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Meyniel-Schicklin L, Amaudrut J, Mallinjoud P, Guillier F, Mangeot PE, Lines L, Aublin-Gex A, Scholtes C, Punginelli C, Joly S, Vasseur F, Manet E, Gruffat H, Henry T, Halitim F, Paparin JL, Machin P, Darteil R, Sampson D, Mikaelian I, Lane L, Navratil V, Golinelli-Cohen MP, Terzi F, André P, Lotteau V, Vonderscher J, Meldrum EC, de Chassey B. Viruses traverse the human proteome through peptide interfaces that can be biomimetically leveraged for drug discovery. Proc Natl Acad Sci U S A 2024; 121:e2308776121. [PMID: 38252831 PMCID: PMC10835127 DOI: 10.1073/pnas.2308776121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
We present a drug design strategy based on structural knowledge of protein-protein interfaces selected through virus-host coevolution and translated into highly potential small molecules. This approach is grounded on Vinland, the most comprehensive atlas of virus-human protein-protein interactions with annotation of interacting domains. From this inspiration, we identified small viral protein domains responsible for interaction with human proteins. These peptides form a library of new chemical entities used to screen for replication modulators of several pathogens. As a proof of concept, a peptide from a KSHV protein, identified as an inhibitor of influenza virus replication, was translated into a small molecule series with low nanomolar antiviral activity. By targeting the NEET proteins, these molecules turn out to be of therapeutic interest in a nonalcoholic steatohepatitis mouse model with kidney lesions. This study provides a biomimetic framework to design original chemistries targeting cellular proteins, with indications going far beyond infectious diseases.
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Affiliation(s)
| | | | | | | | - Philippe E. Mangeot
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Anne Aublin-Gex
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Caroline Scholtes
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Claire Punginelli
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Florence Vasseur
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Evelyne Manet
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Henri Gruffat
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Thomas Henry
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | | | | | | | | | - Ivan Mikaelian
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon69373, France
| | - Lydie Lane
- Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics, Lausanne1015, Switzerland
| | - Vincent Navratil
- Pôle Rhône-Alpes de bioinformatique, Rhône-Alpes Bioinformatics Center, Université Lyon 1, Villeurbanne69622, France
- European Virus Bio-informatiques Center, Jena07743, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry91057, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Gif-sur-Yvette91198, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
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Perrin-Cocon L, Vidalain PO, Jacquemin C, Aublin-Gex A, Olmstead K, Panthu B, Rautureau GJP, André P, Nyczka P, Hütt MT, Amoedo N, Rossignol R, Filipp FV, Lotteau V, Diaz O. A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity. Commun Biol 2021; 4:217. [PMID: 33594203 PMCID: PMC7886870 DOI: 10.1038/s42003-021-01749-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
During the cancerous transformation of normal hepatocytes into hepatocellular carcinoma (HCC), the enzyme catalyzing the first rate-limiting step of glycolysis, namely the glucokinase (GCK), is replaced by the higher affinity isoenzyme, hexokinase 2 (HK2). Here, we show that in HCC tumors the highest expression level of HK2 is inversely correlated to GCK expression, and is associated to poor prognosis for patient survival. To further explore functional consequences of the GCK-to-HK2 isoenzyme switch occurring during carcinogenesis, HK2 was knocked-out in the HCC cell line Huh7 and replaced by GCK, to generate the Huh7-GCK+/HK2− cell line. HK2 knockdown and GCK expression rewired central carbon metabolism, stimulated mitochondrial respiration and restored essential metabolic functions of normal hepatocytes such as lipogenesis, VLDL secretion, glycogen storage. It also reactivated innate immune responses and sensitivity to natural killer cells, showing that consequences of the HK switch extend beyond metabolic reprogramming. Many cancers fuel their rapid growth by replacing glucokinase with its higher affinity isoenzyme, hexokinase 2 (HK2), making HK2 an attractive drug target. In this study, Perrin-Cocon and Vidalain et al. use CRISPR/Cas-9 gene editing to reverse this enzymatic switch in human liver cancer cells, and find this restores innate immune function as well as reversing cancer-associated metabolic reprogramming.
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Affiliation(s)
- Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France
| | - Anne Aublin-Gex
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France
| | - Keedrian Olmstead
- Cancer Systems Biology, Institute for Diabetes and Cancer, Helmholtz Zentrum München, Ingolstädter Landstraße 1, München, D-85764, Germany
| | - Baptiste Panthu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France.,Univ Lyon, CarMeN Laboratory, Inserm, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Hôpital Lyon Sud, Bâtiment CENS ELI-2D, 165 Chemin du grand Revoyet, Pierre-Bénite, F-69310, France
| | - Gilles Jeans Philippe Rautureau
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN), FRE 2034, 5 rue de la Doua, Villeurbanne, F-69100, France
| | - Patrice André
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France
| | - Piotr Nyczka
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, Bremen, D-28759, Germany
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, Bremen, D-28759, Germany
| | - Nivea Amoedo
- CELLOMET, Centre de Génomique Fonctionnelle de Bordeaux, 146 Rue Léo Saignat, Bordeaux, F-33000, France
| | - Rodrigue Rossignol
- CELLOMET, Centre de Génomique Fonctionnelle de Bordeaux, 146 Rue Léo Saignat, Bordeaux, F-33000, France.,Univ. Bordeaux, Inserm U1211, MRGM, Centre hospitalier universitaire Pellegrin, place Amélie Raba Léon, Bordeaux, F-33076, France
| | - Fabian Volker Filipp
- Cancer Systems Biology, Institute for Diabetes and Cancer, Helmholtz Zentrum München, Ingolstädter Landstraße 1, München, D-85764, Germany.,School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, Freising, D-85354, Germany
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France.
| | - Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 21 Avenue Tony Garnier, Lyon, F-69007, France.
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3
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Perrin-Cocon L, Aublin-Gex A, Diaz O, Ramière C, Peri F, André P, Lotteau V. Toll-like Receptor 4-Induced Glycolytic Burst in Human Monocyte-Derived Dendritic Cells Results from p38-Dependent Stabilization of HIF-1α and Increased Hexokinase II Expression. J Immunol 2018; 201:1510-1521. [PMID: 30037846 DOI: 10.4049/jimmunol.1701522] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
Abstract
Cell metabolism now appears as an essential regulator of immune cells activation. In particular, TLR stimulation triggers metabolic reprogramming of dendritic cells (DCs) with an increased glycolytic flux, whereas inhibition of glycolysis alters their functional activation. The molecular mechanisms involved in the control of glycolysis upon TLR stimulation are poorly understood for human DCs. TLR4 activation of human monocyte-derived DCs (MoDCs) stimulated glycolysis with an increased glucose consumption and lactate production. Global hexokinase (HK) activity, controlling the initial rate-limiting step of glycolysis, was also increased. TLR4-induced glycolytic burst correlated with a differential modulation of HK isoenzymes. LPS strongly enhanced the expression of HK2, whereas HK3 was reduced, HK1 remained unchanged, and HK4 was not expressed. Expression of the other rate-limiting glycolytic enzymes was not significantly increased. Exploring the signaling pathways involved in LPS-induced glycolysis with various specific inhibitors, we observed that only the inhibitors of p38-MAPK (SB203580) and of HIF-1α DNA binding (echinomycin) reduced both the glycolytic activity and production of cytokines triggered by TLR4 stimulation. In addition, LPS-induced HK2 expression required p38-MAPK-dependent HIF-1α accumulation and transcriptional activity. TLR1/2 and TLR2/6 stimulation increased glucose consumption by MoDCs through alternate mechanisms that are independent of p38-MAPK activation. TBK1 contributed to glycolysis regulation when DCs were stimulated via TLR2/6. Therefore, our results indicate that TLR4-dependent upregulation of glycolysis in human MoDCs involves a p38-MAPK-dependent HIF-1α accumulation, leading to an increased HK activity supported by enhanced HK2 expression.
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Affiliation(s)
- Laure Perrin-Cocon
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
| | - Anne Aublin-Gex
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
| | - Olivier Diaz
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
| | - Christophe Ramière
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
| | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Patrice André
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, Biologie Cellulaire des Infections Virales, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France; and
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de Chassey B, Aublin-Gex A, Ruggieri A, Meyniel-Schicklin L, Pradezynski F, Davoust N, Chantier T, Tafforeau L, Mangeot PE, Ciancia C, Perrin-Cocon L, Bartenschlager R, André P, Lotteau V. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication. PLoS Pathog 2013; 9:e1003440. [PMID: 23853584 PMCID: PMC3701712 DOI: 10.1371/journal.ppat.1003440] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/06/2013] [Indexed: 12/24/2022] Open
Abstract
Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution. Viruses are obligate intracellular parasites that rely on cellular functions for efficient replication. As most biological processes are sustained by protein-protein interactions, the identification of interactions between viral and host proteins can provide a global overview about the cellular functions engaged during viral replication. Influenza viruses express 13 viral proteins, including NS1 and NS2, which are translated from an alternatively spliced RNA derived from the same genome segment. We present here a comprehensive overview of possible interactions of cellular proteins with NS1 and NS2 from 9 viral strains. Seventy nine cellular proteins were identified to interact with NS1, NS2 or both NS1 and NS2. These interacting host cell proteins are potentially involved in many steps of the virus life cycle and 7 can directly control the viral replication. Most of the cellular targets are shared by the majority of the virus strains, especially the double-stranded RNA binding domain protein family that is strikingly targeted by NS1. One of its members, ADAR1, is essential for influenza virus replication. ADAR1 colocalizes with NS1 in nuclear structures and its editing activity is enhanced by NS1 expressed on its own and during virus infection. A similar phenomenon is observed for dengue virus whose NS3 protein also interacts with ADAR1, suggesting a parallel virus-host co-evolution.
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Affiliation(s)
- Benoît de Chassey
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
| | - Anne Aublin-Gex
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Alessia Ruggieri
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Laurène Meyniel-Schicklin
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Fabrine Pradezynski
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Nathalie Davoust
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Thibault Chantier
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Lionel Tafforeau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Philippe-Emmanuel Mangeot
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Claire Ciancia
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Patrice André
- Hospices Civils de Lyon, Hôpital de la Croix Rousse, Laboratory of Virology, Lyon, France
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, EVIR Team, Université de Lyon, Lyon, France
- Inserm, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
- * E-mail:
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de Chassey B, Meyniel-Schicklin L, Aublin-Gex A, André P, Lotteau V. Genetic screens for the control of influenza virus replication: from meta-analysis to drug discovery. Mol Biosyst 2012; 8:1297-303. [PMID: 22307679 DOI: 10.1039/c2mb05416g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Current anti-influenza virus drugs target two viral proteins and induce a selective pressure for the generation of drug resistant variants. This stresses the need for additional therapeutic strategies including drug targeting of cellular factors that are essential for viral replication. Reverse genetics approaches can be used to identify these factors and recently six independent genomic initiatives have led to the identification of 925 host factors that are essential for the replication of influenza viruses. Here we report a meta-analysis of this dataset, first revealing that these screens are poorly overlapping at the gene level. However, a strong convergence was observed at the level of biological processes which was further supported by an interactomic analysis showing a high interconnectivity of the essential host factors in the human protein network. Plugging virus-host protein interaction data on this dataset reveals a significant targeting of these factors by viral proteins, further validating the cellular targets. Combining this information, the first drug-influenza virus target network was constructed by retrieving from DrugBank 298 molecules interacting with 100 essential host factors. Of these, 204 are FDA-approved offering interesting potential for rapid drug repositioning in the treatment of flu.
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Pellet J, Tafforeau L, Lucas-Hourani M, Navratil V, Meyniel L, Achaz G, Guironnet-Paquet A, Aublin-Gex A, Caignard G, Cassonnet P, Chaboud A, Chantier T, Deloire A, Demeret C, Le Breton M, Neveu G, Jacotot L, Vaglio P, Delmotte S, Gautier C, Combet C, Deleage G, Favre M, Tangy F, Jacob Y, Andre P, Lotteau V, Rabourdin-Combe C, Vidalain PO. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Res 2009; 38:D371-8. [PMID: 20007148 PMCID: PMC2808970 DOI: 10.1093/nar/gkp1000] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such ‘ORFeome’ resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway® system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins.
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Affiliation(s)
- J Pellet
- INSERM U851, Lyon, IFR128-BioSciences, Université Lyon 1, Université de Lyon, Lyon, France
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