304 results on '"Naffakh, Nadia"'
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2. The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome
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Krischuns, Tim, Arragain, Benoît, Isel, Catherine, Paisant, Sylvain, Budt, Matthias, Wolff, Thorsten, Cusack, Stephen, and Naffakh, Nadia
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- 2024
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3. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication
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Dupont, Maud, primary, Krischuns, Tim, additional, Gianetto, Quentin Giai, additional, Paisant, Sylvain, additional, Bonazza, Stefano, additional, Brault, Jean-Baptiste, additional, Douché, Thibaut, additional, Arragain, Benoît, additional, Florez-Prada, Alberto, additional, Perez-Perri, Joel I, additional, Hentze, Matthias W, additional, Cusack, Stephen, additional, Matondo, Mariette, additional, Isel, Catherine, additional, Courtney, David G, additional, and Naffakh, Nadia, additional
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- 2024
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4. Host succinate inhibits influenza virus infection through succinylation and nuclear retention of the viral nucleoprotein
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Guillon, Antoine, Brea‐Diakite, Deborah, Cezard, Adeline, Wacquiez, Alan, Baranek, Thomas, Bourgeais, Jérôme, Picou, Frédéric, Vasseur, Virginie, Meyer, Léa, Chevalier, Christophe, Auvet, Adrien, Carballido, José M, Nadal Desbarats, Lydie, Dingli, Florent, Turtoi, Andrei, Le Gouellec, Audrey, Fauvelle, Florence, Donchet, Amélie, Crépin, Thibaut, Hiemstra, Pieter S, Paget, Christophe, Loew, Damarys, Herault, Olivier, Naffakh, Nadia, Le Goffic, Ronan, and Si‐Tahar, Mustapha
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- 2022
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5. Human MX1 induces the cytoplasmic sequestration of neo-synthesized influenza A virus vRNPs
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McKellar, Joe, primary, García de Gracia, Francisco, additional, Aubé, Corentin, additional, Chaves Valadão, Ana Luiza, additional, Tauziet, Marine, additional, Arnaud-Arnould, Mary, additional, Rebendenne, Antoine, additional, Neyret, Aymeric, additional, Labaronne, Emmanuel, additional, Ricci, Emiliano, additional, Delaval, Bénédicte, additional, Gaudin, Raphaël, additional, Naffakh, Nadia, additional, Gallois-Montbrun, Sarah, additional, Moncorgé, Olivier, additional, and Goujon, Caroline, additional
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- 2024
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6. A polarized cell system amenable to subcellular resolution imaging of influenza virus infection
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Brault, Jean-Baptiste, primary, Thouvenot, Catherine, additional, Cannata Serio, Magda, additional, Paisant, Sylvain, additional, Fernandes, Julien, additional, Gény, David, additional, Danglot, Lydia, additional, Mallet, Adeline, additional, and Naffakh, Nadia, additional
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- 2024
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7. Destabilization of the human RED–SMU1 splicing complex as a basis for host-directed antiinfluenza strategy
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Ashraf, Usama, Tengo, Laura, Le Corre, Laurent, Fournier, Guillaume, Busca, Patricia, McCarthy, Andrew A., Rameix-Welti, Marie-Anne, Gravier-Pelletier, Christine, Ruigrok, Rob W. H., Jacob, Yves, Vidalain, Pierre-Olivier, Pietrancosta, Nicolas, Crépin, Thibaut, and Naffakh, Nadia
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- 2019
8. Structural insights into influenza A virus ribonucleoproteins reveal a processive helical track as transcription mechanism
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Coloma, Rocío, Arranz, Rocío, de la Rosa-Trevín, José M., Sorzano, Carlos O. S., Munier, Sandie, Carlero, Diego, Naffakh, Nadia, Ortín, Juan, and Martín-Benito, Jaime
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- 2020
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9. Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing
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Ashraf, Usama, Benoit-Pilven, Clara, Lacroix, Vincent, Navratil, Vincent, and Naffakh, Nadia
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- 2019
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10. High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit
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Cusack, Stephen, primary, Naffakh, Nadia, additional, Krischuns, Tim, additional, and Drncova, Petra, additional
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- 2023
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11. A community effort in SARS‐CoV‐2 drug discovery
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Schimunek, Johannes, primary, Seidl, Philipp, additional, Elez, Katarina, additional, Hempel, Tim, additional, Le, Tuan, additional, Noé, Frank, additional, Olsson, Simon, additional, Raich, Lluís, additional, Winter, Robin, additional, Gokcan, Hatice, additional, Gusev, Filipp, additional, Gutkin, Evgeny M., additional, Isayev, Olexandr, additional, Kurnikova, Maria G., additional, Narangoda, Chamali H., additional, Zubatyuk, Roman, additional, Bosko, Ivan P., additional, Furs, Konstantin V., additional, Karpenko, Anna D., additional, Kornoushenko, Yury V., additional, Shuldau, Mikita, additional, Yushkevich, Artsemi, additional, Benabderrahmane, Mohammed, additional, Bousquet-Melou, Patrick, additional, Bureau, Ronan, additional, Charton, Beatrice, additional, Cirou, Bertrand, additional, Gil, Gérard, additional, Allen, William J., additional, Sirimulla, Suman, additional, Watowich, Stanley, additional, Antonopoulos, Nick, additional, Epitropakis, Nikolaos, additional, Krasoulis, Agamemnon, additional, Pitsikalis, Vassilis, additional, Theodorakis, Stavros, additional, Kozlovskii, Igor, additional, Maliutin, Anton, additional, Medvedev, Alexander, additional, Popov, Petr, additional, Zaretckii, Mark, additional, Eghbal-zadeh, Hamid, additional, Halmich, Christina, additional, Hochreiter, Sepp, additional, Mayr, Andreas, additional, Ruch, Peter, additional, Widrich, Michael, additional, Berenger, Francois, additional, Kumar, Ashutosh, additional, Yamanishi, Yoshihiro, additional, Zhang, Kam, additional, Bengio, Emmanuel, additional, Bengio, Yoshua, additional, Jain, Moksh, additional, Korablyov, Maksym, additional, Liu, Cheng-Hao, additional, Gilles, Marcous, additional, Glaab, Enrico, additional, Barnsley, Kelly, additional, Iyengar, Suhasini M., additional, Ondrechen, Mary Jo, additional, Haupt, V. Joachim, additional, Kaiser, Florian, additional, Schroeder, Michael, additional, Pugliese, Luisa, additional, Albani, Simone, additional, Athanasiou, Christina, additional, Beccari, Andrea, additional, Carloni, Paolo, additional, D'Arrigo, Giulia, additional, Gianquinto, Eleonora, additional, Goßen, Jonas, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Kokh, Daria B., additional, Kovachka, Sandra, additional, Manelfi, Candida, additional, Mukherjee, Goutam, additional, Muñiz-Chicharro, Abraham, additional, Musiani, Francesco, additional, Nunes-Alves, Ariane, additional, Paiardi, Giulia, additional, Rossetti, Giulia, additional, Sadiq, S. Kashif, additional, Spyrakis, Francesca, additional, Talarico, Carmine, additional, Tsengenes, Alexandros, additional, Wade, Rebecca, additional, Copeland, Conner, additional, Gaiser, Jeremiah, additional, Olson, Daniel R., additional, Roy, Amitava, additional, Venkatraman, Vishwesh, additional, Wheeler, Travis J., additional, Arthanari, Haribabu, additional, Blaschitz, Klara, additional, Cespugli, Marco, additional, Durmaz, Vedat, additional, Fackeldey, Konstantin, additional, Fischer, Patrick D., additional, Gorgulla, Christoph, additional, Gruber, Christian, additional, Gruber, Karl, additional, Hetmann, Michael, additional, Kinney, Jamie E., additional, Das, Krishna M. Padmanabha, additional, Pandita, Shreya, additional, Singh, Amit, additional, Steinkellner, Georg, additional, Tesseyre, Guilhem, additional, Wagner, Gerhard, additional, Wang, Zi-Fu, additional, Yust, Ryan J., additional, Druzhilovskiy, Dmitry S., additional, Filimonov, Dmitry, additional, Pogodin, Pavel V., additional, Poroikov, Vladimir, additional, Rudik, Anastassia V., additional, Stolbov, Leonid A., additional, Veselovsky, Alexander V., additional, De Rosa, Maria, additional, Simone, Giada De, additional, Gulotta, Maria R., additional, Lombino, Jessica, additional, Mekni, Nedra, additional, Perricone, Ugo, additional, Casini, Arturo, additional, Embree, Amanda, additional, Gordon, D. Benjamin, additional, Lei, David, additional, Pratt, Katelin, additional, Voigt, Christopher A., additional, Chen, Kuang-Yu, additional, Jacob, Yves, additional, Krischuns, Tim, additional, Lafaye, Pierre, additional, Zettor, Agnès, additional, Rodríguez, M. Luis, additional, White, Kris M., additional, Fearon, Daren, additional, von Delft, Frank, additional, Walsh, Martin A., additional, Horvath, Dragos, additional, Brooks, Charles L., additional, Falsafi, Babak, additional, Ford, Bryan, additional, García-Sastre, Adolfo, additional, Lee, Sang Yup, additional, Naffakh, Nadia, additional, Varnek, Alexandre, additional, Klambauer, Guenter, additional, and Hermans, Thomas M., additional
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- 2023
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12. Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation
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Camacho-Zarco, Aldo R., primary, Yu, Lefan, additional, Krischuns, Tim, additional, Dedeoglu, Selin, additional, Maurin, Damien, additional, Bouvignies, Guillaume, additional, Crépin, Thibaut, additional, Ruigrok, Rob W. H., additional, Cusack, Stephan, additional, Naffakh, Nadia, additional, and Blackledge, Martin, additional
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- 2023
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13. A community effort to discover small molecule SARS-CoV-2 inhibitors
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Schimunek, Johannes, primary, Seidl, Philipp, additional, Elez, Katarina, additional, Hempel, Tim, additional, Le, Tuan, additional, Noé, Frank, additional, Olsson, Simon, additional, Raich, Lluís, additional, Winter, Robin, additional, Gokcan, Hatice, additional, Gusev, Filipp, additional, Gutkin, Evgeny M., additional, Isayev, Olexandr, additional, Kurnikova, Maria G., additional, Narangoda, Chamali H., additional, Zubatyuk, Roman, additional, Bosko, Ivan P., additional, Furs, Konstantin V., additional, Karpenko, Anna D., additional, Kornoushenko, Yury V., additional, Shuldau, Mikita, additional, Yushkevich, Artsemi, additional, Benabderrahmane, Mohammed B., additional, Bousquet-Melou, Patrick, additional, Bureau, Ronan, additional, Charton, Beatrice, additional, Cirou, Bertrand C., additional, Gil, Gérard, additional, Allen, William J., additional, Sirimulla, Suman, additional, Watowich, Stanley, additional, Antonopoulos, Nick A., additional, Epitropakis, Nikolaos E., additional, Krasoulis, Agamemnon K., additional, Pitsikalis, Vassilis P., additional, Theodorakis, Stavros T., additional, Kozlovskii, Igor, additional, Maliutin, Anton, additional, Medvedev, Alexander, additional, Popov, Petr, additional, Zaretckii, Mark, additional, Eghbal-zadeh, Hamid, additional, Halmich, Christina, additional, Hochreiter, Sepp, additional, Mayr, Andreas, additional, Ruch, Peter, additional, Widrich, Michael, additional, Berenger, Francois, additional, Kumar, Ashutosh, additional, Yamanishi, Yoshihiro, additional, Zhang, Kam Y.J., additional, Bengio, Emmanuel, additional, Bengio, Yoshua, additional, Jain, Moksh J., additional, Korablyov, Maksym, additional, Liu, Cheng-Hao, additional, Marcou, Gilles, additional, Glaab, Enrico, additional, Barnsley, Kelly, additional, Iyengar, Suhasini M., additional, Ondrechen, Mary Jo, additional, Haupt, V. Joachim, additional, Kaiser, Florian, additional, Schroeder, Michael, additional, Pugliese, Luisa, additional, Albani, Simone, additional, Athanasiou, Christina, additional, Beccari, Andrea, additional, Carloni, Paolo, additional, D'Arrigo, Giulia, additional, Gianquinto, Eleonora, additional, Goßen, Jonas, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Kokh, Daria B., additional, Kovachka, Sandra, additional, Manelfi, Candida, additional, Mukherjee, Goutam, additional, Muñiz-Chicharro, Abraham, additional, Musiani, Francesco, additional, Nunes-Alves, Ariane, additional, Paiardi, Giulia, additional, Rossetti, Giulia, additional, Sadiq, S. Kashif, additional, Spyrakis, Francesca, additional, Talarico, Carmine, additional, Tsengenes, Alexandros, additional, Wade, Rebecca C., additional, Copeland, Conner, additional, Gaiser, Jeremiah, additional, Olson, Daniel R., additional, Roy, Amitava, additional, Venkatraman, Vishwesh, additional, Wheeler, Travis J., additional, Arthanari, Haribabu, additional, Blaschitz, Klara, additional, Cespugli, Marco, additional, Durmaz, Vedat, additional, Fackeldey, Konstantin, additional, Fischer, Patrick D., additional, Gorgulla, Christoph, additional, Gruber, Christian, additional, Gruber, Karl, additional, Hetmann, Michael, additional, Kinney, Jamie E., additional, Padmanabha Das, Krishna M., additional, Pandita, Shreya, additional, Singh, Amit, additional, Steinkellner, Georg, additional, Tesseyre, Guilhem, additional, Wagner, Gerhard, additional, Wang, Zi-Fu, additional, Yust, Ryan J., additional, Druzhilovskiy, Dmitry S., additional, Filimonov, Dmitry A., additional, Pogodin, Pavel V., additional, Poroikov, Vladimir, additional, Rudik, Anastassia V., additional, Stolbov, Leonid A., additional, Veselovsky, Alexander V., additional, De Rosa, Maria, additional, De Simone, Giada, additional, Gulotta, Maria R., additional, Lombino, Jessica, additional, Mekni, Nedra, additional, Perricone, Ugo, additional, Casini, Arturo, additional, Embree, Amanda, additional, Gordon, D. Benjamin, additional, Lei, David, additional, Pratt, Katelin, additional, Voigt, Christopher A., additional, Chen, Kuang-Yu, additional, Jacob, Yves, additional, Krischuns, Tim, additional, Lafaye, Pierre, additional, Zettor, Agnès, additional, Rodríguez, M. Luis, additional, White, Kris M., additional, Fearon, Daren, additional, Von Delft, Frank, additional, Walsh, Martin A., additional, Horvath, Dragos, additional, Brooks III, Charles L., additional, Falsafi, Babak, additional, Ford, Bryan, additional, García-Sastre, Adolfo, additional, Lee, Sang Yup, additional, Naffakh, Nadia, additional, Varnek, Alexandre, additional, Klambauer, Günter, additional, and Hermans, Thomas M., additional
- Published
- 2023
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14. The RBPome of influenza A virus mRNA reveals a role for TDP-43 in viral replication
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Dupont, Maud, primary, Krischuns, Tim, additional, Giai Gianetto, Quentin, additional, Paisant, Sylvain, additional, Bonazza, Stefano, additional, Brault, Jean-Baptiste, additional, Douche, Thibaut, additional, Perez-Perri, Joel I, additional, Hentze, Matthias W, additional, Cusack, Stephen, additional, Matondo, Mariette, additional, Isel, Catherine, additional, Courtney, David, additional, and Naffakh, Nadia, additional
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- 2023
- Full Text
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15. Metal-Tagging Transmission Electron Microscopy and Immunogold Labeling on Tokuyasu Cryosections to Image Influenza A Virus Ribonucleoprotein Transport and Packaging
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Sachse, Martin, primary, de Castro, Isabel Fernández, additional, Fournier, Guillaume, additional, Naffakh, Nadia, additional, and Risco, Cristina, additional
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- 2018
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16. High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing
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Chen, Kuang-Yu, primary, Karuppusamy, Jayaprakash, additional, O’Neill, Mary B., additional, Opuu, Vaitea, additional, Bahin, Mathieu, additional, Foulon, Sophie, additional, Ibanez, Pablo, additional, Quintana-Murci, Lluis, additional, Ozawa, Tatsuhiko, additional, van der Werf, Sylvie, additional, Nghe, Philippe, additional, Naffakh, Nadia, additional, Griffiths, Andrew, additional, and Isel, Catherine, additional
- Published
- 2023
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17. Correction: Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD
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Krischuns, Tim, primary, Isel, Catherine, additional, Drncova, Petra, additional, Lukarska, Maria, additional, Pflug, Alexander, additional, Paisant, Sylvain, additional, Navratil, Vincent, additional, Cusack, Stephen, additional, and Naffakh, Nadia, additional
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- 2023
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18. Design and Synthesis of Naturally-Inspired SARS-CoV-2 Inhibitors
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Hassan, Haitham, primary, Chiaravalli, Jeanne, additional, Hassan, Afnan, additional, Bedda, Loay, additional, Krischuns, Tim, additional, Chen, Kuang-Yu, additional, Li, Alice Shi Ming, additional, Delpal, Adrien, additional, Decroly, Etienne, additional, Vedadi, Masoud, additional, Naffakh, Nadia, additional, Agou, Fabrice, additional, Mallart, Sergio, additional, Arafa, Reem K., additional, and Arimondo, Paola B., additional
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- 2023
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19. Resistance Development to Influenza Virus Sialidase Inhibitors
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Rameix-Welti, Marie-Anne, Munier, Sandie, Naffakh, Nadia, and von Itzstein, Mark, editor
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- 2012
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20. Structural basis of an essential interaction between influenza polymerase and Pol II CTD
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Lukarska, Maria, Fournier, Guillaume, Pflug, Alexander, Resa-Infante, Patricia, Reich, Stefan, Naffakh, Nadia, and Cusack, Stephen
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- 2017
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21. Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD
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Krischuns, Tim, primary, Isel, Catherine, additional, Drncova, Petra, additional, Lukarska, Maria, additional, Pflug, Alexander, additional, Paisant, Sylvain, additional, Navratil, Vincent, additional, Cusack, Stephen, additional, and Naffakh, Nadia, additional
- Published
- 2022
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22. The metabolite succinate inhibits influenza virus replication through succinylation and nuclear retention of the viral nucleoprotein
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Cezard, Adeline, primary, Guillon, Antoine, additional, Bréa-Diakite, Deborah, additional, Wacquiez, Alan, additional, Baranek, Thomas, additional, Bourgeais, Jérôme, additional, Picou, Frédéric, additional, Vasseur, Virginie, additional, Meyer, Léa, additional, Auvet, Adrien, additional, Carballido, José M, additional, Nadal Desbarats, Lydie, additional, Dingli, Florent, additional, Turtoi, Andrei, additional, Le Gouellec, Audrey, additional, Fauvelle, Florence, additional, Donchet, Amélie, additional, Crépin, Thibaut, additional, Hiemstra, Pieter S., additional, Paget, Christophe, additional, Loew, Damarys, additional, Hérault, Olivier, additional, Naffakh, Nadia, additional, Le Goffic, Ronan, additional, and Si-Tahar, Mustapha, additional
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- 2022
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23. Influenza viruses and coronaviruses: Knowns, unknowns, and common research challenges
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Terrier, Olivier, primary, Si-Tahar, Mustapha, additional, Ducatez, Mariette, additional, Chevalier, Christophe, additional, Pizzorno, Andrés, additional, Le Goffic, Ronan, additional, Crépin, Thibaut, additional, Simon, Gaëlle, additional, and Naffakh, Nadia, additional
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- 2021
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24. Synthèse sur la détection des produits issus des nouvelles technologies génomiques (NGT) appliquées aux plantes. Paris, Paris, le 26 novembre 2021
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Comité Scientifique Du Haut Conseil Des Biotechnologies, ., Angevin, Frédérique, Bagnis, Claude, Bar-Hen, Avner, Barny, Marie-Anne, Boireau, Pascal, Brévault, Thierry, Chauvel, Bruno, Couvet, Denis, Dassa, Elie, de Verneuil, Hubert, Demeneix, Barbara, Franche, Claudine, Guerche, Philippe, Guillemain, Joël, Hernandez Raquet, Guillermina, Khalife, Jamal, Klonjkowski, Bernard, Lavielle, Marc, Le Corre, Valérie, Lefèvre, François, Lemaire, Olivier, Lereclus, Didier, Maximilien, Rémy, Meurs, Eliane, Naffakh, Nadia, Négre, Didier, Ochatt, Sergio, Pages, Jean-Christophe, Raynaud, Xavier, Regnault-Roger, Catherine, Renard, Michel, Renault, Tristan, Saindrenan, Patrick, Simonet, Pascal, Troadec, Marie-Bérengère, Vaissière, Bernard, Vilotte, Jean-Luc, Haut Conseil des Biotechnologies (HCB), Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Etablissement Français du Sang, Université Paris-Sud - Paris 11 (UP11), Université Paris Descartes - Paris 5 (UPD5), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction des Ressources Humaines et du Développement Durable (DRHDD), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Muséum national d'Histoire naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence nationale de sécurité du médicament et des produits de santé [Saint-Denis] (ANSM), Université Francois Rabelais [Tours], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Modélisation en pharmacologie de population (XPOP), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Pasteur [Paris] (IP), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Abeilles et environnement (AE), Génétique Animale et Biologie Intégrative (GABI), Haut Conseil des Biotechnologies, Commanditaire : Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt (France), Type de commande : Commande avec contrat/convention/lettre de saisine, Type de commanditaire ou d'auteur de la saisine : Ministères, parlements et les structures qui leur sont directement rattachées, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Massart, Isabelle, Institut Pasteur [Paris], Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest
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Plant Breeding ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,New Genomic Technics ,[SDV.BIO] Life Sciences [q-bio]/Biotechnology - Abstract
Synthèse sur la détection des produits issus des nouvelles technologies génomiques (NGT) appliquées aux plantesLa question du statut réglementaire des NGT (New Genomic Techniques), qui ont été définies comme techniques de modification du génome « apparues » depuis 2001 , est actuellement débattue en Europe. Ces techniques n’existaient pas, ou étaient peu développées lors de l’adoption des directives et règlements européens qui encadrent actuellement les organismes génétiquement modifiés (OGM). A l’époque le législateur européen avait choisi de réglementer les techniques de transgénèse et d’exempter les méthodes de mutagénèse notamment sur la base d’une expérience d’usage n’ayant révélé aucun problème particulier. Certaines NGT pouvant être utilisées pour induire une mutagenèse, ciblée ou non , la questionde leur soumission à la réglementation européenne en vigueur fait l’objet de discussions juridiques et politiques depuis quelques années. Les données scientifiques relatives à ces technologies (définitions, méthodes et résultats) doivent permettre de guider ces discussions.
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- 2021
25. Single-Cell and Bulk RNA-Sequencing Reveal Differences in Monocyte Susceptibility to Influenza A Virus Infection Between Africans and Europeans
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O’neill, Mary, Quach, Hélène, Pothlichet, Julien, Aquino, Yann, Bisiaux, Aurélie, Zidane, Nora, Deschamps, Matthieu, Libri, Valentina, Hasan, Milena, Zhang, Shen-Ying, Zhang, Qian, Matuozzo, Daniela, Cobat, Aurélie, Abel, Laurent, Casanova, Jean-Laurent, Naffakh, Nadia, Rotival, Maxime, Quintana-Murci, Lluis, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Diaccurate SAS, Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris], Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Rockefeller University [New York], Howard Hughes Medical Institute (HHMI), Biologie des ARN et virus influenza - RNA Biology of Influenza Virus, Collège de France (CdF (institution)), This work was supported by the Institut Pasteur, the Collège de France, the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10- LABX-62-IBEID) and 'Milieu Intérieur' (ANR-10-LABX-69-01), the Fondation de France (n°00106080), and the Fondation pour la Recherche Médicale (Equipe FRM DEQ20180339214). MO’N was supported by a European Molecular Biology Organization long-term fellowship (ALTF 229-2017)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Éco-Anthropologie (EA), Collège Doctoral, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Biologie des ARN et virus influenza - RNA Biology of Influenza Virus (CNRS-UMR3569), Collège de France - Chaire Génomique humaine et évolution, European Project: ALTF 229-2017, Gestionnaire, Hal Sorbonne Université, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Laboratoires d'excellence - GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE - - MILIEU INTERIEUR2010 - ANR-10-LABX-0069 - LABX - VALID, and European Molecular Biology Organization long-term fellowship - ALTF 229-2017 - INCOMING
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Adult ,[SDV.IMM] Life Sciences [q-bio]/Immunology ,Immunology ,population ,Black People ,GPI-Linked Proteins ,Monocytes ,influenza virus ,White People ,transcriptomics ,Young Adult ,Hypothesis and Theory ,Influenza, Human ,Immunology and Allergy ,Humans ,Sequence Analysis, RNA ,ancestry ,Receptors, IgG ,Middle Aged ,single-cell ‘omics ,Influenza A virus ,[SDV.IMM]Life Sciences [q-bio]/Immunology ,Cytokines ,single-cell 'omics ,Single-Cell Analysis ,Ribosomes - Abstract
International audience; There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use single-cell RNA-sequencing to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. We show widespread inter-individual variability in the percentage of IAV-infected monocytes. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3 , MX1 and OAS3 . Upon IAV challenge, we find that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. We also uncover a stronger resistance of CD16 + monocytes to IAV infection, together with CD16 + -specific mRNA expression of IL6 and TNF in response to IAV. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16 + monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Based on these data, we hypothesize that higher basal monocyte activation, driven by environmental factors and/or weak-effect genetic variants, underlies the lower cellular susceptibility to IAV infection of individuals of African ancestry relative to those of European ancestry. Further studies are now required to investigate how such cellular differences in IAV susceptibility translate into population differences in clinical outcomes and susceptibility to severe influenza.
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- 2021
26. AVIS en réponse à la saisine HCB - dossier 2020-172. Paris, le 06 septembre 2021
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Comité Scientifique Du Haut Conseil Des Biotechnologies, ., Angevin, Frédérique, Bagnis, Claude, Bar-Hen, Avner, Barny, Marie-Anne, Boireau, Pascal, Brévault, Thierry, Chauvel, Bruno, Collonnier, Cécile, Couvet, Denis, Dassa, Elie, de Verneuil, Hubert, Franche, Claudine, Guerche, Philippe, Guillemain, Joël, Hernandez Raquet, Guillermina, Khalife, Jamal, Klonjkowski, Bernard, Lavielle, Marc, Le Corre, Valérie, Lefèvre, François, Lemaire, Olivier, Lereclus, Didier, Maximilien, Rémy, Meurs, Eliane, Naffakh, Nadia, Négre, Didier, Ochatt, Sergio, Pages, Jean-Christophe, Raynaud, Xavier, Regnault-Roger, Catherine, Renard, Michel, Renault, Tristan, Saindrenan, Patrick, Simonet, Pascal, Troadec, Marie-Bérengère, Vaissière, Bernard, Vilotte, Jean-Luc, Haut Conseil des Biotechnologies (HCB), Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Etablissement Français du Sang, Université Paris-Sud - Paris 11 (UP11), Université Paris Descartes - Paris 5 (UPD5), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction des Ressources Humaines et du Développement Durable (DRHDD), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Muséum national d'Histoire naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Agence nationale de sécurité du médicament et des produits de santé [Saint-Denis] (ANSM), Université Francois Rabelais [Tours], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Modélisation en pharmacologie de population (XPOP), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Pasteur [Paris] (IP), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Abeilles et environnement (AE), Génétique Animale et Biologie Intégrative (GABI), Haut Conseil des Biotechnologies, Commanditaire : Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt (France), Type de commande : Commande avec contrat/convention/lettre de saisine, Type de commanditaire ou d'auteur de la saisine : Ministères, parlements et les structures qui leur sont directement rattachées, Massart, Isabelle, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest
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[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,[SDV.BIO] Life Sciences [q-bio]/Biotechnology - Abstract
Le Haut Conseil des biotechnologies (HCB) a été saisi le 22 juin 2021 par les autorités compétentes françaises (Ministère de l'Agriculture et de l'Alimentation) d'une demande d'avis relative au dossier EFSA-GMO-NL-2020-172 de demande d'autorisation de mise sur le marché du maïs génétiquement modifié DP915635 à des fins d'importation, transformation et alimentation humaine et animale. Ce dossier a été déposé par la société Pioneer Hi-Bred International, Inc. auprès des autorités compétentes néerlandaises sur le fondement du règlement (CE) n° 1829/2003. Dans le cadre de ce règlement, l'évaluation des dossiers de demande de mise sur le marché est confiée à l'Autorité européenne de sécurité des aliments (EFSA). Les Etats membres disposent de trois mois pour envoyer leurs commentaires à l'EFSA en contribution à l'évaluation du dossier. Dans ce contexte, le HCB est invité à proposer des commentaires à destination de l'EFSA au plus tard le 07 septembre 2021.
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- 2021
27. High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing.
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Kuang-Yu Chen, Jayaprakash Karuppusamy, O'Neill, Mary B., Opuu, Vaitea, Bahin, Mathieu, Foulon, Sophie, Ibanez, Pablo, Quintana-Murci, Lluis, Tatsuhiko Ozawa, van der Werf, Sylvie, Nghe, Philippe, Naffakh, Nadia, Griffiths, Andrew, and Isel, Catherine
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RNA sequencing ,INFLUENZA A virus ,INFLUENZA viruses ,H1N1 influenza ,MIXED infections ,REMANUFACTURING - Abstract
The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of eight genomic segments from distinct parental viruses. Existing data indicate that reassortant genotypes are not equiprobable; however, the low throughput of available virology techniques does not allow quantitative analysis. Here, we have developed a high-throughput single-cell droplet microfluidic system allowing encapsulation of IAV-infected cells, each cell being infected by a single progeny virion resulting from a coinfection process. Customized barcoded primers for targeted viral RNA sequencing enabled the analysis of 18,422 viral genotypes resulting from coinfection with two circulating human H1N1pdm09 and H3N2 IAVs. Results were highly reproducible, confirmed that genetic reassortment is far from random, and allowed accurate quantification of reassortants including rare events. In total, 159 out of the 254 possible reassortant genotypes were observed but with widely varied prevalence (from 0.038 to 8.45%). In cells where eight segments were detected, all 112 possible pairwise combinations of segments were observed. The inclusion of data from single cells where less than eight segments were detected allowed analysis of pairwise cosegregation between segments with very high confidence. Direct coupling analysis accurately predicted the fraction of pairwise segments and full genotypes. Overall, our results indicate that a large proportion of reassortant genotypes can emerge upon coinfection and be detected over a wide range of frequencies, highlighting the power of our tool for systematic and exhaustive monitoring of the reassortment potential of IAVs. [ABSTRACT FROM AUTHOR]
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- 2023
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28. RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes
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Boussier, Jeremy, Munier, Sandie, Achouri, Emna, Meyer, Bjoern, Crescenzo-Chaigne, Bernadette, Behillil, Sylvie, Enouf, Vincent, Vignuzzi, Marco, van Der Werf, Sylvie, Naffakh, Nadia, Immunobiologie des Cellules dendritiques, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], École Doctorale Bio Sorbonne Paris Cité [Paris] (ED BioSPC), Université Sorbonne Paris Cité (USPC)-Université de Paris (UP), Populations virales et Pathogenèse - Viral Populations and Pathogenesis, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris], Pasteur International Bioresources network (PIBNet), Plateforme de Microbiologie Mutualisée (PIBnet) - Mutualized Platform for Microbiology (P2M), This work was supported by the LabEx IBEID (grant 10-LABX-0062) to Sylvie van der Werf and the ANR (grant ANR-18-CE11-0028) to Nadia Naffakh. This work was funded inpart by the DARPA INTERCEPT program managed by Dr. JimGimlett, Dr. Brad Ringiesen, and Dr. Seth Cohen and administered through DARPA Cooperative Agreement #HR0011-17-2-0023 to Marco Vignuzzi (the content of the information does not necessarily reflect the position or the policy of the U.S. government, and no official endorsement should be inferred). J.B. was supported by a grant from the Ecole normale supérieure and by the école doctorale Frontières du vivant—programme Bettencourt, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-18-CE11-0028,FluTranscript,Mécanisme moléculaire de transcription par la polymérase du virus de la grippe(2018), Naffakh, Nadia, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Mécanisme moléculaire de transcription par la polymérase du virus de la grippe - - FluTranscript2018 - ANR-18-CE11-0028 - AAPG2018 - VALID, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), École Doctorale Bio Sorbonne Paris Cité [Paris] (ED562 - BioSPC), Université Sorbonne Paris Cité (USPC)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP), and Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur)
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[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,transcription-defective mutants ,Defective Viruses ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Genome, Viral ,[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Orthomyxoviridae ,Virus Replication ,Article ,amplification bias ,Influenza, Human ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,defective viral genomes ,Humans ,RNA, Viral ,RNA-seq ,influenza - Abstract
L'article est placé en CC-BY, 1 an après la publication du numéro; International audience; Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the molecular mechanisms that underlie the production and biological activity of DVGs is conditioned upon the sensitivity and accuracy of detection methods, that is, next-generation sequencing (NGS) technologies and related bioinformatics algorithms. Although many algorithms were developed, their sensitivity and reproducibility were mostly assessed on simulated data. Here, we introduce DG-seq, a time-efficient pipeline for DVG detection and quantification, and a set of biological controls to assess the performance of not only our bioinformatics algorithm but also the upstream NGS steps. Using these tools, we provide the first rigorous comparison of the two commonly used sample processing methods for RNA-seq, with or without a PCR preamplification step. Our data show that preamplification confers a limited advantage in terms of sensitivity and introduces size- but also sequence-dependent biases in DVG quantification, thereby providing a strong rationale to favor preamplification-free methods. We further examine the features of DVGs produced by wild-type and transcription-defective (PA-K635A or PA-R638A) influenza viruses, and show an increased diversity and frequency of DVGs produced by the PA mutants compared to the wild-type virus. Finally, we demonstrate a significant enrichment in DVGs showing direct, A/T-rich sequence repeats at the deletion breakpoint sites. Our findings provide novel insights into the mechanisms of influenza virus DVG production.
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- 2020
29. Influenza Virus RNA-Dependent RNA Polymerase and the Host Transcriptional Apparatus
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Krischuns, Tim, primary, Lukarska, Maria, additional, Naffakh, Nadia, additional, and Cusack, Stephen, additional
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- 2021
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30. Influenza B Virus Infection Is Enhanced Upon Heterotypic Co-infection With Influenza A Virus
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Malausse, Nicolas, van Der Werf, Sylvie, Naffakh, Nadia, Munier, Sandie, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Sorbonne Paris Cité (USPC), This work was supported by the LabEx Integrative Biology of Emerging Infectious Diseases (10-LABX-0062)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
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animal structures ,co-infection ,embryonic structures ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,viral interference ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,heterotypic ,Microbiology ,influenza B virus ,influenza virus ,Original Research - Abstract
International audience; Homotypic co-infections with influenza viruses are described to increase genetic population diversity, to drive viral evolution and to allow genetic complementation. Less is known about heterotypic co-infections between influenza A (IAV) and influenza B (IBV) viruses. Previous publications showed that IAV replication was suppressed upon co-infection with IBV. However, the effect of heterotypic co-infections on IBV replication was not investigated. To do so, we produced by reverse genetics a pair of replication-competent recombinant IAV (A/WSN/33) and IBV (B/Brisbane/60/2008) expressing a GFP and mCherry fluorescent reporter, respectively. A549 cells were infected simultaneously or 1 h apart at a high MOI with IAV-GFP or IBV-mCherry and the fluorescence was measured at 6 h post-infection by flow cytometry. Unexpectedly, we observed that IBV-mCherry infection was enhanced upon co-infection with IAV-GFP, and more strongly so when IAV was added 1 h prior to IBV. The same effect was observed with wild-type viruses and with various strains of IAV. Using UV-inactivated IAV or type-specific antiviral compounds, we showed that the enhancing effect of IAV infection on IBV infection was dependent on transcription/replication of the IAV genome. Our results, taken with available data in the literature, support the hypothesis that the presence of IAV proteins can enhance IBV genome expression and/or complement IBV defective particles.
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- 2021
31. Design and synthesis of naturally-inspired SARS-CoV-2 inhibitorsElectronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2md00149g
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Hassan, Haitham, Chiavaralli, Jeanne, Hassan, Afnan, Bedda, Loay, Krischuns, Tim, Chen, Kuang-Yu, Li, Alice Shi Ming, Delpal, Adrien, Decroly, Etienne, Vedadi, Masoud, Naffakh, Nadia, Agou, Fabrice, Mallart, Sergio, Arafa, Reem K., and Arimondo, Paola B.
- Abstract
A naturally inspired chemical library of 25 molecules was synthesised guided by 3-D dimensionality and natural product likeness factors to explore a new chemical space. The synthesised chemical library, consisting of fused-bridged dodecahydro-2a,6-epoxyazepino[3,4,5-c,d]indole skeletons, followed lead likeness factors in terms of molecular weight, C-sp3fraction and Clog P. Screening of the 25 compounds against lung cells infected with SARS-CoV-2 led to the identification of 2 hits. Although the chemical library showed cytotoxicity, the two hits (3b, 9e) showed the highest antiviral activity (EC50values of 3.7 and 1.4 μM, respectively) with an acceptable cytotoxicity difference. Computational analysis based on docking and molecular dynamics simulations against main protein targets in SARS-CoV-2 (main protease Mpro, nucleocapsid phosphoprotein, non-structural protein nsp10–nsp16 complex and RBD/ACE2 complex) were performed. The computational analysis proposed the possible binding targets to be either Mproor the nsp10–nsp16 complex. Biological assays were performed to confirm this proposition. A cell-based assay for Mproprotease activity using a reverse-nanoluciferase (Rev-Nluc) reporter confirmed that 3btargets Mpro. These results open the way towards further hit-to-lead optimisations.
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- 2023
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32. Host restriction of avian influenza viruses at the level of the ribonucleoproteins
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Naffakh, Nadia, Tomoiu, Andru, Rameix-Welti, Marie-Anne, and van der Werf, Sylvie
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Disease transmission -- Methods ,Host-virus relationships -- Physiological aspects ,Avian influenza viruses -- Physiological aspects ,Avian influenza viruses -- Genetic aspects ,Ribonucleoproteins -- Properties ,Biological sciences - Published
- 2008
33. Structural Insights Into Influenza A Virus Ribonucleoproteins Reveal a Processive Helical Track as Transcription Mechanism
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Ministerio de Ciencia, Innovación y Universidades (España), Sorzano, Carlos Óscar S. [0000-0002-9473-283X], Ortín, Juan [0000-0002-6200-4678], Martín-Benito, Jaime [0000-0002-8541-4709], Coloma, Rocío, Arranz, Rocío, Rosa-Trevín, José María de la, Sorzano, Carlos Óscar S., Munier, Sandie, Carlero, Diego, Naffakh, Nadia, Ortín, Juan, Martín-Benito, Jaime, Ministerio de Ciencia, Innovación y Universidades (España), Sorzano, Carlos Óscar S. [0000-0002-9473-283X], Ortín, Juan [0000-0002-6200-4678], Martín-Benito, Jaime [0000-0002-8541-4709], Coloma, Rocío, Arranz, Rocío, Rosa-Trevín, José María de la, Sorzano, Carlos Óscar S., Munier, Sandie, Carlero, Diego, Naffakh, Nadia, Ortín, Juan, and Martín-Benito, Jaime
- Abstract
The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein arranged in a double helical conformation. vRNPs are macromolecular machines responsible for messenger RNA synthesis and genome replication, that is, the formation of progeny vRNPs. Here, we describe the structural basis of the transcription process. The mechanism, which we call the 'processive helical track', is based on the extreme flexibility of the helical part of the vRNP that permits a sliding movement between both antiparallel nucleoprotein-RNA strands, thereby allowing the polymerase to move over the genome while bound to both RNA ends. Accordingly, we demonstrate that blocking this movement leads to inhibition of vRNP transcriptional activity. This mechanism also reveals a critical role of the nucleoprotein in maintaining the double helical structure throughout the copying process to make the RNA template accessible to the polymerase.
- Published
- 2020
34. Heterogeneity of monocyte subsets and susceptibility to influenza virus contribute to inter-population variability of protective immunity
- Author
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O'Neill, Mary, primary, Quach, Helene, additional, Pothlichet, Julien, additional, Aquino, Yann, additional, Bisiaux, Aurelie, additional, Zidane, Nora, additional, Deschamps, Matthieu, additional, Libri, Valentina, additional, Hasan, Milena, additional, Zhang, Shen-Ying, additional, Zhang, Qian, additional, Matuozzo, Daniela, additional, Cobat, Aurelie, additional, Abel, Laurent, additional, Casanova, Jean-Laurent, additional, Naffakh, Nadia, additional, Rotival, Maxime, additional, and Quintana-Murci, Lluis, additional
- Published
- 2020
- Full Text
- View/download PDF
35. Resistance Development to Influenza Virus Sialidase Inhibitors
- Author
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Rameix-Welti, Marie-Anne, primary, Munier, Sandie, additional, and Naffakh, Nadia, additional
- Published
- 2011
- Full Text
- View/download PDF
36. Influenza virus infection induces widespread alterations of host cell splicing
- Author
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Ashraf, Usama, primary, Benoit-Pilven, Clara, additional, Navratil, Vincent, additional, Ligneau, Cécile, additional, Fournier, Guillaume, additional, Munier, Sandie, additional, Sismeiro, Odile, additional, Coppée, Jean-Yves, additional, Lacroix, Vincent, additional, and Naffakh, Nadia, additional
- Published
- 2020
- Full Text
- View/download PDF
37. Detection and Quantification of Influenza Virus Defective Viral Genomes from NGS Datasets Obtained after RT or RT-PCR Product Sequencing
- Author
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Boussier, Jeremy, primary, Munier, Sandie, additional, Crescenzo-Chaigne, Bernadette, additional, Behillil, Sylvie, additional, Enouf, Vincent, additional, Werf, Sylvie van der, additional, and Naffakh, Nadia, additional
- Published
- 2020
- Full Text
- View/download PDF
38. La dimérisation, une nouvelle propriété de l’ARN polymérase des virus influenza
- Author
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Isel, Catherine, primary, Chen, Kuang-Yu, additional, and Naffakh, Nadia, additional
- Published
- 2020
- Full Text
- View/download PDF
39. Influenza virus genome reaches the plasma membrane via a modified endoplasmic reticulum and Rab11-dependent vesicles
- Author
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Martini, Isabel Fernandez de Castro, Fournier, Guillaume, Sachse, Martin, Pizarro Cerda, Javier, Risco, Cristina, Naffakh, Nadia, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), EA 302, Université Paris Diderot - Paris 7 (UPD7), Populations virales et Pathogenèse - Viral Populations and Pathogenesis, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Yersinia, Centre National de Référence de la Peste et autres Yersinioses - National Reference Center Plague and Yersinioses (CNR), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), French National Research Agency [ANR-10-INSB-04-01], EU FP7 PRE-DEMICS project [278433], Spanish Ministry of Economy, Industry and Competitiveness [BIO2015-68758-R], Institut Carnot Pasteur Maladies Infectieuses, PREDEMICS project, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
replication ,[SDV]Life Sciences [q-bio] ,Science ,Endosomes ,Endoplasmic Reticulum ,a virus ,Article ,ribonucleoprotein ,Madin Darby Canine Kidney Cells ,Viral Proteins ,Dogs ,trafficking ,viral-rna ,Animals ,Humans ,RNA, Small Interfering ,lcsh:Science ,Cell Membrane ,rab11 ,Microscopy, Electron ,Protein Transport ,HEK293 Cells ,Ribonucleoproteins ,A549 Cells ,Influenza A virus ,rab GTP-Binding Proteins ,transport ,cells ,RNA Interference ,lcsh:Q ,protein ,electron-microscopy - Abstract
Transport of neo-synthesized influenza A virus (IAV) viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the precise mechanism remains poorly understood. We used metal-tagging and immunolabeling to visualize viral proteins and cellular endomembrane markers by electron microscopy of IAV-infected cells. Unexpectedly, we provide evidence that the vRNP components and the Rab11 protein are present at the membrane of a modified, tubulated endoplasmic reticulum (ER) that extends all throughout the cell, and on irregularly coated vesicles (ICVs). Some ICVs are found very close to the ER and to the plasma membrane. ICV formation is observed only in infected cells and requires an active Rab11 GTPase. Against the currently accepted model in which vRNPs are carried onto Rab11-positive recycling endosomes across the cytoplasm, our findings reveal that the endomembrane organelle that is primarily involved in the transport of vRNPs is the ER., Transport of neo-synthesized influenza A virus viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the mechanism is unclear. Here the authors show that vRNPs are transported through a modified Rab11-positive endoplasmic reticulum and Rab11-dependent vesicles.
- Published
- 2017
40. Sensitivity of H5N1 influenza viruses to oseltamivir: an update
- Author
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Rameix-Welti, Marie-Anne, van der Werf, Sylvie, and Naffakh, Nadia
- Published
- 2008
- Full Text
- View/download PDF
41. Avis en réponse à la saisine du HCB sur le dossier EFSA-GMO-RX-013. Paris, le 30 janvier 2019
- Author
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Comité Scientifique du Haut Conseil des Biotechnologies, ., Angevin, Frédérique, Bagnis, Claude, Bar-Hen, Avner, Barny, Marie-Anne, Boireau, Pascal, Brévault, Thierry, Chauvel, Bruno, Collonnier, Cécile, Couvet, Denis, Dassa, Elie, De Verneuil, Hubert, Demeneix, Barbara, Franche, Claudine, Guerche, Philippe, Guillemain, Joël, Hernandez Raquet, Guillermina, Khalife, Jamal, Klonjkowski, Bernard, Lavielle, Marc, Le Corre, Valérie, Lefèvre, François, Lemaire, Olivier, Lereclus, Didier, Maximilien, Rémy, Meurs, Eliane, Naffakh, Nadia, Négre, Didier, Noyer, Jean-Louis, Ochatt, Sergio, Pages, Jean-Christophe, Raynaud, Xavier, Regnault-Roger, Catherine, Renard, Michel, Renault, Tristan, Saindrenan, Patrick, Simonet, Pascal, Troadec, Marie-Bérengère, Vaissière, Bernard, Vilotte, Jean Luc, Haut Conseil des Biotechnologies (HCB), Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Etablissement Français du Sang, Université Paris-Sud - Paris 11 (UP11), Université Paris Descartes - Paris 5 (UPD5), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), UAR 0241 Direction des Ressources Humaines, Institut National de la Recherche Agronomique (INRA)-Direction des Ressources Humaines (DRH)-Direction des Ressources Humaines (DRH), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Muséum national d'Histoire naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), Agence nationale de sécurité du médicament et des produits de santé [Saint-Denis] (ANSM), Université Francois Rabelais [Tours], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Modélisation en pharmacologie de population (XPOP), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Pasteur [Paris], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UR 406 Abeilles & Environnement, Génétique Animale et Biologie Intégrative (GABI), Haut Conseil des Biotechnologies, Commanditaire : Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt (France), Type de commande : Commande avec contrat/convention/lettre de saisine, and Type de commanditaire ou d'auteur de la saisine : Ministères, parlements et les structures qui leur sont directement rattachées
- Subjects
[SDV]Life Sciences [q-bio] ,[SDE]Environmental Sciences ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,[SHS]Humanities and Social Sciences - Published
- 2019
42. Avis en réponse à la saisine de l’ANSM. Paris le 20 décembre 2019
- Author
-
Bagnis, Claude, Boireau, Pascal, Dassa, Elie, Verneuil, Hubert De, Franche, Claudine, Guerche, Philippe, Khalife, Jamal, Klonjkowski, Bernard, Lefevre, François, Lemaire, Olivier, Lereclus, Didier, Meurs, Eliane, Naffakh, Nadia, Négre, Didier, Pages, Jean-Christophe, Renault, Tristan, Saindrenan, Patrick, Simonet, Pascal, Troadec, Marie-Berengere, Vilotte, Jean-Luc, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), retraité, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), NXP Semiconductors, IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), Institut Pasteur [Paris] (IP), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU de Tours), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Paris-Sud - Paris 11 (UP11), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génétique Animale et Biologie Intégrative (GABI), and Haut Conseil des Biotecjnologies
- Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology - Abstract
L'ANSM a récemment initié une réflexion en vue de la modification des modalités de qualification et de suivi des organismes et produits entrant dans la catégorie des micro-organismes et toxines, appelés MOT, devant nécessiter une déclaration d'utilisation. Au-delà de cette déclaration obligatoire, qui astreint à des mesures spécifiques de sécurité de manipulation et de stockage entre autres, l'ANSM déploie des mesures de contrôle des organismes déclarants. Outre les organismes et toxines mentionnés dans les listes officielles, des fragments de génomes de ces MOT peuvent faire l'objet d'études, en particulier par clonage et expression. Ces manipulations seraient alors à l'origine d'une catégorie particulière d'OGM (y compris des MGM) dont certains pourraient avoir des caractéristiques biologiques qui relèveraient d'une classification MOT. Aussi l'ANSM sollicite-t-elle le HCB afin qu'il produise une expertise permettant d'identifier et de caractériser ces OGM-MOT (Le HCB a été saisi 1 le 27 septembre 2019 par l'ANSM). La saisine est reproduite en annexe 1.
- Published
- 2019
43. Codon conservation in the influenza A virus genome defines RNA packaging signals
- Author
-
Gog, Julia R., Afonso, Emmanuel Dos Santos, Dalton, Rosa M., Leclercq, India, Tiley, Laurence, Elton, Debra, von Kirchbach, Johann C., Naffakh, Nadia, Escriou, Nicolas, and Digard, Paul
- Published
- 2007
44. Single-Cell and Bulk RNA-Sequencing Reveal Differences in Monocyte Susceptibility to Influenza A Virus Infection Between Africans and Europeans.
- Author
-
O'Neill, Mary B., Quach, Hélène, Pothlichet, Julien, Aquino, Yann, Bisiaux, Aurélie, Zidane, Nora, Deschamps, Matthieu, Libri, Valentina, Hasan, Milena, Zhang, Shen-Ying, Zhang, Qian, Matuozzo, Daniela, Cobat, Aurélie, Abel, Laurent, Casanova, Jean-Laurent, Naffakh, Nadia, Rotival, Maxime, and Quintana-Murci, Lluis
- Subjects
VIRUS diseases ,INFLUENZA A virus ,GENE expression ,RNA sequencing ,INFLUENZA viruses ,CD14 antigen - Abstract
There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use single-cell RNA-sequencing to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. We show widespread inter-individual variability in the percentage of IAV-infected monocytes. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3 , MX1 and OAS3. Upon IAV challenge, we find that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. We also uncover a stronger resistance of CD16
+ monocytes to IAV infection, together with CD16+ -specific mRNA expression of IL6 and TNF in response to IAV. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16+ monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Based on these data, we hypothesize that higher basal monocyte activation, driven by environmental factors and/or weak-effect genetic variants, underlies the lower cellular susceptibility to IAV infection of individuals of African ancestry relative to those of European ancestry. Further studies are now required to investigate how such cellular differences in IAV susceptibility translate into population differences in clinical outcomes and susceptibility to severe influenza. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
45. Expression of a foreign gene by stable recombinant influenza viruses harboring a dicistronic genomic segment with an internal promoter
- Author
-
Machado, Alexandre Vieira, Naffakh, Nadia, Werf, Sylvie van der, and Escriou, Nicolas
- Published
- 2003
- Full Text
- View/download PDF
46. Avis en réponse à la saisine HCB - dossier EFSA-GMO-RX009. Paris, le 4 juin 2018
- Author
-
Haut Conseil des Biotechnologies, Angevin, Frédérique, Bagnis, Claude, Bar-Hen, Avner, Barny, Marie-Anne, Boireau, Pascal, Brevault, Thierry, Chauvel, Bruno, Collonnier, Cécile, Couvet, Denis, Dassa, Elie, De Verneuil, Hubert, Demeneix, Barbara, Franche, Claudine, Guerche, Philippe, Guillemain, Joël, Hernandez Raquet, Guillermina, Khalife, Jamal, Klonjkowski, Bernard, Lavielle, Marc, Le Corre, Valérie, Lefèvre, François, Lemaire, Olivier, Lereclus, Didier, Maximilien, Rémy, Meurs, Eliane, Naffakh, Nadia, Nègre, Didier, Noyer, Jean-Louis, Ochatt, Sergio, Pagès, Jean-Christophe, Raynaud, Xavier, Regnault-Roger, Catherine, Renard, Michel, Renault, Tristan, Saindrenan, Patrick, Simonet, Pascal, Troadec, Marie-Bérengère, Vaissière, Bernard, and Vilotte, Jean Luc
- Published
- 2018
47. Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer
- Author
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Chen, Kuang-Yu, primary, Santos Afonso, Emmanuel Dos, additional, Enouf, Vincent, additional, Isel, Catherine, additional, and Naffakh, Nadia, additional
- Published
- 2019
- Full Text
- View/download PDF
48. Comparative Profiling of Ubiquitin Proteasome System Interplay with Influenza A Virus PB2 Polymerase Protein Recapitulating Virus Evolution in Humans
- Author
-
Biquand, Elise, Poirson, Juline, Karim, Marwah, Declercq, Marion, Malausse, Nicolas, Cassonnet, Patricia, Barbezange, Cyril, Straub, Marie-Laure, Jones, Louis, Munier, Sandie, Naffakh, Nadia, van der Werf, Sylvie, Jacob, Yves, Masson, Murielle, Demeret, Caroline, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the Institut Pasteur in the framework of PTR call 2015 (PTR no. 546), EU FP7 PREDEMICS (grant agreement 278433), and Labex IBEID. E.B. and M.D. were recipients of a MENRT Ph.D. fellowship, J.P. was a recipient of a Ph.D. fellowship from the Ligue Nationale Contre le Cancer and Alsace Contre le Cancer. M.K. received funding from the European Union Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement 665850., European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), European Project: 665850,H2020,H2020-MSCA-COFUND-2014,INSPIRE(2015), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris]
- Subjects
comparative interactomics ,viruses ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,influenza viruses ,ubiquitination ,Microbiology ,QR1-502 ,Research Article ,Host-Microbe Biology ,virus-host interactions - Abstract
Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adaptation to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin proteasome system (UPS). We found that the PB2 protein engages in an extended interplay with the UPS that evolved along with the virus’s adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches., The optimized exploitation of cell resources is one cornerstone of a successful infection. Differential mapping of host-pathogen protein-protein interactions (PPIs) on the basis of comparative interactomics of multiple strains is an effective strategy to highlight correlations between host proteome hijacking and biological or pathogenic traits. Here, we developed an interactomic pipeline to deliver high-confidence comparative maps of PPIs between a given pathogen and the human ubiquitin proteasome system (UPS). This subarray of the human proteome represents a range of essential cellular functions and promiscuous targets for many viruses. The screening pipeline was applied to the influenza A virus (IAV) PB2 polymerase proteins of five strains representing different levels of virulence in humans. An extensive PB2-UPS interplay has been detected that recapitulates the evolution of IAVs in humans. Functional validation with several IAV strains, including the seasonal H1N1pdm09 and H3N2 viruses, confirmed the biological relevance of most identified UPS factors and revealed strain-independent and strain-specific effects of UPS factor invalidation on IAV infection. This strategy is applicable to proteins from any other virus or pathogen, providing a valuable resource with which to explore the UPS-pathogen interplay and its relationship with pathogenicity. IMPORTANCE Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adaptation to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin proteasome system (UPS). We found that the PB2 protein engages in an extended interplay with the UPS that evolved along with the virus’s adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches.
- Published
- 2017
49. Differential Effect of Nucleotide Substitutions in the 3′ Arm of the Influenza A Virus vRNA Promoter on Transcription/Replication by Avian and Human Polymerase Complexes Is Related to the Nature of PB2 Amino Acid 627
- Author
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Crescenzo-Chaigne, Bernadette, van der Werf, Sylvie, and Naffakh, Nadia
- Published
- 2002
- Full Text
- View/download PDF
50. Hemagglutinin Residues of Recent Human A(H3N2) Influenza Viruses That Contribute to the Inability to Agglutinate Chicken Erythrocytes
- Author
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Medeiros, Rita, Escriou, Nicolas, Naffakh, Nadia, Manuguerra, Jean-Claude, and van der Werf, Sylvie
- Published
- 2001
- Full Text
- View/download PDF
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