Paramecium cilia. As many as 34 posttranslationally added glycine residues have been located in the C-terminal domains of Paramecium alpha- and beta-tubulin. In this study, post source decay matrix-assisted laser desorption/ionization mass spectrometry (PSD MALDI MS) and electrospray ionization on a hybrid quadrupole orthogonal time-of-flight tandem mass spectrometer (ESI Q-TOF MS/MS) were both used to demonstrate that a single molecule of beta-tubulin, from either dynamic cytoplasmic microtubules or stable axonemal microtubules, can be glycylated on each of the last four C-terminal glutamate residues Glu437, Glu438, Glu439, and Glu441 in the sequence 427DATAEEEGEFEEEGEQ442. In both dynamic and stable microtubules the most abundant beta-tubulin isoform contains six posttranslationally added glycine residues: two glycine residues on both Glu437 and Glu438 and one glycine residue on both Glu439 and Glu441. The number and relative abundance of glycylated isoforms of beta-tubulin in both cytoplasmic and axonemal microtubules were compared by MALDI MS.1 The abundance of the major glycylated isoforms in axonemal tubulin decreases regularly with glycylation levels from 6 to 19 whereas it drops abruptly in cytoplasmic tubulin with glycylation levels from 6 to 9. However, the polyglycine chains are similarly distributed on the four C-terminal glutamate residues of cytoplasmic and axonemal tubulin. The polyglycylation results in bulky C-terminal domains with negatively charged surfaces, all surrounding the microtubular structure.
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Affiliation(s)
- J Vinh
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Laboratoire de Neurobiologie, CNRS UMR 7637, Paris, France.
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Bré MH, Redeker V, Vinh J, Rossier J, Levilliers N. Tubulin polyglycylation: differential posttranslational modification of dynamic cytoplasmic and stable axonemal microtubules in paramecium. Mol Biol Cell 1998; 9:2655-65. [PMID: 9725918 PMCID: PMC25538 DOI: 10.1091/mbc.9.9.2655] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [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: 11/11/2022] Open
Abstract
Polyglycylation, a posttranslational modification of tubulin, was discovered in the highly stable axonemal microtubules of Paramecium cilia where it involves the lateral linkage of up to 34 glycine units per tubulin subunit. The observation of this type of posttranslational modification mainly in axonemes raises the question as to its relationship with axonemal organization and with microtubule stability. This led us to investigate the glycylation status of cytoplasmic microtubules that correspond to the dynamic microtubules in Paramecium. Two anti-glycylated tubulin monoclonal antibodies (mAbs), TAP 952 and AXO 49, are shown here to exhibit different affinities toward mono- and polyglycylated synthetic tubulin peptides. Using immunoblotting and mass spectrometry, we show that cytoplasmic tubulin is glycylated. In contrast to the highly glycylated axonemal tubulin, which is recognized by the two mAbs, cytoplasmic tubulin reacts exclusively with TAP 952, and the alpha- and beta- tubulin subunits are modified by only 1-5 and 2-9 glycine units, respectively. Our analyses suggest that most of the cytoplasmic tubulin contains side chain lengths of 1 or 2 glycine units distributed on several glycylation sites. The subcellular partition of distinct polyglycylated tubulin isoforms between cytoplasmic and axonemal compartments implies the existence of regulatory mechanisms for glycylation. By following axonemal tubulin immunoreactivity with anti-glycylated tubulin mAbs upon incubation with a Paramecium cellular extract, the presence of a deglycylation enzyme is revealed in the cytoplasm of this organism. These observations establish that polyglycylation is reversible and indicate that, in vivo, an equilibrium between glycylating and deglycylating enzymes might be responsible for the length of the oligoglycine side chains of tubulin.
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Affiliation(s)
- M H Bré
- Laboratoire de Biologie Cellulaire 4, CNRS URA 2227, Université Paris-Sud, 91405 Orsay Cedex, France.
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Redeker V, Toullec JY, Vinh J, Rossier J, Soyez D. Combination of peptide profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and immunodetection on single glands or cells. Anal Chem 1998; 70:1805-11. [PMID: 9599581 DOI: 10.1021/ac971309c] [Citation(s) in RCA: 53] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The combination of two sensitive and powerful analytical techniques on the same biological sample was examined: (i) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which gives informative peptide profiling on complex samples such as organs or cells; (ii) immunological tools such as enzyme-linked immunosorbent assay (ELISA) and immunocytochemistry to probe for specific peptides in biological extracts or cells. The cellular expression of the two precursors of the hyperglycemic hormone (cHH) was analyzed in neurosecretory cells (30-micron diameter) from the crayfish Orconectes limosus. Neurohemal organs were used to optimize the sample preparation and to demonstrate that, after peptide fingerprinting by MALDI-TOF MS, the sample can be recovered from the MALDI plate for further immunological analysis by ELISA. It was also established that, after immunocytochemistry following 4% paraformaldehyde fixation of the organ, the stained tissue could be recovered for further MALDI-TOF MS analysis. This dual characterization was successfully scaled down to the level of a single crayfish neurosecretory cell. Direct peptide profiling by MALDI-TOF MS on a single cHH-producing cell previously identified by immunocytochemistry demonstrated that both procHH isoforms were expressed in each cell analyzed.
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Affiliation(s)
- V Redeker
- Laboratoire de Neurobiologie, Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, CNRS UMR 7637, France.
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Vinh J, Loyaux D, Redeker V, Rossier J. Sequencing branched peptides with CID/PSD MALDI-TOF in the low-picomole range: application to the structural study of the posttranslational polyglycylation of tubulin. Anal Chem 1997; 69:3979-85. [PMID: 9322434 DOI: 10.1021/ac970449j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [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: 02/05/2023]
Abstract
Sequencing conditions for postsource decay and collision-induced dissociation/postsource decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have been optimized to elucidate the structure of polyglycylation of tubulin. This posttranslational modification involves the linkage of multiple glycine residues through the gamma-carboxyl of glutamic acid residues in the carboxyl termini of the protein. Individual alpha- and beta-tubulin polypeptides contain respectively three and four potential glycylation sites. The sample preparation we used was the thin-layer preparation of the target specimen in the presence of alpha-cyano-4-hydroxycinnamic acid and nitrocellulose. The study of different synthetic polyglycylated peptides fragmentation (modified peptides with the linear sequence DATAEEEGEFEEEGEQ) shows that the peptides fragment regularly to form major fragments of b- and y-type ions with negligible side-chain fragmentation. The rules were applied to the structural elucidation of a Paramecium beta-tubulin hexaglycylated peptide available in the subpicomole range. Polyglycylation was identified on the last four glutamic acid residues.
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Affiliation(s)
- J Vinh
- Laboratoire de Neurobiologie, Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, CNRS URA 2054, France.
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