1 / Fatma Aboulnasr

Hepatitis C virus (HCV), a positive-sense RNA virus that chronically infects between 2.7 and 3.9 million Americans, is highly mutational, making the HCV infection difficult to treat. Thus, it is of high interest to search for highly conserved therapeutic targets within the HCV genome. Two such sequences are located within the 5' untranslated region (UTR) of HCV, being complementary for the microRNA miR-122, a liver microRNA essential for the production of the infectious virus. The use of peptide nucleic acids (PNAs) as therapeutic agents has become a promising area of study in recent years. In this study, we characterized the interactions between miR-122 and the HCV 5'UTR and designed PNAs to disrupt these interactions and thus, inhibit RNA replication and translation. Our results show that the PNAs effectively disrupt the interactions involving miR-122 and the 5'UTR, thereby increasing the possibility of a new therapeutic option against HCV. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / MS / Thesis

MicroRNAs (miRNAs) are non-coding small RNAs that regulate eukaryotic gene activity at the post-transcriptional level by a process termed miRNA gene suppression. MicroRNA-122 (miR-122) is predominantly expressed in human liver cells and recent studies indicated that miR-122 promotes Hepatitis C Virus (HCV) replication and translation through physical interaction with two tandem binding sites located in the 5 untranslated region (5UTR) of the HCV genome (Jopling, et al., 2006; Jopling, et al., 2008). It has been reported that host genes that are also implicated in the miRNA gene suppression pathway are key regulators of HCV replication (Randall, et al., 2007). Two proteins, Dicer, a key RNaseIII enzyme, and its binding partner TRBP are essential proteins for miRNA activity. They are part of a protein complex called the RNA induced silencing complex (RISC) which also includes Argonaute proteins, and function in miRNA biogenesis loading the miRNA into RISC. As such, they are intriguing targets to study host-viral interplay during HCV replication.<p> In our study, we designed siRNAs to knock down Dicer and TRBP and then observed the effects of gene knockdown on full length J6/JFH-1-RLuc HCV (genotype 2a chimeric genome) replication and translation. The results showed that knocking down Dicer and TRBP reduced wild type (wt) J6/JFH-1-RLuc replication but had almost no effects on HCV translation in human liver cells. However, since knocking down Dicer and TRBP did not significantly alter miR-122 levels in the cell, it appears that the role of Dicer and TRBP was not solely the biogenesis of miR-122. This was confirmed by an experiment in which we observed that knocking down Dicer and TRBP also attenuated replication of a mutant virus in which replication is dependent on a exogenously supplied miRNA instead of endogenous miR-122.<p> Taken together, the results supported the hypotheses that Dicer and TRBP facilitate HCV infection mainly through HCV replication but not translation. The effects of Dicer and TRBP on HCV replication are not solely due to miR-122 biogenesis, and may be due to RISC loading functions in steps of miRNA gene suppression.<p> This study has set some essential groundwork for investigating potential roles of host factors in the RNAi machinery modulating HCV replication/translation and exploring novel antiviral targets.

MicroRNAs (miRNAs) are non-coding small RNAs that regulate eukaryotic gene activity at the post-transcriptional level by a process termed miRNA gene suppression. MicroRNA-122 (miR-122) is predominantly expressed in human liver cells and recent studies indicated that miR-122 promotes Hepatitis C Virus (HCV) replication and translation through physical interaction with two tandem binding sites located in the 5 untranslated region (5UTR) of the HCV genome (Jopling, et al., 2006; Jopling, et al., 2008). It has been reported that host genes that are also implicated in the miRNA gene suppression pathway are key regulators of HCV replication (Randall, et al., 2007). Two proteins, Dicer, a key RNaseIII enzyme, and its binding partner TRBP are essential proteins for miRNA activity. They are part of a protein complex called the RNA induced silencing complex (RISC) which also includes Argonaute proteins, and function in miRNA biogenesis loading the miRNA into RISC. As such, they are intriguing targets to study host-viral interplay during HCV replication.<p> In our study, we designed siRNAs to knock down Dicer and TRBP and then observed the effects of gene knockdown on full length J6/JFH-1-RLuc HCV (genotype 2a chimeric genome) replication and translation. The results showed that knocking down Dicer and TRBP reduced wild type (wt) J6/JFH-1-RLuc replication but had almost no effects on HCV translation in human liver cells. However, since knocking down Dicer and TRBP did not significantly alter miR-122 levels in the cell, it appears that the role of Dicer and TRBP was not solely the biogenesis of miR-122. This was confirmed by an experiment in which we observed that knocking down Dicer and TRBP also attenuated replication of a mutant virus in which replication is dependent on a exogenously supplied miRNA instead of endogenous miR-122.<p> Taken together, the results supported the hypotheses that Dicer and TRBP facilitate HCV infection mainly through HCV replication but not translation. The effects of Dicer and TRBP on HCV replication are not solely due to miR-122 biogenesis, and may be due to RISC loading functions in steps of miRNA gene suppression.<p> This study has set some essential groundwork for investigating potential roles of host factors in the RNAi machinery modulating HCV replication/translation and exploring novel antiviral targets.

Hepatitis C virus (HCV) is a serious global health problem with an estimate of 170 million carriers worldwide. Most individuals exposed to this blood-borne pathogen develop chronic infection, which may result in severe liver complications as well as end-stage liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options are suboptimal with no effective vaccines available to date. Development of a readily accessible mouse model that is permissive to natural HCV infection is important to facilitate drug and vaccine discovery, and also to better understand the viral pathogenesis. The inherent difficulty is that HCV displays very limited tropism, infecting only livers from humans or chimpanzees. An attempt was made to elucidate the key determinants in rendering the murine intracellular environment permissive to HCV replication. The results revealed that deletion of the interferon regulatory factor-3 and overexpression of microRNA-122 can independently enhance viral subgenomic replication in murine fibroblasts, with microRNA-122 being the stronger determinant. Interestingly, the phenotype established by these genetic manipulations was insufficient to support full-length HCV genome replication. Murine hepatic cell lines, with or without microRNA-122 expression, were also non-permissive to genomic HCV replication, despite the fact that translation of viral RNA was observed. These results suggest that additional host-specific factor(s) are required to support replication of full-length HCV RNA. These studies provide insight on the essential factors capable of influencing permissiveness of rodent cells to HCV replication, and also suggest genetic modifications to be considered when modeling the complete viral life cycle in a rodent animal model.

The aim of these studies was to identify circulating miRNAs that can be used as biomarkers in patients with paracetamol-induced liver injury. Whether the miRNAs discovered in humans could be back-translated to zebrafish with the aim of developing a liver toxicity model to replace rodent use was also investigated. First, the miRNA signature of DILI induced by paracetamol was defined. Plasma miRNAs were quantified in paracetamol overdose patients. A signature of 16 miRNAs was discovered that best separated patients with liver injury from those without liver injury. This signature was tested in a second cohort and resulted in the detection of paracetamol-induced liver injury with high specificity and sensitivity. At first presentation to hospital miR-122-5p was the most sensitive single miRNA and superior to ALT activity in predicting liver injury. In order to further qualify miR-122-5p, three detailed studies relevant to possible clinical scenarios were performed. The effect of acute alcohol ingestion (commonly co-ingested with paracetamol overdose) on circulating concentrations of miR-122-5p in healthy volunteers was investigated. Alcohol ingestion induced a small, non-clinically relevant, increase in miR-122-5p. The effect of chronic kidney disease (CKD) and haemodialysis (HD) on circulating miR-122-5p concentrations was explored because kidney dysfunction has been associated with a reduction in the concentration of circulating miRNAs. HD patients had lower concentrations of miR- 122-5p compared to healthy volunteers and CKD patients. To facilitate miRNA measurement outwith hospitals, miR-122-5p was measured in a blood drop from a finger prick. miR-122-5p was readily measurable in finger prick samples and concentrations were significantly higher in the blood drop from DILI patients compared with healthy volunteers. To complement miR-122-5p as a marker of toxicity, circulating paracetamol metabolites were measured in plasma samples from paracetamol overdose patients. A higher percentage of circulating metabolites formed by cytochrome P450 enzymes were present in patients with liver injury and these metabolites were superior to both ALT and paracetamol concentration with regard to early patient stratification. To reduce need for rodent studies, miRNAs were back-translated into zebrafish. In order to study circulating miR-122-5p in adult zebrafish, a bloodletting method by collecting blood retro-orbitally was developed. After studying different dosing regimens of paracetamol in adult and larvae zebrafish the model was determined to be too variable with regard to liver injury. A new drug, triptolide, originating from traditional Chinese medicine and responsible for DILI in China, was tested as an alternative model for drug-induced liver injury in zebrafish larvae. miRNA-122-5p decreased in zebrafish larvae after triptolide treatment and triptolide-induced liver injury could be tracked by fluorescent microscopy. Selective plane illumination microscopy was able to track the decrease in liver volume during triptolide exposure. In order to identify the toxic pathways involved in triptolide-induced liver injury, RNA-sequencing was performed. This identified KEGG pathways including ribosome, spliceosome and notch signalling as pathways affected by triptolide. In summary, miRNAs can be used as highly sensitive biomarkers to detect acute liver injury in patients and zebrafish. Zebrafish may represent an alternative model species to study DILI, further work is needed.

Estima-se que 3% da população mundial esteja infectada pelo vírus da hepatite C (HCV). O HCV tem como alvo o tecido hepático e a maioria dos pacientes infectados desenvolvem infecção crônica. Nos últimos anos, estudos in vitro têm demonstrado interações entre o miRNA-122 (miR-122) da célula hospedeira e dois sítios localizados na região 5\' UTR do genoma do vírus da hepatite C (HCV), os quais são essenciais ao processo de replicação viral. O miR-122 é altamente expresso no fígado, onde atua na regulação do metabolismo de lipídios juntamente com outro miRNA, o miRNA-33a (miR-33a), porém, o mecanismo envolvido nesta regulação ainda é pouco conhecido. Sabe-se que a infecção pelo HCV altera a expressão de genes envolvidos na biossíntese e transporte de lipídios, resultando na estimulação do metabolismo de lipídios e criando um ambiente favorável para sua replicação. Neste contexto os objetivos deste trabalho foram avaliar a expressão de miR-33a e miR-122 em indivíduos cronicamente infectados pelo HCV-1 e HCV-3 em amostras obtidas antes do início da terapia. Os miRNAs foram isolados a partir de amostras de sangue periférico e de tecido hepático. A quantificação da expressão relativa de ambos miRNAs foi pela técnica de PCR em tempo real. Os níveis de miR-33a no sangue periférico foram mais elevados do que no tecido hepático em indivíduos infectados pelo HCV-1(p < 0,0001) e HCV-3 (p=0,0025). Observou-se uma correlação inversa entre os níveis de miR-33a no sangue periférico e tecido hepático dos indivíduos infectados pelo HCV-1 (r=-0,281, p=0,039) e correlação positiva para os indivíduos infectados pelo HCV-3 (r=0,9286, p < 0,0001). Correlação inversa entre os níveis hepáticos de miR-33a com o nível sérico de insulina (r=-0,371, p =0,005) nos indivíduos infectados pelo HCV-1 e correlação positiva entre os níveis no sangue periférico com os níveis séricos de GGT (r=0,553, p=0,049) foram observadas. Em relação ao miR-122, de maneira geral o nível hepático foi mais elevado do que o sérico (p < 0,0001). Entretanto, o nível hepático de miR-122 em indivíduos infectados pelo HCV-3 foi maior quando comparado aos infectados pelo HCV-1 (6,22 vezes, p < 0,001). Uma correlação inversa entre os níveis séricos de ApoA-II e os níveis de expressão de miR-122 no sangue (r=-0,330; p=0,014) e tecido hepático (r=-0,311; p=0,020) foi observada nos pacientes infectados pelo HCV-1. Os pacientes infectados pelo HCV- 3 mostraram correlação positiva entre os níveis hepáticos de miR-122 e os níveis de HDL (r=0,412, p=0,036) e insulina (r=0,478, p=0,044). O miR-33a e o miR-122 atuam regulando genes que controlam o metabolismo dos lipídios no fígado. Até o presente momento, não existem relatos que associem a expressão do miR-33a e do miR-122 com o perfil lipídico na infecção pelo HCV. Além disso, o acúmulo de lipídio (esteatose) intensamente descrito na infecção pelo HCV-3 pode sugerir interação diferenciada desse genótipo com os mecanismos envolvidos na regulação do metabolismo lipídico, envolvendo o miR-33a e miR-122 / The prevalence of infection by hepatitis C virus (HCV) is about 3% of the world population. HCV targets the liver tissue and the majority of infected patients develop chronic infection. In recent years, in vitro studies have demonstrated interactions between miRNA-122 (miR-122) the host cell to two places located in the 5\' untranslated region of the HCV genome which are essential for virus replication process. miR-122 is highly expressed in the liver, which has been implicated as a fatty acid metabolism regulator. Another mine has also been described as a key regulator of lipid metabolism, miRNA-33a (miR-33a), however, the mechanisms involved in this regulation are still little known. It is known that HCV infection changes the expression of genes involved in the biosynthesis and transport of lipids, resulting in stimulation of the lipid metabolism and creating a favorable environment for replication of the virus. To our knowledge, there are no reports linking the expression of miR-33a with lipid profile in HCV infection. In this context the objectives of this study were to evaluate the expression of miR-33a and miR-122 in chronically infected individuals with HCV-1 and HCV-3 in samples obtained prior to initiation of therapy. MiRNAs were isolated from peripheral blood samples and liver tissue. The quantification of relative expression of both miRNAs was by PCR in real time. MiR-33a levels in peripheral blood were higher than in liver tissue in patients infected with HCV-1 (p < 0.0001) and HCV-3 (p=0.0025). Levels in the peripheral blood of miR-33a were lower in patients infected with HCV-3 (p=0.0169). There was an inverse correlation between hepatic levels of miR-33a with serum insulin levels (p=0.005) in individuals infected with HCV-1 and a positive correlation between the levels in the peripheral blood serum levels of GGT (p=0.049). Hepatic levels of miR-122 were higher than the levels in the peripheral blood of individuals infected by HCV-1 and HCV-3 (p < 0.0001). Hepatic miR-122 levels were higher in patients infected with HCV-3 than those infected with HCV-1 (6.22 times, p < 0.001). There was a positive correlation between miR-122 levels in the blood and liver tissue of patients infected with HCV-1 (r=0.302, p=0.026). An inverse correlation between serum ApoA-II was observed in these patients the levels of expression of miR-122 in blood (r=-0.330; p =0.014) and liver tissue (r=-0.311; p=0.020). Patients infected with HCV-3 showed a positive correlation between hepatic miR-122 levels to HDL levels (r=0.412, p=0.036) and insulin levels (r=0.478, p=0.044). The miR-33a and miR-122 act by regulating genes that control lipid metabolism in the liver. The different interactions with lipid metabolism exerted by HCV-3 may explain why his relationship with the miR-33a and miR-122 was different when compared with HCV-1

Estima-se que 3% da população mundial esteja infectada pelo vírus da hepatite C (HCV). O HCV tem como alvo o tecido hepático e a maioria dos pacientes infectados desenvolvem infecção crônica. Nos últimos anos, estudos in vitro têm demonstrado interações entre o miRNA-122 (miR-122) da célula hospedeira e dois sítios localizados na região 5\' UTR do genoma do vírus da hepatite C (HCV), os quais são essenciais ao processo de replicação viral. O miR-122 é altamente expresso no fígado, onde atua na regulação do metabolismo de lipídios juntamente com outro miRNA, o miRNA-33a (miR-33a), porém, o mecanismo envolvido nesta regulação ainda é pouco conhecido. Sabe-se que a infecção pelo HCV altera a expressão de genes envolvidos na biossíntese e transporte de lipídios, resultando na estimulação do metabolismo de lipídios e criando um ambiente favorável para sua replicação. Neste contexto os objetivos deste trabalho foram avaliar a expressão de miR-33a e miR-122 em indivíduos cronicamente infectados pelo HCV-1 e HCV-3 em amostras obtidas antes do início da terapia. Os miRNAs foram isolados a partir de amostras de sangue periférico e de tecido hepático. A quantificação da expressão relativa de ambos miRNAs foi pela técnica de PCR em tempo real. Os níveis de miR-33a no sangue periférico foram mais elevados do que no tecido hepático em indivíduos infectados pelo HCV-1(p < 0,0001) e HCV-3 (p=0,0025). Observou-se uma correlação inversa entre os níveis de miR-33a no sangue periférico e tecido hepático dos indivíduos infectados pelo HCV-1 (r=-0,281, p=0,039) e correlação positiva para os indivíduos infectados pelo HCV-3 (r=0,9286, p < 0,0001). Correlação inversa entre os níveis hepáticos de miR-33a com o nível sérico de insulina (r=-0,371, p =0,005) nos indivíduos infectados pelo HCV-1 e correlação positiva entre os níveis no sangue periférico com os níveis séricos de GGT (r=0,553, p=0,049) foram observadas. Em relação ao miR-122, de maneira geral o nível hepático foi mais elevado do que o sérico (p < 0,0001). Entretanto, o nível hepático de miR-122 em indivíduos infectados pelo HCV-3 foi maior quando comparado aos infectados pelo HCV-1 (6,22 vezes, p < 0,001). Uma correlação inversa entre os níveis séricos de ApoA-II e os níveis de expressão de miR-122 no sangue (r=-0,330; p=0,014) e tecido hepático (r=-0,311; p=0,020) foi observada nos pacientes infectados pelo HCV-1. Os pacientes infectados pelo HCV- 3 mostraram correlação positiva entre os níveis hepáticos de miR-122 e os níveis de HDL (r=0,412, p=0,036) e insulina (r=0,478, p=0,044). O miR-33a e o miR-122 atuam regulando genes que controlam o metabolismo dos lipídios no fígado. Até o presente momento, não existem relatos que associem a expressão do miR-33a e do miR-122 com o perfil lipídico na infecção pelo HCV. Além disso, o acúmulo de lipídio (esteatose) intensamente descrito na infecção pelo HCV-3 pode sugerir interação diferenciada desse genótipo com os mecanismos envolvidos na regulação do metabolismo lipídico, envolvendo o miR-33a e miR-122 / The prevalence of infection by hepatitis C virus (HCV) is about 3% of the world population. HCV targets the liver tissue and the majority of infected patients develop chronic infection. In recent years, in vitro studies have demonstrated interactions between miRNA-122 (miR-122) the host cell to two places located in the 5\' untranslated region of the HCV genome which are essential for virus replication process. miR-122 is highly expressed in the liver, which has been implicated as a fatty acid metabolism regulator. Another mine has also been described as a key regulator of lipid metabolism, miRNA-33a (miR-33a), however, the mechanisms involved in this regulation are still little known. It is known that HCV infection changes the expression of genes involved in the biosynthesis and transport of lipids, resulting in stimulation of the lipid metabolism and creating a favorable environment for replication of the virus. To our knowledge, there are no reports linking the expression of miR-33a with lipid profile in HCV infection. In this context the objectives of this study were to evaluate the expression of miR-33a and miR-122 in chronically infected individuals with HCV-1 and HCV-3 in samples obtained prior to initiation of therapy. MiRNAs were isolated from peripheral blood samples and liver tissue. The quantification of relative expression of both miRNAs was by PCR in real time. MiR-33a levels in peripheral blood were higher than in liver tissue in patients infected with HCV-1 (p < 0.0001) and HCV-3 (p=0.0025). Levels in the peripheral blood of miR-33a were lower in patients infected with HCV-3 (p=0.0169). There was an inverse correlation between hepatic levels of miR-33a with serum insulin levels (p=0.005) in individuals infected with HCV-1 and a positive correlation between the levels in the peripheral blood serum levels of GGT (p=0.049). Hepatic levels of miR-122 were higher than the levels in the peripheral blood of individuals infected by HCV-1 and HCV-3 (p < 0.0001). Hepatic miR-122 levels were higher in patients infected with HCV-3 than those infected with HCV-1 (6.22 times, p < 0.001). There was a positive correlation between miR-122 levels in the blood and liver tissue of patients infected with HCV-1 (r=0.302, p=0.026). An inverse correlation between serum ApoA-II was observed in these patients the levels of expression of miR-122 in blood (r=-0.330; p =0.014) and liver tissue (r=-0.311; p=0.020). Patients infected with HCV-3 showed a positive correlation between hepatic miR-122 levels to HDL levels (r=0.412, p=0.036) and insulin levels (r=0.478, p=0.044). The miR-33a and miR-122 act by regulating genes that control lipid metabolism in the liver. The different interactions with lipid metabolism exerted by HCV-3 may explain why his relationship with the miR-33a and miR-122 was different when compared with HCV-1

Generally Hepatitis C Virus tropism is limited to hepatocytes. This limited tropism is a result of the receptors HCV requires for cellular entry and other host cellular factors including, uniquely, a liver specific miRNA, miR-122. The relationship between HCV and miR-122 is interesting, as commonly, miRNA are associated with suppression of function, but in the case of HCV, miR-122 actively promotes HCV proliferation. In-depth studies have demonstrated that miR-122 along with the RNA induced silencing complex (RISC) protein Argonaute 2 (Ago2) binds directly to two seed sequences separated by 8-9 nucleotides on HCV 5’UTR. Binding to the 5’UTR results in an increase in viral replication and translation. The method by which miR-122 promotes HCV translation and replication is not fully understood but evidence suggests that part of the function of miR-122 is to stabilize the HCV genome and protect it from exonuclease degradation by Xrn1, but other mechanisms remain to be identified. The reliance of HCV on miR-122 is best exemplified by the fact that removal of miR-122 by a miR-122 antagonist drastically impedes HCV viral titers in Chimpanzees and humans with no indication of escape mutants. The observation that HCV augmentation of the HCV life cycle by miR-122 requires Ago2 suggests that other components downstream in the miRNA suppression pathway may also be part of the mechanism of action. Our studies focused specifically on the processing body (p-body) associated DEAD-box helicase DDX6. DDX6 is essential for p-body assembly, required for robust miRNA suppression activity and elevated in HCV associated hepatocellular carcinomas. As such we hypothesized that DDX6 and p-bodies were directly or in-directly associated with the mechanism of action of miR-122. Knocking down DDX6 with siRNA indicated that DDX6 augments both HCV replication and translation. To examine whether DDX6 augmentation of HCV replication was related to the effects of miR-122 on the HCV life cycle, HCV replication and translation were assessed in the presence or absence of miR-122 when DDX6 was knocked down. Our data indicated that HCV replication and translation were augmented equally by miR-122 whether DDX6 was present or not. Our data also demonstrated that HCV replication and translation that was occurring independent of miR-122 was also still affected by DDX6 knockdown. Taken together our observations strongly suggest that the role DDX6 has on HCV is independent of HCV and miR-122’s relationship. In order to better understand miR-122’s relationship with HCV, we hypothesized that targeting the miR-122 binding region with siRNA would inhibit HCV replication initially, but that over the course of several rounds of treatment with the same siRNA, HCV would mutate to escape the siRNA, producing escape mutants that replicate without a dependency on miR-122. These escape mutants could be evaluated on how they replicate without using miR-122, shedding light on miR-122 and HCV’s relationship. Conversely if no escape mutants arose the siRNA could be further studied as a potential therapeutic for HCV. siRNA designed to target the miR-122 binding region inhibited HCV replication, confirming that the designed siRNAs could access the miR-122 binding region and function as an siRNA. Interestingly, when the siRNAs were used against a replication competent HCV RNA having a single nucleotide mutation in the first miR-122 binding site, instead of abolishing siRNA knockdown, two of the siRNA showed enhanced inhibition activity. The target sequences of these siRNAs spanned both miR-122 binding sites and we speculate that their inhibitory activity was due to competition for miR-122 binding to site 2. This observation indicates that siRNA targeting the miR-122 binding region have dual activity, by siRNA induced cleavage, and as a competitive inhibitor of miR-122 binding. Selection for viral escape mutants of the miR-122-binding site targeting siRNAs revealed viral RNAs having mutations within the miR-122 binding sites, in the surrounding region, and to other areas within the HCV IRES. The mutant viruses will be used to assess the influence of miR-122 binding site mutations on HCV replicative fitness, and to determine if the virus can evolve to replicate independent from augmentation by miR-122.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20985号 / 医博第4331号 / 新制||医||1027(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 妹尾 浩, 教授 湊谷 謙司, 教授 野田 亮 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM