Swine influenza viruses (SIV) are a common and an important cause of respiratory disease in pigs. Pigs can serve as mixing vessels for the evolution of reassortment viruses containing both avian and human signatures, which have the potential to cause pandemics. NS1 protein of influenza A viruses is a major antagonist of host defence and it regulates multiple functions during infection by interacting with a variety of host proteins. Therefore, it is important to study swine viruses and NS1-interacting host factors in order to understand the mechanisms by which NS1 regulates virus replication and exerts its host defense functions. Influenza A viruses enter the host through the respiratory tract and infect epithelial cells in the respiratory tract, which form the primary sites of virus replication in the host. Thus, studying SIV infection in primary swine respiratory epithelial cells (SRECs) would resemble conditions similar to natural infection. The objectives of this study were to identify NS1-interacting host factors in the virus-infected SRECs and to understand the physiological role of at least one of the factors in influenza virus infection. The approaches to meet this objective were to generate a recombinant SIV carrying a Strep-tag in the NS1 protein, infect SRECs with the Strep-tag virus, purify NS1-interacting host protein complex from the infected cells by pull-down using strep-tactin resin and then study the physiological role of one of the NS1-interacting partners during influenza infection. Using a reverse-genetics strategy, a recombinant virus carrying the Strep-tag NS1 was successfully rescued and the SRECs were infected with this recombinant virus. The Strep-tag in the NS1 protein facilitated the isolation of an intact NS1-interacting protein complex and the proteins present in the complex were identified by liquid chromatography-tandem mass spectrometry. The identified proteins were grouped to enrich for different functions using bioinformatics. This gave an insight into the different functions that NS1 may regulate during infection and the potential host partners involved in these functions. Among the host proteins identified as potential interaction partners, RNA helicases were particularly of interest to study. Influenza being an RNA virus, RNA helicases could have important functions in the virus life cycle. Among the identified RNA helicases, DDX3 has been shown to regulate IFNβ induction and affect the life cycle of a number of viruses. However, its function in influenza A virus life cycle has not been studied. Hence, this study explored whether DDX3 has any role in the influenza A virus life cycle. Immunoprecipitation studies revealed viral proteins NP and NS1 as direct interaction partners with DDX3. DDX3 is a known component of stress granules (SGs) and influenza A virus lacking the NS1 gene is reported to induce SG formation. Therefore, the role of DDX3 in SG formation, induced by PR8 influenza A virus lacking NS1 (PR8 del NS1) was explored. The results from this study showed that DDX3 co-localized with NP in SGs indicating that DDX3 may interact with NP in the SGs. NS1 protein was found to inhibit virus-induced SGs and DDX3 downregulation impaired virus-induced SG formation. The contribution of the different domains of DDX3 to viral protein interaction and virus-induced SG formation was also studied. While DDX3 helicase domain did not interact with NS1 and NP, it was essential for DDX3 localization in virus induced SGs. Moreover, DDX3 downregulation resulted in the increased replication of PR8 del NS1virus, accompanied by an impairment of SG induction in infected cells. Since DDX3 is reported to regulate IFNβ induction, the role of DDX3 in influenza A virus induced IFNβ induction was also examined. Using small molecule inhibitors and siRNA-mediated gene knockdown, the RIG-I pathway was identified as the major contributor of influenza induced IFNβ induction in newborn porcine tracheal epithelial (NPTr) cells. DDX3 downregulation and overexpression also showed that DDX3 has an inhibitory effect on IFNβ expression induced by both influenza infection and low molecular weight (LMW) poly I:C treatment, which is also a RIG-I ligand. RNA competition assay to identify the mechanism of DDX3-mediated inhibition, showed that RIG-I binding affinity to its ligands LMW poly I:C and influenza viral RNA (vRNA) is much higher than that of DDX3. Furthermore, DDX3 downregulation enhanced titers of the PR8 del NS1 virus, while it did not affect the titers of the wild-type strains of PR8 and SIV/SK viruses. Overall, the results show that DDX3 has an antiviral role and the SG regulatory function of DDX3 has a profound effect on virus replication than the IFNβ regulatory function.

Le virus Influenza de type A (IAV) est un agent pathogène hypervariable responsable d’une infection respiratoire aiguë appelée la grippe. L’hyper-variabilité de ce virus IAV lui permet d’être résistant aux traitements antiviraux et est responsable de l’apparition des épidémies de grippe saisonnières. Il est donc essentiel d’établir de nouveaux traitements curatifs « à spectre large » insensibles aux variations du virus de la grippe. Les nanoparticules d’argent (NPs-Ag) sont les nanomatériaux métalliques les plus présents dans le secteur de la santé. En effet, leurs propriétés physico-chimiques leur confèrent de nombreuses capacités telles que la modulation des réponses immunitaires au niveau du poumon et des effets antimicrobiens. Quelques études ont démontré le potentiel anti-IAV des NPs-Ag lorsqu’elles sont placées directement en contact avec le virus IAV. Cependant, aucune de ces études ne porte sur les effets des NPs-Ag dans un contexte physiologique constitué d’une infection grippale suivie d’un traitement. D’autre part, au jour d’aujourd’hui, on ignore les mécanismes d’action mis en place par ces NPs-Ag et les effets induits par l’interaction de ces NPs-Ag avec le système immunitaire dans le contexte d’une infection par l’IAV. Dans ce travail de thèse, l’objectif est d’identifier les mécanismes d’action mis en place par les NPs-Ag au cours de l’infection par le virus IAV et également d’identifier si ces NPs-Ag pourraient être utilisées comme traitement curatif.Dans ce manuscrit de thèse, nous avons pu identifier, dans les cellules épithéliales pulmonaires, un nouveau mécanisme de modulation des NPs-Ag sur la réponse anti-IAV précoce médiée, entre autres, par la sécrétion de la chimiokine CCL5 et de l’IFN-. En effet, les NPs-Ag ciblent spécifiquement la voie de signalisation RIG-I-MAVS-IRFs, activée suite à l’infection par l’IAV et qui est liée à la mitochondrie. Ces NPs-Ag ciblent également en parallèle, à la fois le réseau mitochondrial et le flux autophagique. L’ensemble de ces effets conduit à une redistribution des facteurs de régulation des IFNs (IRFs), les empêchant potentiellement d’interagir avec d’autres facteurs de la voie de signalisation RIG-I/MAVS, ce qui pourrait expliquer l’inhibition de la sécrétion de CCL5 et de l’IFN-b, induite par le virus influenza de type A, par les nanoparticules d’argent. / The Influenza A virus (IAV) is a hyper-variable pathogen causing acute respiratory infection known as Flu. Its hyper-variability allows it to be resistant to antiviral treatment. It is therefore essential to establish new curative "broad spectrum" treatments. Silver nanoparticles (NPs-Ag) are the most metallic nanomaterials present in the health sector and are potent microbicidal agents with major concerns about their use on humans because of their toxicity. Some studies have shown the antiviral effect of NPs-Ag against IAV, but not in a physiological context of Flu. Moreover, the antiviral and immunomodulation mechanisms of NPs-Ag during infection by IAV is still unclear. Here, we show that intra-tracheal administration of AgNPs to influenza infected mice or treatment of human lung epithelial cells with AgNPs resulted in exacerbated inflammation, reduced viral clearance and enhanced mortality associated to different regulation of KC (pro-inflammatory cytokine functionally homologue to human IL-8) and CCL-5 (interferon-related cytokine) in the lung. In this PhD thesis, we identified in lung epithelial cells, a new mechanism explaining dampening of mitochondrial antiviral immunity by AgNPs through alteration of the mitochondrial network leading to redistribution of IFNs regulatory factors 7, which prevents nuclear translocation of these factors. Finally, AgNPs increased LC3 positive vesicles and p62 expression, indicating that AgNPs modify the autophagy flux in lung epithelial cells. Thus, the NPs-Ag Ag inhibited the early anti-IAV response by specifically targeting the RIG-I/MAVS/IRFs signaling pathway resulting in down- regulation of CCL-5 and IFN-ß expression induced by IAV.

Bei Autoimmunkrankheiten wie der Multiplen Sklerose (MS) kommt es zu einer fehlgesteuerten Immunantwort mit Aktivierung und Persistenz autoreaktiver T-Zellen. Apoptose-regulierende Mechanismen wie das CD95-Rezeptor/CD95-Ligand- und TRAIL-Rezeptor/TRAIL-System könnten dabei eine wichtige Rolle spielen. Die lösliche Form des CD95-Rezeptor (sCD95) kann an CD95L binden und so die Apoptose aktivierter T-Zellen verhindern. Die systemische Blockade von TRAIL führt zur Exazerbation von Autoimmunerkrankungen in Tierversuchen. In der vorliegenden Arbeit wurden deshalb die Expression, Regulation und Bedeutung sowohl von sCD95 als auch von löslichem TRAIL (sTRAIL) und membranständigem TRAIL bei gesunden Probanden und Patienten mit schubförmig remittierender MS (RRMS) untersucht. Zytokine wurden mit ELISAs, Zelloberflächenproteine sowie Apoptose im Durchflusszytometer gemessen. Die Untersuchungen mit magnetisch gereinigten humanen Leukozytensubpopulationen und Zelllinien zeigten, dass sCD95 lediglich von zelltyp-spezifisch aktivierten humanen T-Zellen, sezerniert wird. TRAIL wurde vor allem von Monozyten, die mit IFN-beta stimuliert waren, sezerniert und auf der Zelloberfläche exprimiert. Zellkulturüberstände, die sTRAIL enthielten, lösten Apoptose in suszeptiblen Tumorzellen aus. TRAIL führte zu einer signifikanten Inhibition der Proliferation und der Produktion von Th1- und Th2-spezifischen Zytokinen bei humanen (auto)antigenspezifischen T-Zellen. Weder für die sCD95- noch für die TRAIL-Expression wurden Unterschiede zwischen RRMS-Patienten und gesunden Probanden nachgewiesen. Die Ergebnisse dieser Arbeit zeigen ein komplexes Regulations- und Expressionsmuster von sCD95 und TRAIL, ohne jedoch Anhaltspunkte für Unterschiede zwischen MS-Patienten und Gesunden zu liefern. Es ergaben sich wichtige Hinweise darauf, dass der protektive immunomodulatorische Effekt einer systemischen IFN-beta-Therapie bei MS durch TRAIL vermittelt werden könnte. / Autoimmune disorders such as Multiple Sclerosis (MS) are characterized by an aberrant immune response with activation and persistence of autoreactive T-cells. Apoptosis-regulating mechanism such as the CD95-Rezeptor/CD95-Ligand- and the TRAIL-Rezeptor/TRAIL-System may play a major role in this process. The soluble CD95 receptor (sCD95) can bind to CD95L and subsequently inhibit apoptosis of activated T-cells. The systemic blockade of TRAIL leads to the exacerbation of autoimmune disease in animal experiments. In this work I investigated the expression, regulation and significance of sCD95, soluble TRAIL (sTRAIL) and membrane-bound TRAIL in patients with remitting-relapsing MS (RRMS), and in healthy controls. Cytokines were measured by ELISA, membrane bound proteins and apoptosis were measured by flow cytometry. The experiments with magnetically sorted human leucocyte subpopulations and cell lines showed, that only cell-type specific activated human T-cells secrete sCD95. Both forms of TRAIL were expressed by monocytes stimulated with IFN-beta. Cell supernatants containing sTRAIL induced apoptosis in susceptible tumour cells. Furthermore TRAIL inhibited proliferation of (auto)antigen-specific T cells and the production of Th-1 and Th-2 specific cytokines. There were no differences in the expression of sCD95 and TRAIL between RRMS patients and healthy controls. This work shows a complex regulation pattern of sCD95 and TRAIL without being able to detect differences between MS patients and healthy controls. However, results point out that TRAIL could be an important mediator of the immunomodulatory effects of systemic IFN-beta therapy in MS.

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