Gene therapy, although a young field, has become an intense area of study for the potential treatment of many inborn or acquired diseases, including cancer. The systemic or intratumoural delivery of cytokines and other immune system modulators has shown that protective, specific immunity to tumours is possible and effective. Adenovirus is an extremely useful vehicle for the transfer of genes, due to the ease of its preparation, its ability to be grown to high concentrations, and its capacity to infect a wide variety of cell types, including nonproliferating cells. Although a great deal of research has been done, there are a number of possible improvements, specifically, the consistency and range of transgene expression. The HCMV IE promoter/enhancer, used in a wide range of vector systems, has proven to drive lower levels of transgene expression in murine cells as compared to human cells. The use of the MCMV IE promoter/enhancer within the context of an adenovirus vector system has been investigated to see if more consistent transgene expression is possible in murine models. Studies with a luciferase reporter gene have demonstrated that in all cell types, the MCMV IE promoter/enhancer drives transgene expression to equivalent or higher levels than the HCMV IE promoter/enhancer. Our lab has investigated adenovirus as an intrtumoural gene delivery vehicle for various cytokines, including IL-12. However, the current IL-12-expressing vector carries the IL-12p35 subunit in E1 and the IL-12p40 subunit in E3. A homologous recombination event between E1 sequences in the viral genome and those that are integrated into 293 cells, would produce a replication-competent adenovirus expressing high levels of the p40 subunit, which is a potential antagonist to IL-12. A bicistronic adenovirus vector using the poliovirus IRES was constructed containing all IL-12 coding sequences in E1 to avoid this potential hazard. This virus expressed between 60 ng to 2.5 μg of IL-12/10⁶ cells, depending on the cell type. These levels of expression, however are 7-30-fold lower than those driven by previous IL-12 vector. Although this new virus is not appropriate for tumour immunotherapy, the shuttle plasmids developed during its construction have many potential uses. / Thesis / Master of Science (MS)

The improving of our understanding of cancer development still depends on cancer research at the molecular level. In his project, bigenic vectors for animal models of breast and prostate cancer are created. Bigenic constructs are useful because they create animals expressing two genes of interest at a time, with one injection step and no need for crossings. In order to produce these vectors, previous animal models have been analyzed, and the elements that worked successfully in previous models were gathered in a new arrangement for the creation of an improved model. In order to create a bigenic vector, the viral internal ribosomal entry site was utilized, as a means of obtaining two protein products from one transcript. One vector, the MMTV-Neu1842-IRES-Cre was successful in generating a line of transgenic mice. Female founders of this line already express the expected phenotype, tumors of the mammary tissue. Once this line is established, it can be crossed with the Rosa26 line, to determine the pattern of Cre expression. Other vectors were created for models of prostate cancer, using the probasin promoter and the MT oncogene. While transgenic mice were attempted, there were no phenotype differences between wild type and transgenic mice. All created vectors were tested for expression ofthe two genes carried in tissue culture experiments. All the experiments were successful, indicating a working oncogene (by means of a focus assay) and Cre activity (by excission assay). The new breast cancer animal model carrying the MMTV-Neu1842-IRESCre construct is promising and can be used in combination with existing models to answer some of the remaining questions regarding breast cancer signaling pathways. / Thesis / Master of Science (MSc)

Abstract In eukaryotic cells, fatty acids are mainly synthesized in the cytoplasm, but recently, in yeast and in humans, the ability to synthesize fatty acids has been characterized in mitochondria. This mitochondrial pathway is similar to bacterial type II fatty acid synthesis (FAS). The main feature of mitochondrial FAS in yeast is the respiratory deficient phenotype and loss of cytochromes when any of genes encoding enzymes for mitochondrial FAS is deleted. Mitochondrial FAS has been demonstrated to have an important role in lipoic acid production, namely it synthesizes octanoyl-ACP, which is used as a precursor for lipoic acid. However, the role and function of mitochondrial FAS is not yet fully understood. Many components of the mitochondrial FAS pathway in yeast have been identified according to their similarity to bacterial counterparts, but 3-hydroxyacyl-ACP dehydratase does not show any easily recognizable similarity to bacterial dehydratases and thus remained unidentified. In this study 3-hydroxyacyl-ACP dehydratases of mitochondrial FAS were characterized from the yeast Saccharomyces cerevisiae, humans, and the human pathogen Trypanosoma brucei. The yeast 3-hydroxyacyl-ACP dehydratase (Htd2p) was identified by using a genetic screen, and this protein was shown to be encoded by open reading frame (ORF) YHR067w. The product of this gene shows mitochondrial localization and exhibits hydratase 2 activity. The deletion of HTD2 leads to a respiratory deficient phenotype, loss of cytochromes, reduced lipoic acids levels and changes in mitochondrial morphology. The ORF encoding human 3-hydroxyacyl-ACP hydratase (HsHTD2) was identified by functional complementation of the respiratory deficient phenotype of the yeast htd2 mutant with a human cDNA library. The complementing cDNA was previously identified as the RPP14 transcript encoding the 14 kDa subunit of the human RNase P complex. It was found that this transcript contains another 3' ORF, which encodes a protein that displays hydratase 2 activity and has mitochondrial localization. The bicistronic nature of the transcript is conserved in vertebrates and indicates a genetic link between mitochondrial FAS and RNA processing. The mitochondrial 3-hydroxyacyl-ACP hydratase in T. brucei is homologous to human HTD2, can complement the yeast respiratory deficient phenotype, exhibits hydratase 2 activity and localizes to the T. brucei mitochondrion.

The link between polyadenylation (pA) and various biological, behavioral, and pathological events of eukaryotes underlines the need to develop in vivo polyadenylation assay methods for characterization of the cis-acting elements, trans-acting factors and environmental stimuli that affect polyadenylation efficiency and/or relative usage of two alternative polyadenylation (APA) sites. The current protein-based CAT or luciferase reporter systems can measure the polyadenylation efficiency of a single pA site or candidate cis element but not the choice of two APA sites. To address this issue, we developed a set of four new bicistronic reporter vectors that harbor either two luciferase or fluorescence protein open reading frames connected with one Internal Ribosome Entry Site (IRES). Transfection of single or dual insertion constructs of these vectors into mammalian cells demonstrated that they could be utilized not only to quantify the strength of a single candidate pA site or cis element, but also to accurately measure the relative usage of two APA sites at both the mRNA (qRT-PCR) and protein levels. This represents the first reporter system that can study polyadenylation efficiency of a single pA site or element and regulation of two APA sites at both the mRNA and protein levels.

Considerando que várias mutações gênicas estão envolvidas no estabelecimento dos tumores, surge a idéia de que o alcance da melhor eficiência no tratamento do câncer é dado pela entrega de múltiplos genes. Este trabalho apresenta a construção, produção e caracterização funcional in vitro e in vivo do vetor adenoviral bicistrônico Adp16IRESp53 e dos monocistrônicos Adp16 e Adp53 em modelo de câncer de pulmão. Nossos resultados indicam uma forte indução de morte celular nas células H358 transduzidas com Adp16IRESp53 em comparação com vetores monocistrônicos Adp16, Adp53 ou o reporter AdeGFP e/ou AdLacZ. Nos ensaios in vivo, utilizando modelo xenografico onde as células H358 foram implantadas no subcutâneo de camundongos atímicos Balb/C nude, pudemos confirmar também in vivo a significativa inibição do crescimentos dos tumores tratados com Adp16IRESp53. Em conclusão, a remediação simultânea de p16INK4a e p53, mediada pelo arranjo bicistrônico, pode ser considerada como uma estratégia promissora para terapia gênica do câncer de pulmão. / This work presents the construction, production and functional evaluation in vitro and in vivo of the bicistronic adenoviral vector Ap16IRESp53 as well as the monocistronic vectors Adp16 and Adp53 in a lung cancer model. Considering that several mutation events are involved in tumorigenesis, comes the idea that a greater efficiency in cancer treatment would be reached with delivery of multiples genes. Our data demonstrate a strong cell death effect in H358 cells transduced with Adp16IRESp53 when compared with Adp16, Adp53 or the reporter AdeGFP and/or AdLacZ. For the in vivo studies, we have used H358 cells implanted subcutaneously in athymic Balb/c nude mice. Our data show significant suppression of tumors treated with the therapeutic adenoviral vector, Adp16IRESp53. In conclusion, the simultaneous replacement of p16INK4a and p53, mediated by the bicistronic vector, may prove to be a promising strategy for gene therapy of lung cancer.

Considerando que várias mutações gênicas estão envolvidas no estabelecimento dos tumores, surge a idéia de que o alcance da melhor eficiência no tratamento do câncer é dado pela entrega de múltiplos genes. Este trabalho apresenta a construção, produção e caracterização funcional in vitro e in vivo do vetor adenoviral bicistrônico Adp16IRESp53 e dos monocistrônicos Adp16 e Adp53 em modelo de câncer de pulmão. Nossos resultados indicam uma forte indução de morte celular nas células H358 transduzidas com Adp16IRESp53 em comparação com vetores monocistrônicos Adp16, Adp53 ou o reporter AdeGFP e/ou AdLacZ. Nos ensaios in vivo, utilizando modelo xenografico onde as células H358 foram implantadas no subcutâneo de camundongos atímicos Balb/C nude, pudemos confirmar também in vivo a significativa inibição do crescimentos dos tumores tratados com Adp16IRESp53. Em conclusão, a remediação simultânea de p16INK4a e p53, mediada pelo arranjo bicistrônico, pode ser considerada como uma estratégia promissora para terapia gênica do câncer de pulmão. / This work presents the construction, production and functional evaluation in vitro and in vivo of the bicistronic adenoviral vector Ap16IRESp53 as well as the monocistronic vectors Adp16 and Adp53 in a lung cancer model. Considering that several mutation events are involved in tumorigenesis, comes the idea that a greater efficiency in cancer treatment would be reached with delivery of multiples genes. Our data demonstrate a strong cell death effect in H358 cells transduced with Adp16IRESp53 when compared with Adp16, Adp53 or the reporter AdeGFP and/or AdLacZ. For the in vivo studies, we have used H358 cells implanted subcutaneously in athymic Balb/c nude mice. Our data show significant suppression of tumors treated with the therapeutic adenoviral vector, Adp16IRESp53. In conclusion, the simultaneous replacement of p16INK4a and p53, mediated by the bicistronic vector, may prove to be a promising strategy for gene therapy of lung cancer.

Contrairement à la vision classique des ARNms eucaryotes qui ne contiendrait qu’une seule séquence codante, de nombreuses évidences expérimentales montrent que ces ARNms contiennent plusieurs séquences codantes qui permettraient l’expression de plusieurs protéines différentes. Les ARNms sont donc multicodants et contiennent des cadres de lectures alternatifs (AltORFs pour alternative open reading frames). Ces ORFs alternatifs sont présents dans les régions non-traduites (UTRs) ou chevauchant le RefORF (cadre de lecture ouvert de référence) dans les cadres de lectures non-canoniques +2 et +3. Le protéome est donc plus complexe que ce que l’on pense. Toutefois, le rôle et la fonction de ces nouvelles protéines restent à être investigués. Au cours de mon projet de recherche à la maîtrise, j’ai commencé la caractérisation de la protéine alternative AltMiD51, codée dans le 5’UTR du gène bicistronique MIEF1/SMCR7L/MID51 et co-exprimée avec sa protéine de référence MiD51. Par des approches variées de biologie moléculaire, cellulaire et biochimique, j’ai d’abord démontré et confirmé la localisation cellulaire de la protéine AltMiD51 à la mitochondrie. Par la suite, j’ai pu démontrer que la présence d’AltMiD51 affecte significativement la morphologie mitochondriale en fragmentant celle-ci. De plus, j’ai pu davantage cibler la région qui contient l’information de sa localisation ainsi que son effet de fragmentation, soit seulement les 23 premiers acides aminés de sa séquence. J’ai également observé que cette région Nterminale (a.a.23) est encore plus efficace pour induire la fragmentation des mitochondries. J’ai pu démontrer que le motif protéique L-Y-R est essentiel pour l’activité de fragmentation. J’ai également validé l’interaction in vivo de AltMID51 avec sa protéine partenaire ACPM (Acyl carrier protein) dans des foci mitochondriaux. En conclusion, mes travaux à la maîtrise ont permis de mettre en évidence que la protéine AltMiD51 est un nouveau facteur impliqué dans la fission mitochondriale. Ces résultats ouvrent de nouvelles perspectives en ce qui concerne la caractérisation de nouvelles protéines alternatives et par leur contribution dans la biologie moléculaire de la cellule. / Abstract : Challenging the dogma that eukaryotic mRNAs contain a single coding sequence, an ever-growing number of studies highlight the possibility for these mRNAs to have several coding sequences, and thereby code for multiple proteins. Thus, eukaryotic mRNAs are multicoding and present alternative open reading frames (AltORFs). These alternative ORFs are present in the non-translated region (UTRs), and within or overlapping the RefORF (reference open reading frame) in non-canonical frames (+2 and +3). The proteome is indeed more complex than we initially thought. However, the role and biological function of these proteins remain to be elucidated. Over the course of my MPhil, I started characterizing the alternative protein AltMiD51, encoded in the 5’UTR of the bicistronic MIEF1/SMCR7L/MID51 gene, and coexpressed with its reference protein (MiD51). Using a wide range of molecular biology, cellular and biochemistry assays, I first demonstrated AltMiD mitochondrial localisation. I then proved AltMiD51 expression alters mitochondrial dynamics, enhancing a fragmented morphology. Moreover, I further characterized the sequence region responsible for AltMiD51 localisation and mitochondrial fragmentation, namely the first 23 amino acids. I also observed that this N-terminal region alone presents a stronger phenotype of mitochondrial fragmentation. In addition, I proved the L-Y-R domain is essential for AltMiD51 fragmentation activity, and I validated AltMiD51 in vivo interaction with ACPM (Acyl Carrier Mitochondrial Protein) within mitochondrial foci. Eventually, the work presented here highlighted AltMiD51 as a novel factor involved in mitochondrial fragmentation. These results shed light on new perspectives regarding the characterisation of alternative proteins and their contribution to the cellular metabolism.

Initiation der Translation ist ein komplexer und stark regulierter Prozess, bei dem Ribosomen die mRNA binden. Die überwiegende Mehrheit eukaryotischer mRNAs wird durch einen 5‘-Cap-abhängigen Mechanismus translatiert. Dazu bindet der eIF4F-Proteinkomplex die mRNA an der 5'-Cap-Struktur, um weitere eIFs und die kleine ribosomale Untereinheit zu rekrutieren, welche dann die 5'UTR von 5'- in 3'-Richtung bis zu einem Startcodon scannt. Anschließend trifft die große ribosomale Untereinheit dazu und die Proteinsynthese beginnt. Darüber hinaus kann die Translation durch IRES, interne ribosomale Eintrittsstellen, vermittelt werden, welche das Ribosom unabhängig von Cap und 5‘-Ende zum Startcodon rekrutieren. Die zelluläre IRES-vermittelte Translation gilt als ineffizient unter physiologischen Bedingungen, wird aber durch Stress aktiviert. Da die Regulation dieses Mechanismus weitaus unbekannt ist, haben wir die zelluläre, Cap-unabhängige Translationsinitiation untersucht. Dafür haben wir eine embryonale Stammzelllinie generiert, welche eine dominant-negative Mutante von 4E-BP1 exprimiert. 4E-BP1 bindet das 5‘-Cap-bindende Protein, sodass eIF4F nicht am 5'-Cap andocken kann. Wir haben das Proteom während der Überexpression von 4E-BP1 und der neuronalen Differenzierung bestimmt, um Translationsdynamiken systemisch zu erfassen. Gene mit verminderter Sensitivität für die Cap-abhängige Translation wurden so identifiziert und in bicistronischen Reporter-Assays getestet. Nach strenger Validierung wurde eine Cap-unabhängig translatierte mRNA, Pqbp1, entdeckt. Der zweite Teil dieser Studie untersuchte die Cap-unabhängige Translation einer circRNA, welche keine freien Enden hat und daher per IRES translatiert werden muss. Wir konnten bestätigen, dass circMbl in vitro translatiert wird und konnten so innerhalb eines Kooperationsprojekts zu der Erkenntnis beitragen, dass circRNAs im Fliegengehirn translatiert werden. / Translation initiation is a complex and highly regulated process which involves the assembly of an elongation competent ribosome on the mRNA. The vast majority of eukaryotic mRNAs is translated by a canonical cap-dependent mechanism. This requires the eIF4F protein complex to bind the mRNA at the 5’-cap to recruit further eIFs and the small ribosomal subunit which then scans the 5’UTR in 5’ to 3’ direction until a start codon is encountered. Afterwards the large ribosomal subunit joins and protein synthesis begins. Besides that, translation of mRNAs can be mediated by IRESs, internal ribosome entry sites, which recruit the ribosome in a cap and 5’-end-independent manner to the start codon. Such cellular IRES-mediated translation is thought to be inefficient under physiological conditions but activated during stress. As the regulation of this mechanism is not well understood, we aimed to elucidate cellular cap-independent translation events. Therefore, we generated a mouse embryonic stem cell line with inducible overexpression of a dominant negative mutant of 4E-BP1. 4E-BP1 sequesters the cap-binding protein eIF4E so that the eIF4F protein complex fails to assemble at the 5’-cap. We performed shotgun proteomics during 4E‑BP1 overexpression and neuronal differentiation to globally monitor translation dynamics. Genes with reduced sensitivity for cap-dependent translation were identified and tested for internal translation initiation in bicistronic reporter assays. After stringent validation one cap-independently translated mRNA, Pqbp1, was discovered. The second part of this study investigated cap-independent translation initiation on a circRNA, which by nature lacks free ends and thus requires IRES-mediated translation. We could show that circMbl is translated in vitro and thus contributed to the scientific evidence for the translation of circRNAs in fly brain, which was studied in a collaboration project.

Hepatitis C virus (HCV) is a worldwide spread pathogen infecting up to 3 % of the human population. Nowadays, research of new drugs against this virus is focused on the individual steps in its life cycle, including the translation initiation. In the case of HCV translation initiation is dependent on the internal ribosome entry site (IRES). Besides of components of the translational machinery also other components of the cell, so called IRES trans-acting factors (ITAF), contribute to its proper progress. This work continues in previous research of our laboratory focused on searching for new ITAF. In order to search for potential ITAF increasing HCV IRES activity new recombinant plasmid vectors and reference strains were prepared and selection conditions of the selection system were optimized. The differences in the growth characteristics of the reference strains were analyzed and quantified under selective and non-selective conditions. A set of pilot high efficiency transformations of the yeast strain pJ69-4A carrying bicistronic construct with HCV IRES were conducted using human expression cDNA library in order to optimize the efficiency of transformation and selection conditions and to attempt to identify new ITAF. Several dozens of randomly selected clones from these transformations obtained under...