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Article ; Online: A polarized cell system amenable to subcellular resolution imaging of influenza virus infection.

Brault, Jean-Baptiste / Thouvenot, Catherine / Cannata Serio, Magda / Paisant, Sylvain / Fernandes, Julien / Gény, David / Danglot, Lydia / Mallet, Adeline / Naffakh, Nadia

PloS one

2024 Volume 19, Issue 1, Page(s) e0292977

Abstract: The life cycle of influenza A viruses (IAV), and notably intracellular trafficking of the viral genome, depends on multiple interactions with the cellular cytoskeleton and endomembrane system. A limitation of the conventional cellular models used for ... ...

Abstract	The life cycle of influenza A viruses (IAV), and notably intracellular trafficking of the viral genome, depends on multiple interactions with the cellular cytoskeleton and endomembrane system. A limitation of the conventional cellular models used for mechanistic study and subcellular imaging of IAV infection is that they are cultured in two dimensions (2D) under non-polarizing conditions, and therefore they do not recapitulate the intracellular organization of the polarized respiratory epithelial cells naturally targeted by IAVs. To overcome this limitation, we developed an IAV-infection assay in a 3D cell culture system which allows imaging along the baso-lateral axis of polarized cells, with subcellular resolution. Here we describe a protocol to grow polarized monolayers of Caco2-TC7 cells on static Cytodex-3 microcarrier beads, infect them with IAV, and subsequently perform immunostaining and confocal imaging, or electron microscopy, on polarized IAV-infected cells. This method can be extended to other pathogens that infect human polarized epithelial cells.
MeSH term(s)	Humans ; Influenza, Human ; Caco-2 Cells ; Orthomyxoviridae Infections ; Influenza A virus ; Epithelial Cells/metabolism ; Virus Replication
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292977
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Article ; Online: The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome.

Krischuns, Tim / Arragain, Benoît / Isel, Catherine / Paisant, Sylvain / Budt, Matthias / Wolff, Thorsten / Cusack, Stephen / Naffakh, Nadia

Nature communications

2024 Volume 15, Issue 1, Page(s) 1064

Abstract: The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation and activity towards transcription or replication of the ... ...

Abstract	The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation and activity towards transcription or replication of the viral genome, respectively. Here, we provide evidence that the FluPol-RNAP II binding interface, beyond its well-acknowledged function in cap-snatching during transcription initiation, has also a pivotal role in replication of the viral genome. Using a combination of cell-based and in vitro approaches, we show that the RNAP II C-terminal-domain, jointly with ANP32, enhances FluPol replication activity. We observe successive conformational changes to switch from a transcriptase to a replicase conformation in the presence of the bound RNPAII C-terminal domain and propose a model in which the host RNAP II is the anchor for transcription and replication of the viral genome. Our data open new perspectives on the spatial coupling of viral transcription and replication and the coordinated balance between these two activities.
MeSH term(s)	RNA Polymerase II/metabolism ; RNA-Dependent RNA Polymerase/metabolism ; RNA, Viral/genetics ; Orthomyxoviridae/genetics ; DNA-Directed RNA Polymerases ; Virus Replication/genetics
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; RNA, Viral ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2024-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45205-2
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Article ; Online: Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.

Krischuns, Tim / Isel, Catherine / Drncova, Petra / Lukarska, Maria / Pflug, Alexander / Paisant, Sylvain / Navratil, Vincent / Cusack, Stephen / Naffakh, Nadia

PLoS pathogens

2022 Volume 18, Issue 5, Page(s) e1010328

Abstract: During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs ( ... ...

Abstract	During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results suggest that the CTD-binding modes of IAV and IBV may represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery.
MeSH term(s)	Humans ; Influenza A virus/genetics ; Influenza B virus/metabolism ; Influenza, Human ; Phylogeny ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA-Dependent RNA Polymerase/genetics ; Virus Replication/genetics
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-05-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010328
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Article ; Online: The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication.

Dupont, Maud / Krischuns, Tim / Gianetto, Quentin Giai / Paisant, Sylvain / Bonazza, Stefano / Brault, Jean-Baptiste / Douché, Thibaut / Arragain, Benoît / Florez-Prada, Alberto / Perez-Perri, Joel I / Hentze, Matthias W / Cusack, Stephen / Matondo, Mariette / Isel, Catherine / Courtney, David G / Naffakh, Nadia

Nucleic acids research

2024

Abstract: Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, ... ...

Abstract	Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
Language	English
Publishing date	2024-04-30
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae291
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Article ; Online: A distinct cardiopharyngeal mesoderm genetic hierarchy establishes antero-posterior patterning of esophagus striated muscle.

Comai, Glenda / Heude, Eglantine / Mella, Sebastian / Paisant, Sylvain / Pala, Francesca / Gallardo, Mirialys / Langa, Francina / Kardon, Gabrielle / Gopalakrishnan, Swetha / Tajbakhsh, Shahragim

eLife

2019 Volume 8

Abstract: In most vertebrates, the upper digestive tract is composed of muscularized jaws linked to the esophagus that permits food ingestion and swallowing. Masticatory and esophagus striated muscles (ESM) share a common cardiopharyngeal mesoderm (CPM) origin, ... ...

Abstract	In most vertebrates, the upper digestive tract is composed of muscularized jaws linked to the esophagus that permits food ingestion and swallowing. Masticatory and esophagus striated muscles (ESM) share a common cardiopharyngeal mesoderm (CPM) origin, however ESM are unusual among striated muscles as they are established in the absence of a primary skeletal muscle scaffold. Using mouse chimeras, we show that the transcription factors
MeSH term(s)	Animals ; Body Patterning ; Esophagus/embryology ; Gene Expression Regulation, Developmental ; Hepatocyte Growth Factor/metabolism ; LIM-Homeodomain Proteins/metabolism ; Mesoderm/embryology ; Mice ; Muscle, Striated/embryology ; Proto-Oncogene Proteins c-met/metabolism ; Signal Transduction ; T-Box Domain Proteins/metabolism ; Transcription Factors/metabolism
Chemical Substances	HGF protein, mouse ; LIM-Homeodomain Proteins ; T-Box Domain Proteins ; Tbx1 protein, mouse ; Transcription Factors ; insulin gene enhancer binding protein Isl-1 ; Hepatocyte Growth Factor (67256-21-7) ; Proto-Oncogene Proteins c-met (EC 2.7.10.1)
Language	English
Publishing date	2019-09-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.47460
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Article ; Online: A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors

Chen, Kuang-Yu / Krischuns, Tim / Ortega Varga, Laura / Harigua-Souiai, Emna / Paisant, Sylvain / Zettor, Agnes / Chiaravalli, Jeanne / Courtney, David / O'Brien, Amornrat / Baker, Susan / Isel, Catherine / Agou, Fabrice / Jacob, Yves / Blondel, Arnaud / Naffakh, Nadia

bioRxiv

Abstract: Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is ... ...

Abstract	Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC50 values in the 4-21 micromolar range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
Keywords	covid19
Language	English
Publishing date	2021-12-21
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.12.18.473303
Database	COVID19

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Article ; Online: Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors.

Bar-Nur, Ori / Gerli, Mattia F M / Di Stefano, Bruno / Almada, Albert E / Galvin, Amy / Coffey, Amy / Huebner, Aaron J / Feige, Peter / Verheul, Cassandra / Cheung, Priscilla / Payzin-Dogru, Duygu / Paisant, Sylvain / Anselmo, Anthony / Sadreyev, Ruslan I / Ott, Harald C / Tajbakhsh, Shahragim / Rudnicki, Michael A / Wagers, Amy J / Hochedlinger, Konrad

Stem cell reports

2018 Volume 10, Issue 5, Page(s) 1505–1521

Abstract: Skeletal muscle harbors quiescent stem cells termed satellite cells and proliferative progenitors termed myoblasts, which play pivotal roles during muscle regeneration. However, current technology does not allow permanent capture of these cell ... ...

Abstract	Skeletal muscle harbors quiescent stem cells termed satellite cells and proliferative progenitors termed myoblasts, which play pivotal roles during muscle regeneration. However, current technology does not allow permanent capture of these cell populations in vitro. Here, we show that ectopic expression of the myogenic transcription factor MyoD, combined with exposure to small molecules, reprograms mouse fibroblasts into expandable induced myogenic progenitor cells (iMPCs). iMPCs express key skeletal muscle stem and progenitor cell markers including Pax7 and Myf5 and give rise to dystrophin-expressing myofibers upon transplantation in vivo. Notably, a subset of transplanted iMPCs maintain Pax7 expression and sustain serial regenerative responses. Similar to satellite cells, iMPCs originate from Pax7
MeSH term(s)	Animals ; Biomarkers/metabolism ; Cell Differentiation/drug effects ; Cell Self Renewal/drug effects ; Cellular Reprogramming/drug effects ; Fibroblasts/cytology ; Fibroblasts/drug effects ; Mice ; Muscle Development/drug effects ; Muscle Fibers, Skeletal/drug effects ; Muscle Fibers, Skeletal/pathology ; Muscle, Skeletal/cytology ; Muscular Dystrophy, Animal/pathology ; MyoD Protein/metabolism ; PAX7 Transcription Factor/metabolism ; Regeneration/drug effects ; Satellite Cells, Skeletal Muscle/metabolism ; Small Molecule Libraries/pharmacology ; Stem Cell Niche/drug effects ; Stem Cell Transplantation ; Stem Cells/cytology ; Stem Cells/drug effects ; Transgenes
Chemical Substances	Biomarkers ; MyoD Protein ; PAX7 Transcription Factor ; Small Molecule Libraries
Language	English
Publishing date	2018-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2018.04.009
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Article ; Online: Distinct regulatory cascades govern extraocular and pharyngeal arch muscle progenitor cell fates.

Sambasivan, Ramkumar / Gayraud-Morel, Barbara / Dumas, Gérard / Cimper, Clémire / Paisant, Sylvain / Kelly, Robert G / Kelly, Robert / Tajbakhsh, Shahragim

Developmental cell

2009 Volume 16, Issue 6, Page(s) 810–821

Abstract: Genetic regulatory networks governing skeletal myogenesis in the body are well understood, yet their hierarchical relationships in the head remain unresolved. We show that either Myf5 or Mrf4 is necessary for initiating extraocular myogenesis. Whereas ... ...

Abstract	Genetic regulatory networks governing skeletal myogenesis in the body are well understood, yet their hierarchical relationships in the head remain unresolved. We show that either Myf5 or Mrf4 is necessary for initiating extraocular myogenesis. Whereas Mrf4 is dispensable for pharyngeal muscle progenitor fate, Tbx1 and Myf5 act synergistically for governing myogenesis in this location. As in the body, Myod acts epistatically to the initiating cascades in the head. Thus, complementary pathways, governed by Pax3 for body, and Tbx1 for pharyngeal muscles, but absent for extraocular muscles, activate the core myogenic network. These diverse muscle progenitors maintain their respective embryonic regulatory signatures in the adult. However, these signatures are not sufficient to ensure the specific muscle phenotypes, since the expected differentiated phenotype is not manifested when satellite cells are engrafted heterotopically. These findings identify novel genetic networks that may provide insights into myopathies which often affect only subsets of muscles.
MeSH term(s)	Animals ; Branchial Region/cytology ; Branchial Region/metabolism ; Cell Lineage ; Cell Survival ; Eye/cytology ; Eye/metabolism ; Eye/transplantation ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Head ; Mice ; Muscle Development ; Muscles/cytology ; Muscles/metabolism ; Mutation/genetics ; MyoD Protein/metabolism ; Myogenic Regulatory Factor 5/genetics ; Myogenic Regulatory Factor 5/metabolism ; Myogenic Regulatory Factors/genetics ; Myogenic Regulatory Factors/metabolism ; Phenotype ; Satellite Cells, Skeletal Muscle/cytology ; Somites/cytology ; Somites/metabolism ; Stem Cell Transplantation ; Stem Cells/cytology ; Stem Cells/metabolism ; T-Box Domain Proteins/genetics ; T-Box Domain Proteins/metabolism ; Transplantation, Heterotopic
Chemical Substances	Myf5 protein, mouse ; MyoD Protein ; Myogenic Regulatory Factor 5 ; Myogenic Regulatory Factors ; T-Box Domain Proteins ; Tbx1 protein, mouse ; myogenic factor 6
Language	English
Publishing date	2009-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2009.05.008
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Zs.A 5742: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 76: Show issues

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Article: Efficient control of gene expression in the hematopoietic system using a single Tet-on inducible lentiviral vector.

Barde, Isabelle / Zanta-Boussif, Maria Antonietta / Paisant, Sylvain / Leboeuf, Marylene / Rameau, Philippe / Delenda, Christophe / Danos, Olivier

Molecular therapy : the journal of the American Society of Gene Therapy

2006 Volume 13, Issue 2, Page(s) 382–390

Abstract: This work addresses the problem of efficient control of gene expression in the context of viral vectors, which still represents a difficult challenge. A number of lentiviral vectors incorporating the different elements of regulatable transcriptional ... ...

Abstract	This work addresses the problem of efficient control of gene expression in the context of viral vectors, which still represents a difficult challenge. A number of lentiviral vectors incorporating the different elements of regulatable transcriptional systems have been described, but they fail to perform satisfactorily either because of a poor dynamic range of transcription levels or because they display high background activities in the uninduced state and mediocre inducer response. We report here on the systematic comparison of vector designs containing the elements of the doxycycline-inducible Tet-on system in their most advanced versions (rtTA2S-M2 transactivator and tTS(Kid) repressor). We show that a simple "all-in-one" vector can be obtained and used for efficient control of transgene expression in long-term tissue culture and in the hematopoietic system of mice following bone marrow transplantation. Using this vector, the uninduced state can be kept at background levels and induction factors of 100-fold are repeatedly obtained over months both in tissue culture and in vivo. Interestingly, the low background activity of the all-in-one vector renders the use of the tTS repressor dispensable, avoiding the problem of progressive loss of inducibility over time associated with irreversible modifications of the chromatin surrounding proviral sequences.
MeSH term(s)	Animals ; CHO Cells ; Cell Line ; Cricetinae ; Cricetulus ; Doxycycline/pharmacology ; Gene Expression Regulation, Viral/physiology ; Genes, Reporter ; Genetic Vectors/administration & dosage ; Genetic Vectors/biosynthesis ; HCT116 Cells ; Hematopoietic Stem Cells/metabolism ; Hematopoietic Stem Cells/virology ; Humans ; Lentivirus/genetics ; Mice ; Mice, Inbred C57BL ; NIH 3T3 Cells ; Promoter Regions, Genetic/genetics ; Regulatory Elements, Transcriptional/genetics ; Time Factors ; Transduction, Genetic
Chemical Substances	Doxycycline (N12000U13O)
Language	English
Publishing date	2006-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2005.09.012
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