Resumo: A composição de quasiespécies do vírus da Hepatite C (HCV) pode ter implicações importantes com relação à persistência viral e à resposta a terapia baseada em Interferon. A região NS5A completa foi analisada para avaliar se a composição de quasiespécies do HCV 1a/1b está relacionada à resposta ao tratamento combinado de interferon peguilado (PEGIFN) e ribavirina. Seiscentos e noventa seqüências correspondentes a região não estrutural 5A (NS5A) completa foram geradas a partir de amostras coletadas antes, durante a após a administração da terapia de pacientes respondedores, não respondedores e respondedores ao final do tratamento. Este estudo apresenta evidências de que a homogeneidade da composição de quasiespécies, e a baixa complexidade e diversidade da região NS5A em amostras préterapia estão associados à resposta virológica sustentada. Portanto, a alta diversidade e complexidade de quasiespécies podem fornecer ao vírus melhores oportunidades de evadir a terapia antiviral. Análises filogenéticas não demonstraram o agrupamento das seqüências de acordo os padrões específicos de resposta ao tratamento. Contudo, o agrupamento distinto de seqüências pré e pós-terapia foi observado, sugerindo que um processo adaptativo ocorreu durante o período analisado. Adicionalmente, a dinâmica evolutiva da composição de quasiespécies demonstrou estar sob pressão seletiva purificadora ou purificadora relaxada, o que é condizente com a população de quasiespécies diversificada no pré-terapia, seguida de um aumento em freqüência de quasiespécies predominantes nas amostras pós-tratamento, provavelmente devido a conferirem alguma vantagem ao vírus. Estes resultados sugerem que a diversidade de quasiespécies da região NS5A pode ser importante para o entendimento dos mecanismos de baixa resposta virológica sustentada em pacientes com Hepatite C crônica / Abstract: The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy. Six hundred and ninety full-length NS5A sequences were generated from samples collected before, during and after treatment from virological sustained responder, non-responder and the end-of-treatment responder patients. This study provides evidence that homogeneity of quasispecies composition, low diversity and less complexity of the NS5A region pre-therapy are associated with viral clearance. Therefore, higher diversity and complexity of quasispecies could offer the virus a better opportunity of evading anti-viral therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed, suggesting that an evolutionary process occurred during the time course examined. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. This could explain the initial diversified composition of quasispecies at baseline, followed by an increase in the frequency of a predominant quasispecies in 'after treatment' samples of non-responders and end-of-treatment responders, probably because it offers some advantage for the virus. These results suggest that quasispecies diversity of the NS5A region could be important for elucidating the mechanism underlying treatment failure in patients infected with chronic hepatitis C / Orientador: Paula Rahal / Coorientador: Isabel Maria Vicente Guedes Carvalho-Mello / Banca: Camila Malta Romano / Banca: Jonny Yokosawa / Banca: Maurício Lacerda Nogueira / Banca: Fátima Pereira de Souza / Doutor

Dendrimers are synthetic macromolecules with branches-upon-branches structures, nanoscale dimensions and a high density of surface groups. Presence of multiple cationic sites in dendrimers permits their efficient nucleic acid complexation and cellular internalization through endocytic pathways. PETIM dendrimers of are characterized by tertiary amine branch points, and ether linkages. A third generation PETIM dendrimer, G3(NH2)24, with nitrogen at the core and twenty four peripheral primary amines was synthesized through alternate Michael addition and reduction reactions. The ability of G3(NH2)24 to interact with DNA was ascertained by spectroscopic and bio-physical techniques. These studies established the formation of dendrimer-DNA, and complex formation was also shown to protect the plasmid DNA from nucleases. Toxicity studies in cell culture, as well as, in female Balb/c mice established the non-toxic properties of the dendrimer. G3(NH2)24 was able to mediate efficient transfection in mammalian cells and in vivo. Targeted delivery of small interfering RNA (siRNA) to hepatocytes, in order to combat hepatitis C virus (HCV) infection was undertaken to expand the scope of PETIM dendrimer based gene delivery. Functionalization of the dendrimer periphery with galactose units ensured preferential delivery to the liver through multivalent interactions with the asialoglycoprotein receptors on the liver cell surface. The delivery of siRNA to the perinuclear region, in close proximity to the HCV RNA replication site resulted in ~75% decrease in viral RNA levels in replicon containing cells, as well as, JFH-1 infectious virus systems. The dendrimer-siRNA complexes were preferentially delivered to mice liver and were active in vivo. Physico-chemical studies of the protonation pattern of PETIM dendrimer indicated that the protonation of the dendrimer amines proceeded in a shell-wise pattern from the periphery to the core. The primary amines of the dendrimer as well as the outer shell tertiary amines with pKa values ~7-10 were protonated at physiological pH and were cationic sites for nucleic acid condensation. The inner shell tertiary amines with a pKa of ~4-6 were protonated at endosomal pH and aided ‘endosomal escape’ due to the high buffering capacity of 3.5. Work described in the Thesis establish a new synthetic dendrimer vector, namely, the series of PETIM dendrimers, as a high value gene delivery vector, making in-roads towards pre-clinical and possible clinical trials in future studies.

Environ 30% des patients infectés par le virus de l’hépatite C guérissent spontanément. Le but de ce travailétait (i) d’examiner l’évolution des protéines d’enveloppe en cas de guérison spontanée (ii) de comparerl’infectivité des variants présents aux stades précoces (iii) d’explorer la capacité neutralisante des anticorps(Ac) vis-à-vis des variants majoritaires et minoritaires. Nous avons sélectionné 2 patients avec une hépatiteaigue C suivie d’une guérison très rapide. Pour explorer la capacité d’entrée de ces variants et leur aptitude àêtre neutralisés, nous avons produit des pseudo-particules rétrovirales portant les enveloppes de différentsvariants. Pour le 1er patient, une réponse neutralisante autologue était détectable précocement, avec unmaximum entre le 2ème et le 3èmemois suivant la cytolyse. Elle était encore détectable au 30ème mois. Pourle 2ème patient, des Ac vis-à-vis du variant majoritaire étaient détectés dans le sérum prélevé 4 jours après lacytolyse et dans les sérums plus tardifs. Le titre des Ac était maximum au 5ème mois. La réponse neutralisanteest d’apparition précoce et persiste même après l’élimination virale. Ces observations nous questionnent parrapport au rôle éventuel joué par ces Ac dans les cas de recontamination. / Only 30% of Hepatitis C virus infected individuals recover spontaneously. We investigated the mechanismsleading to early HCV clearance. The purpose of this work was: (i) to explore the diversity and the early geneticevolution of the HCV envelope glycoproteins, and the infectivity spectrum of isolated variants and (ii) toanalyze the ability of the autologous neutralizing response to control these variants. We selected two patientswho developed an acute HCV infection. To explore the impact of mutations on infectivity and neutralization,retroviral pseudoparticules were produced with representative E1 and E2 sequences. For the first case, themaximum neutralizing activity was observed in the serum collected between 2 and 3 months post ALT peak,the activity was still detectable after 30 months. For the second case, autologous neutralizing activity wasdetected in every serum collected between 4 days and 13 months after. A gradual increase of neutralizationactivity was observed over time with a maximum 5 to 6 months. We have shown that the neutralizing responsewas detectable at early stages of primoinfection and was sustained beyond the time at which the virus wascleared. These observations raise interesting questions about the role of such antibodies in case of re-exposure.

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Le virus de l’hépatite C (VHC) est l’une des causes majeures de cirrhose du foie et de carcinome hépatocellulaire. Au courant de la première partie de ma thèse, nous nous sommes intéressés à caractériser plus en détail le rôle de SR-BI dans l’infection par le VHC. Bien que les mécanismes impliquant SR-BI dans la liaison du virus à l’hépatocyte aient été partiellement caractérisés, le rôle de SR-BI dans les étapes suivant la liaison du VHC reste encore largement méconnu. Afin de mieux caractériser le rôle de l’interaction VHC/SR-BI dans l’infection par le VHC, notre laboratoire à généré une nouvelle classe d’anticorps monoclonaux anti-SR-BI inhibant l’infection virale. Nous avons pu démontrer que SR-BI humain jouait un rôle dans le processus d’entrée du virus à la fois lorsde l’étape de liaison du virus à la cellule hôte mais aussi au cours d’étapes suivant cette liaison. Ainsi il serait intéressant de cibler cette fonction de SR-BI dans le cadre d’une stratégie antivirale pour lutter contre l’infection parle VHC. Dans la seconde partie de ma thèse, nous avions pour but de caractériser les mécanismes moléculaires intervenant dans la réinfection du greffon lors de la transplantation hépatique (TH). Nous avons ainsi identifiés 3 mutations adaptatives dans la glycoprotéine d’enveloppe E2 responsables de l’entrée virale augmentée du variant hautement infectieux. Ces mutations influent sur la dépendance au récepteur CD81 du VHC résultant en une entrée virale accrue. L’identification de ces mécanismes va nous permettre une meilleure compréhension de la pathogénèse de l’infection par le VHC, et est un premier pas pour le développement d’une stratégie préventive antivirale ou vaccinale. / Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. In the first part of my PhD, we aimed to further characterize the role of scavenger receptor class B type I (SR-BI) in HCV infection. While the SR-BI determinants involved in HCV binding have been partially characterized, the post-binding function of SR-BI remains remained largely unknown. To further explore the role of HCV-SR-BI interaction during HCV infection, we generated a novel class of anti-SR-BI monoclonal antibodies inhibiting HCV infection. We demonstrated that human SR-BI plays a dual role in the HCV entry process during both binding and post-binding steps. Targeting the post-binding function of SR-BI thus represents an interesting antiviral strategy against HCV infection. In the second part of my PhD, we aimed to characterize the molecular mechanisms underlying HCV re-infection of the graft after liver transplantation (LT). We identified threeadaptive mutations in envelope glycoprotein E2 mediating enhanced entry and evasion of a highly infectious escape variant. These mutations markedly modulated CD81 receptor dependency resulting in enhanced viral entry. The identification of these mechanisms advances our understanding of the pathogenesis of HCV infection and paves the way for the development of novel antiviral strategies and vaccines.

A infecção pelo vírus da hepatite C (VHC) é uma das mais comuns infecções ao redor do mundo. Aproximadamente, 20% dos pacientes infectados eliminam espontaneamente o vírus, porém a maioria dos indivíduos infectados desenvolve infecção crônica com amplo espectro de lesões hepáticas, desde inflamação leve até cirrose. A resposta imune do hospedeiro exerce grande influência sobre o desfecho da infecção pelo VHC. O objetivo deste trabalho foi analisar a influência dos polimorfismos genéticos de citocinas na susceptibilidade ou persistência da infecção por VHC e no clareamento espontâneo em uma amostra de pacientes da população do Rio de Janeiro (Brasil). Os polimorfismos genéticos das citocinas TNFA (-308), TGFB1 (codon 10 e 25), IL10 (-1082, -592), IL6 (-174) e IFNG (+874) foram analisados por PCR-SSP em 245 pacientes com hepatite C crônica (HCC), 41 pacientes que alcançaram o clareamento viral espontâneo e 189 indivíduos controle saudáveis. Além disso, os polimorfismos próximos ao gene da citocina IL28B (rs12979860, rs12980275 e rs8099917) foram analisados por PCR em tempo real em todos os grupos. O grau de fibrose e inflamação, a resposta ao tratamento e o genótipo do vírus também foram levados em consideração quanto ao desfecho da HCC Os genótipos IL28B rs12979860 CC e CT e rs12980275 AA e AG foram significativamente associados ao clareamento espontâneo e à resposta à terapia anti-viral. Da mesma forma, o alelo C (rs12979860) e o alelo A (rs12980275) foram significativamente maior no grupo Clareamento. O alelo C de IL6 (-174) foi associado com o Clareamento. Nenhuma associação entre as demais citocinas e o desfecho da HCC foi encontrada. O Genótipo TNFA (-308) GG parece estar associado com menor grau de inflamação. Além disso, a etnia auto declarada influencia a distribuição dos polimorfismos em IL6 (-174) e IL28B rs12979860 e rs8099917. Nossas observações indicam que os polimorfismos próximos ao gene da IL28B estão associados com o clareamento viral e resposta ao tratamento na população do Rio de Janeiro. Além disso, nossos resultados podem ser úteis para futuras investigações entre os polimorfismos de citocinas e a infecção por VHC numa população heterogênea como a Brasileira. / Hepatitis C virus infection is one of the most common blood-borne infections worldwide. Approximately, 20% of infected patients successfully eliminate the virus, whereas the majority of patients develop chronic infection with a wide spectrum of liver lesions, ranging from a minimal inflammation to cirrhosis. The host's immune response is an important correlate of HCV infection outcome and disease progression. The aim of this study was to explore the possibility of the inheritance of cytokine gene polymorphisms as a candidate for susceptibility to persistent HCV infection or HCV clearance in a sample of Rio de Janeiro (Brazil) population. Genetic polymorphisms in the cytokines TNFA (-308), TGFB1 (codon 10 and 25), IL10 (-1082, -592), IL6 (-174) and IFNG (+874) were analyzed by polymerase chain reaction-sequence-specific primer (SSP) in 245 chronic hepatitis C (HCC) patients, 41 spontaneous recovery (SR) patients and 189 healthy volunteers. Further, IL28B (rs12979860, rs12980275 and rs8099917) were assessed by real-time PCR in all groups. Liver fibrosis and inflammation staging, response to treatment and virus genotype were also tested to influence in HCV chronic infection. IL28B rs12989760 CC and rs12980275 AA genotypes were significantly associated with spontaneous recovery of HCV infection and response to therapy. Likewise, C allele (rs12979860) and A allele (rs12980275) were also more frequent in SR group, while C allele of IL6 (-174) is associated with persistence to HCC. No association was found between other cytokine gene polymorphism and susceptibility to HCV infection and response to treatment. Multivariate analysis showed male, IL28B rs12979860 CT and TT and TGFB1 (codon 10) TC genotypes to be factors associated with HCC. TNFA (-308) GG genotype seems to be associated with moderate stage of inflammation. Also, ethnicity according self-declared is supposed to influence the distribution IL6 (-174) and IL28B rs12979860 and rs8099917 polymorphisms. These results suggest that the IL28B polymorphisms are associated with spontaneous clearance of HCV and response to therapy in a Brazilian population. Moreover, these results could be useful to further association between cytokine polymorphism and HCV infection outcome in Brazilian admixture population.

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-25Bitstream added on 2014-06-13T20:03:27Z : No. of bitstreams: 1 jardim_acg_dr_sjrp.pdf: 1650863 bytes, checksum: 6ecdc00802358d3e90fac9c3024108d4 (MD5) / A composição de quasiespécies do vírus da Hepatite C (HCV) pode ter implicações importantes com relação à persistência viral e à resposta a terapia baseada em Interferon. A região NS5A completa foi analisada para avaliar se a composição de quasiespécies do HCV 1a/1b está relacionada à resposta ao tratamento combinado de interferon peguilado (PEGIFN) e ribavirina. Seiscentos e noventa seqüências correspondentes a região não estrutural 5A (NS5A) completa foram geradas a partir de amostras coletadas antes, durante a após a administração da terapia de pacientes respondedores, não respondedores e respondedores ao final do tratamento. Este estudo apresenta evidências de que a homogeneidade da composição de quasiespécies, e a baixa complexidade e diversidade da região NS5A em amostras préterapia estão associados à resposta virológica sustentada. Portanto, a alta diversidade e complexidade de quasiespécies podem fornecer ao vírus melhores oportunidades de evadir a terapia antiviral. Análises filogenéticas não demonstraram o agrupamento das seqüências de acordo os padrões específicos de resposta ao tratamento. Contudo, o agrupamento distinto de seqüências pré e pós-terapia foi observado, sugerindo que um processo adaptativo ocorreu durante o período analisado. Adicionalmente, a dinâmica evolutiva da composição de quasiespécies demonstrou estar sob pressão seletiva purificadora ou purificadora relaxada, o que é condizente com a população de quasiespécies diversificada no pré-terapia, seguida de um aumento em freqüência de quasiespécies predominantes nas amostras pós-tratamento, provavelmente devido a conferirem alguma vantagem ao vírus. Estes resultados sugerem que a diversidade de quasiespécies da região NS5A pode ser importante para o entendimento dos mecanismos de baixa resposta virológica sustentada em pacientes com Hepatite C crônica / The quasispecies composition of Hepatitis C virus (HCV) could have important implications with regard to viral persistence and response to interferon-based therapy. The complete NS5A was analyzed to evaluate whether the composition of NS5A quasispecies of HCV 1a/1b is related to responsiveness to combined interferon pegylated (PEG-IFN) and ribavirin therapy. Six hundred and ninety full-length NS5A sequences were generated from samples collected before, during and after treatment from virological sustained responder, non-responder and the end-of-treatment responder patients. This study provides evidence that homogeneity of quasispecies composition, low diversity and less complexity of the NS5A region pre-therapy are associated with viral clearance. Therefore, higher diversity and complexity of quasispecies could offer the virus a better opportunity of evading anti-viral therapy. Phylogenetic relationships concerning complete NS5A sequences obtained from patients did not demonstrate clustering associated with specific response patterns. However, distinctive clustering of pre/post-therapy sequences was observed, suggesting that an evolutionary process occurred during the time course examined. In addition, the evolution of quasispecies over time was subjected to purifying or relaxed purifying selection. This could explain the initial diversified composition of quasispecies at baseline, followed by an increase in the frequency of a predominant quasispecies in ‘after treatment’ samples of non-responders and end-of-treatment responders, probably because it offers some advantage for the virus. These results suggest that quasispecies diversity of the NS5A region could be important for elucidating the mechanism underlying treatment failure in patients infected with chronic hepatitis C

En combinant un nouveau système de culture cellulaire à partir d'hépatocytes différenciés avec du virus de l’hépatite C (VHC) purifié, nous pouvons induire un profil transcriptomique caractéristique des patients à risque élevé de développer un carcinome hépatocellulaire (CHC). En utilisant ce modèle, nous avons découvert le rôle fonctionnel de l'EGFR comme élément moteur de la signature du risque de développement d'un CHC. De plus, nous avons identifié des gènes candidats impliqués dans le développement du CHC. Pour étudier les maladies du foie in vivo, nous avons caractérisé l'expression des protéines phosphatases dans des biopsies hépatiques de patients infectés par le VHC. Nous avons observé une régulation négative de PTPRD, un suppresseur de tumeur, causé par une augmentation de miR-135a-5p qui cible l'ARNm de PTPRD. Par ailleurs, l'analyse in silico montre que l'expression de PTPRD dans le tissu hépatique est corrélée à la survie chez les patients atteints de CHC. / By combining a cell culture system of hepatocyte-like cells with purified hepatitis C virus (HCV), we effectively simulated chronic infection in vitro. We found this infection model induces a transcriptomic profile of chronic HCV patients at high risk of developing hepatocellular carcinoma (HCC). Using this model, we have uncovered the functional role of EGFR as a driver of the HCC risk signature and revealed candidate drivers of the molecular recalibration of hepatocytes leading to liver cancer. In an approach to study liver disease in vivo, we opted to screen for protein phosphatase expression in liver biopsies of chronic HCV patients. We observed a downregulation of PTPRD, a well-known tumor suppressor. We demonstrated that this effect is mediated by an increase in miR-135a-5p which targets PTPRD mRNA. Moreover, in silico analysis shows that PTPRD expression in adjacent liver tissue of HCC patients correlates with survival and reduced tumor recurrence after surgical resection.

Hepatitis C virus (HCV) infection globally affects 130-150 million people. It causes both acute and chronic infections. Due to the severe side effects and low success rates of interferon based treatments, which formed the standard treatment for HCV, the treatment paradigm shifted to direct acting antivirals (DAAs). DAAs have revolutionized the treatment of hepatitis C virus infection. Clinical trials with combinations of DAAs have recorded >90% response with shorter treatment durations and fewer side effects than earlier treatments involving IFN. Outside the controlled setting of a clinical trial, however, response rates with DAA combinations are much lower (<70%). DAAs can fail if HCV accumulates mutations that confer drug resistance. Interestingly, the pre-existence of mutant frequency in the virus appears not to influence treatment outcome. A better predictor for DAA treatment outcome is yet to be unravelled. Surprisingly, individuals who respond poorly to IFN appear to be more likely to fail DAA treatment. IFN is a generic antiviral that improves immune responses and is expected not to have any bearing on DAA treatment outcomes. Why individuals with poor IFN sensitivity fail DAA treatment remains a mystery. In a recent study of the IFN signalling network, HCV has been shown to compromise IFN activity. It induces bistability in the network leading to distinct phenotypic responses of cells to IFN exposure. In particular, individuals who respond poorly to IFN tend to have a higher percentage of cells that are refractory to IFN; these cells allow viral persistence despite IFN exposure. We hypothesized here that in such individuals, greater ongoing replication would allow increased development of resistance and thus lead to the failure of DAAs. We constructed a model of viral dynamics that accounts for the distinct phenotypic responses of cells to IFN, viral replication and mutation, and the development of resistance to DAAs. Our model predicted that although the relative prevalence of pre- existing mutants is unaffected by IFN sensitivity, in agreement with observations, the growth of drug resistant mutants is accelerated in individuals with poor IFN sensitivity. Based on a distribution of IFN sensitivity across individuals, our model accurately described clinical observations of the response rates to different current treatment protocols. With this model, we predict that the common strategy of increasing the genetic barrier by adding more drugs to the combination was not necessary to avert the development of drug resistance. Instead, an optimised increase in DAA dosage alone or DAA+PR or PR dosage depending on the patient’s IFN sensitivity could help achieve success.