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1. Platelets favor the outgrowth of established metastases

Author

Garcia-Leon, Maria J., Liboni, Cristina, Mittelheisser, Vincent, Bochler, Louis, Follain, Gautier, Mouriaux, Clarisse, Busnelli, Ignacio, Larnicol, Annabel, Colin, Florent, Peralta, Marina, Osmani, Naël, Gensbittel, Valentin, Bourdon, Catherine, Samaniego, Rafael, Pichot, Angélique, Paul, Nicodème, Molitor, Anne, Carapito, Raphaël, Jandrot-Perrus, Martine, Lefebvre, Olivier, Mangin, Pierre H., and Goetz, Jacky G.

Published
2024
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2. Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia

Author

Schleiss, Cedric, Carapito, Raphael, Fornecker, Luc-Matthieu, Muller, Leslie, Paul, Nicodème, Tahar, Ouria, Pichot, Angelique, Tavian, Manuela, Nicolae, Alina, Miguet, Laurent, Mauvieux, Laurent, Herbrecht, Raoul, Cianferani, Sarah, Freund, Jean-Noel, Carapito, Christine, Maumy-Bertrand, Myriam, Bahram, Seiamak, Bertrand, Frederic, and Vallat, Laurent

Published
2021
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6. Tenascin‐C immobilizes infiltrating T lymphocytes through CXCL12 promoting breast cancer progression

Author

Murdamoothoo, Devadarssen, Sun, Zhen, Yilmaz, Alev, Riegel, Gilles, Abou‐Faycal, Chérine, Deligne, Claire, Velazquez‐Quesada, Ines, Erne, William, Nascimento, Marine, Mörgelin, Matthias, Cremel, Gérard, Paul, Nicodème, Carapito, Raphael, Veber, Romain, Dumortier, Hélène, Yuan, Jingping, Midwood, Kim S, Loustau, Thomas, and Orend, Gertraud

Published
2021
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7. Hemodynamic Forces Tune the Arrest, Adhesion, and Extravasation of Circulating Tumor Cells

Author

Follain, Gautier, Osmani, Naël, Azevedo, Ana Sofia, Allio, Guillaume, Mercier, Luc, Karreman, Matthia A., Solecki, Gergely, Garcia Leòn, Marìa Jesùs, Lefebvre, Olivier, Fekonja, Nina, Hille, Claudia, Chabannes, Vincent, Dollé, Guillaume, Metivet, Thibaut, Hovsepian, François Der, Prudhomme, Christophe, Pichot, Angélique, Paul, Nicodème, Carapito, Raphaël, Bahram, Siamak, Ruthensteiner, Bernhard, Kemmling, André, Siemonsen, Susanne, Schneider, Tanja, Fiehler, Jens, Glatzel, Markus, Winkler, Frank, Schwab, Yannick, Pantel, Klaus, Harlepp, Sébastien, and Goetz, Jacky G.

Published
2018
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9. Data from Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma

Author

Spenlé, Caroline, primary, Loustau, Thomas, primary, Murdamoothoo, Devadarssen, primary, Erne, William, primary, Beghelli-de la Forest Divonne, Stephanie, primary, Veber, Romain, primary, Petti, Luciana, primary, Bourdely, Pierre, primary, Mörgelin, Matthias, primary, Brauchle, Eva-Maria, primary, Cremel, Gérard, primary, Randrianarisoa, Vony, primary, Camara, Abdouramane, primary, Rekima, Samah, primary, Schaub, Sebastian, primary, Nouhen, Kelly, primary, Imhof, Thomas, primary, Hansen, Uwe, primary, Paul, Nicodème, primary, Carapito, Raphael, primary, Pythoud, Nicolas, primary, Hirschler, Aurélie, primary, Carapito, Christine, primary, Dumortier, Hélène, primary, Mueller, Christopher G., primary, Koch, Manuel, primary, Schenke-Layland, Katja, primary, Kon, Shigeyuki, primary, Sudaka, Anne, primary, Anjuère, Fabienne, primary, Van Obberghen-Schilling, Ellen, primary, and Orend, Gertraud, primary

Published
2023
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10. Supplementary Data from Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma

Author

Spenlé, Caroline, primary, Loustau, Thomas, primary, Murdamoothoo, Devadarssen, primary, Erne, William, primary, Beghelli-de la Forest Divonne, Stephanie, primary, Veber, Romain, primary, Petti, Luciana, primary, Bourdely, Pierre, primary, Mörgelin, Matthias, primary, Brauchle, Eva-Maria, primary, Cremel, Gérard, primary, Randrianarisoa, Vony, primary, Camara, Abdouramane, primary, Rekima, Samah, primary, Schaub, Sebastian, primary, Nouhen, Kelly, primary, Imhof, Thomas, primary, Hansen, Uwe, primary, Paul, Nicodème, primary, Carapito, Raphael, primary, Pythoud, Nicolas, primary, Hirschler, Aurélie, primary, Carapito, Christine, primary, Dumortier, Hélène, primary, Mueller, Christopher G., primary, Koch, Manuel, primary, Schenke-Layland, Katja, primary, Kon, Shigeyuki, primary, Sudaka, Anne, primary, Anjuère, Fabienne, primary, Van Obberghen-Schilling, Ellen, primary, and Orend, Gertraud, primary

Published
2023
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11. Supplementary Data from Matrix-Targeting Immunotherapy Controls Tumor Growth and Spread by Switching Macrophage Phenotype

Author

Deligne, Claire, primary, Murdamoothoo, Devadarssen, primary, Gammage, Anís N., primary, Gschwandtner, Martha, primary, Erne, William, primary, Loustau, Thomas, primary, Marzeda, Anna M., primary, Carapito, Raphael, primary, Paul, Nicodème, primary, Velazquez-Quesada, Inés, primary, Mazzier, Imogen, primary, Sun, Zhen, primary, Orend, Gertraud, primary, and Midwood, Kim S., primary

Published
2023
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12. Data from Matrix-Targeting Immunotherapy Controls Tumor Growth and Spread by Switching Macrophage Phenotype

Author

Deligne, Claire, primary, Murdamoothoo, Devadarssen, primary, Gammage, Anís N., primary, Gschwandtner, Martha, primary, Erne, William, primary, Loustau, Thomas, primary, Marzeda, Anna M., primary, Carapito, Raphael, primary, Paul, Nicodème, primary, Velazquez-Quesada, Inés, primary, Mazzier, Imogen, primary, Sun, Zhen, primary, Orend, Gertraud, primary, and Midwood, Kim S., primary

Published
2023
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13. Identification of early-induced broadly neutralizing activities against transmitted founder HIV strains

Author

Lucas, Julie, primary, Lin, Li-Yun, additional, Paul, Nicodème, additional, Laumond, Géraldine, additional, Klingler, Jéromine, additional, Schmidt, Sylvie, additional, Frappier, Julia, additional, Essat, Asma, additional, Meyer, Laurence, additional, Gordon, Alicia Castro, additional, Goujard, C.é.cile, additional, Bahram, Seiamak, additional, and Moog, Christiane, additional

Published
2022
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14. Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond–like features

Author

Carapito, Raphael, Konantz, Martina, Paillard, Catherine, Miao, Zhichao, Pichot, Angélique, Leduc, Magalie S., Yang, Yaping, Bergstrom, Katie L., Mahoney, Donald H., Shardy, Deborah L., Alsaleh, Ghada, Naegely, Lydie, Kolmer, Aline, Paul, Nicodème, Hanauer, Antoine, Rolli, Véronique, Müller, Joëlle S., Alghisi, Elisa, Sauteur, Loïc, Macquin, Cécile, Morlon, Aurore, Sancho, Consuelo Sebastia, Amati-Bonneau, Patrizia, Procaccio, Vincent, Mosca-Boidron, Anne-Laure, Marle, Nathalie, Osmani, Naël, Lefebvre, Olivier, Goetz, Jacky G., Unal, Sule, Akarsu, Nurten A., Radosavljevic, Mirjana, Chenard, Marie-Pierre, Rialland, Fanny, Grain, Audrey, Béné, Marie-Christine, Eveillard, Marion, Vincent, Marie, Guy, Julien, Faivre, Laurence, Thauvin-Robinet, Christel, Thevenon, Julien, Myers, Kasiani, Fleming, Mark D., Shimamura, Akiko, Bottollier-Lemallaz, Elodie, Westhof, Eric, Lengerke, Claudia, Isidor, Bertrand, and Bahram, Seiamak

Published
2017
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16. Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort

Author

Carapito, Raphael, primary, Li, Richard, additional, Helms, Julie, additional, Carapito, Christine, additional, Gujja, Sharvari, additional, Rolli, Véronique, additional, Guimaraes, Raony, additional, Malagon-Lopez, Jose, additional, Spinnhirny, Perrine, additional, Lederle, Alexandre, additional, Mohseninia, Razieh, additional, Hirschler, Aurélie, additional, Muller, Leslie, additional, Bastard, Paul, additional, Gervais, Adrian, additional, Zhang, Qian, additional, Danion, François, additional, Ruch, Yvon, additional, Schenck, Maleka, additional, Collange, Olivier, additional, Chamaraux-Tran, Thiên-Nga, additional, Molitor, Anne, additional, Pichot, Angélique, additional, Bernard, Alice, additional, Tahar, Ouria, additional, Bibi-Triki, Sabrina, additional, Wu, Haiguo, additional, Paul, Nicodème, additional, Mayeur, Sylvain, additional, Larnicol, Annabel, additional, Laumond, Géraldine, additional, Frappier, Julia, additional, Schmidt, Sylvie, additional, Hanauer, Antoine, additional, Macquin, Cécile, additional, Stemmelen, Tristan, additional, Simons, Michael, additional, Mariette, Xavier, additional, Hermine, Olivier, additional, Fafi-Kremer, Samira, additional, Goichot, Bernard, additional, Drenou, Bernard, additional, Kuteifan, Khaldoun, additional, Pottecher, Julien, additional, Mertes, Paul-Michel, additional, Kailasan, Shweta, additional, Aman, M. Javad, additional, Pin, Elisa, additional, Nilsson, Peter, additional, Thomas, Anne, additional, Viari, Alain, additional, Sanlaville, Damien, additional, Schneider, Francis, additional, Sibilia, Jean, additional, Tharaux, Pierre-Louis, additional, Casanova, Jean-Laurent, additional, Hansmann, Yves, additional, Lidar, Daniel, additional, Radosavljevic, Mirjana, additional, Gulcher, Jeffrey R., additional, Meziani, Ferhat, additional, Moog, Christiane, additional, Chittenden, Thomas W., additional, and Bahram, Seiamak, additional

Published
2022
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17. A mouse model of MSU-induced acute inflammation in vivo suggests imiquimod-dependent targeting of Il-1β as relevant therapy for gout patients

Author

Mariotte, Alexandre, De Cauwer, Aurore, Po, Chrystelle, Abou-Faycal, Chérine, Pichot, Angélique, Paul, Nicodème, Aouadi, Ismael, Carapito, Raphael, Frisch, Benoit, Macquin, Cécile, Chatelus, Emmanuel, Sibilia, Jean, Armspach, Jean-Paul, Bahram, Seiamak, and Georgel, Philippe

Subjects
Inflammation, Mice, Knockout, Imiquimod, Gout, Administration, Topical, Injections, Subcutaneous, Interleukin-1beta, Magnetic Resonance Imaging, Antioxidants, Uric Acid, Disease Models, Animal, Mice, Adjuvants, Immunologic, Acute Disease, Animals, Cytokines, Research Paper
Abstract

Rationale: The role of Monosodium Urate (MSU) crystals in gout pathophysiology is well described, as is the major impact of IL-1β in the inflammatory reaction that constitutes the hallmark of the disease. However, despite the discovery of the NLRP3 inflammasome and its role as a Pattern Recognition Receptor linking the detection of a danger signal (MSU) to IL-1β secretion in vitro, the precise mechanisms leading to joint inflammation in gout patients are still poorly understood. Methods: Acute urate crystal inflammation was obtained by subcutaneous injections of MSU crystals in mice. Symptoms were followed by scoring, cytokine quantification by ELISA and western blot, gene expression by RT-qPCR and RNAseq; Magnetic Resonance Imaging was also used to assess inflammation. Results: We provide an extensive clinical, biological and molecular characterization of an acute uratic inflammation mouse model which accurately mimics human gout. We report the efficacy of topical imiquimod treatment and its impact on Interferon-dependent down modulation of Il-1β gene expression in this experimental model. Conclusion: Our work reveals several key features of MSU-dependent inflammation and identifies novel therapeutic opportunities for gout patients.

Published
2020

21. Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes

Author

Spenlé, Caroline, primary, Loustau, Thomas, additional, Burckel, Hélène, additional, Riegel, Gilles, additional, Abou Faycal, Chérine, additional, Li, Chengbei, additional, Yilmaz, Alev, additional, Petti, Luciana, additional, Steinbach, Fanny, additional, Ahowesso, Constance, additional, Jost, Camille, additional, Paul, Nicodème, additional, Carapito, Raphael, additional, Noël, Georges, additional, Anjuère, Fabienne, additional, Salomé, Nathalie, additional, and Orend, Gertraud, additional

Published
2021
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22. Identification of driver genes for severe forms of COVID-19 in a deeply phenotyped young patient cohort

Author

Carapito, Raphael, primary, Li, Richard, additional, Helms, Julie, additional, Carapito, Christine, additional, Gujja, Sharvari, additional, Rolli, Véronique, additional, Guimaraes, Raony, additional, Malagon-Lopez, Jose, additional, Spinnhirny, Perrine, additional, Mohseninia, Razieh, additional, Hirschler, Aurélie, additional, Muller, Leslie, additional, Bastard, Paul, additional, Gervais, Adrian, additional, Zhang, Qian, additional, Danion, François, additional, Ruch, Yvon, additional, Schenck-Dhif, Maleka, additional, Collange, Olivier, additional, Chamaraux-Tran, Thiên-Nga, additional, Molitor, Anne, additional, Pichot, Angélique, additional, Bernard, Alice, additional, Tahar, Ouria, additional, Bibi-Triki, Sabrina, additional, Wu, Haiguo, additional, Paul, Nicodème, additional, Mayeur, Sylvain, additional, Larnicol, Annabel, additional, Laumond, Géraldine, additional, Frappier, Julia, additional, Schmidt, Sylvie, additional, Hanauer, Antoine, additional, Macquin, Cécile, additional, Stemmelen, Tristan, additional, Simons, Michael, additional, Mariette, Xavier, additional, Hermine, Olivier, additional, Fafi-Kremer, Samira, additional, Goichot, Bernard, additional, Drenou, Bernard, additional, Kuteifan, Khaldoun, additional, Pottecher, Julien, additional, Mertes, Paul-Michel, additional, Kailasan, Shweta, additional, Aman, M. Javad, additional, Pin, Elisa, additional, Nilsson, Peter, additional, Thomas, Anne, additional, Viari, Alain, additional, Sanlaville, Damien, additional, Schneider, Francis, additional, Sibilia, Jean, additional, Tharaux, Pierre-Louis, additional, Casanova, Jean-Laurent, additional, Hansmann, Yves, additional, Lidar, Daniel, additional, Radosavljevic, Mirjana, additional, Gulcher, Jeffrey R., additional, Meziani, Ferhat, additional, Moog, Christiane, additional, Chittenden, Thomas W., additional, and Bahram, Seiamak, additional

Published
2021
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23. NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation and hyperinflammation Running title: NCKAP1L deficiency

Author

Castro, Carla, Rosenzwajg, Michelle, Carapito, Raphael, Shahrooei, Mohammad, Konantz, Martina, Khan, Amjad, Miao, Zhichao, Gross, Miriam, Tranchant, Thibaud, Radosavljevic, Mirjana, Paul, Nicodème, Stemmelen, Tristan, Pitoiset, Fabien, Hirschler, Aurélie, Nespola, Benoit, Molitor, Anne, Rolli, Véronique, Pichot, Angélique, Faletti, Laura, Rinaldi, Bruno, Friant, Sylvie, Mednikov, Mark, Karauzum, Hatice, Javad Aman, M, CARAPITO, Christine, Lengerke, Claudia, Ziaee, Vahid, Eyaid, Wafaa, Ehl, Stephan, Alroqi, Fayhan, Parvaneh, Nima, Bahram, Seiamak, Centre d’Investigation Clinique intégré en Biothérapies et immunologie [AP-HP pitié-salpêtrière, Paris] (CIC-BTi), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Equipe Plate-forme GENOMAX (Inserm U1109), Fédération Hospitalo-Universitaire OMICARE-Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA)-Université de Strasbourg (UNISTRA)-Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Engineering and Technology [Peshawar] (UET), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), 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
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience

Published
2020
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24. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

Author

Domingo-Calap, Pilar, Schubert, Benjamin, Joly, Mélanie, Solis, Morgane, Untrau, Meiggie, Carapito, Raphael, Georgel, Philippe, Caillard, Sophie, Fafi-Kremer, Samira, Paul, Nicodème, Kohlbacher, Oliver, González-Candelas, Fernando, Bahram, Seiamak, Agencia Estatal de Investigación (España), Agence Nationale de la Recherche (France), Institut National de la Santé et de la Recherche Médicale (France), Institut Universitaire de France, Université de Strasbourg, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat Valenciana, Domingo-Calap, Pilar [0000-0003-2829-8809], Schubert, Benjamin [0000-0003-3412-1102], Joly, Mélanie [0000-0003-0316-5065], Untrau, Meiggie [0000-0002-0054-8741], Georgel, Philippe [0000-0001-6853-7080], Paul, Nicodème [0000-0003-4680-3012], Kohlbacher, Oliver [0000-0003-1739-4598], González-Candelas, Fernando [0000-0002-0879-5798], Bahram, Seiamak [0000-0002-6928-9952], Domingo-Calap, Pilar, Schubert, Benjamin, Joly, Mélanie, Untrau, Meiggie, Georgel, Philippe, Paul, Nicodème, Kohlbacher, Oliver, González-Candelas, Fernando, and Bahram, Seiamak

Subjects
RNA viruses, 0301 basic medicine, Mutation rate, Physiology, viruses, Urine, Pathology and Laboratory Medicine, medicine.disease_cause, Biochemistry, Medicine and Health Sciences, Biology (General), Amino Acids, Genome Evolution, Phylogeny, Data Management, Mutation, Organic Compounds, High-Throughput Nucleotide Sequencing, Phylogenetic Analysis, DNA virus, Genomics, Body Fluids, BK virus, Phylogenetics, Chemistry, Medical Microbiology, Viral Pathogens, Viral evolution, Viruses, Physical Sciences, Evolutionary Rate, Pathogens, Anatomy, Research Article, Computer and Information Sciences, Evolutionary Processes, QH301-705.5, Immunology, Genome, Viral, HLA-C Antigens, Biology, Microbiology, Molecular Evolution, Viral Evolution, Virus, Deep sequencing, 03 medical and health sciences, Virology, Genetics, medicine, Humans, Evolutionary Systematics, Microbial Pathogens, Molecular Biology, Taxonomy, Evolutionary Biology, Polyomavirus Infections, Organic Chemistry, Organisms, Chemical Compounds, Biology and Life Sciences, Computational Biology, Proteins, Organ Transplantation, RC581-607, 030112 virology, Organismal Evolution, Peptide Fragments, Polyomaviruses, 030104 developmental biology, Amino Acid Substitution, BK Virus, Microbial Evolution, Parasitology, Immunologic diseases. Allergy, DNA viruses
Abstract

Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus., This work has been published under the framework of the Laboratoire d’Excellence (LABEX) TRANSPLANTEX [ANR-11-LABX0070_TRANSPLANTEX] and benefits from a funding from the French government, managed by the French National Research Agency (ANR) as part of the « Investments for the future » program (SB)(http://www.agence-nationale-recherche.fr/investissementsdavenir/). Additional support was received from the Strasbourg High Throughput Next Generation Sequencing facility (GENOMAX) (SB)(no URL available), the Institut National de la Sante et de la Recherche Medicale (INSERM)(SB) (www.inserm.fr), Initiative d’Excellence (IDEX) fund of the University of Strasbourg (UNISTRA)(SB) (www.unistra.fr), the Institut Universitaire de France (IUF)(SB)(http://www.iufrance.fr), projects BFU2014-58656R and BFU2017-89594R from Ministry of Economy and Competitiveness (MINECO; Spanish Government) (http://www.idi. mineco.gob.es)(FGC) and the project PROMETEO/2016/122 from the Generalitat Valenciana (FGC) (www.gva.es/).

Published
2018

25. Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes

Author

Ghoroghi, Shima, primary, Mary, Benjamin, additional, Larnicol, Annabel, additional, Asokan, Nandini, additional, Klein, Annick, additional, Osmani, Naël, additional, Busnelli, Ignacio, additional, Delalande, François, additional, Paul, Nicodème, additional, Halary, Sébastien, additional, Gros, Frédéric, additional, Fouillen, Laetitia, additional, Haeberle, Anne-Marie, additional, Royer, Cathy, additional, Spiegelhalter, Coralie, additional, André-Grégoire, Gwennan, additional, Mittelheisser, Vincent, additional, Detappe, Alexandre, additional, Murphy, Kendelle, additional, Timpson, Paul, additional, Carapito, Raphaël, additional, Blot-Chabaud, Marcel, additional, Gavard, Julie, additional, Carapito, Christine, additional, Vitale, Nicolas, additional, Lefebvre, Olivier, additional, Goetz, Jacky G, additional, and Hyenne, Vincent, additional

Published
2021
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26. Author response: Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes

Author

Ghoroghi, Shima, primary, Mary, Benjamin, additional, Larnicol, Annabel, additional, Asokan, Nandini, additional, Klein, Annick, additional, Osmani, Naël, additional, Busnelli, Ignacio, additional, Delalande, François, additional, Paul, Nicodème, additional, Halary, Sébastien, additional, Gros, Frédéric, additional, Fouillen, Laetitia, additional, Haeberle, Anne-Marie, additional, Royer, Cathy, additional, Spiegelhalter, Coralie, additional, André-Grégoire, Gwennan, additional, Mittelheisser, Vincent, additional, Detappe, Alexandre, additional, Murphy, Kendelle, additional, Timpson, Paul, additional, Carapito, Raphaël, additional, Blot-Chabaud, Marcel, additional, Gavard, Julie, additional, Carapito, Christine, additional, Vitale, Nicolas, additional, Lefebvre, Olivier, additional, Goetz, Jacky G, additional, and Hyenne, Vincent, additional

Published
2020
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27. Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma

Author

Spenlé, Caroline, primary, Loustau, Thomas, additional, Murdamoothoo, Devadarssen, additional, Erne, William, additional, Beghelli-de la Forest Divonne, Stephanie, additional, Veber, Romain, additional, Petti, Luciana, additional, Bourdely, Pierre, additional, Mörgelin, Matthias, additional, Brauchle, Eva-Maria, additional, Cremel, Gérard, additional, Randrianarisoa, Vony, additional, Camara, Abdouramane, additional, Rekima, Samah, additional, Schaub, Sebastian, additional, Nouhen, Kelly, additional, Imhof, Thomas, additional, Hansen, Uwe, additional, Paul, Nicodème, additional, Carapito, Raphael, additional, Pythoud, Nicolas, additional, Hirschler, Aurélie, additional, Carapito, Christine, additional, Dumortier, Hélène, additional, Mueller, Christopher G., additional, Koch, Manuel, additional, Schenke-Layland, Katja, additional, Kon, Shigeyuki, additional, Sudaka, Anne, additional, Anjuère, Fabienne, additional, Van Obberghen-Schilling, Ellen, additional, and Orend, Gertraud, additional

Published
2020
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29. Matrix-Targeting Immunotherapy Controls Tumor Growth and Spread by Switching Macrophage Phenotype

Author

Deligne, Claire, primary, Murdamoothoo, Devadarssen, additional, Gammage, Anís N., additional, Gschwandtner, Martha, additional, Erne, William, additional, Loustau, Thomas, additional, Marzeda, Anna M., additional, Carapito, Raphael, additional, Paul, Nicodème, additional, Velazquez-Quesada, Inés, additional, Mazzier, Imogen, additional, Sun, Zhen, additional, Orend, Gertraud, additional, and Midwood, Kim S., additional

Published
2020
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30. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

Author

Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Institut National de la Santé et de la Recherche Médicale (France), Institut Universitaire de France, Université de Strasbourg, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat Valenciana, Domingo-Calap, Pilar [0000-0003-2829-8809], Schubert, Benjamin [0000-0003-3412-1102], Joly, Mélanie [0000-0003-0316-5065], Untrau, Meiggie [0000-0002-0054-8741], Georgel, Philippe [0000-0001-6853-7080], Paul, Nicodème [0000-0003-4680-3012], Kohlbacher, Oliver [0000-0003-1739-4598], González-Candelas, Fernando [0000-0002-0879-5798], Bahram, Seiamak [0000-0002-6928-9952], Domingo-Calap, Pilar, Schubert, Benjamin, Joly, Mélanie, Solis, Morgane, Untrau, Meiggie, Carapito, Raphael, Georgel, Philippe, Caillard, Sophie, Fati-Kremer, Samira, Paul, Nicodème, Kohlbacher, Oliver, González-Candelas, Fernando, Bahram, Seiamak, Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Institut National de la Santé et de la Recherche Médicale (France), Institut Universitaire de France, Université de Strasbourg, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat Valenciana, Domingo-Calap, Pilar [0000-0003-2829-8809], Schubert, Benjamin [0000-0003-3412-1102], Joly, Mélanie [0000-0003-0316-5065], Untrau, Meiggie [0000-0002-0054-8741], Georgel, Philippe [0000-0001-6853-7080], Paul, Nicodème [0000-0003-4680-3012], Kohlbacher, Oliver [0000-0003-1739-4598], González-Candelas, Fernando [0000-0002-0879-5798], Bahram, Seiamak [0000-0002-6928-9952], Domingo-Calap, Pilar, Schubert, Benjamin, Joly, Mélanie, Solis, Morgane, Untrau, Meiggie, Carapito, Raphael, Georgel, Philippe, Caillard, Sophie, Fati-Kremer, Samira, Paul, Nicodème, Kohlbacher, Oliver, González-Candelas, Fernando, and Bahram, Seiamak

Abstract

Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus.

Published
2018

31. A mouse model of MSU-induced acute inflammation in vivo suggests imiquimod-dependent targeting of Il-1 beta as relevant therapy for gout patients

Author

Mariotte, Alexandre, de Cauwer, Aurore, Po, Chrystelle, Abou-Faycal, Cherine, Pichot, Angelique, Paul, Nicodème, Aouadi, Ismaïl, Carapito, Raphael, Frisch, Benoit, Macquin, Cecile, Chatelus, Emmanuel, Sibilia, Jean, Armspach, Jean-Paul, Bahram, Seiamak, Georgel, Philippe, univOAK, Archive ouverte, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-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 la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Conception et application de molécules bioactives (CAMB), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie des Systèmes Fonctionnels, and Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire
Abstract

Rationale : The role of Monosodium Urate (MSU) crystals in gout pathophysiology is well described, as is the major impact of IL-1β in the inflammatory reaction that constitutes the hallmark of the disease. However, despite the discovery of the NLRP3 inflammasome and its role as a Pattern Recognition Receptor linking the detection of a danger signal (MSU) to IL-1β secretion in vitro, the precise mechanisms leading to joint inflammation in gout patients are still poorly understood. Methods : Acute urate crystal inflammation was obtained by subcutaneous injections of MSU crystals in mice. Symptoms were followed by scoring, cytokine quantification by ELISA and western blot, gene expression by RT-qPCR and RNAseq; Magnetic Resonance Imaging was also used to assess inflammation. Results : We provide an extensive clinical, biological and molecular characterization of an acute uratic inflammation mouse model which accurately mimics human gout. We report the efficacy of topical imiquimod treatment and its impact on Interferon-dependent down modulation of Il-1β gene expression in this experimental model. Conclusion : Our work reveals several key features of MSU-dependent inflammation and identifies novel therapeutic opportunities for gout patients.

Published
2020
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32. NLRP3- and AIM2-autonomy in a mouse model of MSU crystal-induced acute inflammation in vivo highlights imiquimod-dependent targeting of Il-1E expression as relevant therapy for gout patients

Author

Mariotte, Alexandre, De Cauwer, Aurore, Po, Chrystelle, Abou-Fayçal, Cherine, Pichot, Angélique, Paul, Nicodème, Aouadi, Ismael, Carapito, Raphael, Frisch, Benoit, Macquin, Cécile, Chatelus, Emmanuel, Sibilia, Jean, Armspach, Jean-Paul, Bahram, Seiamak, Georgel, Philippe, Frisch, Benoit, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Equipe 2 - Bases Moléculaires de la Progression des Cancers du Poumon, Inserm U823, Institut d'oncologie/développement Albert Bonniot de Grenoble (INSERM U823), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Equipe Plate-forme GENOMAX (Inserm U1109), Fédération Hospitalo-Universitaire OMICARE-Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA)-Université de Strasbourg (UNISTRA)-Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Conception et application de molécules bioactives (CAMB), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Service de Rhumatologie, Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de Référence pour les Maladies Systémiques Autoimmunes Rares, Rhumatologie, CHU Strasbourg, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ICube Laboratory, University of Strasbourg, CNRS, France, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Fédération Hospitalo-Universitaire OMICARE-Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA)-Université de Strasbourg (UNISTRA), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-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 la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract

L'article est publié dans la revue sous le titre définitif :"A mouse model of MSU-induced acute inflammation in vivo suggests imiquimod-dependent targeting of Il-1β as relevant therapy for gout patients"; International audience; The role of Monosodium Urate (MSU) crystals in gout pathophysiology is well described, as is the major impact of IL-1 in the inflammatory reaction that constitutes the hallmark of the disease. However, despite the discovery of the NLRP3 inflammasome and its role as a Pattern Recognition Receptor linking the detection of a danger signal (MSU) to IL-1 secretion in vitro, the precise mechanisms leading to joint inflammation in gout patients are still poorly understood. Here, we provide an extensive clinical, biological and molecular characterization of the acute uratic inflammation mouse model induced by subcutaneous injection of MSU crystals, which accurately mimics human gout. Our work reveals several key features of MSU-dependent inflammation and identifies novel therapeutic opportunities, among which the use of topical application of imiquimod to promote interferon-dependent anti-inflammatory action maybe relevant. All rights reserved. No reuse allowed without permission. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Published
2020

33. ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder

Author

Carapito, Raphael, Ivanova, Ekaterina L., Morlon, Aurore, Meng, Linyan, Molitor, Anne, Erdmann, Eva, Kieffer, Bruno, Pichot, Angélique, Naegely, Lydie, Kolmer, Aline, Paul, Nicodème, Hanauer, Antoine, Tran Mau-Them, Frédéric, Jean-Marçais, Nolwenn, Hiatt, Susan M., Cooper, Gregory M., Tvrdik, Tatiana, Muir, Alison M., Dimartino, Clémantine, Chopra, Maya, Amiel, Jeanne, Gordon, Christopher T., Dutreux, Fabien, Garde, Aurore, Thauvin-Robinet, Christel, Wang, Xia, Leduc, Magalie S., Phillips, Meredith, Crawford, Heather P., Kukolich, Mary K., Hunt, David, Harrison, Victoria, Kharbanda, Mira, Smigiel, Robert, Gold, Nina, Hung, Christina Y., Viskochil, David H., Dugan, Sarah L., Bayrak-Toydemir, Pinar, Joly-Helas, Géraldine, Guerrot, Anne-Marie, Schluth-Bolard, Caroline, Rio, Marlène, Wentzensen, Ingrid M., McWalter, Kirsty, Schnur, Rhonda E., Lewis, Andrea M., Lalani, Seema R., Mensah-Bonsu, Noël, Céraline, Jocelyn, Sun, Zijie, Ploski, Rafal, Bacino, Carlos A., Mefford, Heather C., Faivre, Laurence, Bodamer, Olaf, Chelly, Jamel, Isidor, Bertrand, and Bahram, Seiamak

Published
2019
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34. ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder

Author

Carapito, Raphael, primary, Ivanova, Ekaterina L., additional, Morlon, Aurore, additional, Meng, Linyan, additional, Molitor, Anne, additional, Erdmann, Eva, additional, Kieffer, Bruno, additional, Pichot, Angélique, additional, Naegely, Lydie, additional, Kolmer, Aline, additional, Paul, Nicodème, additional, Hanauer, Antoine, additional, Tran Mau-Them, Frédéric, additional, Jean-Marçais, Nolwenn, additional, Hiatt, Susan M., additional, Cooper, Gregory M., additional, Tvrdik, Tatiana, additional, Muir, Alison M., additional, Dimartino, Clémantine, additional, Chopra, Maya, additional, Amiel, Jeanne, additional, Gordon, Christopher T., additional, Dutreux, Fabien, additional, Garde, Aurore, additional, Thauvin-Robinet, Christel, additional, Wang, Xia, additional, Leduc, Magalie S., additional, Phillips, Meredith, additional, Crawford, Heather P., additional, Kukolich, Mary K., additional, Hunt, David, additional, Harrison, Victoria, additional, Kharbanda, Mira, additional, Smigiel, Robert, additional, Gold, Nina, additional, Hung, Christina Y., additional, Viskochil, David H., additional, Dugan, Sarah L., additional, Bayrak-Toydemir, Pinar, additional, Joly-Helas, Géraldine, additional, Guerrot, Anne-Marie, additional, Schluth-Bolard, Caroline, additional, Rio, Marlène, additional, Wentzensen, Ingrid M., additional, McWalter, Kirsty, additional, Schnur, Rhonda E., additional, Lewis, Andrea M., additional, Lalani, Seema R., additional, Mensah-Bonsu, Noël, additional, Céraline, Jocelyn, additional, Sun, Zijie, additional, Ploski, Rafal, additional, Bacino, Carlos A., additional, Mefford, Heather C., additional, Faivre, Laurence, additional, Bodamer, Olaf, additional, Chelly, Jamel, additional, Isidor, Bertrand, additional, and Bahram, Seiamak, additional

Published
2020
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36. Identification of clustered microRNAs using an ab initio prediction method

Author

Brownstein Michael J, Pfeffer Sébastien, Aravin Alexei, Landgraf Pablo, Paul Nicodème, Sewer Alain, Tuschl Thomas, van Nimwegen Erik, and Zavolan Mihaela

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds of them have been identified in the last five years and very recent works indicate that their total number is still larger. Therefore miRNAs gene discovery remains an important aspect of understanding this new and still widely unknown regulation mechanism. Bioinformatics approaches have proved to be very useful toward this goal by guiding the experimental investigations. Results In this work we describe our computational method for miRNA prediction and the results of its application to the discovery of novel mammalian miRNAs. We focus on genomic regions around already known miRNAs, in order to exploit the property that miRNAs are occasionally found in clusters. Starting with the known human, mouse and rat miRNAs we analyze 20 kb of flanking genomic regions for the presence of putative precursor miRNAs (pre-miRNAs). Each genome is analyzed separately, allowing us to study the species-specific identity and genome organization of miRNA loci. We only use cross-species comparisons to make conservative estimates of the number of novel miRNAs. Our ab initio method predicts between fifty and hundred novel pre-miRNAs for each of the considered species. Around 30% of these already have experimental support in a large set of cloned mammalian small RNAs. The validation rate among predicted cases that are conserved in at least one other species is higher, about 60%, and many of them have not been detected by prediction methods that used cross-species comparisons. A large fraction of the experimentally confirmed predictions correspond to an imprinted locus residing on chromosome 14 in human, 12 in mouse and 6 in rat. Our computational tool can be accessed on the world-wide-web. Conclusion Our results show that the assumption that many miRNAs occur in clusters is fruitful for the discovery of novel miRNAs. Additionally we show that although the overall miRNA content in the observed clusters is very similar across the three considered species, the internal organization of the clusters changes in evolution.

Published
2005
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37. Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency

Author

Carapito, Raphael, Carapito, Christine, Morlon, Aurore, Paul, Nicodème, Vaca Jacome, Alvaro Sebastian, Alsaleh, Ghada, Rolli, Véronique, Tahar, Ouria, Aouadi, Ismaïl, Rompais, Magali, Delalande, Francois, Pichot, Angélique, Georgel, Philippe, Messer, Laurent, Sibilia, Jean, Cianférani, Sarah, Van Dorsselaer, Alain, Bahram, Seiamak, Immuno-Rhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), 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), Functional Genomics and Cancer, Service de rhumatologie (Hôpitaux Civils de Colmar), Service de rhumatologie [Strasbourg], CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Immunorhumathologie moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Gaillard, Brigitte, and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Adult, Proteomics, Genes, Modifier, gene polymorphism, Gene Expression Profiling, Mutation, Missense, Middle Aged, Polymorphism, Single Nucleotide, Phenotype, STAT1 Transcription Factor, inflammation, [CHIM] Chemical Sciences, Humans, [CHIM]Chemical Sciences, Exome, Female, Mevalonate Kinase Deficiency, Basic and Translational Research, familial mediterranean fever
Abstract

International audience; Objectives The objective of the present study was to explain why two siblings carrying both the same homozygous pathogenic mutation for the autoinflammatory disease hyper IgD syndrome, show opposite phenotypes, that is, the first being asymptomatic, the second presenting all classical characteristics of the disease.Methods Where single omics (mainly exome) analysis fails to identify culprit genes/mutations in human complex diseases, multiomics analyses may provide solutions, although this has been seldom used in a clinical setting. Here we combine exome, transcriptome and proteome analyses to decipher at a molecular level, the phenotypic differences between the two siblings.Results This multiomics approach led to the identification of a single gene—STAT1—which harboured a rare missense variant and showed a significant overexpression of both mRNA and protein in the symptomatic versus the asymptomatic sister. This variant was shown to be of gain of function nature, involved in an increased activation of the Janus kinase/signal transducer and activator of transcription signalling (JAK/STAT) pathway, known to play a critical role in inflammatory diseases and for which specific biotherapies presently exist. Pathway analyses based on information from differentially expressed transcripts and proteins confirmed the central role of STAT1 in the proposed regulatory network leading to an increased inflammatory phenotype in the symptomatic sibling.Conclusions This study demonstrates the power of a multiomics approach to uncover potential clinically actionable targets for a personalised therapy. In more general terms, we provide a proteogenomics analysis pipeline that takes advantage of subject-specific genomic and transcriptomic information to improve protein identification and hence advance individualised medicine.This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

Published
2018
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38. HIV-Specific B Cell Frequency Correlates with Neutralization Breadth in Patients Naturally Controlling HIV-Infection

Author

Rouers, Angeline, Klingler, Jéromine, Su, Bin, Samri, Assia, Laumond, Géraldine, Even, Sophie, Avettand-Fenoel, Véronique, Richetta, Clemence, Paul, Nicodème, Boufassa, Faroudy, Hocqueloux, Laurent, Mouquet, Hugo, Rouzioux, Christine, Lambotte, Olivier, Autran, Brigitte, Graff-Dubois, Stéphanie, Moog, Christiane, Moris, Arnaud, Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Casrouge, Armanda, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg (UNISTRA), Capital University of Medical Sciences [Beijing] (CUMS), Infection à VIH, réservoirs, diversité génétique et résistance aux antirétroviraux (ARV) (EA 7327), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Hôpital La Source [Orléans] (HLSO), Réponse humorale aux pathogènes, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Infectious Diseases Models for Innovative Therapies (IDMIT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Hôpitaux Universitaires Paris Sud [AP-HP] (HUPS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and This work was granted by the ANRS (Agence nationale de recherches sur le SIDA et les hépatites virales). We thank the Dormeur Foundation, Vaduz, for providing AID ELISPOT Reader.

Subjects
immunoglobulin G (n)Ab, [SDV]Life Sciences [q-bio], intermediate memory B cells MZ-like B cells, lcsh:Medicine, HIV Infections, antibody secreting cell AM, RM, resting memory B cells, TLM B cells, tissue like memory B cells, immunoglobulin G, ADCC, antibody-dependent cell-mediated cytotoxicity, activated memory B cells RM, cART, combined antiretroviral therapy, marginal zone-like B cells, transmitted/founder virus PBMC, marginal zone-like B cells TLM B cells, TLM B cells, B-Lymphocytes, lcsh:R5-920, antibody secreting cell, human immunodeficiency virus, B cell-ELISPOT, virus diseases, tissue like memory B cells, peripheral blood mononuclear cells, HIV Elite controllers Memory B cells B cell-ELISPOT Neutralization Tier-2 virus IgG HIV, transmitted/founder virus, Env, HIV envelope protein, HIV, human immunodeficiency virus, [SDV] Life Sciences [q-bio], PBMC, peripheral blood mononuclear cells, ASC, antibody secreting cell, (neutralizing) antibody, lcsh:Medicine (General), ADCC, resting memory B cells IM, Research Paper, Env, RM, T/F, transmitted/founder virus, IgG, MZ-like B cells, marginal zone-like B cells, T/F, IgG, immunoglobulin G, combined antiretroviral therapy, cART, CTL, cytotoxic T cell, antibody-dependent cell-mediated cytotoxicity, activated memory B cells, peripheral blood mononuclear cells ASC, ASC, cytotoxic T cell T/F, Neutralization, (neutralizing) antibody ADCC, human immunodeficiency virus Env, (n)Ab, (neutralizing) antibody, Humans, Alleles, intermediate memory B cells, elite controller IgG, EC, resting memory B cells, EC, elite controller, AM, activated memory B cells, antibody-dependent cell-mediated cytotoxicity CTL, lcsh:R, PBMC, elite controller, HIV, combined antiretroviral therapy EC, IM, Memory B cells, HIV envelope protein, (n)Ab, AM, IM, intermediate memory B cells, Elite controllers, HLA-B Antigens, CTL, Tier-2 virus, HIV envelope protein cART, MZ-like B cells, cytotoxic T cell
Abstract

HIV-specific broadly neutralizing antibodies (bnAbs) have been isolated from patients with high viremia but also from HIV controllers that repress HIV-1 replication. In these elite controllers (ECs), multiple parameters contribute to viral suppression, including genetic factors and immune responses. Defining the immune correlates associated with the generation of bnAbs may help in designing efficient immunotherapies. In this study, in ECs either positive or negative for the HLA-B*57 protective allele, in treated HIV-infected and HIV-negative individuals, we characterized memory B cell compartments and HIV-specific memory B cells responses using flow cytometry and ELISPOT. ECs preserved their memory B cell compartments and in contrast to treated patients, maintained detectable HIV-specific memory B cell responses. All ECs presented IgG1 + HIV-specific memory B cells but some individuals also preserved IgG2 + or IgG3 + responses. Importantly, we also analyzed the capacity of sera from ECs to neutralize a panel of HIV strains including transmitted/founder virus. 29% and 21% of HLA-B*57 + and HLA-B*57 − ECs, respectively, neutralized at least 40% of the viral strains tested. Remarkably, in HLA-B*57 + ECs the frequency of HIV-Env-specific memory B cells correlated positively with the neutralization breadth suggesting that preservation of HIV-specific memory B cells might contribute to the neutralizing responses in these patients., Highlights • In contrast to treated HIV-infected patients, elite controllers (ECs) maintain HIV-specific memory B cell responses. • In HLA-B*57 + ECs, HIV-specific B cell frequency correlates positively with the neutralization breadth of tier-2 HIV strains. • In HLA-B*57 + and HLA-B*57 − ECs different antibody functions are probably involved in suppressing HIV replication. A fraction of HIV-1-infected individuals (so-called elite controllers, ECs) naturally control HIV-1 replication maintaining undetectable viral loads. Understanding the mechanisms implicated in natural control of HIV-1 infection will help in developing efficient HIV vaccines. In ECs, we analyzed the influence of B cell antibody responses. We show that in contrast to successfully treated HIV-1-infected patients, ECs preserve memory B cell compartments and maintain HIV-specific B cell responses. In ECs positive for the protective HLA-B*57 allele, HIV-specific memory B cell responses are positively associated with the breadth of HIV neutralization. These findings will help develop novel immunotherapies to fight HIV.

Published
2017
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39. Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma

Author

Fornecker, Luc-Matthieu, primary, Muller, Leslie, additional, Bertrand, Frédéric, additional, Paul, Nicodème, additional, Pichot, Angélique, additional, Herbrecht, Raoul, additional, Chenard, Marie-Pierre, additional, Mauvieux, Laurent, additional, Vallat, Laurent, additional, Bahram, Seiamak, additional, Cianférani, Sarah, additional, Carapito, Raphaël, additional, and Carapito, Christine, additional

Published
2019
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40. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

Author

Domingo-Calap, Pilar, primary, Schubert, Benjamin, additional, Joly, Mélanie, additional, Solis, Morgane, additional, Untrau, Meiggie, additional, Carapito, Raphael, additional, Georgel, Philippe, additional, Caillard, Sophie, additional, Fafi-Kremer, Samira, additional, Paul, Nicodème, additional, Kohlbacher, Oliver, additional, González-Candelas, Fernando, additional, and Bahram, Seiamak, additional

Published
2018
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41. Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements

Author

Argemi, Xavier, Martin, Véronique, Loux, Valentin, Dahyot, Sandrine, Lebeurre, Jérémie, Guffroy, Aurélien, Martin, Mickael, Velay, Aurélie, Keller, Daniel, Riegel, Philippe, Hansmann, Yves, Paul, Nicodème, and Prévost, Gilles

Subjects
next generation sequencing, Recombination, Genetic, plasmids, Genomic Islands, Virulence Factors, Prophages, Staphylococcus lugdunensis, Aucun, Molecular Sequence Annotation, Staphylococcal Infections, Sciences du Vivant [q-bio]/Microbiologie et Parasitologie, Genome Report, virulence, Interspersed Repetitive Sequences, Genome, Bacterial
Abstract

Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements. S. lugdunensis also bears various putative virulence genes but only one complete genome with extensive analysis has been published with one prophage sequence (φSL2) and a unique plasmid was previously described. In this study, we performed de novo sequencing, whole genome assembly and annotation of seven strains of S. lugdunensis from VISLISI clinical trial. We searched for the presence of virulence genes and mobile genetics elements using bioinformatics tools. We identified four new prophages, named φSL2 to φSL4, belonging to the Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three plasmids are homologous to known plasmids that include, amongst others, one S. aureus plasmid. The two other plasmids were not described previously. This study provides a new context for the study of S. lugdunensis virulence suggesting the occurrence of several genetic recombination' with other staphylococci.

Published
2017

42. Reduced DICER1 Expression Bestows Rheumatoid Arthritis Synoviocytes Proinflammatory Properties and Resistance to Apoptotic Stimuli

Author

Alsaleh, Ghada, Nehmar, Ramzi, Blüml, Stephan, Schleiss, Cédric, Ostermann, Eleonore, Dillenseger, Jean-Philippe, Sayeh, Amira, Choquet, Philippe, Dembélé, Doulaye, François, Antoine, Salmon, Jean-Hugues, Paul, Nicodème, Schabbauer, Gernot, Bierry, Guillaume, Meyer, Alain, Gottenberg, Jacques-Eric, Haas, Gabrielle, Pfeffer, Sébastien, Vallat, Laurent, Sibilia, Jean, Bahram, Seiamak, Georgel, Philippe, Physiopathologie des arthrites, Université Louis Pasteur - Strasbourg I, Research Center for Molecular Medicine of the Austrian Academy of Sciences [Vienna, Austria] (CeMM ), Austrian Academy of Sciences (OeAW), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagerie Préclinique-UF6237, Pôle d'imagerie [Strasbourg], Les Hôpitaux Universitaires de Strasbourg (HUS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Reims (CHU Reims), Service de neuroradiologie [Lille], Hôpital Roger Salengro [Lille]-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Rheumatology [CHU Strasbourg], CHU Strasbourg, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Immunologie cellulaire et tissulaire, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de rhumatologie [Strasbourg], and CHU Strasbourg-Hôpital de Hautepierre [Strasbourg]

Subjects
Inflammation, Ribonuclease III, [SDV]Life Sciences [q-bio], Physique [physics]/Mécanique [physics], Apoptosis, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Synoviocytes, Arthritis, Rheumatoid, DEAD-box RNA Helicases, Mice, Sciences du Vivant [q-bio]/Autre [q-bio.OT], Gene Expression Regulation, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

OBJECTIVE: While the regulatory role of individual microRNAs (miRNAs) in rheumatoid arthritis (RA) is well established, the role of DICER1 in the pathogenesis of the disease has not yet been investigated. The purpose of this study was to analyze the expression of factors involved in miRNA biogenesis in fibroblast-like synoviocytes (FLS) from RA patients and to monitor the arthritis triggered by K/BxN serum transfer in mice deficient in the Dicer gene (Dicer(d/d) ). METHODS: The expression of genes and precursor miRNAs was quantified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). MicroRNA macroarray profiling was monitored by qRT-PCR. Cytokines were quantified by enzyme-linked immunosorbent assay. Experimental arthritis in mice was achieved by the transfer of serum from K/BxN donors. Apoptosis was quantified using an enzyme-linked immunosorbent assay. RESULTS: We found decreased DICER1 and mature miRNA expression in synovial fibroblasts from RA patients. These cells were hyperresponsive to lipopolysaccharide, as evidenced by their increased interleukin-6 secretion upon stimulation. Experimental serum-transfer arthritis in Dicer(d/d) mice confirmed that an unbalanced biogenesis of miRNAs correlated with an enhanced inflammatory response. Synoviocytes from both RA patients and Dicer(d/d) mice exhibited increased resistance to apoptotic stimuli. CONCLUSION: The findings of this study further substantiate the important role of DICER1 in the maintenance of homeostasis and the regulation of inflammatory responses.

Published
2016
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43. Hemodynamic forces tune the arrest, adhesion and extravasation of circulating tumor cells

Author

Follain, Gautier, primary, Osmani, Naël, additional, Azevedo, Sofia, additional, Allio, Guillaume, additional, Mercier, Luc, additional, Karreman, Matthia A., additional, Solecki, Gergely, additional, Garcia-Leon, Maria Jesus, additional, Lefebvre, Olivier, additional, Fekonja, Nina, additional, Hille, Claudia, additional, Chabannes, Vincent, additional, Dollé, Guillaume, additional, Metivet, Thibaut, additional, Der Hovsepian, François, additional, Prudhomme, Christophe, additional, Pichot, Angélique, additional, Paul, Nicodème, additional, Carapito, Raphaël, additional, Bahram, Siamak, additional, Ruthensteiner, Bernhard, additional, Kemmling, André, additional, Siemonsen, Susanne, additional, Schneider, Tanja, additional, Fiehler, Jens, additional, Glatzel, Markus, additional, Winkler, Frank, additional, Schwab, Yannick, additional, Pantel, Klaus, additional, Harlepp, Sébastien, additional, and Goetz, Jacky G., additional

Published
2017
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44. Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements

Author

Argemi, Xavier, primary, Martin, Véronique, additional, Loux, Valentin, additional, Dahyot, Sandrine, additional, Lebeurre, Jérémie, additional, Guffroy, Aurélien, additional, Martin, Mickael, additional, Velay, Aurélie, additional, Keller, Daniel, additional, Riegel, Philippe, additional, Hansmann, Yves, additional, Paul, Nicodème, additional, and Prévost, Gilles, additional

Published
2017
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45. A new MHC-linked susceptibility locus for primary Sjögren’s syndrome: MICA

Author

Carapito, Raphael, primary, Gottenberg, Jacques-Eric, additional, Kotova, Irina, additional, Untrau, Meiggie, additional, Michel, Sandra, additional, Naegely, Lydie, additional, Aouadi, Ismail, additional, Kwemou, Marius, additional, Paul, Nicodème, additional, Pichot, Angélique, additional, Locke, James, additional, Bowman, Simon J., additional, Griffiths, Bridget, additional, Sivils, Kathy L., additional, Sibilia, Jean, additional, Inoko, Hidetoshi, additional, Micelli-Richard, Corinne, additional, Nocturne, Gaétane, additional, Ota, Masao, additional, Ng, Wan-Fai, additional, Mariette, Xavier, additional, and Bahram, Seiamak, additional

Published
2017
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46. Protein-altering MYH3 variants are associated with a spectrum of phenotypes extending to spondylocarpotarsal synostosis syndrome

Author

Carapito, Raphael, primary, Goldenberg, Alice, additional, Paul, Nicodème, additional, Pichot, Angélique, additional, David, Albert, additional, Hamel, Antoine, additional, Dumant-Forest, Clémentine, additional, Leroux, Julien, additional, Ory, Benjamin, additional, Isidor, Bertrand, additional, and Bahram, Seiamak, additional

Published
2016
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47. Multi-OMICS analyses unveil as a potential modifier gene in mevalonate kinase deficiency.

Author

Carapito, Raphael, Carapito, Christine, Morlon, Aurore, Paul, Nicodème, Jacome, Alvaro Sebastian Vaca, Alsaleh, Ghada, Rolli, Véronique, Tahar, Ouria, Aouadi, Ismail, Rompais, Magali, Delalande, François, Pichot, Angélique, Georgel, Philippe, Messer, Laurent, Sibilia, Jean, Cianferani, Sarah, Van Dorsselaer, Alain, Bahram, Seiamak, and Vaca Jacome, Alvaro Sebastian

Abstract

Objectives: The objective of the present study was to explain why two siblings carrying both the same homozygous pathogenic mutation for the autoinflammatory disease hyper IgD syndrome, show opposite phenotypes, that is, the first being asymptomatic, the second presenting all classical characteristics of the disease.Methods: Where single omics (mainly exome) analysis fails to identify culprit genes/mutations in human complex diseases, multiomics analyses may provide solutions, although this has been seldom used in a clinical setting. Here we combine exome, transcriptome and proteome analyses to decipher at a molecular level, the phenotypic differences between the two siblings.Results: This multiomics approach led to the identification of a single gene-STAT1-which harboured a rare missense variant and showed a significant overexpression of both mRNA and protein in the symptomatic versus the asymptomatic sister. This variant was shown to be of gain of function nature, involved in an increased activation of the Janus kinase/signal transducer and activator of transcription signalling (JAK/STAT) pathway, known to play a critical role in inflammatory diseases and for which specific biotherapies presently exist. Pathway analyses based on information from differentially expressed transcripts and proteins confirmed the central role of STAT1 in the proposed regulatory network leading to an increased inflammatory phenotype in the symptomatic sibling.Conclusions: This study demonstrates the power of a multiomics approach to uncover potential clinically actionable targets for a personalised therapy. In more general terms, we provide a proteogenomics analysis pipeline that takes advantage of subject-specific genomic and transcriptomic information to improve protein identification and hence advance individualised medicine. [ABSTRACT FROM AUTHOR]

Published
2018
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49. A de novo ADCY5 mutation causes early‐onset autosomal dominant chorea and dystonia

Author

Carapito, Raphael, primary, Paul, Nicodème, additional, Untrau, Meiggie, additional, Le Gentil, Marion, additional, Ott, Louise, additional, Alsaleh, Ghada, additional, Jochem, Pierre, additional, Radosavljevic, Mirjana, additional, Le Caignec, Cédric, additional, David, Albert, additional, Damier, Philippe, additional, Isidor, Bertrand, additional, and Bahram, Seiamak, additional

Published
2014
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50. A new mutation in the C-SH2 domain of PTPN11 causes Noonan syndrome with multiple giant cell lesions

Author

Carapito, Raphael, primary, Paul, Nicodème, additional, Untrau, Meiggie, additional, Ott, Louise, additional, Corradini, Nadège, additional, Poignant, Sylvaine, additional, Geffroy, Loïc, additional, Caldagues, Emmanuelle, additional, Heymann, Marie-Françoise, additional, Cassagnau, Elisabeth, additional, Isidor, Bertrand, additional, and Bahram, Seiamak, additional

Published
2013
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