Les Henipavirus sont des paramyxovirus zoonotiques émergents hautement pathogènes. Ils sont capables d’infecter un large spectre d’hôtes incluant notamment la chauve-souris frugivore (réservoir naturel), le porc et l’homme. Etant donné leur très grande dangerosité et en l’absence de traitements curatifs ou prophylactiques efficaces, ces virus doivent être manipulés dans un laboratoire de classe P4. Dans une première partie, nous étudions l’effet de composés glyco-amino-glycanes sur l’infection par les Henipavirus ainsi que leur potentielle application en tant que traitement. Dans une seconde partie, nous nous attachons à comprendre les interactions entre le système immunitaire de l’hôte et le virus. Afin de mieux comprendre ces interactions, nous avons utilisé une approche basée sur l’utilisation de souris déficientes pour certaines voies de l’immunité. En effet, bien que les récepteurs cellulaires au virus (EFN B2 et B3) soient fonctionnels chez la souris, celle-ci est résistante à l’infection par voie intrapéritonéale. Nous avons analysé la susceptibilité au virus Nipah (NiV) de souris privées de différentes voies du système immunitaire inné et adaptatif. Les résultats obtenus permettent d’envisager certaines lignées de ces souris comme nouveaux modèles animaux pour l’étude de l’immunopathogénèse du NiV. Cette étude suggère aussi que le système interféron de type I joue un rôle crucial dans la limitation de la propagation virale vers le cerveau et que les lymphocytes T sont nécessaires à la complète élimination du virus. Les macrophages jouent, quant à eux, un rôle central et indispensable, à l’interface entre système inné et adaptatif. Enfin, nous abordons les prémices d’un projet visant à identifier les différences d’interactions au niveau moléculaire entre les protéines non-structurales du virus et les protéines du système immunitaire inné chez l’Homme et la souris afin de voir s’il se dégage des différences d’interactions pouvant expliquer les différences de pathogénie. Ces travaux ont donc permis d’identifier de nouveaux modèles animaux et de mieux caractériser les interactions entre le pathogène et le système immunitaire de l’hôte, de l’échelle moléculaire à l’échelle de l’organisme entier. Néanmoins, les mécanismes précis de ces interactions restent à élucider et permettront certainement de mieux comprendre la grande diversité de pathogénie des Henipavirus. / Henipaviruses are highly pathogenic emerging zoonotic paramyxoviruses. They can infect a broad spectrum of mammals including flying foxes (Pteropus fruit bats), its reservoir, pigs and humans. As there are neither therapeutic drugs nor efficient prophylactic treatment towards these highly lethal viruses, they have to be manipulated in biosafety level-4 laboratories. In the first part of this thesis, we study the role of glyco-amino-glycans on Henipavirus infection and their potential use as treatment. In the second part, we describe the interaction between the host immune system and the pathogen. To investigate these interactions, we took advantage of different transgenic mouse models deficient for some immune pathways. Indeed, although mice possess the viral entry receptor for Henipaviruses, they do not succumbed to intraperitoneal infection. We analyzed the susceptibility to Nipah virus (NiV) infection of mice deleted for different components of innate and adaptive immune systems. Obtained results showed that some of these mice can be used as new models for NiV immunopathogenesis study. This study also suggests that type I interferon system plays a major role in limitation of viral spreading to the brain and that T cells are necessary for full viral clearance. Macrophages act at the crossroad of immunity, between innate and adaptive system. Finally, we deal with the preliminary phases of a project which aims to identify the differences, at a molecular level, of interaction between non-structural viral proteins and innate immunity proteins in mice and human. Such differences could explain the different clinical patterns that are observed in these species. In conclusion, this thesis allowed to identify new animal models and to better characterize host-pathogen interactions, from molecular to whole organism level. However, the precise mecanisms of these interactions remain to be elucidated and would probably help to understand the great diversity of pathogeny of Henipaviruses.

Brucella est une bactérie à Gram négatif, responsable de la brucellose, une zoonose ré-émergente. Sans traitement efficace, la pathologie peut devenir chronique et atteindre une grande variété de cellules et d'organes. Il a été montré que cette capacité à persister dans l'organisme pourrait être facilitée par son aptitude à se répliquer dans les cellules dendritiques (DCs) et à contrôler leur maturation in vitro. Les DCs sont considérées comme les cellules présentatrices d'antigènes les plus efficaces du système immunitaire. Elles forment un réseau complexe de cellules composé de plusieurs populations qui différent par leur origine, leur fonction ou leur localisation. Ainsi l'étude des interactions entre Brucella et les DCs doit être approfondie à ces différents sous-types. Dans ce but, nous avons utilisé différents modèles d'obtention de DCs in vitro précédemment décrits dans la littérature. Ces différentes méthodes de culture nous permettent d'obtenir plusieurs populations de cellules qui partagent des caractéristiques phénotypiques et fonctionnelles avec les sous-types observés in vivo. Nous avons ensuite comparé l'infection par Brucella entre le modèle classique utilisant du GMCSF à des méthodes utilisant du Flt3l ou du GMCSF combiné au Flt3l, à l'IL15 encore à l'IL4. Les résultats obtenus montrent que le contrôle de la maturation des DCs n'est pas un phénomène retrouvé dans toutes les populations. Nous avons pu montrer que dans certaines conditions la réplication de Brucella est moins efficace. Le champ d'étude des interactions entre Brucella et les DCs reste étendu et la compréhension de ces mécanismes pourrait fournir des clés pour combattre cette bactérie. / Brucella is a facultative intracellular gram-negative bacterium, responsible for a re-emergent zoonosis called brucellosis. Without effective treatment, the pathology may become chronic and reach a wide variety of cells and organs. This ability to persist into the organism has been pointed out as being presumably facilitated by its aptitude to replicate into dendritic cells (DCs) and to control their in vitro maturation. These cells are regarded as the most efficient antigen-presenting cells of the immune system. They form a complex network of cells consisting of several populations differing from each other from their origin, function or location. As a consequence, the interactions between Brucella and DCs should be studied more deeply as regarding the different subset. For that purpose, we used different models of in vitro DCs from former descriptive studies. These various culture methods allow us to get different population sharing phenotypic and functional features with the subtypes examined in vivo. Then, we compared Brucella infection of classical model using GMCSF to methods using Flt3l or GMCSF combined with Flt3l, IL15 or IL4. The results demonstrate that the control of DCs maturation is not a phenomenon that we can find again in every population. Moreover, we showed that the replication of Brucella is less active under certain conditions. The scope of the study on the interactions between Brucella and DCs remains extensive, and the understanding of those mechanisms might open doors in the fight against this bacterium.

Systemic Lupus Erythematosus (SLE) and Mixed Connective Tissue Disease (MCTD) are chronic, autoimmune disorders that target overlapping autoantigens and exhibit similar clinical manifestations. Despite 40 years of research, a reliable biomarker capable of diagnosing these syndromes has yet to be identified. Previous studies have confirmed that components of the U1 small nuclear ribonucleoprotein complex (U1 snRNP) such as U1A are 1000 fold more autoantigenic than any other nuclear component in SLE patients. Based on these findings, I hypothesize that models derived from the U1 snRNP autoantigenic properties could distinguish SLE from MCTD patients. To test this hypothesis, 30 peptides corresponding to protein regions of the U1 snRNP were tested in triplicates by indirect ELISA in sera from SLE or MCTD subjects. In addition laboratory tests and clinical manifestations data from these patients were included and analyzed in this investigation. Statistical classification methods as well as bioinformatics pattern recognition strategy were employed to determine which combination, if any, of all the variables included in this study provide the best segregation power for SLE and MCTD. The results confirmed that the IgM reactivity for U1 snRNP and U1A have the power to significantly distinguish SLE from MTCD patients as well as identify kidney and lung malfunctions for these subjects (p ≤ 0.05). Furthermore, the data analysis revealed eight novel classification rules for the segregation of SLE and MCTD which are a better classification tool than any of the currently available methods (p ≤ 0.05). Consequently, the results derived from this study support that SLE and MCTD are indeed separate disorders and pioneer the description of eight novel classification criteria capable of significantly discerning between SLE and MCTD patients (p ≤ 0.05).

La cardiopathie rhumatismale (CR) demeure la première cause de cardiopathie acquise chez les enfants et les jeunes adultes à travers le Monde. L'essor de l'échographie cardiaque comme outils de dépistage dans les zones endémiques pose de nouvelles questions. Trois études indépendantes ont été menées en Nouvelle Calédonie dans le cadre de la thèse de 2011 à 2013: " L'étude de cohorte rétrospective en population a évalué une campagne de dépistage national de la CR par échocardiographie visant à inclure tous les enfants scolarisés en classe de CM1 sur l'île de 2008 à 2011. Les méthodes diagnostiques complexes utilisées en recherche ne peuvent être transposées en campagnes de dépistage écho-guidées à l'échelle nationale en raison du nombre élevé d'enfants (~25%) sans diagnostic final. Le pronostic de la CR asymptomatique dépistée par échographie est bénin à moyen terme, quoique les lésions échographiques persistent dans la majorité des cas. Environ 13% des enfants initialement sains présentent des anomalies échocardiographiques à 2 ans de suivi. " Une étude prospective en population a exploré des méthodes simplifiées de dépistage à l'aide de l'échoscopie cardiaque avec des appareils de poche par du personnel paramédical. La sensibilité et la spécificité de cette approche permet de dépister ~80% des cas, avec une sensibilité de ~90% dans le cadre de CR certaine, seul cas de figure où un traitement est nécessaire. " Une cohorte hospitalière contemporaine de patients admis à l'unique centre du pays a permis d'apporter des données épidémiologiques de la CR symptomatique, et d'identifier les facteurs associés à la survenue d'événements cardiovasculaires. Le diagnostic y est encore souvent porté à un stade tardif, révélé par des complications (~25%). Le taux de survie à 8 ans de la CR symptomatique sans complication initiale est élevé (~98%) mais l’incidence annuelle d’événements atteint 59‰ (95% CI 44.35-73.75). La sévérité de la CR au diagnostic (CR moyenne versus modérée HR 3.39 (0.95 – 12.12); CR sévère versus modérée HR 10.81 (3.11 – 37.62), p<0.001) et l’antibioprophylaxie (HR 0.27 (0.12-0.63), p=0.01) sont les deux facteurs associés à la survenue d’événements cardiovasculaires. / Rheumatic heart disease (RHD) remains the leading acquired heart disease in the young worldwide. The advent of echocardiography as a screening tool has raised new questions in the field. This thesis incorporated three studies to explore critical questions regarding the burden of asymptomatic and symptomatic RHD in New Caledonia (2011-2013): Retrospective population-based cohort study assessing the first nationwide echo-screening campaign targeting all children in 4th grade (2008-2011). Methods derived from research may not be applicable as a healthcare policy given the lack of completeness (~25%). Outcomes of children with asymptomatic RHD detected by echocardiography are benign although the majority of valve lesions persist with little clinical implications. RHD being a dynamic condition, 13% of children at high risk of RHD with normal baseline echocardiograms may present with mild echocardiographic lesions at 2 years follow-up. Prospective population-based study assessing sensitivity and specificity to detect asymptomatic RHD of a focused cardiac ultrasound (FCU) compared to echocardiography. FCU includes nurses after a short training scheme using pocket-echocardiographic machines and simplified criteria. Sensitivity and specificity for RHD detection was of ~80% and performed better (sensitivity ~90%) when restricted to definite RHD in which case treatment is recommended. Retrospective hospital-based cohort of patients admitted with symptomatic RHD. RHD remains prevalent and incident. Diagnosis if often made at an advanced stage (~25%). In patients with uncomplicated RHD, the survival rate was ~96% at 8 years with however an annual incidence of 59.05‰ (95% CI 44.35-73.75) major cardiovascular events. The severity of RHD at diagnosis (moderate vs. mild HR 3.39 (0.95 – 12.12); severe vs. mild RHD HR 10.81 (3.11 – 37.62), p<0.001), and ongoing secondary prophylaxis at follow-up (HR 0.27 (0.12-0.63), p=0.01) were the two most influential factors associated with major cardiovascular events.

Commonly used simulation models for predicting outbreaks of re-emerging infectious diseases (EIDs) take an individual-level or a population-level approach to modeling contact dynamics. These approaches are a trade-off between the ability to incorporate individual-level dynamics and computational efficiency. Agent-based network models (ABNM) use an individual-level approach by simulating the entire population and its contact structure, which increases the ability of adding detailed individual-level characteristics. However, as this method is computationally expensive, ABNMs use scaled-down versions of the full population, which are unsuitable for low prevalence diseases as the number of infected cases would become negligible during scaling-down. Compartmental models use differential equations to simulate population-level features, which is computationally inexpensive and can model full-scale populations. However, as the compartmental model framework assumes random mixing between people, it is not suitable for diseases where the underlying contact structures are a significant feature of disease epidemiology. Therefore, current methods are unsuitable for simulating diseases that have low prevalence and where the contact structures are significant. The conceptual framework for a new simulation method, Evolving Contact Network Algorithm (ECNA), was recently proposed to address the above gap. The ECNA combines the attributes of ABNM and compartmental modeling. It generates a contact network of only infected persons and their immediate contacts, and evolves the network as new persons become infected. The conceptual framework of the ECNA is promising for application to diseases with low prevalence and where contact structures are significant. This thesis develops and tests different algorithms to advance the computational capabilities of the ECNA and its flexibility to model different network settings. These features are key components that determine the feasibility of ECNA for application to disease prediction. Results indicate that the ECNA is nearly 20 times faster than ABNM when simulating a population of size 150,000 and flexible for modeling networks with two contact layers and communities. Considering uncertainties in epidemiological features and origin of future EIDs, there is a significant need for a computationally efficient method that is suitable for analyses of a range of potential EIDs at a global scale. This work holds promise towards the development of such a model.

The accessory protein Nef of human immunodeficiency virus type 1 (HIV-1) has long been known to enhance the infectivity of HIV-1 progeny virions. The multipass transmembrane proteins serine incorporator 3 (SERINC3) and SERINC5 were recently identified as novel antiviral proteins that restrict HIV-1 infectivity. Nef enhances HIV-1 infectivity by removing SERINCs from the plasma membrane, which prevents their incorporation into progeny HIV-1 virions. To exploit this potent intrinsic antiretroviral factor for potential therapy development, it is critical to explore the determinants in SERINC5 that govern its downregulation by Nef and its restriction on HIV-1 infectivity. Here I report that the ability to inhibit HIV-1 infectivity is conserved among vertebrate SERINC5 proteins, whereas the sensitivity to downregulation by Nef is not. However, a Nef-resistant SERINC5 became Nef-sensitive when its intracellular loop 4 (ICL4) was replaced by that of Nef-sensitive human SERINC5. Conversely, human SERINC5 became resistant to Nef when its ICL4 was replaced by that of a Nef-resistant SERINC5. In general, ICL4 regions from SERINCs that exhibited resistance to a given Nef conferred resistance to the same Nef when transferred to a sensitive SERINC, and vice versa. I demonstrate that human SERINC5 can be modified to restrict HIV-1 infectivity even in the presence of Nef. Moreover, by generating chimeras between SERINC5 and SERINC2, which does not exhibit antiretroviral activity, I demonstrate that SERINC5’s inhibitory function, unlike the sensitivity to Nef, requires the participation of more than one region. Helix 4 and extracellular loop 5 (ECL5) of SERINC5 are both required for the potent restriction of HIV-1 infectivity. In contrast, a large amino-terminal portion of SERINC5 is not required for its antiretroviral activity of SERINC5. The determinants in ECL5 disperse throughout the loop. Furthermore, the ECL5 of SERINC5 is a hotspot region that determines the Env-dependent antiretroviral activity of SERINC5.

Protective antiviral immune responses require priming of naïve T cells by dendritic cells (DCs) that have matured sufficiently to produce co-stimulatory cell surface molecules and cytokines. Although only low levels of productive HIV-1 infection are detected in ex vivo DCs following HIV-1 challenge, those few cells exhibit innate activation. Experimentally bypassing blocks to entry and replication leads to more efficient transduction of DCs and maturation as indicated by production of interferons and interferon stimulated genes. Furthermore, similar innate activation occurs upon transduction of macrophages or CD4+ T cells. However, the mechanism by which HIV-1 is detected to activate innate immune signaling is not clear. The purpose of this thesis is to incorporate my data and observations into the understanding of HIV-1 innate detection and attempt to resolve seemingly conflicting observations. Reverse transcription and genomic integration are necessary for innate activation implying the need de novo transcription. Coding sequences are unnecessary save for those cis-acting sequences necessary for the HIV-1 life cycle. CRM1 dependent, HIV-1 unspliced RNA export is essential for innate activation. As intact viral sequence is unnecessary for transcription and export, defective proviruses may contribute to systemic inflammation seen in chronically infected individuals. These insights, are hoped to aid in the production of qualitatively better anti-retroviral drugs as well as in the design a protective HIV vaccine.

The clearance of viruses is largely dependent upon the activation of T cells to generate a robust immune response. However, host responses are suppressed during chronic viral infections. In this thesis, we explored the role of Top2α in DNA topology in individuals with chronic HBV, HCV, and HIV infections. We found that Top2α protein expression and activity were low in T cells derived from chronically virus-infected individuals compared to healthy subjects. Using CD4+ T cells treated with Top2α inhibitor or poisoner as a model, we demonstrated that Top2α inhibition disrupts the DNA topology, suppresses DNA repair kinase (ATM), and telomere protein (TRF2) expression, and induces T cell dysfunction. These findings reveal that Top2α inhibition is a mechanism by which viruses evade the host responses and establish persistent infection, and thus, restoring Top2α levels could be a way of boosting immune responses during chronic viral infections.

Viruses are pathogenic agents which affect all varieties of organisms, including plants, animals and humans. These microscopic particles are genetically simple organisms which encode a limited number of proteins that undertake a wide range of functions. While structurally distinct, viruses often share common characteristics that have evolved to aid in their infectious life cycles. A commonly underappreciated characteristic of many deadly viruses is a lipid envelope coat that surrounds them. Lipid enveloped viruses comprise a diverse range of pathogenic viruses, known to cause disease in both animals and human which often leads to high fatality rates, many of which lack effective and approved therapeutics. This report focuses on learning how a multifunctional protein within lipid enveloped viruses, the matrix protein, interacts with the plasma membrane of cells to enter and exit cells. Specifically, four viruses are investigated, Measles virus and Nipah virus (within the <i>Paramyxoviridae</i> family) and Ebola virus and Marburg virus (within the <i>Filoviridae</i> family). Through numerous <i>in vitro </i>experiments, functional cellular assays, a myriad of microscopy techniques, and experiments in high containment bio-safety level 4 settings, this report identifies specific lipids at play during the viral assembly process for each virus. Moreover, mechanistic insight is presented as to how each matrix protein interacts with the plasma membrane to facilitate: membrane association, viral matrix protein oligomerization and assembly, the rearrangement of lipids within the plasma membrane, and viral production. Lastly, numerous small molecule inhibitors targeting specific lipids, (e.g. phosphatidylserine and phosphatidylinositol 4,5 bisphosphate) within the cell were investigated for their efficacy in inhibiting matrix protein-dependent viral like particle production and viral spread in cells. As a whole, these projects lend credence to the significant role that lipids and the plasma membrane play throughout lipid enveloped viral life cycles, and provide compelling evidence for the merit of future drug-development research geared at targeting the matrix protein-plasma membrane interaction.

Signal Transducers and Activators of Transcription (STATs) are latent transcription factors that mediate several cellular responses. This protein family consists of seven members, STAT1 – 6 including two closely related molecules, STAT5a and STAT5b, that show 96% amino acid sequence homology and are critical for lymphoid, myeloid and erythroid cell development and function. Activated STAT proteins dimerize and translocate to the nucleus, where they bind to high-affinity DNA motifs to modulate gene expression. We recently identified STAT5b as the critical regulator of IgE-mediated cytokine production in mast cells. STAT5b knockout (KO) cells show decreased sensitivity to IgE-mediated passive systemic anaphylaxis accompanied with decreased production of IL-6 and IL-13 compared to wild type counterparts. Interestingly, STAT5b KO mice demonstrated elevated levels of serum IgE but a normal response to histamine-mediated passive systemic anaphylaxis. The current work demonstrates that STAT5b regulates mast cell function both in vivo and in vitro. Additionally, activated STAT proteins can also form tetramers through an N-terminal domain-mediated oligomerization process when bound to low-affinity tandem motifs. Dr. Warren Leonard’s laboratory generated STAT5a-STAT5b double knock-in (DKI) mice in which STAT5 proteins are phosphorylated and can form dimers but not tetramers. We have now found that bone marrow-derived mast cells from STAT5 DKI mice are defective in IgE-induced cytokine and chemokine production and exhibit defective stem cell factor (SCF)-induced migration and survival responses in vitro. Similarly, IgE-mediated passive systemic anaphylaxis is decreased in STAT5 DKI mice. These data indicate that Stat5 tetramers are critical for some aspects of mast cell function in allergic and inflammatory disease.