Cancer is a leading cause of death worldwide, accounting for around 13% of all death [1]. Traditional cancer therapeutics usually require careful selection of one or more intervention, such as surgery, radiotherapy, and chemotherapy, which have made momentous progress, but have ample limitations [2]. The next generation of cancer therapeutics will specifically target processes responsible for the growth and survival of cancer cells. Among the most promising of these molecularly-targeted therapeutics are short interfering RNAs (siRNAs). These siRNAs serve as the effectors of RNA interference, a naturally occurring and highly specific mechanism for regulating gene expression through sequence-specific degradation of messenger RNA. However, the native structure of RNA is plagued with undesirable chemical properties. For example, the sugar-phosphate backbone contains a negative charge which hinders its ability to cross the negatively charged lipid bilayer. Furthermore, the phosphodiester backbone is a substrate for nucleases, which catalytically cleaves the phosphate-oxygen bond, thus degrading the native RNA [3]. As such, there is widespread interest in chemically modifying the backbone of siRNAs in order to overcome some of the inherent problems with its native structure. There have been only two reports that have employed amide-bond linkages as phosphate replacements within siRNAs [4, 5]. In both of these studies, the amide bond containing monomer units were placed at the 3’-overhangs and not within the internal Watson-Crick region of the double stranded siRNA due to the limitation of standard solid-phase oligonucleotide synthesis. In this thesis, we proposed to utilize phosphoramidite chemistry to localize internal amide-bond modifications [6]. A practical synthesis of a peptide nucleic acid unit combined with an RNA nucleoside (PNA-RNA dimer, UaU) is reported [7]. Using this PNA-RNA dimer phosphoramidite allows us to control the site-specific location of the internal amide-bond modification throughout the desired RNA strand. Polyacrylamide gel (PAGE) and mass spectrometry analysis were performed to ensure the formation of full-length modified siRNA molecules. The effects of these modifications were explored with respect to the biophysical and biological properties of the modified siRNAs. The techniques used in this work included hybridization affinity assays (melting temperature), secondary structure determination (circular dichroism), cell-based luciferase assays, and nuclease stability assays. Melting temperature experiment reveals that localizing a UaU dimer unit within the RNA oligonucleotides has an overall destabilizing effect, whereas UaU modifications at the 3’-overhang positions show little change in thermal stability. Circular dichroism experimental results illustrate that all chemically modified siRNAs exhibit the standard A-form helix. In cell-based luciferase assays, we utilized two different target sequences and our results highlight the compatibility of utilizing a neutral amide-bond backbone within siRNAs. Specifically, the internal amide-bond modification is compatible within the RNAi machinery when placed at 3’-overhang position in the sense strand of the double-stranded siRNA. However, poor efficacy is observed when this unit is placed adjacent the Ago 2 cleavage site on the antisense strand. The nuclease stability assays reveal that the introduction of a PNA-RNA dimer at the 3’-end of the siRNA where the exonuclease cleaves the terminal nucleotide, increased markedly the resistance to serum-derived nucleases. To the best of our knowledge, this is the first report that involves amide-bonds as phosphate backbone replacements within the internal regions of siRNAs and thus opens the future possibility for examining and utilizing this modification in studying new structure-function relationships. / UOIT

A raiva é uma zoonose que afeta todos os mamíferos e causa cerca de 55.000 mortes humanas por ano, causada pelo vírus da raiva. O vírus da raiva pertence à Ordem Mononegavirales, Família Rhabdoviridae e o Gênero Lissavirus. Atualmente, o tratamento humano se baseia no uso do Protocolo de Milwaukee composto de indução do paciente ao coma e uso de massiva terapia antiviral. O protocolo, apesar de ter sido utilizado duas vezes com sucesso, inclusive em um caso brasileiro, ainda requer aprimoramentos. Neste sentido, a interferência por RNA (RNAi) é uma nova abordagem para terapia de doenças virais. O objetivo deste trabalho foi avaliar a inibição da replicação do vírus da raiva in vitro e in vivo utilizando RNAi. Para tanto, foram utilizados três siRNAs (siRNA 124, siRNA 750, siRNA B) com a fita antisenso complementar ao mRNA da nucleoproteína (N) do vírus da raiva. Para o ensaio in vitro foram utilizadas a cepa PV do vírus da raiva e as células de BHK-21 (Baby hamster kidney). As monocamadas celulares foram infectadas com a cepa PV e depois de 2 horas de incubação transfectadas com cada um dos siRNAs em combinação com Lipofectamine 2000®. Depois de 22 horas as placas teste e controle foram submetidas à imunofluorescência direta (IFD) com conjugado globulina de coelho anti-nucleocapsídeo do vírus da raiva/isotiocianato de fluoresceína (BIO-RADTM). Os resultados revelaram títulos de 5,71logTCID50/ml, 5,56logTCID50/ml e 5,65logTCID50/ml para os siRNAs 124, B e 750, respectivamente, enquanto que, para a placa controle, o título foi 6,43logTCID50/ml. Para o ensaio in vivo, foram usados camundongos albino suíços de 21 dias com peso entre 11 e 14g, infectados com a cepa PV via intracerebral. Duas horas depois da infecção foi inoculada por via intracerebral uma solução do \"pool\" dos três siRNAs com Lipofectamine 2000® . Os animais com paralisia foram sacrificados e aqueles sobreviventes foram observados até completar 30 dias de observação quando foram, então, sacrificados. O sistema nervoso central de todos os animas foi recolhido e submetido a IFD. O título viral do grupo teste foi 7.03logLD50%/ml e do grupo controle 7.13logLD50%/ml. O resultado do ensaio in vitro demonstra que os siRNAs utilizados são efetivos em inibir a replicação do vírus da raiva, com eficiências equivalentes. A utilização do \"pool\" dos três siRNA em camundongos resultou em 30% de animais sobreviventes frente a 100 DL50% do vírus PV, enquanto que a mesma dose levou a 100% de mortalidade nos animais não tratados. Pode-se atribuir a menor eficiência em inibir a replicação do vírus da raiva in vivo quando se compara com os resultados in vitro possivelmente às elevadas doses virais utilizadas. Estes resultados, ainda que indiquem a necessidade de mais estudos, permitem concluir que a RNAi é uma tecnologia promissora como antiviral contra a raiva. / Rabies is a zoonotic disease that affects all mammals and causes more than 55.000 human deaths every year, caused by rabies virus (RABV) a virus of the Mononegavirales order, Family Rhabdoviridae and the Lissavirus genus. After the onset of the symptoms, the illness has a fast progression and the patients feel intense physical suffering. Currently, human rabies treatment has been based on the Milwaukee Protocol which consists on the induction of coma and massive antiviral therapy. Despite this protocol has been successful in two cases, including a Brazilian case (Recife State), more studies on antiviral for human rabies treatment are required. RNA interference is a new antiviral approach, which gives hope to the possibility of rabies antiviral treatment. The aim of this study was to assess the decrease in the titer of rabies virus in vitro and in vivo using short-interfering RNAs. For this purpose, three siRNAs (siRNA 124, siRNA B, siRNA 750) were used with antisense strands complementary to rabies virus nucleoprotein (N) mRNA. Pasteur virus strain (PV) of rabies virus and BHK-21 cells were used, and the monolayers were transfected with each of tree RNAs with Lipofectamine-2000. After 22 hours, the siRNA-treated and the control plates were tested by direct fluorescent antibody test (DFAT) with anti-rabies virus nucleocapsid antibody conjugate with fluorescein isothiocianate. Virus titers were calculated by the Spearman-Karber method. The results revealed that all three siRNAs reduced the titer of PV strain and a more intense effect was obtained with siRNA B. The titer of the PV strain in the control plate was 6.43lg TCID50%/ml and 5.56lg TCID50%/ml in the plate treated with siRNA B, respectively. The similar result was obtained in plates treated with siRNAs 124 and 750. The title of PV strain of these plates was 5.71lg TCID50%/ml of siRNA 124 and 5.65lg TCID50%/ml of siRNA750, respectively. No cytopathic or cytotoxic effect was observed in the monolayers treated with Lipofectamine-2000®. Swiss albino mice with 21 days weighing between 11 and 14g infected with strain PV by the intracerebral route used in this in vivo essay. After two hours of infection, a pool solution of 3 siRNAs with lipofectamine was also inoculated by the intracerebral route. The animals with paralysis were euthanized and those which survived were observed until the 30th day when they were also euthanized. The central nervous system of all animals were collected and induced to IFD. The title viral test group was 7.03logLD50%/ml and the control group was 7.13logLD50%/ml. The in vitro test results indicate that siRNAS are effective in inhibiting the replication of rabies virus with similar efficiencies. The use of the pool of three siRNA in mice resulted in 30% of survivors for 100 LD50% of PV virus, while the same dose led to 100% mortality in untreated animals. A lower efficiency in inhibiting the replication of rabies virus in vivo when compared with results in vitro could be possibly due to the high viral doses used. These results, although indicative of the need for further studies, show that RNAi is a promising technology as antiviral against rabies.

A raiva é uma zoonose que afeta todos os mamíferos e causa cerca de 55.000 mortes humanas por ano, causada pelo vírus da raiva. O vírus da raiva pertence à Ordem Mononegavirales, Família Rhabdoviridae e o Gênero Lissavirus. Atualmente, o tratamento humano se baseia no uso do Protocolo de Milwaukee composto de indução do paciente ao coma e uso de massiva terapia antiviral. O protocolo, apesar de ter sido utilizado duas vezes com sucesso, inclusive em um caso brasileiro, ainda requer aprimoramentos. Neste sentido, a interferência por RNA (RNAi) é uma nova abordagem para terapia de doenças virais. O objetivo deste trabalho foi avaliar a inibição da replicação do vírus da raiva in vitro e in vivo utilizando RNAi. Para tanto, foram utilizados três siRNAs (siRNA 124, siRNA 750, siRNA B) com a fita antisenso complementar ao mRNA da nucleoproteína (N) do vírus da raiva. Para o ensaio in vitro foram utilizadas a cepa PV do vírus da raiva e as células de BHK-21 (Baby hamster kidney). As monocamadas celulares foram infectadas com a cepa PV e depois de 2 horas de incubação transfectadas com cada um dos siRNAs em combinação com Lipofectamine 2000®. Depois de 22 horas as placas teste e controle foram submetidas à imunofluorescência direta (IFD) com conjugado globulina de coelho anti-nucleocapsídeo do vírus da raiva/isotiocianato de fluoresceína (BIO-RADTM). Os resultados revelaram títulos de 5,71logTCID50/ml, 5,56logTCID50/ml e 5,65logTCID50/ml para os siRNAs 124, B e 750, respectivamente, enquanto que, para a placa controle, o título foi 6,43logTCID50/ml. Para o ensaio in vivo, foram usados camundongos albino suíços de 21 dias com peso entre 11 e 14g, infectados com a cepa PV via intracerebral. Duas horas depois da infecção foi inoculada por via intracerebral uma solução do \"pool\" dos três siRNAs com Lipofectamine 2000® . Os animais com paralisia foram sacrificados e aqueles sobreviventes foram observados até completar 30 dias de observação quando foram, então, sacrificados. O sistema nervoso central de todos os animas foi recolhido e submetido a IFD. O título viral do grupo teste foi 7.03logLD50%/ml e do grupo controle 7.13logLD50%/ml. O resultado do ensaio in vitro demonstra que os siRNAs utilizados são efetivos em inibir a replicação do vírus da raiva, com eficiências equivalentes. A utilização do \"pool\" dos três siRNA em camundongos resultou em 30% de animais sobreviventes frente a 100 DL50% do vírus PV, enquanto que a mesma dose levou a 100% de mortalidade nos animais não tratados. Pode-se atribuir a menor eficiência em inibir a replicação do vírus da raiva in vivo quando se compara com os resultados in vitro possivelmente às elevadas doses virais utilizadas. Estes resultados, ainda que indiquem a necessidade de mais estudos, permitem concluir que a RNAi é uma tecnologia promissora como antiviral contra a raiva. / Rabies is a zoonotic disease that affects all mammals and causes more than 55.000 human deaths every year, caused by rabies virus (RABV) a virus of the Mononegavirales order, Family Rhabdoviridae and the Lissavirus genus. After the onset of the symptoms, the illness has a fast progression and the patients feel intense physical suffering. Currently, human rabies treatment has been based on the Milwaukee Protocol which consists on the induction of coma and massive antiviral therapy. Despite this protocol has been successful in two cases, including a Brazilian case (Recife State), more studies on antiviral for human rabies treatment are required. RNA interference is a new antiviral approach, which gives hope to the possibility of rabies antiviral treatment. The aim of this study was to assess the decrease in the titer of rabies virus in vitro and in vivo using short-interfering RNAs. For this purpose, three siRNAs (siRNA 124, siRNA B, siRNA 750) were used with antisense strands complementary to rabies virus nucleoprotein (N) mRNA. Pasteur virus strain (PV) of rabies virus and BHK-21 cells were used, and the monolayers were transfected with each of tree RNAs with Lipofectamine-2000. After 22 hours, the siRNA-treated and the control plates were tested by direct fluorescent antibody test (DFAT) with anti-rabies virus nucleocapsid antibody conjugate with fluorescein isothiocianate. Virus titers were calculated by the Spearman-Karber method. The results revealed that all three siRNAs reduced the titer of PV strain and a more intense effect was obtained with siRNA B. The titer of the PV strain in the control plate was 6.43lg TCID50%/ml and 5.56lg TCID50%/ml in the plate treated with siRNA B, respectively. The similar result was obtained in plates treated with siRNAs 124 and 750. The title of PV strain of these plates was 5.71lg TCID50%/ml of siRNA 124 and 5.65lg TCID50%/ml of siRNA750, respectively. No cytopathic or cytotoxic effect was observed in the monolayers treated with Lipofectamine-2000®. Swiss albino mice with 21 days weighing between 11 and 14g infected with strain PV by the intracerebral route used in this in vivo essay. After two hours of infection, a pool solution of 3 siRNAs with lipofectamine was also inoculated by the intracerebral route. The animals with paralysis were euthanized and those which survived were observed until the 30th day when they were also euthanized. The central nervous system of all animals were collected and induced to IFD. The title viral test group was 7.03logLD50%/ml and the control group was 7.13logLD50%/ml. The in vitro test results indicate that siRNAS are effective in inhibiting the replication of rabies virus with similar efficiencies. The use of the pool of three siRNA in mice resulted in 30% of survivors for 100 LD50% of PV virus, while the same dose led to 100% mortality in untreated animals. A lower efficiency in inhibiting the replication of rabies virus in vivo when compared with results in vitro could be possibly due to the high viral doses used. These results, although indicative of the need for further studies, show that RNAi is a promising technology as antiviral against rabies.

<p>The Arabidopsis root apical meristem (RAM) is a complex tissue capable of generating all the cell types that ultimately make up the root. The work presented in this thesis takes advantage of the versatility of high-throughput sequencing to address two independent questions about the root meristem. Although a lot of information is known regarding the cell fate decisions that occur at the RAM, cortex specification and differentiation remain poorly understood. In the first part of this thesis, I used an ethylmethanesulfonate (EMS) mutagenized marker line to perform a forward genetics screen. The goal of this screen was to identify novel genes involved in the specification and differentiation of the cortex tissue. Mapping analysis from the results obtained in this screen revealed a new allele of BRASSINOSTEROID4 with abnormal marker expression in the cortex tissue. Although this allele proved to be non-cortex specific, this project highlights new technology that allows mapping of EMS-generated mutations without the need to map-cross or back-cross. In the second part of this thesis, using fluorescence activated cell sorting (FACS) coupled with high throughput sequencing, my collaborators and I generated single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and smallRNA transcriptomes for six different populations of cell types in the Arabidopsis root meristem. We were able to discover that the columella is hypermethylated in the CHH context within transposable elements. This hypermethylation is accompanied by upregulation of the RNA-dependent DNA methylation pathway (RdDM), including higher levels of 24-nt silencing RNAs (siRNAs). In summary, our studies demonstrate the versatility of high-throughput sequencing as a method for identifying single mutations or to perform complex comparative genomic analyses.</p> / Dissertation

Submitted by Tatiana Silva (tsilva@icict.fiocruz.br) on 2012-12-26T18:35:05Z No. of bitstreams: 1 juliana_f_lopes_ioc_bcm_0034_2010.pdf: 2515209 bytes, checksum: 7753044e364addb6c4a32fb5a7c5b298 (MD5) / Made available in DSpace on 2012-12-26T18:35:05Z (GMT). No. of bitstreams: 1 juliana_f_lopes_ioc_bcm_0034_2010.pdf: 2515209 bytes, checksum: 7753044e364addb6c4a32fb5a7c5b298 (MD5) Previous issue date: 2009 / Fundação Oswaldo Cruz.Instituto Oswaldo Cruz. Rio de janeiro, RJ, Brasil / O vírus da hepatite A (HAV) possui genoma RNA de fita simples de 7,5 Kb e polaridade positiva. Este vírus pertence à família Picornaviridae, gênero Hepatovirus, com propriedades biológicas únicas, em particular, o crescimento lento em cultura celular com ausência de efeito citopático. O HAV causa uma infecção autolimitada normalmente com pouco ou nenhum sintoma em pacientes jovens (abaixo de 5 anos). Já em pacientes adultos, sintomas graves podem aparecer com 1% dos casos podendo evoluir para uma hepatite fulminante. A inibição da replicação viral pode retardar a infecção pelo vírus prevenindo uma hepatite fulminante. Pequenos RNAs de interferência (siRNAs) que agem com base na degradação seqüência-específica do genoma, pode constituir uma nova estratégia para a inibição específica de vários tipos de vírus. A interferência por siRNA é um processo onde fitas duplas de RNA (dsRNA) são capazes de silenciar as funções específicas de um gene alvo. A via de siRNA pode ser induzida em células por transfecção de oligômeros sintéticos de 21-23 nucleotídeos. O objetivo deste estudo foi avaliar o silenciamento produzido por três seqüências específicas de siRNAs, uma para região 2C (helicase), e duas para 3D (protease) do genoma do HAV. Vinte e quatro horas antes da transfecção, células FRHK-4 foram cultivadas em placas de 24 poços, com meio 199 e densidade de 10 5 células por poço. Em seguida, as células foram transfectadas por 4 horas com cada siRNA e suas combinações. Após isto, as células foram infectadas com o HAV (10 5 cópias/ml) e cultivadas por cinco dias consecutivos à 37°C. Seqüências não-específicas foram utilizadas como controle negativo. O RNA total foi extraído e a análise foi realizada por RT-PCR, sendo o silenciamento confirmado por imunofluorescência. Todas as seqüências mostraram-se com capacidade inibitória. A melhor taxa de silenciamento ocorreu no segundo dia com as três sequências em conjunto, atingindo 85% de inibição da replicação viral. Tal resultado foi confirmado pela diminuição da intensidade da fluorescência para o HAV. As combinações foram mais eficazes do que cada sequência utilizada isoladamente. Os siRNAs foram eficazes na diminuição da expressão da helicase e protease do HAV / Hepatitis A virus (HAV) has a single-stranded RNA genome of 7.5 kb with positive polarity.This virus belongs the Picornaviridae family, genus Hepatovirus with unique biological properties, in particular, slow growth in cell culture without cytopathic effect. HAV causes a self-limiting liver infection with usually mild or no symptoms in young patients. Whereas adult patients might suffer from severe symptoms and 1% of cases can evolue to fulminant hepatitis. Inhibition of viral replication can improve viral infection and thus prevent fulminant failure. Small interference RNA (siRNA) based on specific sequence may present a novel and specific approach strategy for inhibit of various types of virus. RNA interference is a process by double-stranded (dsRNA) is able to silence specific gene functions. The siRNA pathway can be induced in mammalian cells by transfection of short synthetic sequence-specific oligomers with 21-23 nucleotides. The aim of this study was to evaluate the silencing produced by three specific sequences of siRNAs, one for region 2C (helicase), and two for 3D (protease) of the HAV. Twenty-four hours before transfection, FRHK-4 cells were cultivated in 24-well plate in 199 medium with density of 10 5 cells per well. After that, cells were transfected for 4 hours with each siRNA and its combinations following by infection with HAV (10 5 cópies/ml) and grown for five consecutive days. Non-specific sequences were used as negative control. The total RNA was extracted (with commercial kit) and analysis was performed by RT-PCR and silencing was confirmed by immunofluorescence. All sequences showed inhibitory capacity. The best silencing occurred in the second day using the three sequences together reaching 85% of inhibition viral replication. This result was confirmed with the decrease in fluorescence intensity for HAV. The combination of the sequences was more effective than the sequences used alone. The siRNAs could knockdown the expression of helicase and protease of HAV

Das Harnblasenkarzinom (BCa) ist die zweithäufigste bösartige urologische Tumorerkrankung sowie die siebthäufigste tumorbedingte Todesursache bei Männern. Zur Senkung des erheblichen Rezidiv- und Progressionsrisikos oberflächlicher BCa kommen lokale Immun- oder Chemotherapeutika zum Einsatz, die jedoch starke Nebenwirkungen verursachen können bzw. ungenügende langfristige Effekte bewirken. Eine neuartige Therapieoption besteht in der gezielten Expressionshemmung von Genen, die den Tumorzellen einen Wachstumsvorteil vermitteln. Hierfür eignen sich besonders synthetische Nukleinsäuren wie Antisense-Oligodesoxynukleotide (AS-ODN) und small interfering RNAs (siRNAs). In der vorliegenden Arbeit wurde die Expressionshemmung des potenziellen Targetgens hTERT (humane Telomerase Reverse Transkriptase) mit AS-ODN und siRNAs in BCa-Zellen untersucht. Die Tumorspezifität der hTERT-mRNA-Expression konnte zunächst an tumor- und tumorfreien Gewebeproben von BCa-Patienten gezeigt werden. Die verwendeten AS-ODN reduzierten die hTERT-mRNA-Expression auf bis zu 40%, womit eine Verringerung der Telomeraseaktivität einherging. Die AS-ODN-Behandlung bewirkte des Weiteren eine konzentrationsabhängige Viabilitätsreduktion verschiedener BCa-Zelllinien sowie eine verminderte Zellkoloniebildungsrate. Diese antiproliferativen Effekte waren auf eine Apoptoseinduktion zurückzuführen. Durch eine Vorbehandlung von vier BCa-Zelllinien mit hTERT-AS-ODN konnten die zytotoxischen Effekte der für das BCa relevanten Chemotherapeutika Cisplatin, Mitomycin C und Gemcitabin signifikant verstärkt werden. Nach Untersuchung der AS-ODN-Wirkung in vitro erfolgte die Etablierung eines subkutanen Xenotransplantantmodells der Nacktmaus. Die Eignung einer intraperitonealen Applikation wurde mit fluoreszenzmarkierten AS-ODN belegt. In weiteren Zellkulturexperimenten kamen hTERT-siRNAs, als alternative Methode der Geninhibition, zum Einsatz. Die Reduktion der hTERT-mRNA-Expression auf 50% war mit der durch AS-ODN bewirkten Inhibition vergleichbar. Im Gegensatz zur AS-ODN-Behandlung induzierten siRNAs keine unmittelbare Apoptose. Eine Kombination der siRNAs mit Cisplatin und Mitomycin C bewirkte jedoch eine Verdopplung der Apoptoserate. Um die molekularen Mechanismen der Wirkung der nukleinsäurebasierten hTERT-Inhibitoren und den Einfluss targetunabhängiger Effekte zu untersuchen, wurden transkriptomweite Expressionsanalysen mittels Oligonukleotid-Microarrays durchgeführt. Hierbei zeigte sich, dass die AS-ODN-Behandlung vorwiegend zu einer gesteigerten Expression von Genen führte, die mit einer zellulären Stressantwort assoziiert sind (u.a. ATF3, EGR1, GADD45). Diese Expressionsmuster stimmten in hohem Maße mit denen überein, die durch Transfektion mit AS-ODN gegen andere Targets erhalten wurden. Diese Ergebnisse deuten auf eine, zumindest teilweise, durch off-Targeteffekte ausgelöste Wachstumshemmung hin. Die siRNA-Behandlungen gegen unterschiedliche Targets zeigten relativ geringe Übereinstimmungen in den Expressionsmustern und somit eine höhere Spezifität. Außerdem wurde erstmalig gezeigt, dass eine hTERT-Inhibition mit siRNAs zur trankriptionellen Hemmung der Onkogene EGFR und FOSL1 führt. Diese Daten sowie die Ergebnisse anderer Arbeitsgruppen deuten auf einen wechselseitigen Zusammenhang zwischen hTERT und EGFR in der Regulation der EGFR-stimulierten Proliferation von BCa-Zellen hin. Zusammenfassend lässt sich feststellen, dass hTERT als tumorspezifisch exprimierter und funktionell relevanter Faktor ein hervorragendes Target für eine nukleinsäurebasierte BCa-Therapieoption darstellt. Im Vergleich zu AS-ODN wirken siRNAs grundsätzlich targetspezifischer. Die therapeutische Wertigkeit der lokal applizierten Inhibitoren, insbesondere in Kombination mit herkömmlichen Chemotherapeutika, sollte in nachfolgenden Experimenten im Rahmen eines orthotopen BCa-Xenotransplantatmodells untersucht werden.

Frontotemporal Dementia with parkinsonism linked to chromosome 17 (FTDP-17) (OMIM # 600274) is a tauopathy caused by mutations in the MAPT gene. This gene encodes for Tau protein and its alternative splicing normally produces 6 different isoforms with three (3R) or four (4R) repeats of microtubule-binding domains, originated from the alternative splicing of exon 10 in the MAPT transcript. In normal adult brain, neurons and glia cells contain both 3R and 4R splicing isoforms in a 1:1 ratio. Several mutations in the MAPT gene impair exon 10 splicing, causing unbalance between 4R and 3R Tau isoforms (4R &gt; 3R), leading to Tau 4R protein accumulation as insoluble neuronal deposits. Therapeutical correction of MAPT splicing isoforms balance is, in principle, possible using either exon-specific siRNAs, which degrade exon-10-containing mRNA in the cytoplasm, or splice-switching antisense RNAs, that induce skipping of exon 10 during the splicing of MAPT pre-mRNA in the nucleus. Both approaches have been explored in the Laboratory of RNA Biology and Biotechnology at CIBIO (University of Trento) using splicing reporters. Subsequently, several siRNAs and antisense RNAs have been demonstrated to efficiently engage their target (pre-)mRNA and restore 4R:3R balance in neuroblastoma cell lines in culture. Aim of the present work is to obtain pre-clinical evidence of the efficiency of the two approaches, in order to move towards clinical studies. To this purpose, I set up a disease model consisting in hiPSCs-derived neurons carrying a mutation in intron 10, where a C is substituted with a T in position 16 (MAPT IVS10+16; EBiSC, depositor Sigma-Aldrich SIGi001-A-12) and compared them with the appropriate isogenic healthy control (EBiSC; depositor Sigma-Aldrich SIGi001-A-1). 3R and 4R Tau mRNA and protein levels were evaluated at various days of differentiation and neuronal maturation. In my hands, IVS10+16 neurons showed increase 4R Tau mRNA expression at 120 days of differentiation, resembling the patient’s phenotype. The unbalance 4R:3R is reflected in the Tau protein, as assessed by Western blotting . I am presently evaluating other outcome measures of disease in this cellular model, such as synaptic impairment and electrophysiology . The Laboratory of RNA Biology and Biotechnology has reported that microRNAs (miRNAs) can be used as biomarkers of Frontotemporal Dementia (FTD). In particular, we recently reported that miR-92a-3p, miR-320a and miR-320b are misregulated in the plasma of FTD patients in comparison to healthy individuals (manuscript under review). I set out to measure these miRNAs in d120 IVS10+16 and isogenic neurons and in their conditioned medium. I found that all three miRNAs of interest were significantly increased in IVS10+16 samples compared to WT neurons, therefore representing a useful measure of therapeutical efficacy in our protocols. With the use of fluorescently labelled siRNAs, I then tackled the problem of delivering siRNA molecules to mature neurons and set up a protocol for their efficient delivery. Consequently, day120 IVS10+16 and WT neurons were transfected with different concentration of scramble and therapeutic siRNAs and the restoration of the 4R:3R Tau balance was assessed. My results suggest a promising potential for the use of isoform-specific siRNAs in FTDP-17 and possibly in other tauopathies. At the same time, I intended to validate in the same hiPSC-derived neuronal disease model, U1 and U7 chimeric splice-switching antisense RNAs that had been previously tested by plasmid transfection in neuroblastoma cell lines. To overcome the limitation represented by poor plasmid transfection efficiency in mature neurons, I encapsulated them into recombinant adeno-associated viruses (rAAVs). After having optimized the production of rAAVs and set the transduction conditions, IVS10+16 mature neurons were transduced with AAV expressing chimeric splice-switching antisense RNAs. Although neurons successfully got transduced and the cassette transcribed, there was no therapeutic effect when viruses were tested in d130 IVS10+16 neurons. I am presently exploring different experimental paradigms, to test the hypothesis that the 4R:3R unbalance can be prevented in mature neurons.

Das Harnblasenkarzinom (BCa) ist die zweithäufigste bösartige urologische Tumorerkrankung sowie die siebthäufigste tumorbedingte Todesursache bei Männern. Zur Senkung des erheblichen Rezidiv- und Progressionsrisikos oberflächlicher BCa kommen lokale Immun- oder Chemotherapeutika zum Einsatz, die jedoch starke Nebenwirkungen verursachen können bzw. ungenügende langfristige Effekte bewirken. Eine neuartige Therapieoption besteht in der gezielten Expressionshemmung von Genen, die den Tumorzellen einen Wachstumsvorteil vermitteln. Hierfür eignen sich besonders synthetische Nukleinsäuren wie Antisense-Oligodesoxynukleotide (AS-ODN) und small interfering RNAs (siRNAs). In der vorliegenden Arbeit wurde die Expressionshemmung des potenziellen Targetgens hTERT (humane Telomerase Reverse Transkriptase) mit AS-ODN und siRNAs in BCa-Zellen untersucht. Die Tumorspezifität der hTERT-mRNA-Expression konnte zunächst an tumor- und tumorfreien Gewebeproben von BCa-Patienten gezeigt werden. Die verwendeten AS-ODN reduzierten die hTERT-mRNA-Expression auf bis zu 40%, womit eine Verringerung der Telomeraseaktivität einherging. Die AS-ODN-Behandlung bewirkte des Weiteren eine konzentrationsabhängige Viabilitätsreduktion verschiedener BCa-Zelllinien sowie eine verminderte Zellkoloniebildungsrate. Diese antiproliferativen Effekte waren auf eine Apoptoseinduktion zurückzuführen. Durch eine Vorbehandlung von vier BCa-Zelllinien mit hTERT-AS-ODN konnten die zytotoxischen Effekte der für das BCa relevanten Chemotherapeutika Cisplatin, Mitomycin C und Gemcitabin signifikant verstärkt werden. Nach Untersuchung der AS-ODN-Wirkung in vitro erfolgte die Etablierung eines subkutanen Xenotransplantantmodells der Nacktmaus. Die Eignung einer intraperitonealen Applikation wurde mit fluoreszenzmarkierten AS-ODN belegt. In weiteren Zellkulturexperimenten kamen hTERT-siRNAs, als alternative Methode der Geninhibition, zum Einsatz. Die Reduktion der hTERT-mRNA-Expression auf 50% war mit der durch AS-ODN bewirkten Inhibition vergleichbar. Im Gegensatz zur AS-ODN-Behandlung induzierten siRNAs keine unmittelbare Apoptose. Eine Kombination der siRNAs mit Cisplatin und Mitomycin C bewirkte jedoch eine Verdopplung der Apoptoserate. Um die molekularen Mechanismen der Wirkung der nukleinsäurebasierten hTERT-Inhibitoren und den Einfluss targetunabhängiger Effekte zu untersuchen, wurden transkriptomweite Expressionsanalysen mittels Oligonukleotid-Microarrays durchgeführt. Hierbei zeigte sich, dass die AS-ODN-Behandlung vorwiegend zu einer gesteigerten Expression von Genen führte, die mit einer zellulären Stressantwort assoziiert sind (u.a. ATF3, EGR1, GADD45). Diese Expressionsmuster stimmten in hohem Maße mit denen überein, die durch Transfektion mit AS-ODN gegen andere Targets erhalten wurden. Diese Ergebnisse deuten auf eine, zumindest teilweise, durch off-Targeteffekte ausgelöste Wachstumshemmung hin. Die siRNA-Behandlungen gegen unterschiedliche Targets zeigten relativ geringe Übereinstimmungen in den Expressionsmustern und somit eine höhere Spezifität. Außerdem wurde erstmalig gezeigt, dass eine hTERT-Inhibition mit siRNAs zur trankriptionellen Hemmung der Onkogene EGFR und FOSL1 führt. Diese Daten sowie die Ergebnisse anderer Arbeitsgruppen deuten auf einen wechselseitigen Zusammenhang zwischen hTERT und EGFR in der Regulation der EGFR-stimulierten Proliferation von BCa-Zellen hin. Zusammenfassend lässt sich feststellen, dass hTERT als tumorspezifisch exprimierter und funktionell relevanter Faktor ein hervorragendes Target für eine nukleinsäurebasierte BCa-Therapieoption darstellt. Im Vergleich zu AS-ODN wirken siRNAs grundsätzlich targetspezifischer. Die therapeutische Wertigkeit der lokal applizierten Inhibitoren, insbesondere in Kombination mit herkömmlichen Chemotherapeutika, sollte in nachfolgenden Experimenten im Rahmen eines orthotopen BCa-Xenotransplantatmodells untersucht werden.

When conspecific individuals are crossed, the ensuing hybridization creates a spectrum of phenotypes in the resulting offspring. Many of hybrid traits will be additive, similar to the parental phenotypes. In some cases however, transgressive phenotypes are formed, outside the range of that of the parental phenotypes. Transgressive phenotypes can either be restricted to the F1 generation or be heritable throughout the hybrid lineage. While the mechanism behind heritable transgressive phenotyped is yet to be determined, transgressive gene expression is thought to be the root cause of their formation. Epigenetics modifications, heritable variation separate to the DNA code, can alter gene expression, persist through generations, and vary between individuals and over time. This makes them ideal candidates to be involved in the formation of transgressive phenotypes. RNA silencing is an epigenetic mechanism of gene regulation relying on 20Q24nt single stranded small RNAs (sRNAs). Small RNAs, due to their ability to set up persistent epigenetic marks at a locus, have the potential to create heritable transgressive gene expression. For example, when genetic variation from one parental genome presents novel targets to the sRNAs of the other parental genome, new epigenetic marks such as DNA methylation or secondary sRNAs can be created at target sites. In order to understand the potential of small RNAs to influence hybrid phenotype, I designed crossing experiments with Chlamydomonas reinhardtii, choosing this unicellular alga due to the genetic tools available and the haploid nature of its vegetative cells. The specific aim of the experiment was to identify transgressively expressed sRNA populations. Crossing two geographically distinct strains of C. reinhardtii, and sequencing both the genomes and sRNAomes of parents and recombinants, I was able catalogue both genetic and epigenetic variation in the parental strains providing unique insight into the inheritance of small RNAs in this alga. In this thesis, I first compare the genomes of the parental strains, identifying polymorphisms and assessing genetic variation in RNA silencing pathway components. I then describe the sRNA profiles of the parental strains, identifying differentially expressed sRNA loci. I then describe my approach to identifying transgressively expressed sRNA loci in the hybrids. While many sRNA loci in the recombinants exhibit additive sRNA expression, I found multiple transgressively expressed sRNA loci. Using the available bioinformatics tools, I identified potential miRNAs and phased secondary sRNAs within the list of transgressively expressed loci. Target analysis of one of the transgressively expressed miRNAs linked it with the transgressive expression of certain phased loci, suggesting a potential for sRNAs to be able to set up heritable epigenetic marks in recombinant C. reinhardtii cells.

Le carcinome à cellules rénales claires métastatique (CCC) demeure résistant aux thérapies actuelles. Les travaux précédents ont montré des similitudes mécanistiques entre tumorigenèse et néphrogenèse. Parmi les cibles de la voie oncogénique Sonic Hedgehog-Gli, le facteur développemental Lim1 a été identifié comme un nouvel oncogène dans le CCC. Les études préliminaires suggèrent que Lim1 aurait un rôle dans l’invasion cellulaire. Aucun inhibiteur de Lim1 n’est disponible; l’ARN interférence reste l’outil le plus efficace et le plus spécifique pour l’extinction des gènes. Dans le but de développer un nouvel outil d’inhibition de Lim1 applicable en clinique, basée sur des siRNAs véhiculés par des systèmes nanométriques, une nouvelle génération de véhicules de siRNAs a été étudiée. Il s’agit de polymères diacétyléniques photo-polymérisables sous forme de nanofibres (PDA-Nf). Ces travaux démontrent le rôle invasif de Lim1 dans la dissémination métastatique et identifient les PDA-Nf comme un nouvel outil de délivrance de siRNAs très prometteur en clinique. L’avantage du ciblage de Lim1 avec cette approche, est l’absence de son expression à l’âge adulte. / Clear cell renal cell carcinoma (CCC) remains resistant to current therapies, despite the development of anti-angiogenic and the new immunotherapeutic approaches. Previous work of the laboratory has shown mechanistic similarities between tumorigenesis and nephrogenesis. Among the targets of the Sonic Hedgehog-Gli pathway which is found oncogenic in CCC, the developmental factor Lim1 has been identified as a new oncogene in CCC. Preliminary studies suggest that Lim1 would have a role in cell invasion. No Lim1 inhibitors are available; RNA interference remains the most effective and specific tool for gene silencing. In order to develop a new clinically applicable inhibition tool for Lim1, based on siRNAs carried by nanoparticles, a new generation of siRNA vehicles has been investigated. These are photo-polymerizable diacetylenic polymers in the form of nanofibers (PDA-Nf). These works demonstrate the invasive role of Lim1 in metastatic dissemination and identifies PDA-Nf as a new promising siRNA delivery tool in clinical practice. The advantage of targeting Lim1 with this nano-carrier approach is that Lim1 is not expressed in adulthood.