Introdução: O câncer de próstata (CaP) é o tumor mais comum do homem nos países ocidentais e a segunda causa de óbito por câncer em homens nos EUA, Europa e Brasil. O câncer localizado tem sobrevida câncer especifica elevada quando tratado adequadamente, porém a doença metastática ainda apresenta tratamentos pouco eficientes com sobrevida global de 28%. Os microRNAs (miRNAs) são um grupo de moléculas pequenas de RNA que contém entre 19 a 25 nucleotídeos não codificantes de proteína, com ação fundamental na regulação da expressão gênica. Eles estão envolvidos em processos essenciais nas células normais e neoplásicas como ciclo celular, proliferação, apoptose, metabolismo energético, invasão e metastatização. Objetivos: Realizar estudos in vitro e in vivo usando miRNA em um modelo de câncer de próstata metastático inédito no nosso meio com intuito de analisar o seu potencial como agente terapêutico dessa neoplasia. Métodos: Nos estudos in vitro, três linhagens celulares foram utilizadas (PC3, DU145 e LNCaP). Essas linhagens foram transfectadas com os miRNAs 100, 145 e 373 e seus respectivos antiMiRs utilizando-se lipofectamina. Analisamos a expressão dos genes alvo mTOR, SMARCA5, KRAS, CMYC, MMP9, CD44 por PCR quantitativo em tempo real (qRT-PCR). Foram realizados também estudos de apoptose, ciclo celular e ploidia utilizando o citômetro de fluxo. Alterações no potencial de invasão foram avaliadas pela técnica do matrigel. O modelo in vivo pré-clínico foi desenvolvido pela injeção intra-cardíaca da linhagem PC-3M-Luc-C6 em camundongos NUDE com 9 semanas. O crescimento tumoral foi avaliado com o sistema de bioluminescência in vivo. Após o pleno estabelecimento das metástases no dia 21, os animais foram tratados com três injeções na veia da cauda contendo o miRNA conjugado com o atelocolágeno. Os animais foram sacrificados e no dia 48 para análise dos tecidos. Resultados: miR-100 aumenta a apoptose na LNCaP, e reduz a apoptose na DU145. Na linhagem DU145 o miR 100 inibiu a proliferação. Na análise da expressão gênica o miR-100 inibe SMARCA5 na DU145 e PC3 e mTOR na LNCaP, o anti-miR 100 estimula mTOR e SMARCA5 na LNCaP. O miR-145 promoveu aumento da apoptose em 24% na DU145. Na linhagem PC3 o miR-145 age inibindo a proliferação, com uma diferença absoluta de 18% em relação ao seu controle. O miR-145 inibe KRAS e CMYC nas três linhagens e o anti-miR-145 estimula CMYC na DU145 e RAS nas três linhagens O miR-373 reduziu a apoptose em 29% na DU145 e diminui a proliferação com uma diferença absoluta de 13% em relação ao controle. O miR- 373 estimula a MMP9 na DU145 e na LNCaP e inibe o CD44 na PC3. O antimiR- 373 inibe MMP9 na DU145 e LNCaP. Nos estudos in vivo de CaP metastático o miR-100 apresenta tendência a redução no crescimento tumoral (p=0,23) e o miR-145 reduz o crescimento de forma significativa no dia 34 (p=0,02). Após esses dias o tumor volta a crescer de forma agressiva. Os animais tratados com anti-miR-373 não apresentaram alterações em relação aos controles. Conclusões: O miR-100 é um miRNA contexto dependente, com papel supressor tumoral em linhagens de tumor de próstata agressivo e o miR- 373 age in vitro como oncomiR. O miR-145 age como supressor tumoral in vitro e em modelo animal de CaP metastático apresentando resposta terapêutica consistente, podendo ser utilizado no arsenal terapêutico contra essa neoplasia. Estudos futuros devem avaliar o uso dos miRNAs isoladamente ou de forma adjuvante no tratamento do CaP metastático / Introduction: Prostate cancer (PCa) is the most common neoplasia of man in Western countries and the second cause of death by cancer in men in the US, Europe and Brazil. The localized cancer has high cancer-specific survival when treated properly, however metastatic disease still presents low effective treatments with 28% of global survival. microRNAs (miRNAs) are a group of small RNA molecules containing from 19 to 25 nucleotides of noncoding protein with fundamental action in the regulation of gene expression. They are involved in key processes in normal and neoplastic cells as cell cycle, proliferation, apoptosis, energy metabolism, invasion and metastasis. Objectives: To carry out studies in vitro and in vivo using miRNA in a novel model of metastatic prostate cancer in our country in order to evaluate its potential as a therapeutic agent of this neoplasia. Methods: In the in vitro studies, three cell lines were used (PC3, DU145 and LNCaP). These cell lines were transfected with miRNAs 100, 145 and 373 and their antiMiRs using lipofectamine. We analyzed the gene expression of mTOR, SMARCA5, KRAS, CMYC, MMP9, CD44 by real-time polymerase chain reaction (qRT-PCR). We also performed studies of apoptosis, cell cycle and ploidy using flow cytometer. Changes in the invasion potential were evaluated by the technique of matrigel. The pre-clinical model in vivo was developed by intracardiac injection of PC-3MLuc-C6 cell line in NUDE mice with 9 weeks. Tumor growth was evaluated with an in vivo image system (IVIS). After the full establishment of metastases on day 21, the animals were treated with three injections into the tail vein containing the miRNA plus atelocollagen. The animals were sacrificed on day 48 for tissues analysis. Results: MiR-100 increases apoptosis in LNCaP and reduces apoptosis in DU145. The anti-miR-100 increased apoptosis in 14% in PC3. In cell line DU145, miR-100 inhibited proliferation. In the analysis of gene expression, the miR-100 inhibits SMARCA5 in DU145 and PC3 and mTOR in LNCaP, anti-miR-100 stimulates mTOR and SMARCA5 in LNCaP. The miR-145 promoted an increased in apoptosis by 24% in DU145. In PC3 cell line miR-145 acts by inhibiting the proliferation, with an absolute difference of 18% compared to control. MiR-145 inhibits KRAS and CMYC in the three cell lines and anti-miR-145 stimulates CMYC in DU145 and KRAS in the three cell lines. The miR-373 reduced apoptosis by 29% in DU145 and reduces proliferation with an absolute difference of 13% relative to control. MiR-373 stimulates MMP9 in DU145 and LNCaP cells and inhibits CD44 in PC3. The anti -miR-373 inhibits MMP9 in DU145 and LNCaP. In the in vivo studies of metastatic PCa, miR-100 shows a tendency to decrease tumor growth (p=0.23) and miR-145 reduces tumor growth on day 34 (p=0.02). After those days, the tumor grows back aggressively. Animals treated with anti-miR-373 showed no changes relative to controls. Conclusion: The miR-100 is a context-dependent miRNA, with tumor suppressor role in aggressive tumor cell lines. The miR-373 acts in vitro as oncomiR and miR-145 acts as a tumor suppressor in vitro and in an animal model with consistent therapeutic response and can be used in the therapeutic arsenal against this neoplasia. Future studies should evaluate the use of miRNAs alone or adjuvant in the treatment of metastatic prostate cancer

O aneurisma de aorta abdominal (AAA) é uma doença assintomática na maioria dos casos, podendo acometer 5% das pessoas do gênero masculino com idade superior a 65 anos, predispondo ao risco de ruptura com mortalidade em torno de 80%. O presente estudo teve como objetivo avaliar os perfis de expressão gênica e de metilação do DNA no tecido, como também os microRNAs no plasma e no tecido de indivíduos com e sem AAA na tentativa de identificar marcadores biológicos e alvos terapêuticos para o diagnóstico, monitoramento e tratamento precoce do AAA. Os perfis de expressão gênica, miRNA e metilação de DNA dos tecidos da aorta abdominal (n=6) obtidos durante a cirurgia aberta para correção de AAA foram comparados com tecidos da aorta abdominal de doadores de órgãos sem AAA (n=6). Também foram comparados os perfis de miRNAs circulantes no plasma do grupo AAA (n=6) com o grupo-controle de voluntários com as características semelhantes, porém sem AAA (n=6). Para a análise da expressão gênica, utilizou-se a qPCR Array, analisando-se genes relacionados ao endotélio vascular humano (PAHS-015Z, QIAGEN®). A análise do perfil de miRNA foi realizada utilizando-se Human miFinder 384HC miScript miRNA PCR Array (MIHS-3001Z, QIAGEN®) e, para análise de metilação do DNA, utilizou-se a qPCR array com 22 genes das vias de estresse e toxicidade EpiTect Methyl II (EAHS-581Z, QIAGEN®). O software Ingenuity Pathway analysis (IPA®) foi utilizado para identificação das prováveis relações entre os microRNAs e a expressão gênica realizada nesta pesquisa. No estudo da expressão gênica, quatro genes (SPHK-1, TYMP, ALOX5 e HIF1A) foram identificados como mais expressos e outros 6 genes (PTGIS, CX3CL1, ITGB1, COL18A-1, FN1 e AGTR1) apresentaram expressão reduzida nos tecidos de AAA. Na análise do perfil de miRNAs, 24 miRNAs foram significantemente mais expressos e 35 miRNAs menos expressos no tecido. No plasma de indivíduos com AAA, 8 miRNAs apresentaram-se mais expressos e 9 miRNAs menos expressos. Dois miRNAs, miR-328-3p e let-7c-5p demonstraram expressões comuns entre tecido e plasma. Quanto ao padrão de metilação de DNA, somente o gene GDF15 teve grau de metilação maior nos tecidos de AAA quando comparado ao grupo-controle. A análise funcional revelou que o gene PTGIS (prostaciclina sintetase), um potente vasodilatador e inibidor da atividade plaquetária, foi reprimido pelo miR-150-5p, que se mostrou 7,5 vezes mais expresso no tecido de AAA, e teve uma possível interação com o miR-328-3p, cuja expressão foi 3,7 vezes mais baixa no tecido. Os genes com expressão reduzida nos tecidos do AAA foram alvos de miRNAs com expressão aumentada, evidenciando a importância e influência dos fatores epigenéticos tanto para o desenvolvimento quanto para a gravidade do AAA. / Abdominal aortic aneurism (AAA) is an asymptomatic disease in the majority of cases that may occur in 5% of males over age 65, predisposing to the risk of rupture leading to a mortality rate of 80%. The aim of this study was to evaluate the DNA metilation and gene expression profile in tissue, and microRNA expression pattern in both plasma and tissue samples from individuals with and without AAA to identify biological markers and therapeutic targets for an early diagnosis and treatment of AAA, respectively. Genes and miRNA expression and DNA metilation profiles in AAA tissues (n= 6) were compared to abdominal aortic tissues obtained from organ donators without AAA (n = 6). We also compared circulating miRNAs profiles in plasma samples, between AAA (n = 6) and the control group without AAA (n = 6). For the gene expression analysis we used a qPCR Array (PAHS-015Z, QIAGEN®) to analyze genes related to human vascular endothelium. For the miRNA expression pattern and for DNA methylation analysis we used the Human miFinder 384HC miScript miRNA PCR Array (MIHS-3001Z, QIAGEN®) and EpiTect Methyl II (EAHS-581Z, QIAGEN®), respectively. The Ingenuity software was used to identify the interactions between the miRNAs and genes evaluated in this study. Four genes (SPHK-1, TYMP, ALOX5 and HIF1A) were upregulated and six other genes (PTGIS, CX3CL1, ITGB1, COL18A-1, FN1 e AGTR1) were downregulated in AAA tissues. In addition, the miRNAs analysis showed 24 miRNAs more expressed and 35 miRNAs less expressed in AAA tissue than controls. Although in plasma samples, AAA group presented 8 miRNAs more expressed and 8 miRNAs less expressed than controls. Only, miR-328-3p and let-7c-5p were differently expressed between AAA and controls in both tissue and plasma samples. DNA methylation analysis showed that the gene GDF15 was hypermethylated in AAA tissues when compared to the control group. Functional analysis revealed that PTGIS, a potent vasodilator and platelet activity inhibitor was supressed by miR-150-5p, which had a seven-fold increase in AAA tissues. Moreover, a possible interaction between PTGIS and miR-328-3p, about 4-fold decreased in AAA tissues, was showed. Thus, the downregulated genes in AAA tissues are targets of miRNAs with increased expression in the same biological sample. These results highlight the importance and influence of epigenetic factors for both development and severity of AAA.

MicroRNAs (miRNAs) are short, non-coding RNAs involved in the regulation of several processes associated with inflammatory diseases and infection. Bacterial infection modulates miRNA expression to subvert innate immune response. In this study, we analyzed bacterial modulation of miRNAs in bone-marrow-derived macrophages (BMMs), in which activity was induced by infection with Porphyromonas gingivalis (Pg) through a microarray analysis. Several miRNA expressions levels were modulated 3 hours post infection (at a multiplicity of infection (MOI) of 25). A bioinformatics analysis was performed to further identify pathways related to the innate immune host-response pathways that are under the influence of the selected miRNAs. To assess the effects of the identified miRNAs on cytokines secretion (pro inflammatory TNF-α and anti-inflammatory IL-10), BMMs were transfected with selected miRNAs mimics or inhibitors. Transfection with mmu-miR-155 and mmu-miR- 2137 did not modify TNF-α secretion while their inhibitors increased it. Inhibitors of mmumiR-2137 and mmu-miR-7674 increased the secretion of the anti-inflammatory IL-10. In Pginfected BMMs, mmu-miR-155-5p significantly decreased TNF-α secretion while inhibitor of mmu-miR-2137 increased IL-10 secretion. In vivo, in a Pg-induced calvarial bone resorption mouse model, injection of mmu-miR-155-5p or anti-mmu-miR-2137 reduced the size of the lesion significantly. Furthermore, anti-mmu-miR-2137 significantly reduced inflammatorycell infiltration, osteoclast activity and bone loss. Bioinformatics analysis demonstrated that pathways related to cytokines and chemokines related pathways but also osteoclast differentiation may be involved in the observed effects. The study highlights the potential therapeutic merits of targeting mmu-miR-155-5p and mmu-miR-2137 to control inflammation induced by Pg infection. To assess the regenerative process in the same animal model, we aimed to compare the effect of Bone Morphogenic Protien 2 (BMP2), Platelets Rich Plasma (PRP), Leukocyte-Platelets Rich Fibrin (L-PRF), and Polygucosamine (PGIcNAc) on bone formation in critical size bone defects in mice. One-hundred-thirty-eight mice were divided into 23 groups (n=6), negative control, different combinations of the PGIcNAc with or without of BMP2, Collagen Sponge (SurgiFoam), PRP, and L-PRF. The 5mm defect, then, was allowed to heal. After six weeks, samples were analyzed for bone formation utilizing radiographs, H&E staining, alkaline phosphatase staining. Our results show that BMP2 were able to produce 90-95% healing of critical size defects after six weeks histologically and radiographically. However, SurgiFoam, PRP and L-PRF with or without PGIcNAc were able to close 60% of the original defect. This study supports that BMP2 is more effective for bone regeneration than SurgiFoam, PRP, L-PRF and PGIcNAc.

O Transtorno do Espectro Autista (TEA), segundo o DSM-5, se enquadra nos Transtornos do Desenvolvimento e é caracterizado por uma díade comportamental: 1) prejuízos na comunicação e interação social e 2) comportamentos repetitivos ou estereotipados. Apesar da etiologia do TEA ser desconhecida, tanto fatores genéticos quanto ambientais já foram associados à desordem, incluindo a utilização de ácido valproico (VPA) durante a gestação. Observando essa relação importante, desenvolveu-se um modelo animal de autismo induzido pela exposição pré-natal ao VPA, o qual já foi amplamente validado em aspectos comportamentais e moleculares. No primeiro capítulo desta tese, utilizamos o modelo animal de autismo obtido através de uma única injeção intraperitoneal de VPA (600mg/kg) no dia E12,5 nas ratas Wistar prenhes e testamos um tratamento pré-natal com resveratrol (RSV), através de injeções subcutâneas (3,6 mg/Kg) administradas nas ratas prenhes nos dias E6,5-E18,5. O tratamento pré-natal com RSV demonstrou ser capaz de prevenir alterações na sociabilidade recíproca, porém não teve impacto nos prejuízos na memória olfativa e comportamentos repetitivos induzidos pelo VPA. No que se refere aos dados de microRNA (miRNA), RSV foi capaz de prevenir a alteração na expressão de miR134-5p, o qual também se observou alterado em pacientes com TEA, juntamente com o miR138-5p, ambos com alvos associados à modulação do citoesqueleto na estrutura de espinhos dendríticos. Em conjunto, esses resultados demonstram que o RSV altera vias importantes no modelo, possivelmente através das suas características antioxidantes e anti-inflamatórias, as quais contrapõem os aspectos inflamatórios do VPA. Este trabalho permitiu o aprimoramento e melhor conhecimento da técnica de RT-qPCR para análise de miRNA, sendo tema do segundo capítulo da presente tese, reunindo diferentes estratégias que auxiliaram a superar potenciais problemas e interferentes no uso dessa técnica. Finalmente, no terceiro capítulo, utilizamos o modelo VPA para avaliar o efeito do tratamento pós-natal com suramina, através de uma única injeção subcutânea (20 mg/kg) administrada nos filhotes machos na idade P30. Este tratamento foi capaz de reverter alterações de sociabilidade, novidade social e comportamento do tipo ansioso, enquanto os prejuízos na sociabilidade recíproca, comportamento exploratório, estereotipia e processamento sensorial não foram revertidos por esse tratamento. Nos dados moleculares, a suramina não foi capaz de reverter o aumento de expressão nos receptores purinérgicos P2X4 (hipocampo e córtex pré-frontal medial) e P2Y2 (hipocampo), porém reverteu o aumento de IL-6 promovido pelo VPA. Assim, possivelmente a modulação comportamental associada à suramina parece não estar associada a interações específicas nos receptores purinérgicos, mas sim com uma modificação neuroimune através da interleucina pró-inflamatória IL-6, demonstrando a importância do sistema imunológico na fisiopatologia do TEA. De forma geral, a tese contribuiu para elucidar mecanismos envolvidos no desenvolvimento das características do tipo autista, demonstrando o papel relevante das alterações neuroimunes e da modulação de alvos por miRNA, as quais, em conjunto, podem contribuir para o desenvolvimento de métodos diagnósticos e adequação de estratégias farmacológicas voltados ao TEA. Palavras-chave: Comportamento animal, microRNA, neuroimune, PCR, resveratrol, sistema purinérgico, suramina, transtorno do espectro autista. / According to DSM-5, Autism Spectrum Disorder (ASD) is a developmental disorder characterized by a behavioral dyad: 1) deficits in communication and social interaction, and 2) repetitive and stereotyped behaviors. Although the etiology of ASD is still unknown, both genetic and environmental factors have been associated with the disorder, including the use of valproic acid (VPA) during gestation. Observing this important relationship, an animal model of autism induced by prenatal exposure to VPA was developed, which has already been widely validated in behavioral and molecular aspects. In the first chapter of this thesis, we used the animal model obtained through a single intraperitoneal injection of VPA (600 mg/kg) at E12.5 in pregnant Wistar rats and tested a prenatal treatment with resveratrol (RSV) by subcutaneous injections (3.6 mg/kg) administered in the pregnant rats at E6.5 to E18.5. The prenatal treatment with RSV was able to prevent changes in the reciprocal sociability, but had no impact on the deficits in olfactory memory and repetitive behavior induced by VPA. Regarding the microRNA (miRNA) data, RSV treatment was able to prevent the alteration in the expression of miR134-5p, which also was altered in ASD patients along with miR138-5p, both with targets associated with cytoskeletal modulation in the structure of dendritic spines. Taken together, these results demonstrate that RSV alters important pathways in the model, possibly through its antioxidant and anti-inflammatory properties, which counteract the inflammatory aspects of VPA. This work allowed the improvement and better knowledge of the RT-qPCR technique for miRNA analysis, which was the theme of the second chapter of this thesis, combining different strategies to overcome potential problems and interferences in this methodology Finally, in the third chapter we used the same animal model to evaluate the effect of postnatal treatment with suramin after a single subcutaneous injection (20 mg/kg) administered to male pups at P30. This treatment was able to revert VPA-induced deficits in sociability, social novelty, and anxiety-like behavior, whilst present no effect on impairments in reciprocal sociability, exploratory behavior, repetitive behavior and sensory processing. In the molecular data, suramin was not able to reverse the increase of expression in the purinergic receptors P2X4 (hippocampus and medial prefrontal cortex) and P2Y2 (hippocampus), but reversed the VPA-induced increase of proinflammatory interleukin IL-6. Thus, behavioral modulation associated with suramin appears to be related not with specific interactions in purinergic receptors, but with a neuroimmune modification through the IL-6, indicating the importance of the immune system in the ASD pathophysiology. In general, the thesis contributed to elucidate the mechanisms involved in the development of autistic-like features, demonstrating the relevant role of neuroimmune alterations and the modulation of targets by miRNA, which, together, may contribute to the development of diagnostic methods and improvement of pharmacological strategies related to ASD.

Le profil d'expression aberrant des micro(mi)ARN est une caractéristique typique de nombreux cancers, dont le carcinome hépatocellulaire (CHC), une tumeur hépatique maligne primaire qui se classe seconde dans le monde en termes de mortalité par cancer. Notre équipe a récemment montré la baisse d’expression de miR-4510 dans des échantillons de patients atteints de CHC et son activité « suppresseur de tumeur ». L'analyse de données protéomiques recueillies à partir de cellules Huh7 transfectées par miR-4510 a révélé une diminution importante de plusieurs oncogènes, dont la sérine / thréonine protéine kinase RAF1. J’ai également découvert que le taux de protéine RAF1 était significativement surexprimé chez les patients atteints de CHC. Le rôle de RAF1 et de miR-4510 dans le CHC étant mal compris, j’ai étudié la fonction du couple RAF1/miR-4510 dans la tumorigenèse du foie. Mes analyses ont montré que miR-4510 régule négativement les taux de protéine RAF1 et d'ARNm. Une analyse par le système de double fluorescence-FunREG a révélé que miR-4510 interagit directement avec la région 3’ non-traduite de l’ARN de RAF1 via un site unique. La déplétion de RAF1 dans deux lignées tumorales de CHC par miR-4510 ou ARN interférant désactive leur caractère tumorigène in vitro et in vivo. Collectivement, mes données suggèrent que miR-4510 participe à la carcinogenèse du foie via son action directe sur RAF1 et la régulation de la voie MAPK/ERK. En conclusion, mon étude soutient l’hypothèse selon laquelle un traitement à base de miR-4510 pourrait être efficace pour traiter les patients atteints de CHC de type avancé ou réfractaire à la chimiothérapie. / Aberrant micro(mi)RNA expression signature is a hallmark of many cancers including hepatocellular carcinoma (HCC), a primary malignant liver disease which ranks second in cancer mortality worldwide. Our team previously reported the downregulation of miR-4510 in HCC samples and identified this miRNA as a strong tumor suppressor in liver. Proteomic data analysis collected from Huh7 cells transfected by miR-4510 showed a significant decrease of multiple oncogenes including RAF1 serine/threonine protein kinase. I also found that RAF1 protein level is significantly increased in HCC patients. The role of RAF1 and miR-4510 in HCC being poorly understood, I studied the function of RAF1/miR-4510 pair in tumorigenesis of the liver. My results showed that miR-4510 overexpression significantly decreases both RAF1 protein and mRNA levels and inhibits MAPK/ERK signaling. The dual fluorescence-FunREG assay revealed that miR-4510 directly interacts with RAF1 3’-untranslated region through a unique site. Silencing of RAF1 in two hepatic cell lines by miR-4510 or a specific small interfering RNA suppressed important tumorigenic features (proliferation, migration….) both in vitro and in vivo. Collectively, my data suggest that miR-4510 participates in liver carcinogenesis through RAF1 targeting and MAPK/ERK signaling inactivation. In addition, my study suggests that miR-4510-based therapy may represent a promising strategy to treat patients with advanced or refractory HCC.

Viruses are obligate intracellular pathogens. Therefore, their successful replication, at every stage from attachment to assembly and egress, is dependent on host cell functions. The host cell in turn engages mechanisms to counteract virus replication. As a result, viruses have evolved mechanisms to evade these counteracting measures as well as ways to reshape the cellular environment into one that’s favourable for successful replication. Systematic studies offer a platform for unravelling virus-cell interactions and in particular can address three important aspects 1) increase our understanding of basic biology of the virus, 2) identify and characterise novel cellular functions 3) provide important leads for novel targets for antiviral therapy. In this study, I investigated two aspects of virus host interaction; the role of microRNAs (miRNAs) in virus infection and the role of interferon inducible genes in virus infection. Human cytomegalovirus (HCMV) is a β herpes virus that infects humans. HCMV maintains a persistent lifelong infection in the host involving a cycle of latency and reactivation. Infection of healthy individuals with HCMV results in relatively minor symptoms. In contrast, infection of individuals with a compromised immune system, as in the case of organ transplant recipients and AIDS patients, can cause significant morbidity and mortality. In common with other herpes viruses, HCMV expresses multiple small regulatory RNAs called miRNAs. HCMV encodes at least 14 miRNAs. Identifying the targets of these miRNAs will help us understand their functional importance during infection. Recently, a biochemical technique called Cross-Linking, Ligation and Sequencing of Hybrids (CLASH), was developed by Tollervey and colleagues, representing the most advanced systematic technique for the identification of miRNA targets. We adapted this approach to identify high confidence miRNA targets during HCMV infection. However, the protocol was sub-optimal and presented us with technical challenges. Although high quality data sets were not generated, the work was crucial for the establishment of the system which is now generating promising data. Virus-cell interactions can also be elucidated by probing for host factors that are important for virus replication. Type I interferon is a highly effective inhibitor of HCMV replication. Treatment of cells with interferon results in up regulation of multiple effectors known as interferon stimulated genes (ISGs). How these genes block HCMV replication is poorly understood. A library of more than 380 ISG expressing lentiviruses was screened to determine the effects of individual ISGs on HCMV replication. The screen was performed in primary human fibroblast cells and a glioblastoma cell line called U373s. Multiple inhibitory ISGs were identified including well characterised ISGs such as cGAS, STAT2, NOD2, DDX60 and HPSE as well as novel candidates TXNIP, ELF1, FAM46C, MT1H and CHMP5. Five ISGs were identified as HCMV replication enhancers including previously published ISGs BST2 and IFITM1 and novel enhancers ODC1, BCL3 and IL28RA. siRNA screens against top hits demonstrated that STAT2, CPT1A and cGAS are dominant inhibitory factors during HCMV infection and knockdown of these genes can partially rescue HCMV replication following interferon treatment. Finally, using a corresponding rhesus ISG library we show that rhesus SAMHD1 effectively inhibits HCMV replication while human SAMHD1 has no effect, suggesting that HCMV expresses a species-specific inhibitor of SAMHD1. This study defines interferon stimulated pathways important for HCMV replication and identifies multiple novel host factors that both restrict and enhance HCMV replication. These studies demonstrate the effectiveness of using systematic approaches for the identification of novel host virus interactions.

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No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_PerfilMicroRna.pdf: 6022695 bytes, checksum: fd2a87ff6ebe80e553d7c993c5fe8f88 (MD5) Previous issue date: 2016-06-30 / CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico / IEC - Instituto Evandro Chagas / A dengue é a arbovirose mais prevalente no mundo, causada pelo vírus dengue (DENV) está presente em todos continentes. Por mais de três décadas tem sido um constante problema de saúde pública frequentemente fatal nos casos de dengue hemorrágica (DHF). A patogenia da dengue é intimamente relacionada à resposta imune do hospedeiro, atingindo quadros de inflamação exacerbada e autoimunidade transitória onde todos tecidos são atingidos, sendo o fígado um dos mais importantes no contexto de evolução dos quadros graves devido a intensa replicação viral nesse órgão e sua função significativa no metabolismo. O estudo de microRNAs (miRNA) como elementos regulatórios do metabolismo e da resposta imune durante a infecção é crucial para o entendimento dos mecanismos de regulação da expressão gênica durante a infecção pelo DENV, e pode auxiliar no desenvolvimento de métodos diagnósticos e terapias anti-virais. Utilizamos a abordagem de miRA-Seq, utilizando a plataforma MySeq (Illumina) para identificar o perfil de miRNAs expressos no tecido hepático parafinizado de dez casos de óbito por DHF, comparando com cinco amostras de tecido sem infecção por DENV. Oito miRNAs apresentaram expressão diferencial no fígado de pacientes com DHF, sendo o miR-126-5p (molécula de regulação da proliferação de células endoteliais), e miR-133a-3p, regulados positivamente na DHF e miR-122-5p (um miRNA hepatoespecífico), miR-146a-5p (regulador de Interferon), miR-10b-5p, miR-204-5p, miR-148a-5p, e miR-423-5p regulados negativamente. A análise funcional de vias KEGG e GO, a partir dos genes alvo preditos dos miRNAs superexpressos, identificou a maioria de vias de regulação daapoptose e da resposta imune com envolvimento de genes MAPK, RAS, CDK e FAS e da resposta imune com destaque para NF-kB, famílias CC e CX, Il e TLR. A mesma análise dos genes alvo dos miRNAs sub-expressos também identificou na maioria vias de apoptose e biossintéticas. No nosso conhecimento, essa é a primeira descrição in vivo do perfil de miRNAs no tecido hepático de pacientes com DHF. Os resultados em conjunto mostram uma provável relação dos miRNAs: miR-126-5p, miR-122-5p e miR-146a-5p com a patogenia do DENV no fígado no quadro de DHF através da regulação do reparo endotelial e permeabilidade vascular, controle da homeostase do fígado e regulação da expressão de citocinas inflamatórias. / Dengue is the most prevalent arbovirosis in the world caused by Dengue virus (DENV) and is present in all continents, for more than three decades has been a constant public health concern and often fatal by dengue hemorrhagic fever (DHF). The pathogenesis of dengue is closely related to the host immune response, reaching exacerbated inflammation and transient autoimmunity. All tissues are affected, which liver is one of the most important in severe conditions, due its intense viral replication and its significant role in metabolism. The study of microRNAs (miRNA) as regulatory elements of metabolism and immune response during infection is crucial to understanding the regulatory mechanisms of gene expression on DENV infection, and can help in diagnostic development of anti-viral therapies. We sequenced the miRNoma in MySeq platform (Illumina) to identify the miRNAs profile expressed in FFPE liver tissue, ten DHF fatal cases were compared to five control cases. Eight miRNAs exhibited differential expression in DHF liver, miR-126-5p, a regulatory molecule of endothelial cells, and miR-133a-3p are upregulated in dengue and miR-122-5p, a liver-specific miRNA, miR- 146a-5p, interferon regulator, miR-10b-5p, miR-204-5p, miR-148a-5p and miR-423-5p were downregulated. Functional analysis of KEGG pathways and GO terms with predicted target genes of overexpressed miRNAs found regulatory pathways of apoptosis and immune response, involving MAPK gene, RAS, CDK and FAS; immune response pathways showed NF- kB, CC and CX families, IL and TLR. The same analysis with target genes of downregulated miRNAs also identified in most pathways of apoptosis and biosynthetic pathways of metabolism. In our knowledge, this is the first description of the liver miRNA profile in DHF, the results together show a feasible relationship of miR-126-5p, miR-122-5p and miR-146a-5p with liver pathogenesis of DHF, through endothelial repair and vascular permeability regulation, control of homeostasis and liver expression regulation of inflammatory cytokines.

By performing microRNA microarrays to globally detect any novel miRNAs in the limbus, eleven microRNAs (hsa-miR-136, hsa-miR-373*, hsa-miR-150, hsa-miR-143, hsa-miR-455, hsa-miR-145, hsa-miR-381, hsa-miR-224, hsa-miR-338, hsa-miR-154, hsa-miR-377) were found to be upregulated while two microRNAs (hsa-miR-122a and hsa-miR-425-3p) were identified as downregulated by more than 2 folds. Among these, hsa-miR-143 and hsa-miR-145 were distingushed to be the most significantly up-regulated limbal miRNAs. Individual assessement of the microarray results of a recently reported stem cell specific microRNA, hsa-miR-21, were also upregulated by more than two thousand fold when comparing limbus and cornea. miR-21, miR-143 and miR-145 were therefore selected as the most likely microRNA candidates in the present study. The expression level of these miRNA candidates were validated and confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). To localize these candidates, we performed in situ hybridization on frozen corneal rim sections using locked nucleic acid (LNA)-modified oligonucleotide probes. Results showed that miR-2I, 143 and 145 were confined in the limbal region with gradation of expression level along the basal-suprabasal line. / Functional roles of these microRNAs were then deciphered by overexpressing human corneal epithelial cell line (HCE) with precursor microRNAs (pre-miRs) through lipophilic transfection. Results showed that high endogenous level of miR-145 could inhibit cell proliferation by 3.5 fold as shown from MTT proliferation assay at day 5, and could generate discrete spherical colonies that resembles the morphology of holoclones at day 8, but not the other two candidate miRNAs. / In conclusion, 1 have identified three novel microRNAs (hsa-miR-21, 143, 145) which were precisely upregulated in the limbus region, while miR-145 was being the most limbal specific. In addition, the functions of miR-145 were found to be inhibitory on cell proliferation, possibly through the indirect regulation of IFNB1. These unprecedented results may suggest a therapeutic potential of miR-145 on limbal stem cell deficiency and limbal tumors because miR-145 can affect cell survival and proliferation. / MicroRNAs is a family of small non-coding RNAs that, in human, binds imperfectly to the 3' untranslated region (UTR) of target mRNAs for translational repression or negative regulation. Recent studies have shown that such negative regulatory pathways may play pivotal roles in the maintenance of asymmetric cell division in embryonic and tissue specific stem cells. Human corneal epithelial progenitor cells (CEPC), a tissue specific stem cell lineage residing between cornea and conjunctiva in the Palisade of Vogt of the limbus region, is known to maintain corneal homeostasis throughout human life. They respond to injury and normal wearing by rapid proliferation and differentiation into transit amplifying cells (TACs) and eventually corneal epithelial cells, though the biological factors controlling this homeostatic switch are still largely unknown. Here I hypothesized that microRNAs can participate in CEPC regulation. Experiments elucidating the anatomical distribution and functional roles of microRNAs on the human cornea rims were performed to testify this proposition. / Protocols aim at enriching the CEPC population were then devised. For the first time a four parameter cell sorting system utilizing ABCG2, Connexin 43, Notch 1 and pyronin Y as markers was established for the prospective in vitro study. Nevertheless, manual microdissection isolating the limbus region and the cornea region was employed for the present study of microRNAs. / This study begins with the phenotypic validation of human cornea rims recruited from the Chinese Hong Kong population using immunohistochemistry. Conventional CEPC markers (p63, EGFR, cytochrome oxidase and cytokeratin 15), embryonic stem cell marker (stat1) and cancer stem cell markers (p73, MDM2 and pStat1) were expressed in the limbus region, suggesting that these specimens contained a source of CEPC for attesting our hypothesis. / To determine the mRNA targets of candidate microRNAs in HCE cells, Whole Human Genome Oligo Microarray Kits (Agilent Technologies) which contained 41K human genes and transcripts were employed. When compared to the scrambled control, HCE cells over-expressed with hsa-miR-21, 143 or 145 revealed differential expression of genes that participate in cell activation, motility and proliferation. Of note, interferon beta 1 fibroblast (IFNB1), a gene that is often deleted or rearranged in cancers, was significantly upregulated by a medium of 1093 fold in pre-miR-145 treated cells as confirmed by real time PCR assays. / Lee, Sharon Ka-wai. / "December 2009." / Advisers: Calvin Chi-Pui Pang; Gary Hin Fai Yam. / Source: Dissertation Abstracts International, Volume: 72-01, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 216-252). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Based on matching analysis between different EBV strains, we found two nucleotide variations in miR-BART21 and four nucleotide changes in miR-BART22. Interestingly, two nucleotide variations upstream of mature miR-BART22 likely favor its biogenesis by Drosha/DGCR8 processing and we experimentally confirmed this augmentation by in-vitro Drosha digestion, and thus may underline the high and consistent expression of miR-BART22 in NPC tumors. / Infection with the Epstein-Barr virus (EBV) is a strong predisposing factor in the development of nasopharyngeal carcinoma (NPC). Many viral gene products including EBNA1, LMP1 and LMP2 have been implicated in NPC tumorigenesis, although the de novo control of these viral oncoproteins remain largely unclear. / MicroRNAs (miRNAs) are a class of small, non-coding RNAs with a size around 18--24 nucleotides with significant roles in regulating gene expression by either transcriptional silencing or translational suppression. As gene regulators, recent miRNA studies have emphasized the contribution of aberrant miRNA expression in cancer development. The recent discovery of EBV encoded viral miRNAs (ebv-miRNAs) in lymphoid malignancies has prompted us to examine the NPC-associated EBV miRNAs. In this study, we have systematically examined the NPC associated EBV genome for viral-encoded miRNA expression. By constructing small cDNA libraries from a native EBV positive NPC cell line (C666-1) and a xenograft (X2117), we screened about 3000 clones and detected several small EBV fragments, within which two novel ebv-miRNAs in the BARTs region were identified. These two newly identified miRNAs, now named miR-BART21 and miR-BART22, were proven to be abundantly expressed in most NPC samples by both Northern blot and QRT-PCR analysis. / Taken together, this thesis shows that two newly identified EBV-encoded miRNAs are highly expressed in latent EBV infection in NPC. Frequent expression of miR-BART22 can be explained partially by a specific EBV strain that is associated with NPC in our locality. Our findings emphasize the role of miR-BART22 in modulating LMP-2A expression. Because LMP-2A is a potent immunogenic viral antigen that is recognized by the cytotoxic T cells (CTLs), down-modulation of LMP-2A expression by mir-BART22 may permit escape of EBV-infected cells from host immune surveillance. / We attempted to predict the potential viral and cellular targets of miR-BART21 and miR-BART22 by public available computer programs, miRanda and RNAhybrid. A number of potential cellular mRNA targets were suggested, although many failed to be validated by luciferase reporter assay. However, we found a putative miR-BART22 binding site in the LMP2A-3'UTR. Although the LMP-2A transcript is consistently detected in NPC, only 6 out of 26 (23%) primary NPC tumors show weak LMP-2A expression by immunohistochemistry (IHC). The expression levels of miR-BART22 and LMP-2A mRNA have also been determined in eleven of these tumors. Interestingly, the LMP-2A mRNA expression level did not directly correlate with protein expression, and relatively low expression levels of miR-BART22 miRNA were observed in all 3 LMP-2A positive-primary tumors. The suppressive effect of miR-BART22 on LMP-2A was also experimentally validated by a series of dual luciferase reporter assays using reporter constructs containing the putative or mutated recognition site at the LMP-2A 3'UTR. By co-transfection of different amounts of miR-BART22 with the LMP-2A-3'UTR expression vector in reporter assay, we confirmed that miR-BART22 suppressed the LMP-2A protein level in a dose-dependent manner. Furthermore, transfection of miR-BART22 into HEK293 cells that had been stably transfected with pcDNA3.1-LMP-2A, which contains a complete LMP-2A ORF and 3'UTR, readily suppressed levels of the LMP-2A protein. / Lung, Wai Ming Raymond. / Adviser: To Ka Fai. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 197-226). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Yip, Wing Kit. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 100-119). / Abstract also in Chinese. / Abstract (English version) --- p.i / Abstract (Chinese version) --- p.iii / Acknowledgments --- p.v / Table of Contents --- p.vii / List of Tables --- p.x / List of Figures --- p.xi / List of Abbreviations --- p.xiii / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Hepatocellular Carcinoma --- p.1 / Chapter 1.1.1 --- Epidermiology --- p.1 / Chapter 1.1.2 --- Etiology --- p.1 / Chapter 1.2 --- Hepatitis B Virus --- p.3 / Chapter 1.2.1 --- The Epidermiology of Hepatitis B Virus Infection --- p.3 / Chapter 1.2.2 --- The Morphology and Genome of Hepatitis B Virus --- p.4 / Chapter 1.2.3 --- HBV Genotypes and Their Significance --- p.8 / Chapter 1.3 --- Hepatitis B Virus X Protein --- p.9 / Chapter 1.3.1 --- HBx Alters Various Signal Transduction Pathways --- p.10 / Chapter 1.3.2 --- HBx Interacts with Various Transcription Factors and Co-activators --- p.12 / Chapter 1.3.3 --- HBx Induces Epigenetic Alterations --- p.14 / Chapter 1.3.4 --- Identification of COOH-terminal Truncated HBx in Liver Tumors --- p.15 / Chapter 1.4 --- MicroRNAs --- p.17 / Chapter 1.4.1 --- Transcriptional Regulation and Biogenesis of MicroRNAs --- p.18 / Chapter 1.4.2 --- MicroRNAs and Cancer --- p.21 / Chapter 1.4.3 --- MicroRNAs and HCC --- p.25 / Chapter 1.5 --- Hypothesis and Aims of the Study --- p.29 / Chapter CHAPTER 2 --- MATERIALS and METHODS --- p.30 / Chapter 2.1 --- Patients --- p.30 / Chapter 2.2 --- Cell Lines --- p.30 / Chapter 2.3 --- Cloning of Various HBx Constructs --- p.32 / Chapter 2.3.1 --- PCR Amplification of HBx Fragments --- p.32 / Chapter 2.3.2 --- Cloning of HBx Fragments into TA-vectos --- p.33 / Chapter 2.3.3 --- Heat Shock Transformation --- p.33 / Chapter 2.3.4 --- Sub-cloning of HBx Fragments into Lentiviral Vectors --- p.34 / Chapter 2.4 --- Generation of Lentivirus --- p.37 / Chapter 2.4.1 --- Lentivirus Infection --- p.37 / Chapter 2.5 --- RNA Extraction --- p.38 / Chapter 2.6 --- Western Blot Analysis --- p.39 / Chapter 2.7 --- MiRNA Microarray --- p.40 / Chapter 2.7.1 --- Cyanine3-pCp Labeling of RNA Samples --- p.40 / Chapter 2.7.2 --- Sample Hybridization --- p.41 / Chapter 2.7.3 --- Microarray Wash --- p.41 / Chapter 2.7.4 --- Array Slide Scanning and Processing --- p.41 / Chapter 2.8 --- Detection of HBx Gene Deletion by PCR --- p.43 / Chapter 2.9 --- Immunohistochemistry --- p.44 / Chapter 2.10 --- Quantitative Real-time PCR --- p.45 / Chapter 2.11 --- Proliferation Assay --- p.47 / Chapter 2.12 --- Cell Cycle Analysis --- p.48 / Chapter 2.13 --- Annexin V Apoptosis Assay --- p.49 / Chapter 2.14 --- Colony Formation Assay --- p.50 / Chapter 2.15 --- Statistical Analysis --- p.51 / Chapter CHAPTER 3 --- RESULTS --- p.52 / Chapter 3.1 --- Detection of Full-length and COOH-terminal Truncated HBx in HCC Tissues --- p.52 / Chapter 3.2 --- Confirmation of HBx Expression in HCC Tissues --- p.55 / Chapter 3.3 --- Comparison of HBx from Different HBV Genotypes for Study --- p.61 / Chapter 3.4 --- Functional Characterization of COOH-tterminal Truncated HBx --- p.64 / Chapter 3.4.1 --- Selection of COOH-terminal Truncated HBx --- p.64 / Chapter 3.4.2 --- Generation of Various HBx-expressing Hepatocyte Cell Lines --- p.66 / Chapter 3.4.3 --- Effect of Full-length and COOH-terminal Truncated HBx on Cell Proliferation --- p.69 / Chapter 3.4.4 --- Effect of Full-length and COOH-terminal Truncated HBx Cell Cycle --- p.34 / Chapter 3.4.5 --- Effect of Full-length and COOH-terminal Truncated HBx on Apoptosis --- p.45 / Chapter 3.5 --- MicroRNA Profiling of Various HBx-expressing Hepatocyte Cell Lines --- p.76 / Chapter 3.5.1 --- Identification of Deregulated MicroRNAs by Microarray --- p.76 / Chapter 3.5.2 --- Validation of Deregulated MicroRNAs by Real-time PCR Analysis --- p.80 / Chapter 3.5.3 --- Confirmation of Deregulated MiRNAs in HCC and Adjacent Non-tumor Tissues --- p.84 / Chapter 3.5.4 --- Potential Downstream Targets of the HBx-deregulated MiRNAs --- p.87 / Chapter CHAPTER 4 --- DISCUSSION --- p.91 / Chapter 4.1 --- The Impact of COOH-terminal Truncated HBx in HCC --- p.91 / Chapter 4.2 --- The Biological Significance of COOH-terminal Truncated HBx Induced MiRNAs --- p.94 / Chapter 4.3 --- Limitations of the Present Study --- p.97 / Chapter 4.4 --- Future Studies --- p.98 / Chapter CHAPTER 5 --- CONCLUSION --- p.99 / REFERENCES --- p.100