Orientador: Paulo Inácio da Costa / Banca: Iguatemy Lourenço Brunetti / Banca: Fernanda de Freitas Aníbal / Resumo: Os perfis metabólicos correlacionam-se com a infecção pelo VHC e são prognósticos da resposta viral em pacientes crônicos. Porém, pouco se sabe a respeito da associação entre perfis lipídicos e carga viral do VHC entre infecções dos genótipos 1, 2 ou 3. Portanto, o objetivo deste trabalho foi estudar a influência da viremia e dos genótipos do VHC sobre o metabolismo lipídico através das variações de lipoproteínas séricas (colesterol total, LDL, HDL, VLDL, triglicérides) e apolipoproteína B (Apo B) em hepatopatas crônicos, avaliando se o VHC predispõe os indivíduos ao aparecimento de complicações vasculares. O grupo amostral constituiu-se de um total de 150 pacientes crônicos do VHC com genótipos 1, 2 ou 3, e de um grupo controle de 20 indivíduos saudáveis (10 homens e 10 mulheres) em idade adulta (20 à 50 anos). Os níveis séricos de HDL (28%), VLDL (26%) e triglicérides (26%) nos portadores crônicos do VHC se mostraram diminuídos em relação ao grupo controle, enquanto os níveis de LDL (25%) e Apo B (29%) se mostraram elevados, resultados que foram mais importantes nos portadores do genótipo 3a. Observou-se correlação positiva entre a viremia e alterações nos níveis de apo B (r = 0,5763) nos portadores do genótipo 1b. Assim, foi pressuposto que o risco de pacientes portadores do VHC desenvolverem complicações vasculares é elevado, pois 1% de redução nos níveis de LDL está associado com uma redução de 2-3% no risco de desenvolvimento de doenças cardíacas, e como cerca de 90% da proteína na LDL se constitui de apo B, sua concentração plasmática indica o número total de partículas potencialmente aterogênicas. Desta forma, o perfil lipídico auxilia no diagnóstico da severidade da infecção hepática causada pelo VHC e ainda atua como um bom sinal prognóstico. / Abstract: The metabolic profiles correlate with the hepatitis C virus infection and are prognostics for the viral reply in chronic patients. However, little is known regarding the distinguishing association between lipid profiles and hepatitis C viral load in patients carrying genotypes 1, 2 or 3. Therefore, the objective of this work was to study viremia and genotypes on the lipid metabolism through the serum lipoprotein variations (total cholesterol, LDL, HDL, VLDL, triglycerides) and apolipoprotein B (Apo B) in chronic carriers of this infection, evaluating if the HCV premakes the individual to the lipidic disequilibrium and favors the appearance of vascular complications. The amostral group consisted of 150 HCV chronic patients with genotypes 1, 2 or 3, and a control group consisted of 20 healthful individuals (10 men and 10 women) in adult age (20 to 50 years). The levels of HDL (28%), VLDL (26%) and triglycerides (26%) of the HCV chronic patients were lower than the control group, while the LDL levels (25%) and the Apo B levels (29%) were higher. These findings were more significant in the genotype 3a carrying patients. Positive correlation occurred between the viremia and the alterations in the Apo B levels (r = 0.5763) in the genotype 1b carrying patients. Consequently it was inferred that the risk of HCV patients to develop vascular complication is elevated. In general, 1% of reduction in the LDL levels is associated with a reduction of 2-3% in the risk of development of cardiac illnesses, and, as about 90% of the protein in the LDL is constituted of apo B, its plasmatic concentration indicates the total potentially atherogenics particles number. The lipid profile aids in the diagnosis of the severity of the hepatic infection and equally acts as a good signal prognostic, therefore its analysis must be carried through in all the cases of advanced hepatic infection. / Mestre

L’infection par le Virus de l’Hépatite C (VHC) est un problème majeur de santépublique touchant environ 170 millions de personnes dans le monde. A l’heure actuelle, il n’existe aucun vaccin pour lutter contre le VHC et les traitements curatifs disponibles sont chers, donnent lieu à des effets secondaires très sévères et ne sont efficaces que pour une partie des patients. Le développement de nouvelles stratégies antivirales représente donc un enjeu crucial dans la lutte contre le VHC. Dans le but de développer de nouvelles molécules bloquant différentes étapes du cycle viral, une meilleure compréhension de chacune des ces étapes est nécessaire. Au cours de mon travail de thèse, nous avons étudier le mécanisme d’entrée du VHC dans ses cellules cibles, les hépatocytes. Dans un premier temps nous avons caractérisé un inhibiteur naturel de l’entrée du VHC, appelé EWI-2wint. Ce travail a notamment permis de mettre en évidence l’importance de la dynamique membranaire de l’un des récepteurs du virus, la protéine CD81, dans ce processus. Dans un second axe, nous avons étudié l’effet de la monensine sur l’infection par le VHC. Nous avons ainsi montré que cet inhibiteur pharmacologique bloque une étape tardive du processus d’entrée du VHC.L’ensemble des données accumulées au cours de ma thèse permettent de mieux comprendre le mécanisme d’entrée du VHC et ouvrent la voie au développement de nouveaux outils thérapeutiques. / Hepatitis C, whose causal agent is called Hepatitis C Virus (HCV), is a global health burden with about 170 million people infected. Currently, no vaccine exists again HCV and treatments are effective for only a part of infected people. Therefore, new treatments are urgently needed, as well as a better understanding of the viral life cycle.To do so, we studied the entry process of HCV in its targets cells through the characterisation of HCV entry inhibitors. Firstly, we have shown that EWI-2wint, a natural inhibitor of HCV entry, blocks this process by changing the partitionning of CD81, one of the HCV receptors. In addition, we have studied the effect of monensin on HCV infection and found that this pharmacological inhibitor impairs a late step of HCV entry.Altogether, our results allow a better understading of the HCV entry process and open the way to the development of new therapeutic agents.

Hepatitis C virus (HCV), a blood-borne pathogen, is a small enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family. HCV infection represents one of the major health concerns affecting approximately 170 million people globally. Patients with chronic HCV infection are at risk of developing hepatic fibrosis, cirrhosis and hepatocellular carcinoma. No protective anti-HCV vaccine is available yet. Until recently, standard therapy based on pegylated interferon plus ribavirin, was inadequate in treating all the patients as it results in a sustained virological response in only 40 to 50 percent of patients infected with the most common genotype (gt 1). Advances in understanding host-HCV interactions have helped developing newer anti-HCV agents such as telaprevir and boceprevir. However, treatment success is still limited due to different factors including genotype specificity, high cost, potential drug-drug interactions, substantial side effects etc. The positive-sense single-stranded RNA genome of HCV is approximately 9.6kb long which is flanked by highly structured and conserved 5’ and 3’ untranslated regions (UTRs) at both ends. Unlike cap-dependent translation of host cell mRNAs, HCV translation is mediated by an internal ribosomal entry site (IRES) present majorly within the 5’UTR. Several reports have demonstrated the interaction of different cellular proteins with HCV-5’UTR and/or 3’UTR, which include human La protein, polypyrimidine tract binding protein (PTB), poly (rC)-binding protein 2 (PCBP2) etc. These interactions of trans-acting factors with the UTRs may be important for HCV translation and/or replication. Earlier study from our laboratory revealed the importance of interaction of human La protein, by its central RNA recognition motif (RRM), with the HCV IRES around a tetranucleotide sequence GCAC near initiator AUG in influencing HCV translation. However, the role of this interaction, if any, in HCV RNA replication was not known. In the first part of the thesis, we characterized the interaction between human La protein and the GCAC to understand its role in HCV replication. We incorporated mutation, which altered the binding of La, in the GCAC motif in HCV monocistronic replicon and checked HCV RNA replication by reverse transcriptase polymerase chain reaction (RT-PCR). The mutation drastically inhibited HCV replication. Interestingly, overexpression of La could reverse the effect of this mutation and significantly enhanced HCV RNA levels. Using a bicistronic replicon, we observed that decrease in replication was independent of translation inhibition. Furthermore, mutation at the GCAC motif reduced the association between La and viral polymerase, NS5B as seen in co-immunoprecipitation assays. Moreover, this mutation affected translation to replication switch regulated by the interplay between HCV-NS3 protease and human La protein. Our analyses of point mutations, based on RT-PCR and luciferase assays, revealed distinct roles of each nucleotide of the GCAC motif in HCV replication and translation. Finally, 5’-3’ crosslink assays revealed that specific interaction of the GCAC motif with human La protein is important for linking 5’ and 3’ends of HCV genome. Results clearly demonstrate the mechanism of regulation of HCV replication by interaction of cis-acting element GCAC within the HCV IRES with human La protein. HCV is highly species-specific. Under natural conditions, HCV infects only humans and chimpanzees. This restricted host-tropism has prevented the development of a small animal model to study HCV infection in vivo. Although several human-specific entry factors have been identified to be responsible for this species selectivity, full multiplication of the HCV in animals (other than humans and chimpanzees) is still not possible. In the second part of the thesis, we showed that a post-entry host factor –‘La protein’ may also contribute in determining HCV host tropism. We aligned La protein sequences from different species and interestingly we found that HCV RNA interacting beta-turn sequence (KYKETDL) in central RRM (residues 112-184) is conserved only in human and chimpanzee. Earlier, it was shown from our laboratory that a heptameric peptide comprising of this sequence (derived from human La) could inhibit HCV translation by competing with La interaction with the IRES element. However, in the current study, another peptide corresponding to the mouse La sequence (KYKDTNL) was unable to inhibit HCV RNA translation. Similarly, wild-type mouse La (mLa) failed to stimulate HCV IRES function, but addition of chimeric mouse La protein bearing human beta-turn sequence (mLahN7) significantly increased HCV IRES mediated translation in vitro. Also, exogenous supplementation of mLahN7 enhanced HCV translation in cell culture system. Moreover, quantitative as well as tagged RT-PCR analyses showed an enhanced HCV replication upon overexpression of mLahN7. The findings obtained in this part raise a possibility of creating HCV mouse model using human specific cellular entry factors and a humanized form of La protein. Hepatitis C has emerged as a major challenge to the medical community. Developing more potent and safe anti-HCV regimens is need of the hour. As described above, a linear hepatapeptide (KYKETDL) was synthesized and shown to reduce HCV translation. However, this linear peptide was stable only for a shorter time scale. Therefore, in the third part of the thesis, effect of a more stable cyclic form of this peptide has been described. NMR spectroscopy suggested that the beta turn conformation is preserved in cyclic peptide as well. Also, using in vitro bicistronic reporter assay, we demonstrated that cyclic peptide inhibits HCV translation in a dose dependent manner. In fact, due to its higher stability, cyclic peptide reduced HCV translation and replication more efficiently than the corresponding linear peptide at longer post-treatment time point. Additionally, we observed that cyclic peptide is non-toxic in cell culture system. Our results suggest that cyclic peptide might emerge as a promising lead compound against hepatitis C. Due to availability of only partially effective liver protective drugs in modem medicine, complementary and alternative medicine approach, based on plant derived compounds, is also being utilised against HCV. Plant derived compounds have advantages of having high chemical diversity, drug-likeliness properties and ability of being metabolized by the body with little or no toxicity than synthetic ones. Different studies have shown that phytochemicals may exert anti-HCV activities by acting as direct-acting antivirals and play a potential therapeutic role in treating HCV infection. Also, from our laboratory, it was shown that methanolic extract of Phyllanthus amarus (P. amarus) plant inhibited HCV replication. The fourth part of the thesis describes the study on the anti-HCV properties of several bioactive components from P. amarus extract. Using a fluorimetric assay, we demonstrated that two principal components of this extract, phyllanthin and corilagin reduced the HCV NS3 protease activity significantly in vitro. We also observed a sharp reduction in HCV negative sense RNA levels in cell culture system. Structural knowledge-based molecular docking studies showed interactions of phyllanthin and corilagin with the amino acid residues of the catalytic triad of NS3 protease. Further, these compounds were found to be non-toxic in cell culture. Also, phyllanthin and corilagin displayed antioxidant properties by blocking HCV induced oxidative stress generated by reactive oxygen species suggesting their hepatoprotective nature. More importantly, our in vivo toxicity analyses and pharmacokinetics studies proved their safety, tolerability, metabolic stability, and systemic oral bioavailability and support their potential as novel anti-HCV therapeutic candidates. Altogether, the study deciphers mechanistic details of translation and replication of HCV RNA and demonstrates novel antiviral agents targeting these important viral processes.

Hepatitis C Virus (HCV) is one of the most important causes of chronic liver disease, affecting more than 170 million people worldwide. The mechanisms of hepatitis C pathogenesis are unknown. Viral cytotoxicity and immune mediated mechanisms might play an important role in its pathogenesis. HCV infection and alcohol abuse frequently coexist and together lead to more rapid progression of liver disease, increasing the incidence and prevalence of cirrhosis and hepatocellular carcinoma. The cytopathic effect of HCV proteins, especially the core, E1 and E2 structural proteins, which induce liver steatosis, oxidative stress and cell transformation may be amplified by alcohol abuse. The purpose of this study was to characterize the liver damage mechanisms induced by HCV structural proteins and alcohol and to determine the potential molecular mechanism(s) that may promote chronic, progressive liver damage. A transgenic mouse model expressing HCV core, E1 and E2 was used to investigate whether alcohol increased HCV RNA expression. Real-time RT-PCR analysis of genes involved in lipid metabolism and transport confirmed their abnormal expression in the alcohol-fed transgenic mice. In addition, light and electron microscopy analysis were performed on liver tissues of transgenic mice on an alcoholic diet versus those on a normal diet, in order to identify histological changes. The severe hepatopathy in HCV transgenic mice was exacerbated by alcohol. Mitochondria and endoplasmic reticulum had severe abnormalities in the electron microscopy analysis. The second part of this study focused on adaptive immune responses, which may also play an important role in HCV pathogenesis. I focused my analysis on dendritic cells (DC), which have been the main suspects to explain immune impairment in HCV infection. Their powerful antigen-presenting function allows them to stimulate the antiviral response of CD4+ and CD8+ T cells, the effector cells of the immune system. This unique function of the DC makes them possible targets for immune evasion by the Hepatitis C virus. In this study, DCs were generated from mouse bone marrow cells. I investigated their maturation capacity in the presence of structural proteins of HCV. The impact of HCV core/E1/E2 polyprotein on DCs cytokine expression and ability to activate T-cell lymphocytes was also analyzed. A dysfunctional CD4 T cell response was observed after exposure of DCs to core/E1/E2 polyprotein, indicating inefficient CD4 priming, which might lead to chronic HCV infection in humans. The presence of the core/E1/E2 polyprotein reduced the DC maturation capacity and the expression of certain cytokines (IL-12, IFNg, IL-6, MCP-1) important for stimulation and chemotaxis of T cells and other immune cells. My studies contribute to the understanding of HCV pathogenesis and may have implications to the development of better therapies for HCV infection.

Hepatitis C virus (HCV) infection is a leading cause of liver transplantation and hepatocellular carcinoma worldwide. HCV, like all obligate parasites, relies on host pathways to facilitate its pathogenesis. In particular, the virus possesses an intimate link with hepatic lipid metabolism, promoting a lipid-rich cellular environment conducive to HCV propagation. Clinically, these metabolic perturbations manifest as steatosis in over 50% of patients. The majority of research to-date examining how the virus co-opts hepatic lipid pathways has been focused on coding genes and their protein products. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression, which have been implicated in virtually every cellular process. Through interactions with partially complementary mRNAs, each individual miRNA has the capacity to repress the expression of hundreds of genes and induce significant regulatory effects. Herein, we demonstrate that hepatic miRNAs, including miR-7, miR-27a/b, miR-130b, and miR-185, act as crucial regulatory molecules to the maintenance of hepatic lipid homeostasis. These miRNAs cooperate to regulate fatty acid and cholesterol metabolism. HCV modulates the expression of a subset of these miRNAs (miR-27a/b, miR-130b, and miR-185) to promote hepatocellular lipid accumulation and the HCV life cycle. There appears to be a broad viral requirement for lipids, and the mammalian innate immune response strategically targets host metabolic pathways to restrict virus’ access to key lipid species. We demonstrate that 25-hydroxycholesterol, a broadly anti-viral oxysterol produced as part of the innate anti-viral response, activates miR-185 expression in the liver to deplete virus infected cells of lipids. HCV appears to actively counteract this anti-viral response by suppressing miR-185 expression. Collectively, our results highlight the role of microRNAs in hepatic lipid metabolism and the immunometabolic response to viral infection.

Hepatitis C virus (HCV) is remarkably capable of efficiently hijacking host cell pathways including lipid metabolism in the liver in order to create pro-viral environments for pathogenesis. It is becoming increasingly clear that identifying small molecule inhibitors that target host factors exploited by the virus will expand available HCV treatment options. As such, a thorough understanding of host-virus interactions is critical to the development of alternative therapeutic strategies. Hepatic lipid droplets (LDs) are recruited by HCV to play essential roles in the viral lifecycle. The intracellular location of LDs is modified upon interacting with viral structural core protein. This enables formation of platforms that support viral particle assembly. Because these interactions are non-static, capturing its dynamic processes in order to better understand viral assembly can be achieved with label-free molecular imaging enhanced with live-cell capabilities. Chemical biology approaches that includes CARS microscopy employed in a multi-modal imaging system was used to probe interactions between HCV and host LDs. By successfully tracking LD trajectories, we identified core protein’s ability to alter LD speed and control for LD directionality. Using protein expression model systems that allowed for simultaneous tracking of core protein and LDs, our data revealed that mutations in the core protein region that vary in hydrophobicity and LD binding strengths, are factors that control for differential modulation of LD kinetics. Furthermore, we measured bidirectional LD travels runs and velocities, and observed critical properties by which core protein induces LD migration towards regions of viral particle assembly. Given that many steps in the HCV lifecycle are directly linked to host lipid metabolism, it is not surprising that disrupting lipid biosynthetic pathways would negatively affect viral replication. From this outlook, we explored small molecule inhibitors that targeted several lipid metabolic pathways to study its antiviral properties. Using fluorescent probes covalently labeled to viral RNA, we captured the visualization of disrupted replication complexes upon antagonizing nuclear hormone receptors that are linked to regulating lipid homeostasis. Correspondingly, biochemistry and molecular imaging techniques were also employed to identify novel antiviral mechanisms of small molecule inhibitors that target additional HCV-dependent lipid metabolic pathways.

Hepatitis C virus (HCV) infects an estimated 170 million people worldwide and is a major cause of chronic hepatitis and hepatocellular carcinoma. As there are limited treatment options, the elucidation of novel host-viral interactions during HCV pathogenesis will be critical for the development of new therapeutics. My thesis work has identified cell death-inducing DFF45-like effector B (CIDEB) as a host factor that is disregulated during HCV infection, and has delineated the relevance of CIDEB’s dual roles in apoptosis and lipid metabolism in the context of the HCV lifecycle. Moreover, additional host factors necessary for the HCV lifecycle were investigated using unnatural amino acid (UAA) technology. With this technique, the photo-cross-linking UAA p-azido-phenlyalanine (AZF) and 3’-azibutyl-N-carbamoyl-lysine (Abk) were incorporated into viral proteins by expanding the genetic code of the host organism. This conferred diverse physicochemical and biological properties to these proteins that were exploited to investigate protein structure and function in vitro and in vivo. In summary, gaining insight into the numerous host-viral interactions that take place during HCV infection will both advance our understanding of HCV pathogenesis and uncover potential therapeutic targets.

Immune homeostasis is a host characteristic that maintains biological balance within a host. Humans have evolved many host defence mechanisms that ensure the survival of individuals upon encountering a pathogenic infection, with recovery or persistence from a viral infection being determined by both viral factors and host immunity. Chronic viral infections, such as hepatitis B virus, hepatitis C virus and HIV, often result in chronic fluctuating viraemia in the face of host cellular and humoral immune responses, which are dysregulated by multi-faceted mechanisms that are incompletely understood. This review attempts to illuminate the mechanisms involved in this process, focusing on immune homeostasis in the setting of persistent viral infection from the aspects of host defence mechanism, including interferon-stimulated genes, apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3), autophagy and interactions of various immune cells, cytokines and regulatory molecules.

Hepatitis C virus (HCV) has chronically infected an estimated 170million people worldwide. There are many impediments to the development of an effective vaccine for HCV infection. Dendritic cells (DC) remain the most important antigen-presenting cells for host immune responses, and are capable of either inducing productive immunity or maintaining the state of tolerance to self and non-self antigens. Researchers have recently explored the mechanisms by which DC function is regulated during HCV infection, leading to impaired antiviral T-cell responses and so to persistent viral infection. Recently, DC-based vaccines against HCV have been developed. This review summarizes the current understanding of DC function during HCV infection and explores the prospects of DC-based HCV vaccine. In particular, it describes the biology of DC, the phenotype of DC in HCV-infected patients, the effect of HCV on DC development and function, the studies on new DC-based vaccines against HCV infection, and strategies to improve the efficacy of DC-based vaccines.

No description available.