Hepatitis C virus NS5A is a multi-functional viral protein essential for viral replication and assembly, although the exact role the protein plays in the viral lifecycle remains unclear. A vast array of functions have been attributed to NS5A in recent years, despite the lack of enzymatic activity. NS5A has been found to interact with over 130 host proteins including many which are central to cellular signaling pathways. NS5A is composed of three domains separated by regions of low complexity. All three domains perform important functions in the viral lifecycle. Domains I and II are essential for viral replication whereas domain III is required for viral assembly. However, the role that NS5A and its individual domains may play in modulating viral translation remains controversial. Previous studies have utilized translation reporter systems that do not accurately reflect the role of the viral 3´-UTR in modulating viral translation. We and others have shown that NS5A binds to the poly-U/UC region of the 3´-UTR. In addition to serving as the initiation site for negative strand synthesis the 3´-UTR functions to significantly enhance viral translation. The mechanism of translation enhancement remains unclear but may involve long range RNA-RNA interaction with the IRES, the binding of cellular proteins which stimulate translation and/or the recycling of ribosomes. Therefore, the protein-RNA interaction between NS5A and the poly-U/UC region has the potential to modulate viral translation. Therefore we set out to determine the role of NS5A and its individual domains in modulating viral translation and the role of the NS5A-poly-U/UC region interaction in this modulation. Utilizing monocistronic RNA reporters which contain the viral 5´- and 3´-UTRs and an internal Renilla luciferase reporter gene, we determined that NS5A specifically down-regulates viral translation in a dose-dependent manner through a mechanism dependent upon the presence of the poly-U/UC region in the viral 3´-UTR. Furthermore, we have re-tested the effect using full-length HCV genomic RNA reporters. These results suggest that NS5A is able to interfere with the stimulation of viral translation exerted by the 3´-UTR. This down-regulatory function of NS5A may function in mediating a switch from translation to replication, a step required in the lifecycle of a positive sensed RNA virus. Having established a role for NS5A in modulating viral translation, we then aimed to determine which region of NS5A was responsible for this effect. We found that each of NS5A domains was capable of this modulatory effect on viral translation independently. Although surprising, this finding is not entirely unexpected as each domain has been shown to retain the ability to bind to the poly-U/UC region. Within NS5A domain I we identified a 61 aa. region sufficient for translation down-regulation. Furthermore, we have identified a number of positively charged residues within this region involved in the modulation of viral translation, in particular arginine 112 (R112). This residue has previously been found to be at the domain I dimer contact interface and to form an intermolecular hydrogen bond with glutamic acid 148 (E148). We found that mutations R112A and E148A individually negate the ability of domain I to modulate viral translation and these mutations impede the formation of domain I dimers. Additionally, the R112A mutation appears to affect the ability of domain I to interact with the poly-U/UC region of the viral 3´-UTR alluding to the possible mechanism of translation modulation. Finally this mutation was lethal in an HCV subgenomic replication, confirming the link between NS5A dimerization, RNA binding and viral replication. These results collectively point to a crucial role for the NS5A arginine 112 residue in the modulation of HCV lifecycle by NS5A. Within NS5A domain II, we identified a 47 aa. region sufficient for translation modulation. Through the mutation of positively charged amino acids within this region, we found that lysine 312 (K312) was essential for this effect. The ability of this domain to modulate viral translation was completely lost when K312 was mutated within a full domain II protein fragment. The mechanism behind this modulation remains unclear but the 47 aa. region identified has been previously found to contain a region proposed to make contact with poly-U RNA and the K312 residue was suspected to interact directly with such RNA. Furthermore, this region interacts with the host protein cyclophilin A, an interaction that enhances the RNA binding ability of domain II. These findings strongly suggest that domain II modulates viral translation by binding within the poly-U/UC region. While investigating the modulation of viral translation by NS5A domain III we determined that the C-terminal 31 aa. are sufficient for the effect of this domain on viral translation. Through alanine scanning mutagenesis we identified glutamic acid 446 (E446) as playing a key role in the modulatory function of this region. Within a domain III protein fragment mutation of this E446 residue abolishes the modulatory function of this domain towards HCV translation. The mechanism behind this modulation and the role of E446 in this effect remains to be determined. These findings suggest that in addition to being essential for viral replication and assembly, NS5A has an important role in modulating viral translation through a mechanism requiring the poly-U/UC region of the viral 3´-UTR. Furthermore, each domain of NS5A appears to contribute to this effect. These results support the description of NS5A as a multi-functional protein and the further characterization of its functions may aid in the development of novel antivirals targeting the numerous functions of this complex, and at times puzzling, viral protein.

Le virus de l’Hépatite C (VHC), de la famille Flaviviridae, est à l’origine d’une pandémiemondiale. L’infection par le VHC provoque le dévelopment d’hépatites chroniques, decirrhoses et de carcinomes hépatocellulaires (CHC). Les fonctions de la majorité des protéinesvirales sont connues, mis à part pour NS5A dont la seule fonction directe attribuée à ce jour,équivaut à celle d’un facteur d'activation transcriptionnelle. Notre laboratoire a montréprécédemment que les variants de quasiespèce de NS5A isolés à partir du sérum d’un mêmepatient présentaient des différences significatives dans leurs propriétés intrinsèques detransactivation. Fort de ces résultats, nous avons analysé des variants de NS5A isolés à partirde tissu hépatique d’un patient chroniquement infecté par le VHC de génotype 1b. Cesanalyses ont révélé une compartimentation génétique et fonctionnelle des variants de NS5Aentre le tissu tumoral et le tissu non-tumoral adjacent. Nous avons donc émis l’hypothèse queles propriétés transactivatrices de NS5A pourraient jouer un rôle dans la pathogenèse ainsique dans la réplication virale, et que la variabilité naturelle de NS5A pourrait influencer sespropriétés transactivatrices. L’objectif de ce travail de thèse était d’analyser le rôle despropriétés transactivatrices de NS5A dans la pathogenèse hépatique viro-induite ainsi quedans la réplication virale. Pour étudier le rôle des propriétés de transactivation de NS5A dans la pathogenèse hépatique,nous avons développé des vecteurs lentiviraux pour exprimer dans les hépatocytes primaireshumains les variants choisis de NS5A portants différents potentiels de transactivation. Enutilisant la technologie RNA-Seq d’Illumina, l’analyse des transcriptomes d’hépatocytestransduits exprimant les variants transactivateurs fort et faible de NS5A, sera utiliser pouridentifier les voies cellulaires ciblées par les propriétés transactivatrices de NS5A. Pour lesétudes in vivo, nous avons lancé le développement des souris transgénique permettantl’activation conditionnelle de l’expression des variants de NS5A avec fort et faible potentielde transactivation, spécifiquement dans le foie. Ces souris transgéniques seront utilisées pourétudier le rôle potentiel des propriétés transactivatrices dans la pathogenèse VHC induite etplus particulièrement dans le développement des cancers. Pour étudier le rôle des propriétés de transactivation de NS5A dans la réplication virale, nousavons utilisé le système de réplicon subgénomique de VHC exprimant les variants de NS5Aprécédemment caractérisés. Pour exercer ses propriétés transactivatrices, NS5A doit êtrelocalisée au moins partiellement dans le noyau. Nous avons démontré qu’une partie de NS5Ase retrouve dans noyau et est recruté sur des promoteurs cellulaires, modulant ainsidirectement l’expression de gènes cellulaires essentiels pour la réplication de l’ARN viral.Nous avons observé que les variants de NS5A avec différents potentiels de transactivation,confèrent différentes capacités de réplication au réplicon subgénomique, et corrèlent avec lepotentiel de transactivation de variant correspondant. En accord avec ces observations,l’inhibition de translocation nucléaire de NS5A entraine une inhibition de la réplication virale,suggerant un rôle potentiel des propriétés transactivatrices de NS5A dans la réplication l’ARNvirale. En conclusion, nous avons démontré que l’activation transcriptionnelle des gènes cellulairespar la NS5A est essentielle pour la réplication de l’ARN du VHC. Cette modulation des gènescellulaires pourrait également être impliquée dans les mécanismes de la pathogenèse viroinduite.Nous confirmerons cette hypothèse grâce aux souris NS5A. Par ailleurs, ces résultatspourraient contribuer au développement de nouvelles thérapies anti-VHC, basées surl’inhibition de translocation nucléaire de NS5A / Hepatitis C virus (HCV) causes a chronic infection in the majority of infected patients,ultimately leading to liver cirrhosis and hepatocellular carcinoma (HCC). Although the rolesof the HCV proteins in the viral life cycle are increasingly understood, the precise function ofthe HCV NS5A protein has yet to be elucidated. To date, the only putative direct functionattributed to NS5A is its transcriptional transactivation properties. Our group has previouslyshown that quasispecies variants of NS5A isolated from the serum samples of the samepatient bear different transactivating properties according to their amino acid sequence. Basedon these observations, we performed preliminary phylogenetic and functional analysis ofNS5A variants isolated from liver tissue of individuals infected with HCV of genotype 1b.This analysis revealed genetic and functional compartmentation of NS5A variants in tumoraland adjacent non-tumoral tissue. We hypothesized that the natural variability of NS5A mayimpact its proposed transactivation properties. We also hypothesized that NS5A’s putativetransactivation properties could play a role in HCV replication and in liver pathogenesis. Theaim of the study presented in this thesis was to investigate the role of NS5A transactivationproperties in the development of HCV-induced liver pathogenesis as well as in viralreplication. To study the role of NS5A transcriptional activation properties in liver pathogenesis, wedeveloped lentiviral vectors for the expression of selected NS5A variants bearing differenttransactivation potentials in cultured primary human hepatocytes. We now intend to extendthese preparations using RNAseq technology to analyse the, transcriptome of primaryhepatocytes transduced with lentiviral vectors encoding strongly and weakly transactivatingNS5A variants to identify the cellular pathways targeted by NS5A, allowing us to decipherthe role of NS5A mediated host gene regulation in development of HCV inducedpathogenesis. For in vivo studies, we have begun the development of transgenic mice allowingliver-specific conditional expression of NS5A variants with high and low transactivationpotentials. These transgenic mice will be used to study the possible role of NS5Atransactivation properties in development of HCC. To study the role of NS5A transcriptional activation properties in HCV RNA replication, weused the sub-genomic replicon system expressing previously characterized NS5A sequences..Using this system, we have demonstrated that a subset of NS5A protein can translocate to thenucleus and is recruited to cellular promoters of host cell genes known to be required forefficient replication of HCV replicon RNA as well as those implicated in pathogenesis.Moreover, we have shown that NS5A directly regulate the expression of these genes.Consequently, it was observed that replicons encoding NS5A variants with differenttransactivation potentials exhibited different replication capacities, and that this correlatedwith the transactivation potential of the corresponding NS5A variant. In agreement with theseobservations, inhibition of nuclear translocation of NS5A resulted in the inhibition ofreplication of the HCV subgenomic replicon, further confirming the role of NS5Atransactivation properties in viral RNA replication. In conclusion, we have demonstrated that NS5A-mediated transcriptional regulation ofcellular genes is required for HCV replication. Such NS5A-mediated modulation of cellulargenes may also constitute one of the mechanisms involved in HCV-related liver pathogenesisand development of HCC, an aspect which is currently under investigation using the toolsdeveloped during this project. This study will contribute towards deciphering the role ofNS5A in viral replication as well as providing insight into its role in HCV-induced liverpathogenesis...

La phosphatidylinositol-4-kinase de type IIIα est une kinase de lipide eukaryote ubiquitaire qui synthétise le phosphatidylinositol-4-phosphate PtdIns(4)P de la membrane plasmique. Ce phosphoinositide est d’autant plus important qu’il tient un rôle majeur dans différentes voies de signalisation cellulaire, le traffic vésiculaire ainsi que dans l’identité des organelles. De plus, la PIK4A humaine est un facteur essentiel pour la réplication du virus de l’hépatite C (VHC). En effet, le recrutement du complexe de réplication du VHC par la protéine virale NS5A à la membrane du reticulum endoplasmique permet la formation d’un réseau membranaire à l’origine de la structuration des complexes de replication viraux.La PI4KA est une kinase imposante (2102 résidus, 240 kDa pour la PI4KA humaine) qui possède un domaine kinase C-terminal d’environ 400 résidus précédé d’un domaine formé de répétitions Armadillo pour lequel aucune fonction n’a été determinée. Le rôle ainsi que le repliement des 1500 résidus N-terminaux de PI4KA ne sont pas connus à ce jour.Afin d’en savoir plus sur la structure tri-dimensionnelle de la PI4KA humaine, nous avons utilisé des outils bio-informatiques afin de délimiter et de modéliser les modules et domaines la composant. Nous avons pu ainsi les exprimer et les produire en bactérie et en cellules d’insecte afin de vérifier nos hypothèses. Nous avons pu conclure que PI4KA est composée de deux modules. Le module N-terminal (1100 résidus), est composé de deux domaines dont un solénoïde α. Les résultats obtenus par diffusion des rayons X aux petits angles (SAXS) nous permettent de définir leur agencement potentiel. Le second module (1000 résidus), le module C-terminal, est l’enzyme-core. Son analyse nous a permis d’identifier une similitude remarquable avec les sérine/thréonine kinases PIKKs, comme mTor, apparentées aux phosphatidylinositol-3-kinases. Nous avons défini au début du module C-terminal de PI4KA trois domaines putatifs que nous avons nommés DI, DII et DIII. Nos collaborateurs ont montré qu'ils sont essentiels à l’activité kinase de la protéine ainsi qu’à la replication du VHC. Le domaine DI a été caractérisé et a permis la validation d’une nouvelle paramétrisation de la molécule de N, N-dimethyl-dodecylamine oxide (LDAO) pour des simulations de dynamique moléculaire. Enfin, la PI4KA humaine dans son entier a été exprimée en cellules d’insecte puis purifiée, et un premier test d’interaction avec les membranes a été initié. / The eukaryotic lipid kinase phosphatidylinositol 4-kinase III alpha is a ubiquitous enzyme that synthesizes the plasma membrane pool of phosphatidylinositol 4-phosphate. This important phosphoinositide has key roles in different signalization pathways, vesicular traffic and cellular compartment identity. Moreover, PI4KA is an essential factor for hepatitis C virus (HCV) replication. Indeed, PI4KA's interaction with the non-structural HCV protein NS5A at the endoplasmic reticulum membrane leads to formation of a “membranous web” giving to the membrane the signature necessary to the formation of viral replication machineryPI4KA is a large protein (2102 residues, 240 kDa for human PI4KA) with the kinase domain making up the ca 400 C-terminal residues preceded by an Armadillo domain for which no function is known. There is essentially no structural information about the 1500 N-terminal residues and no clue as to the function of most of this region of PI4KA.We use computational methods in order to delineate fragments of human PI4KA amenable to soluble production in Escherichia coli and insect cells. We clone and express these fragments and evaluate the soluble fraction of each construction. Our results further suggest that PI4KA can be described as a two-module protein. The N-terminal module (1100 residues), is composed of two domains which one is an alpha solenoid. Their potential arrangement was defined by small angle X-ray scattering (SAXS).The second module (1000 residues), the C-terminal module, is the core enzyme. Its analysis leads us to identify similarities with the serine/threonine kinases PIKKs, as mTor, homologous to phosphatidylinositol-3-kinases. Three putative domains were delineate at the beginning of this C-terminal module. We name the DI, DII and DIII. Our collaborators have shown their necessity to the kinase activity of PI4KA and the HCV replication. DI domain was characterized and allowed the validation of a new parametrization of the N, N-dimethyl-dodecylamine oxide molecule (LDAO) for simulation of molecular dynamics. Finally, the full-length human PI4KA was expressed in insect cells, purified and a first interaction experiment with membranes have been initiated.

Hepatitis C infection is a global disease that causes an estimated 399,000 deaths per year. Treatment has improved dramatically in recent years through the development of direct acting antivirals that target specific regions of the Hepatitis C virus (HCV). Unfortunately the virus can have a preexisting resistance or become resistant to these drugs by mutations in the genes that code for the target proteins. These mutations are called resistance-associated substitutions (RASs). Since RASs can cause treatment failure for patients, resistance detection is performed in clinical practice to select the ideal regimen. Currently RASs are detected by using Sanger sequencing and a partly manual workflow that can discriminate the presence of a RAS if it is present in 15-20% of viruses in a patients blood. A new method with the capacity to detect lower ratios of RASs in HCV sequences was developed, which utilizes Pacific Biosciences’ (PacBio’s) sequencing and a bioinformatics analysis software called CLAMP. To validate this new approach, 123 HCV patient samples were sequenced with both methods and then analyzed. The RASs detected with the new method were congruent to what was found with the Sanger-based workflow. The new approach was also shown to correctly genotype the virus samples, identify any co-existing mutations on the same sequences, and detect if there were any mixed genotype infections in the samples. The new procedure was found to be a valid replacement for the Sanger based workflow, with the possibility to perform additional analyses and perform automated and time efficient RAS detection.

Made available in DSpace on 2014-06-11T19:26:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-02-26Bitstream added on 2014-06-13T20:14:38Z : No. of bitstreams: 1 jardim_acg_me_sjrp.pdf: 3983929 bytes, checksum: 587fc4359397e3ed6de6922651160d80 (MD5) / O HCV é uma das maiores causas de doença do fígado, sendo estimado que mais de 2% da população mundial está infectada. Este vírus possui um genoma de RNA (+) fita simples, que devido à falta de atividade corretiva da polimerase viral apresenta variabilidade genética em vários níveis: genótipos, subtipos e quasispecies. O genótipo 1 é o mais prevalente no Brasil e no mundo, sendo preditivo de uma baixa resposta à terapia antiviral, que atualmente é baseada na administração de PEG-IFN e ribavirina. A variabilidade genética da região viral NS5A tem sido relacionada à sensibilidade ou resistência ao IFN. Este estudo teve como objetivo investigar se a possível relação entre a composição de quasispecies da NS5A e a resposta ao tratamento. Foram selecionados 12 pacientes, sendo 4 respondedores (R), 4 não respondedores (NR) e 4 respondedores ao final do tratamento (RFT). As amostras pré-tratamento destes pacientes foram amplificadas, clonadas e seqüenciadas, resultando em 165 seqüências da NS5A completa. Estas seqüências foram alinhadas, editadas e a construção da topologia da árvore filogenética foi realizada. A NS5A e suas regiões específicas CRS, PKR-binding, ISDR, NLS e V3 foram analisadas quanto às substituições e o grau de variabilidade genético. O grupo de pacientes RFT apresentou uma maior taxa de substituições sinônimas em relação aos demais grupos. Uma maior quantidade de mutações foi observada na região downstream à ISDR, principalmente na região V3. Nenhum sítio específico de mutação foi relacionado a um tipo particular de resposta, e não houve agrupamento filogenético das quasispecies de acordo com o tipo de resposta. Estes resultados sugerem que o número de mutações não é suficiente para predizer a sensibilidade ou resistência à terapia baseada em IFN, sendo necessário avaliar se estas mutações conservaram ou não as propriedades químicas dos aminoácidos. / Hepatitis C virus (HCV) is major causes of liver desease and about 2% of world s population are infected. This virus is a single strain RNA genome of approximately 9.6 kb. Genetics variability of HCV exists at several different levels: genotypes, subtypes and quasispecies. The high mutation rates are related to the low fidelity of viral RNA polymerase. Genotype 1 HCV is the most prevalent in Brazil, as well as worldwide. Genotypes 1a and 1b are predictive of lower sustained virological response in peginterferon (PEG-IFN) plus ribavirin combination therapy. Genetic variability of viral NS5A has been related to IFN sensibility or resistance. To evaluate whether HCV NS5A quasispecies composition are related to responsiveness to combined PEG-IFN and ribavirin therapy, this study analyzed before treatment sample of 12 treated patients (4 sustained responders - SR, 4 non responders - NR and 4 end of treatment responder - ETR). Samples were amplified, cloned and sequenced, resulting in 165 sequences of complete NS5A. Sequences were aligned, edited and phylogenetical tree was constructed. Mutations and mean of genetic distance were analyzed to NS5A and specific regions CRS, PKR-binding, ISDR, NLS and V3. The number of synonymous substitutions per synonymous sites was higher in ETR patients than in other patient groups. Mutations were more common downstream ISDR, mainly concentrated in V3 domain. No single amino acid position or motif was associated with different responses to therapy in any NS5A regions analyzed and phylogenetic analysis did not show clustering of nucleotide sequences of viral isolates from SR, NR or ETR. These results suggest that number of mutations is not sufficient to predict sensibility or resistance to IFN based therapy. Other studies are necessary to evaluate whether chemical characteristics of amino acids were altered for the mutations.

Resumo: A infecção pelo vírus da Hepatite C (HCV) é considerada um grande problema de saúde pública, desde a sua descoberta em 1989. Entretanto a terapia mais utilizada atualmente, baseada no uso de Peginterferon, tem sucesso em aproximadamente 50% dos pacientes com o genótipo 1. Embora os mecanismos envolvidos nesta resistência viral ainda não sejam esclarecidos, sugere-se que fatores virais e do hospedeiro participam deste. A proteína não-estrutural 5A (NS5A) está envolvida em diversos processos celulares e é um componente essencial para o HCV. Entretanto, sua estrutura e função ainda não foram bem elucidadas. A partir destes fatos, os objetivos do presente estudo foram elaborar um modelo teórico da NS5A e investigar as propriedades estruturais e funcionais in silico. Foram analisadas 345 sequências da proteína NS5A do HCV de 23 pacientes infectados com o genótipo 1 ou 3. As composições de aminoácidos e de estrutura secundária demonstraram que há diferença entre os genótipos, podendo indicar que há diferenças nas interações proteína-proteína entre os genótipos, o que pode estar relacionado com a diferença da taxa de resistência ao tratamento. A análise funcional foi realizada com o ProtFun, que sugeriu que a NS5A estaria envolvida nas funções celulares de metabolismo intermediário central, tradução, crescimento, tranporte, ligação e hormônio. Estas funções variaram entre os domínios, suportando a hipótese de que a NS5A é uma proteína multifuncional. A análise pelo PROSITE indicou vários sítios de glicosilação, fosforilação e miristoilação, que são altamente conservados e podem ter função importante na estabilização da estrutura e função, sendo assim possíveis alvos de novos antivirais. Alguns deles estão em regiões relacionadas com a resposta ao tratamento. Outro... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Hepatitis C virus (HCV) infects almost 3% of people worldwide and it is considered the main cause of liver chronic diseases and transplants. Until today, there is no effective vaccine and the current most used therapy, based on Peginterferon, is successful only in 50% of patients infected by genotype 1. Although the outcomes of this treatment resistance are unclear, it is suggested host and virus factors may participate in this mechanism. Non-structural 5A (NS5A) protein is involved in several cellular and virus processes and it is a critical component of HCV. However, its structure and function are still uncertain. Regarding these facts, the present study attachments were to elaborate a model of the NS5A protein and to investigate NS5A structural and functional features, using in silico tools. It was analyzed 345 sequences of HCV NS5A protein from 23 patients infected by genotypes 1 or 3. Residues and secondary structure composition of all sequences demonstrated that there are differences between genotypes. It may indicate that there are differences in interactions between genotypes, which could be related with the distinct average of treatment resistance. In addition, among those that varied between genotypes, there were amino acids in regions that studies suggested as related with virus persistence. Functional analysis was performed with ProtFun. It suggested that NS5A is involved with central intermediary metabolism, translation, growth, transport, ligation and hormone functions in the cell. These functions vary between the domains, strengthening the hypothesis that NS5A is a multifunctional protein. Prosite motif search indicated that there are many glicosilation, fosforilation and myristoilation sites, which are highly conserved and may play an important role in structural stabilization and... (Complete abstract click electronic access below) / Orientador: Paula Rahal / Coorientador: Helen Andrade Arcuri / Banca: Fernanda Canduri / Banca: Carlos Alberto Montanari / Mestre

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Introduction : Le virus de l’hépatite C (VHC), est l’une des premières causes de pathologie hépatique dans le monde. Ce virus à ARN est responsable de l’hépatite C qui aboutit au développement de la cirrhose et du cancer du foie. Selon l’Organisation Mondiale de la Santé, le VHC infecte actuellement plus de 170 millions de personnes dans le monde, soit 3% de la population. L’hépatite C chronique connait toujours en Tunisie un taux de guérison faible pour le génotype 1 car le traitement standard actuellement disponible est la bithérapie interféron pégylé associé à la ribavirine. A l’heure actuelle, le développement de différentes molécules ciblant spécifiquement le VHC, appelées les antiviraux à action directe (AAD), apparait comme une potentielle révolution dans le traitement de l’infection par le VHC.Ces AAD comprennent les inhibiteurs de protéase (IP), les inhibiteurs nucléos(t)idiques (IN) et les inhibiteurs non-nucléosidiques (INN) de la polymérase NS5B ainsi que les inhibiteurs de la protéine NS5A. La quasi-espèce virale est formée d’un mélange complexe de variants viraux parmi lesquels se trouvent des variants associés à des degrés variables à la résistance aux AAD. Ces variants peuvent donc exister naturellement en absence de toute pression médicamenteuse et sont susceptibles d’avoir un impact sur la réponse aux différents traitements par AAD. Notre objectif était de déterminer la prévalence des variants associés à la résistance dans les souches tunisiennes circulantes en préambule à l’introduction deces molécules en Tunisie. Méthodes : L’amplification et le séquençage direct de la protéase NS3, de la polymérase NS5B ainsi que la région NS5A ont été effectuées chez 149 patients tunisiens naïfs de traitement et infectés par le VHC de génotype 1 (génotype 1b = 142 ; génotype 1a = 7). Résultats : Douze séquences NS3 (12/131 ; 9,2%) ont montré des mutations connes pour conférer une résistance aux IP. Une seule séquence (1/95 ; 1,1%) a montré la mutation V321I connue pour conférer une résistance aux IN-NS5B. Trente quatre séquences (34/95 ; 35,8%) ont montré des mutations connues pour diminuer la sensibilité des INN-NS5B. Une seule séquence de génotype 1a (1/7 ; 14,3%) et 17 séquences de génotype 1b (17/112 ; 16,2%) ont montré des mutations connues pour conférer une résistance au inhibiteurs de la protéine NS5A. Conclusions : Notre étude a permis de mettre en évidence la présence de substitutions conférant une diminution de la sensibilité aux AAD chez des patients tunisiens naïfs de tout traitement anti-VHC. Des études in situ seront nécessaires pour évaluer l’impact de ces mutations sur la réponse au traitement. / Introduction: Hepatitis C virus (HCV) is a major cause of liver disease worldwide. This RNA virus is responsible for hepatitis C, which leads to the development of cirrhosis and liver cancer. According to the World Health Organization, HCV infects more than 170 million people worldwide, about 3% of the population. Chronic hepatitis C still know in Tunisia low cure rates for genotype 1, because the currently standard treatment available is combination therapy of pegylated interferon plus ribavirin. At present, the development of different molecules that specifically target HCV, called direct-acting antivirals (DAA) appears as a potential revolution in the treatment of HCV infection. These DAA include protease inhibitors (PI), nucleos(t)ide (NI) and non-nucleoside inhibitors (NNI) for NS5B polymerase and NS5A inhibitors. The viral quasispecies is formed by a complex mixture of viral variants including variants associated with variable degrees of resistance to DAA. These variants may therefore exist naturally in absence of drug pressure and may affect response to different treatments by DAA. Our objective was to determine the prevalence of variants associated with resistance in circulating Tunisian strains preamble to the introduction of these molecules in Tunisia. Methods: Amplification and direct sequencing of NS3 protease, NS5B polymerase and NS5A region were performed in 149 Tunisian naïve patients infected with HCV genotype 1 (genotype 1b = 142; genotype 1a = 7) . Results: Twelve sequences NS3 (12/131; 9.2%) showed mutations known to confer resistance to PI. One sequence (1/95; 1.1%) showed the V321I mutation known to confer resistance to NS5B-IN. Thirty four sequences (34/95; 35.8%) showed mutations known to reduce the sensitivity of NS5B-INN. One genotype 1a sequence (1/7; 14.3%) and 17 genotype 1b sequences (17/112; 16.2%) showed mutations known to confer resistance to NS5A inhibitors.Conclusions: Our study highlighted the presence of substitutions conferring decreased susceptibility to DAA in naïve patients infected with HCV genotype 1. Field studies will be needed to evaluate the impact of these mutations on the treatment response.

Le virus de l'Hépatite C (VHC), de la famille Flaviviridae, est à l'origine d'une pandémiemondiale. L'infection par le VHC provoque le dévelopment d'hépatites chroniques, decirrhoses et de carcinomes hépatocellulaires (CHC). Les fonctions de la majorité des protéinesvirales sont connues, mis à part pour NS5A dont la seule fonction directe attribuée à ce jour,équivaut à celle d'un facteur d'activation transcriptionnelle. Notre laboratoire a montréprécédemment que les variants de quasiespèce de NS5A isolés à partir du sérum d'un mêmepatient présentaient des différences significatives dans leurs propriétés intrinsèques detransactivation. Fort de ces résultats, nous avons analysé des variants de NS5A isolés à partirde tissu hépatique d'un patient chroniquement infecté par le VHC de génotype 1b. Cesanalyses ont révélé une compartimentation génétique et fonctionnelle des variants de NS5Aentre le tissu tumoral et le tissu non-tumoral adjacent. Nous avons donc émis l'hypothèse queles propriétés transactivatrices de NS5A pourraient jouer un rôle dans la pathogenèse ainsique dans la réplication virale, et que la variabilité naturelle de NS5A pourrait influencer sespropriétés transactivatrices. L'objectif de ce travail de thèse était d'analyser le rôle despropriétés transactivatrices de NS5A dans la pathogenèse hépatique viro-induite ainsi quedans la réplication virale. Pour étudier le rôle des propriétés de transactivation de NS5A dans la pathogenèse hépatique,nous avons développé des vecteurs lentiviraux pour exprimer dans les hépatocytes primaireshumains les variants choisis de NS5A portants différents potentiels de transactivation. Enutilisant la technologie RNA-Seq d'Illumina, l'analyse des transcriptomes d'hépatocytestransduits exprimant les variants transactivateurs fort et faible de NS5A, sera utiliser pouridentifier les voies cellulaires ciblées par les propriétés transactivatrices de NS5A. Pour lesétudes in vivo, nous avons lancé le développement des souris transgénique permettantl'activation conditionnelle de l'expression des variants de NS5A avec fort et faible potentielde transactivation, spécifiquement dans le foie. Ces souris transgéniques seront utilisées pourétudier le rôle potentiel des propriétés transactivatrices dans la pathogenèse VHC induite etplus particulièrement dans le développement des cancers. Pour étudier le rôle des propriétés de transactivation de NS5A dans la réplication virale, nousavons utilisé le système de réplicon subgénomique de VHC exprimant les variants de NS5Aprécédemment caractérisés. Pour exercer ses propriétés transactivatrices, NS5A doit êtrelocalisée au moins partiellement dans le noyau. Nous avons démontré qu'une partie de NS5Ase retrouve dans noyau et est recruté sur des promoteurs cellulaires, modulant ainsidirectement l'expression de gènes cellulaires essentiels pour la réplication de l'ARN viral.Nous avons observé que les variants de NS5A avec différents potentiels de transactivation,confèrent différentes capacités de réplication au réplicon subgénomique, et corrèlent avec lepotentiel de transactivation de variant correspondant. En accord avec ces observations,l'inhibition de translocation nucléaire de NS5A entraine une inhibition de la réplication virale,suggerant un rôle potentiel des propriétés transactivatrices de NS5A dans la réplication l'ARNvirale. En conclusion, nous avons démontré que l'activation transcriptionnelle des gènes cellulairespar la NS5A est essentielle pour la réplication de l'ARN du VHC. Cette modulation des gènescellulaires pourrait également être impliquée dans les mécanismes de la pathogenèse viroinduite.Nous confirmerons cette hypothèse grâce aux souris NS5A. Par ailleurs, ces résultatspourraient contribuer au développement de nouvelles thérapies anti-VHC, basées surl'inhibition de translocation nucléaire de NS5A