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11 results on '"Karima Chaoui"'

1. Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics

Author

Anne Gonzalez de Peredo, Marie Malissen, Bernard Malissen, Hervé Luche, Guillaume Voisinne, Hui Wang, Liaoxun Lu, Lichen Zhang, Odile Burlet-Schiltz, Laura Girard, Karima Chaoui, Marisa Goncalves Menoita, Romain Roncagalli, Yinming Liang, Kristof Kersse, Youcef Ounoughene, Frédéric Di Fiore, Julie Chaix, Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Wuhan University [China], Centre d'Immunophénomique (CIPHE), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Malissen, Bernard, Xinxiang Medical University, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
CD4-Positive T-Lymphocytes, 0301 basic medicine, [SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV]Life Sciences [q-bio], Transgene, Primary Cell Culture, Immunology, Receptors, Antigen, T-Cell, Mice, Transgenic, Article, Chromatography, Affinity, Mass Spectrometry, Mice, 03 medical and health sciences, 0302 clinical medicine, Antigen, Affinity chromatography, Protein Interaction Mapping, Animals, Immunology and Allergy, Protein Interaction Maps, Receptor, ComputingMilieux_MISCELLANEOUS, Chemistry, T-cell receptor, Acquired immune system, Cell biology, 030104 developmental biology, Cell culture, [SDV.IMM]Life Sciences [q-bio]/Immunology, Signal transduction, Signal Transduction, 030215 immunology
Abstract

The activation of T cells by the T cell antigen receptor (TCR) results in the formation of signaling protein complexes (signalosomes), the composition of which has not been analyzed at a systems level. Here, we isolated primary CD4+ T cells from 15 gene-targeted mice, each expressing one tagged form of a canonical protein of the TCR-signaling pathway. Using affinity purification coupled with mass spectrometry, we analyzed the composition and dynamics of the signalosomes assembling around each of the tagged proteins over 600 s of TCR engagement. We showed that the TCR signal-transduction network comprises at least 277 unique proteins involved in 366 high-confidence interactions, and that TCR signals diversify extensively at the level of the plasma membrane. Integrating the cellular abundance of the interacting proteins and their interaction stoichiometry provided a quantitative and contextual view of each documented interaction, permitting anticipation of whether ablation of a single interacting protein can impinge on the whole TCR signal-transduction network. Malissen and colleagues provide a quantitative systems-level analysis of 15 distinct signalosomes that form within minutes of TCR stimulation of primary CD4+ T cells.

Published
2019
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2. Bisubstrate-Type Chemical Probes Identify GRP94 as a Potential Target of Cytosine-Containing Adenosine Analogs

Author

Gabriela Chiosis, Marie Lopez, Odile Burlet-Schiltz, Fanny Assemat, Pengrong Yan, Dany Pechalrieu, Ludovic Halby, Sahil Sharma, Karima Chaoui, Marlène Marcellin, Paola B. Arimondo, Pharmacochimie de la Régulation Epigénétique du Cancer (ETaC), PIERRE FABRE-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Memorial Sloane Kettering Cancer Center [New York], Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), This work was supported by PlanCancer2014 France (no. EPIG201401), the Centre National pour la Recherche Scientifique (CNRS), the research center Pierre Fabre, the Région Occitanie, Toulouse Métropole, FEDER (Fonds Européens de Développement Régional) and the French Ministry of Research (Programme Investissement d’Avenir, Infrastructures Nationales en Biologie et Santé, Proteomics French Infrastructure project, ANR 10-INBS-08). This work was also funded in part by P01 CA186866 and P30 CA008748 (NCI Core Facility Grant)., ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, 0301 basic medicine, Adenosine, Proteome, Ultraviolet Rays, [SDV]Life Sciences [q-bio], Drug target, Chemical probe, 01 natural sciences, Biochemistry, Article, Cytosine, 03 medical and health sciences, chemistry.chemical_compound, Cell Line, Tumor, medicine, Humans, [CHIM]Chemical Sciences, Membrane Glycoproteins, 010405 organic chemistry, Chemistry, Extramural, Affinity Labels, General Medicine, 0104 chemical sciences, 3. Good health, 030104 developmental biology, Click chemistry, Molecular Medicine, Click Chemistry, medicine.drug
Abstract

International audience; We synthesized affinity-based chemical probes of cytosine-adenosine bisubstrate analogs and identified several potential targets by proteomic analysis. The validation of the proteomic analysis identified the chemical probe as a specific inhibitor of glucose-regulated protein 94 (GRP94), a potential drug target for several types of cancers. Therefore, as a result of the use of bisubstrate-type chemical probes and a chemical-biology methodology, this work opens the way to the development of a new family of GRP94 inhibitors that could potentially be of therapeutic interest.

Published
2020
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3. Human Bone Marrow Is Comprised of Adipocytes with Specific Lipid Metabolism

Author

Philippe Valet, Mohamed Moutahir, Camille Attané, Jason S. Iacovoni, Karima Chaoui, Jill Corre, Nicolas Reina, David Estève, Odile Schiltz, Catherine Muller, ORANGE, Colette, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Proteomics, 0301 basic medicine, medicine.medical_specialty, Proteome, Lipolysis, [SDV]Life Sciences [q-bio], Adipose tissue, General Biochemistry, Genetics and Molecular Biology, Cell Line, Mice, 03 medical and health sciences, chemistry.chemical_compound, Basal (phylogenetics), 0302 clinical medicine, Microscopy, Electron, Transmission, Bone Marrow, Internal medicine, Adipocytes, medicine, Animals, Humans, Protein Interaction Maps, lcsh:QH301-705.5, Cells, Cultured, Caloric Restriction, Chemistry, Cholesterol, Lipid metabolism, Metabolism, Lipid Metabolism, Monoacylglycerol Lipases, [SDV] Life Sciences [q-bio], Monoacylglycerol lipase, 030104 developmental biology, medicine.anatomical_structure, Endocrinology, lcsh:Biology (General), Bone marrow, 030217 neurology & neurosurgery
Abstract

Summary: Under caloric restriction, bone marrow adipocytes (BM-Ads) do not decrease in size compared to white adipocytes, suggesting they harbor unique metabolic properties. We compare human primary BM-Ads with paired subcutaneous adipocytes (SC-Ads) using proteomic and lipidomic approaches. We find that, although SC-Ads and BM-Ads share similar morphological features, they possess distinct lipid metabolism. Although BM-Ad shows enrichment in proteins involved in cholesterol metabolism, correlating with increased free cholesterol content, proteins involved in lipolysis were downregulated. In particular, monoacylglycerol lipase expression is strongly reduced in BM-Ads, leading to monoacylglycerol accumulation. Consequently, basal and induced lipolytic responses are absent in BM-Ads, affirming their differences in metabolic fitness upon caloric restriction. These specific metabolic features are not recapitulated in vitro using common protocols to differentiate bone marrow mesenchymal stem cells. Thus, contrary to classical SC-Ads, BM-Ads display a specific lipid metabolism, as they are devoid of lipolytic activity and exhibit a cholesterol-orientated metabolism. : Attané et al. show that, although human bone marrow adipocytes (BM-Ads) resemble classic white adipocytes on a morphological level, their lipid metabolism is highly specific. They are devoid of lipolytic activity, one of the main metabolic functions of white adipocytes, which explains why they behave like a preserved lipid source under energy-demanding conditions. Keywords: bone marrow adipocytes, cholesterol, lipolysis, monoacylglycerol lipase, proteomic, adipose tissue, bone marrow fat

Published
2020
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4. The costimulatory molecule CD226 signals through VAV1 to amplify TCR signals and promote IL-17 production by CD4 + T cells

Author

Julien Familiades, Guillaume Gaud, Abdelhadi Saoudi, Bernard Monsarrat, Romain Roncagalli, Karima Chaoui, Anne Gonzalez de Peredo, Bernard Malissen, Odile Burlet-Schiltz, Sahar Kassem, Isabelle Bernard, Céline Colacios, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), Centre de Recherches en Cancérologie de Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0301 basic medicine, VAV1, CD226, T cell, [SDV]Life Sciences [q-bio], medicine.disease_cause, Biochemistry, Autoimmunity, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Immune system, medicine, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Chemistry, T-cell receptor, Tyrosine phosphorylation, Cell Biology, 3. Good health, Cell biology, 030104 developmental biology, medicine.anatomical_structure, [SDV.IMM]Life Sciences [q-bio]/Immunology, Interleukin 17, 030215 immunology
Abstract

The activation of T cells requires the guanine nucleotide exchange factor VAV1. Using mice in which a tag for affinity purification was attached to endogenous VAV1 molecules, we analyzed by quantitative mass spectrometry the signaling complex that assembles around activated VAV1. Fifty VAV1-binding partners were identified, most of which had not been previously reported to participate in VAV1 signaling. Among these was CD226, a costimulatory molecule of immune cells. Engagement of CD226 induced the tyrosine phosphorylation of VAV1 and synergized with T cell receptor (TCR) signals to specifically enhance the production of interleukin-17 (IL-17) by primary human CD4(+) T cells. Moreover, co-engagement of the TCR and a risk variant of CD226 that is associated with autoimmunity (rs763361) further enhanced VAV1 activation and IL-17 production. Thus, our study reveals that a VAV1-based, synergistic cross-talk exists between the TCR and CD226 during both physiological and pathological T cell responses and provides a rational basis for targeting CD226 for the management of autoimmune diseases.

Published
2018
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5. The exerkine apelin reverses age-associated sarcopenia

Author

Cédric Dray, Vincent Mouly, Jerome N. Feige, Marco Pahor, Laura Lukjanenko, Philippe Valet, Simon Deleruyelle, Angèle Chopard, Ophélie Pereira, Umji Lee, Nancy Geoffre, Jean-Philippe Pradere, Karima Chaoui, Etienne Mouisel, Mathieu Vigneau, Fabien Pillard, Sonia Karaz, Matteo Cesari, Sophie Le Gonidec, Alizée Dortignac, Mylène Camus, Bruno Vellas, Allan F. Pagano, Sophie Guyonnet, Anne Bigot, Claire Vinel, Aurélie Batut, Odile Burlet-Schiltz, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées, Aging Dept, Nestle Inst Hlth Sci SA, Innovat Pk, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Institut de Myologie, Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Association française contre les myopathies (AFM-Téléthon)-Sorbonne Université (SU), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut des Technologies Avancées en sciences du Vivant (ITAV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Dynamique Musculaire et Métabolisme (DMEM), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM), Gérontopôle, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse], Coll Med, Inst Aging, University of Florida [Gainesville] (UF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Myologie, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse], U1048, Inst Malad Metabol & Cardiovasc, Institut National de la Santé et de la Recherche Médicale (INSERM), UM76, Inst Myol, UMR7215, UMRS 974, Université Pierre et Marie Curie (Paris 6), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), and University of Florida [Gainesville]

Subjects
0301 basic medicine, Aging, Sarcopenia, [SDV]Life Sciences [q-bio], Adipose tissue, physical activity, 0302 clinical medicine, regenerative capacity, Aged, 80 and over, satellite cells, Apelin Receptors, Muscle Weakness, Organelle Biogenesis, Ribosomal Protein S6 Kinases, 70-kDa, General Medicine, 3. Good health, Apelin, adipose tissue, medicine.anatomical_structure, medicine.symptom, Stem cell, Muscle contraction, Adult, medicine.medical_specialty, Adolescent, Satellite Cells, Skeletal Muscle, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Internal medicine, medicine, Animals, Humans, Regeneration, skeletal muscle, Muscle, Skeletal, Exercise, Aged, Muscle Cells, business.industry, Adenylate Kinase, Body Weight, Autophagy, Muscle weakness, Skeletal muscle, medicine.disease, Mice, Inbred C57BL, Kinetics, 030104 developmental biology, Endocrinology, Protein Biosynthesis, business, Proto-Oncogene Proteins c-akt, 030217 neurology & neurosurgery
Abstract

Sarcopenia, the degenerative loss of skeletal muscle mass, quality and strength, lacks early diagnostic tools and new therapeutic strategies to prevent the frailty-to-disability transition often responsible for the medical institutionalization of elderly individuals. Herein we report that production of the endogenous peptide apelin, induced by muscle contraction, is reduced in an age-dependent manner in humans and rodents and is positively associated with the beneficial effects of exercise in older persons. Mice deficient in either apelin or its receptor (APLNR) presented dramatic alterations in muscle function with increasing age. Various strategies that restored apelin signaling during aging further demonstrated that this peptide considerably enhanced muscle function by triggering mitochondriogenesis, autophagy and anti-inflammatory pathways in myofibers as well as enhancing the regenerative capacity by targeting muscle stem cells. Taken together, these findings revealed positive regulatory feedback between physical activity, apelin and muscle function and identified apelin both as a tool for diagnosis of early sarcopenia and as the target of an innovative pharmacological strategy to prevent age-associated muscle weakness and restore physical autonomy.

Published
2018
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6. Determination of differentially regulated proteins upon proteasome inhibition in AML cell lines by the combination of large-scale and targeted quantitative proteomics

Author

Mariette Matondo, Bernard Monsarrat, Odile Burlet-Schiltz, Marlène Marcellin, Marie-Pierre Bousquet-Dubouch, Karima Chaoui, Anne Gonzalez-de-Peredo, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, The work was supported in part by grants from the Région Midi‐Pyrénées, the 'Fondation pour la Recherche Médicale' (programme Grands Equipements), European Fonds (FEDER), Toulouse metropole, 'Fond Social Européen' (FSE) and the 'Ligue contre le cancer' Grants., We thank Dr. Darragh O'Brien from Institut Pasteur for the careful reading of this manuscript., We thank members of the group for insightful comments related to this work. We would like to thank David Bouyssié for MFPAQ software and technical support. We would like also to thank our collaborators Stephane Manenti, for discussion. We Thanks Pr. Dr. Ruedi Aebersold from IMSB (ETH Zurich) for allowing the SRM measurement on the TSQ Vantage., Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, MESH: Gene Ontology, Technology, Leupeptins, Cellular differentiation, Cell Cycle Proteins, Apoptosis, MESH: Cell Cycle / drug effects, Biochemistry, SILAC, MESH: Interleukins / metabolism, Bortezomib, MESH: Leukocytes / drug effects, Leukocytes, MESH: Interleukins / genetics, MESH: Apoptosis Regulatory Proteins / metabolism, Protein Isoforms, Proteasome inhibitor, Phosphorylation, MESH: Proteasome Endopeptidase Complex / drug effects, Targeted proteomics, Heat-Shock Proteins, MESH: Proteasome Endopeptidase Complex / metabolism, MESH: Computational Biology, Chemistry, Gene Expression Regulation, Leukemic, Cell Cycle, MESH: Apoptosis / drug effects, Cell Differentiation, Cell cycle, MESH: Phosphorylation / drug effects, MESH: Cell Cycle Proteins / metabolism, 3. Good health, Cell biology, MESH: Cell Cycle Proteins / genetics, MESH: Heat-Shock Proteins / genetics, Proteasome Inhibitors, medicine.drug, Research Article, Signal Transduction, MESH: Cell Differentiation, Proteasome Endopeptidase Complex, MESH: Cell Line, Tumor, Quantitative proteomics, MESH: Tumor Suppressor Protein p53 / metabolism, MESH: Protein Isoforms / genetics, MESH: Acetylcysteine / pharmacology, MESH: Molecular Sequence Annotation, MESH: Apoptosis Regulatory Proteins / genetics, MESH: Transcription Factors / genetics, MESH: Protein Isoforms / metabolism, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Leukocytes / pathology, Heat shock protein, Cell Line, Tumor, medicine, MESH: Acetylcysteine / analogs & derivatives, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cell Cycle Protein, Molecular Biology, MESH: Proteasome Inhibitors / pharmacology, MESH: Transcription Factors / metabolism, MESH: Humans, MESH: Leupeptins / pharmacology, Gene Expression Profiling, Interleukins, Computational Biology, Molecular Sequence Annotation, MESH: Bortezomib / pharmacology, MESH: Tumor Suppressor Protein p53 / genetics, MESH: Heat-Shock Proteins / metabolism, MESH: Leukocytes / metabolism, Acetylcysteine, 030104 developmental biology, Gene Ontology, Proteasome, MESH: Gene Expression Regulation, Leukemic / drug effects, Tumor Suppressor Protein p53, Apoptosis Regulatory Proteins, Human acute myeloid leukemia (AML) cells, Transcription Factors
Abstract

International audience; The ubiquitin-proteasome pathway (UPP) plays a critical role in the degradation of proteins implicated in cell cycle control, signal transduction, DNA damage response, apoptosis and immune response. Proteasome inhibitors can inhibit the growth of a broad spectrum of human cancer cells by altering the balance of intracellular proteins. However, the targets of these compounds in acute myeloid leukemia (AML) cells have not been fully characterized. Herein, we combined large-scale quantitative analysis by SILAC-MS and targeted quantitative proteomic analysis in order to identify proteins regulated upon proteasome inhibition in two AML cell lines displaying different stages of maturation: immature KG1a cells and mature U937 cells. In-depth data analysis enabled accurate quantification of more than 7000 proteins in these two cell lines. Several candidates were validated by selected reaction monitoring (SRM) measurements in a large number of samples. Despite the broad range of proteins known to be affected by proteasome inhibition, such as heat shock (HSP) and cell cycle proteins, our analysis identified new differentially regulated proteins, including IL-32, MORF family mortality factors and apoptosis inducing factor SIVA, a target of p53. It could explain why proteasome inhibitors induce stronger apoptotic responses in immature AML cells.

Published
2017
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7. Proteomic Analysis of Regulatory T Cells Reveals the Importance of Themis1 in the Control of Their Suppressive Function

Author

Olivier Andreoletti, Odile Burlet-Schiltz, Marlène Marcellin, Renaud Lesourne, Marie Locard-Paulet, Fanny Duguet, Isabelle Bernard, Abdelhadi Saoudi, Karima Chaoui, Anne Gonzalez de Peredo, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Institut National de la Santé et de la Recherche Médicale (INSERM), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centre de Physiopathologie Toulouse Purpan (CPTP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetically modified mouse, Proteomics, Adaptive immunology, Immunology, Médecine humaine et pathologie, chemical and pharmacologic phenomena, Biology, Biochemistry, T-Lymphocytes, Regulatory, Analytical Chemistry, Flow cytometry, Immune tolerance, 03 medical and health sciences, Mice, In vivo, Tandem Mass Spectrometry, Biologie animale, Immunologie, medicine, Immune Tolerance, Animals, Humans, Molecular Biology, Animal biology, medicine.diagnostic_test, Research, [SDV.BA]Life Sciences [q-bio]/Animal biology, Proteins, hemic and immune systems, T lymphocyte, Flow Cytometry, Inflammatory Bowel Diseases, In vitro, Cell biology, Mice, Inbred C57BL, Immunité adaptative, Disease Models, Animal, 030104 developmental biology, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Intercellular Signaling Peptides and Proteins, [SDV.IMM]Life Sciences [q-bio]/Immunology, Human health and pathology, Function (biology), [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Chromatography, Liquid
Abstract

Regulatory T cells (Treg) represent a minor subpopulation of T lymphocytes that is crucial for the maintenance of immune homeostasis. Here, we present a large-scale quantitative mass spectrometry study that defines a specific proteomic "signature" of Treg. Treg and conventional T lymphocyte (Tconv) subpopulations were sorted by flow cytometry and subjected to global proteomic analysis by single-run nanoLC-MS/MS on a fast-sequencing Q-Exactive mass spectrometer. Besides "historical" proteins that characterize Treg, our study identified numerous new proteins that are up- or downregulated in Treg versus Tconv. We focused on Themis1, a protein particularly under-represented in Treg, and recently described as being involved in the pathogenesis of immune diseases. Using a transgenic mouse model overexpressing Themis1, we provided in vivo and in vitro evidence of its importance for Treg suppressive functions, in an animal model of inflammatory bowel disease and in coculture assays. We showed that this enhanced suppressive activity in vitro is associated with an accumulation of Tregs. Thus, our study highlights the usefulness of label free quantitative methods to better characterize the Treg cell lineage and demonstrates the potential role of Themis1 in the suppressive functions of these cells.

Published
2017
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8. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update

Author

Yves Vandenbrouck, Marlène Marcellin, Thomas Fréour, Anne-Marie Hesse, Karima Chaoui, Christine Carapito, Christophe Bruley, Anne Gonzalez de Peredo, Karine Rondel, Emmanuelle Mouton-Barbosa, Thibault Robin, Jérôme Garin, Charlotte Macron, Charles Pineau, Lydie Lane, Sarah Cianférani, Paula D. Duek, Loren Méar, Cecilia Lindskog, Myriam Ferro, Emmanuelle Com, Alain Gateau, Yohann Couté, Odile Burlet-Schiltz, Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Département de science des protéines humaines [Genève], Université de Genève = University of Geneva (UNIGE)-Faculté de médecine [Genève], Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Genève] (SIB), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Proteomics Core Facility (Protim), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Uppsala University, ANR-10-INBS-08, Agence Nationale de la Recherche, Conseil Régional de Bretagne, Biogenouest, ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Genève (UNIGE)-Faculté de médecine [Genève], Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®, Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Bertacchi Griffi, Nathalie, and Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID

Subjects
Male, Proteomics, 0301 basic medicine, human proteome project, Proteome, [SDV]Life Sciences [q-bio], Peptide, Computational biology, Biology, Bioinformatics, Biochemistry, 03 medical and health sciences, Expression pattern, Tandem Mass Spectrometry, Testis, Protein purification, Human proteome project, Humans, ddc:576, Databases, Protein, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 030102 biochemistry & molecular biology, NeXtProt, cilia, General Chemistry, data mining, bioinformatics, Spermatozoa, mass spectrometry proteomics, [SDV] Life Sciences [q-bio], 030104 developmental biology, chemistry, spermatozoon, immunohistochemistry, Human testis, missing proteins, Chromatography, Liquid
Abstract

The Chromosome-Centric Human Proteome Project aims to identify proteins classed as « missing » in the neXtProt knowledgebase. In this article, we present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using a range of protein extraction procedures and LC-MS/MS analysis, we detected a total of 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through a combination of LC-MS/MS and LC-PRM analysis, data mining and immunohistochemistry, we were able to confirm the expression of 206 missing proteins (PE2-4) in line with current HPP guidelines (version 2.0). Parallel Reaction Monitoring (PRM) acquisition combined with synthetic heavy labeled peptides was used to target 36 « one-hit wonder » candidates selected on the basis of prior PSM assessment. Of this subset of candidates, 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for a further 16 missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could potentially be valuable markers with applications in fertility assessment. Strong evidence was also found for the existence of 4 proteins labeled as "uncertain" (PE5); the status of these proteins should therefore be re-examined. Our results show how the use of a range of sample preparation techniques combined with MS-based analysis, expert knowledge and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the Chromosome-Centric Human Proteome Project, we hope the availability of these data will stimulate the continued exploration of the sperm proteome.

Published
2016
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9. Co‐recruitment analysis of the <scp>CBL</scp> and <scp>CBLB</scp> signalosomes in primary T cells identifies <scp>CD</scp> 5 as a key regulator of <scp>TCR</scp> ‐induced ubiquitylation

Author

Romain Roncagalli, Marie Malissen, Bernard Malissen, Antonio García-Blesa, Frédéric Di Fiore, Karima Chaoui, Odile Burlet-Schiltz, Guillaume Voisinne, Anne Gonzalez de Peredo, Elise Bergot, and Laura Girard

Subjects
0301 basic medicine, General Immunology and Microbiology, biology, Applied Mathematics, T-cell receptor, Regulator, General Biochemistry, Genetics and Molecular Biology, Cell biology, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Computational Theory and Mathematics, Ubiquitin, hemic and lymphatic diseases, 030220 oncology & carcinogenesis, biology.protein, CBLB, Signal transduction, CD5, General Agricultural and Biological Sciences, Receptor, Function (biology), Information Systems
Abstract

T-cell receptor (TCR) signaling is essential for the function of T cells and negatively regulated by the E3 ubiquitin–protein ligases CBL and CBLB. Here, we combined mouse genetics and affinity purification coupled to quantitative mass spectrometry to monitor the dynamics of the CBL and CBLB signaling complexes that assemble in normal T cells over 600 seconds of TCR stimulation. We identify most previously known CBL and CBLB interacting partners, as well as a majority of proteins that have not yet been implicated in those signaling complexes. We exploit correlations in protein association with CBL and CBLB as a function of time of TCR stimulation for predicting the occurrence of direct physical association between them. By combining co-recruitment analysis with biochemical analysis, we demonstrated that the CD5 transmem-brane receptor constitutes a key scaffold for CBL-and CBLB-mediated ubiquitylation following TCR engagement. Our results offer an integrated view of the CBL and CBLB signaling complexes induced by TCR stimulation and provide a molecular basis for their negative regulatory function in normal T cells.

Published
2016
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10. Benchmarking quantitative label-free LC–MS data processing workflows using a complex spiked proteomic standard dataset

Author

Marlène Marcellin, Sebastian Vaca, Anne-Marie Hesse, Karima Chaoui, Alain Van Dorssaeler, Christophe Bruley, Christine Schaeffer, Myriam Ferro, Emmanuelle Mouton-Barbosa, Agnès Hovasse, Claire Ramus, Jérôme Garin, Christine Carapito, Anne Gonzalez de Peredo, David Bouyssié, Sarah Cianférani, Yohann Couté, Odile Burlet-Schiltz, Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Spectrométrie de Masse BioOrgan [Université de Strasbourg], Université de Strasbourg (UNISTRA), Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC)

Subjects
0301 basic medicine, False discovery rate, proteomic standard, MS signal analysis, Proteome, Computer science, nanoLC-MS/MS, computational proteomics, Software Validation, Biophysics, computer.software_genre, Sensitivity and Specificity, Biochemistry, Mass Spectrometry, label-free quantification, Workflow, 03 medical and health sciences, Software, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Signal processing, Data processing, Ground truth, spectral counting, Staining and Labeling, business.industry, Reproducibility of Results, Benchmarking, Label-free quantification, 030104 developmental biology, Benchmark (computing), Data mining, business, computer, Chromatography, Liquid
Abstract

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods.Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods.

Published
2016
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11. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods

Author

Marlène Marcellin, David Bouyssié, Jérôme Garin, Christine Carapito, Odile Burlet-Schiltz, Anne Gonzalez de Peredo, Anne-Marie Hesse, Karima Chaoui, Agnès Hovasse, Alain Van Dorssaeler, Christophe Bruley, Emmanuelle Mouton-Barbosa, Yohann Couté, Myriam Ferro, Christine Schaeffer, Sarah Cianférani, Claire Ramus, Sebastian Vaca, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, False discovery rate, Data processing, Ground truth, Multidisciplinary, Computer science, business.industry, [SDV]Life Sciences [q-bio], Context (language use), lcsh:Computer applications to medicine. Medical informatics, computer.software_genre, Identifier, 03 medical and health sciences, 030104 developmental biology, Workflow, Software, ComputingMethodologies_PATTERNRECOGNITION, lcsh:R858-859.7, Spike (software development), Data mining, lcsh:Science (General), business, computer, lcsh:Q1-390, Data Article
Abstract

International audience; This data article describes a controlled, spiked proteomic dataset for which the “ground truth” of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.

Published
2015
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