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The fundamental element of life known to man is the gene. The information contained in genes regulates all cellular functions, in health and disease. The ability to selectively alter genes or their transcript intermediates with designed molecular tools, as synthetic oligonucleotides, represents a paradigm shift in human medicine. The full potential of oligonucleotide therapeutics is however dependent on the development of efficient delivery vectors, due to their intrinsic characteristics, as size, charge and low bioavailability. Cell-penetrating peptides are short sequences of amino acids that are capable of mediating the transport of most types of oligonucleotide therapeutics to the cell interior. It is the interaction of cell-penetrating peptides with oligonucleotides and the transport of their non-covalently formed complexes across the cellular membrane, that constitutes the main subject of this thesis. In Paper I we studied the effects of different types of oligonucleotide cargo in the capacity of cationic and amphipathic peptides to interact with lipid membranes. We found that indeed the cargo sequesters some of the peptide’s capacity to interact with membranes. In Paper II we revealed the simultaneous interaction of different molecular and supramolecular peptide and peptide/oligonucleotide species in equilibrium, with the cellular membrane. In Paper III we developed a series of peptides with improved affinity for oligonucleotide cargo as well as enhanced endosomal release and consequently better delivery capacity. In Paper IV we investigated the effect of saturated fatty acid modifications to a cationic cell-penetrating peptide. The varying amphipathicity of the peptide correlated with the complex physicochemical properties and with its delivery efficiency. This thesis contributes to the field with a set of characterized mechanisms and physicochemical properties for the components of the ternary system – cell-penetrating peptide, oligonucleotide and cell membrane – that should be considered for the future development of gene therapy. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

Cancer testis antigens (CTA) represent attractive targets for targeted radiotherapy and imaging as their expression is restricted to cancer and germ cells. NY-ESO-1, a member of the CTA family, is highly immunogenic and expressed in multiple tumor types including carcinoma of bladder, liver lung. The aim of this study was to develop radioimmunoconjugates (RIC) to target NY-ESO-1 protein in cancer cells. Anti-NY-ESO-1 antibodies were modified by addition of DTPA for 111In-labelling or, in the presence of Iodogen, were 123I-labelled. Delivery of radiolabeled immunoconjugates across the cell membrane was achieved using a protein transfection (PT) reagent (SAINT-PhD) and by chemical linkage with the cell-penetrating and nuclear-localizing peptide, TAT (YGRKKRRQRRR). Cellular internalization, distribution and efflux of 111In-DTPA-anti-NY-ESO-1-TAT-PT and 123I-anti-NY-ESO-1-TAT-PT were investigated in cell fractionation and retention assays. It was shown that protein transfection reagent has promoted the cellular uptake of RICs into SK-MEL-37 and both of 111In-DTPA-anti-NY-ESO-1-TAT-PT and 123I-anti-NY-ESO-1-TAT-PT was retained longer in SK-MEL-37 cells in comparison to their isotope control RIC. In clonogenic assays, 111In-DTPA-anti-NY-ESO-1-TAT-PT significantly reduced surviving fraction of SK-MEL-37 cells. Cytotoxicity was inversely proportional to specific activity and the concentration of cells exposed to 111In-DTPA-anti-NY-ESO-1-TAT-PT. siRNA knock down of NY-ESO-1 resulted in partial reversal of 111In-DTPA-anti-NY-ESO-1-TAT-PT associated cytotoxicity. These promising results obtained from the in vitro study has brought the probe further into in vivo study. In preliminary biodistribution studies in SK-MEL-37 xenograft-bearing mice, tumour:muscle ratio for 111In-DTPA-anti-NY-ESO-1-TAT-PT was statistically significant compared to the control RIC 48 h post injection. This clearly indicated that the probe can be delivered into tumour in in vivo model and the successful uptake of radioactivity increased the chance of causing cytotoxicity to tumour cells through DNA damage. All of these findings have suggested that intracellular cancer associated antigen NY-ESO-1 can be reached by protein transfection reagent and cell penetrating peptide and initiates DNA damage through radio-isotope mediated cytotoxicity. Therefore, it represents a novel approach to the treatment of CTA-expressing cancers.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Actuellement le polyéthylènimine (PEI) est l’agent de transfection transitoire le plus utilisé par l’industrie pharmaceutique pour la production de protéines recombinantes à grande échelle par les cellules de mammifères. Il permet la condensation de l’ADN plasmidique (ADNp) en formant spontanément des nanoparticules positives appelées polyplexes, lui procurant la possibilité de s’attacher sur la membrane cellulaire afin d’être internalisé, ainsi qu’une protection face aux nucléases intracellulaires. Cependant, alors que les polyplexes s’attachent sur la quasi-totalité des cellules seulement 5 à 10 % de l’ADNp internalisé atteint leur noyau, ce qui indique que la majorité des polyplexes ne participent pas à l’expression du transgène. Ceci contraste avec l’efficacité des vecteurs viraux où une seule particule virale par cellule peut être suffisante. Les virus ont évolués afin d’exploiter les voies d’internalisation et de routage cellulaire pour exprimer efficacement leur matériel génétique. Nous avons donc supposé que l’exploitation des voies d’internalisation et de routage cellulaire d’un récepteur pourrait, de façon similaire à plusieurs virus, permettre d’optimiser le processus de transfection en réduisant les quantités d’ADNp et d’agent de transfection nécessaires. Une alternative au PEI pour transfecter les cellules de mammifèreest l’utilisation de protéines possédant un domaine de liaison à l’ADNp. Toutefois, leur utilisation reste marginale à cause de la grande quantité requise pour atteindre l’expression du transgène. Dans cette étude, nous avons utilisé le système E/Kcoil afin de cibler un récepteur membranaire dans le but de délivrer l’ADNp dans des cellules de mammifères. Le Ecoil et le Kcoil sont des heptapeptides répétés qui peuvent interagir ensemble avec une grande affinité et spécificité afin de former des structures coiled-coil. Nous avons fusionné le Ecoil avec des protéines capables d’interagir avec l’ADNp et le Kcoil avec un récepteur membranaire que nous avons surexprimé dans les cellules HEK293 de manière stable. Nous avons découvert que la réduction de la sulfatation de la surface cellulaire permettait l’attachement ciblé sur les cellules par l’intermédiaire du système E/Kcoil. Nous démontrons dans cette étude comment utiliser le système E/Kcoil et une protéine interagissant avec l’ADNp pour délivrer un transgène de manière ciblée. Cette nouvelle méthode de transfection permet de réduire les quantités de protéines nécessaires pour l’expression du transgène. / Pharmaceutical industry often employs polyethylenimine (PEI) for large scale protein production processes by transient transfection of mammalian cells. PEI condenses plasmid DNA (pDNA) by spontaneously forming positive nanoparticles known as polyplexes. Condensed pDNA is favoured for cell surface binding, internalization and protection from intracellular nucleases. While most of the cells efficiently uptake polyplexes, only 5 to 10% of captured pDNA reaches the nucleus for transgene expression. This suggests that polyplexes are hampered in their ability to route and to translocate to the nucleus necessitating large amounts of polyplexes to achieve high expression levels. By contrast, many viruses can efficiently transduce cells with only one or a few viral genome copies. Viruses have evolved to exploit cellular internalization and routing properties to express their own genetic material. We hypothesized that less pDNA would be used in an optimized transfection process if we exploited the internalization and routing properties that viruses use. DNA binding proteins could be used as an alternative to PEI to transfect mammalian cells. However, their usage is marginal due to the large protein quantities required to bind pDNA for transgene expression. If less pDNA is used less binding protein is needed. In this study, we used the E/Kcoil system to target a membrane receptor to deliver pDNA in mammalian cells. The Ecoil and Kcoil are two repeated heptapeptides which interact with a high affinity and specificity to form coiled-coil structures. We fused the Ecoil with a recombinant pDNA-binding protein. The Kcoil was fused to a stably-expressed membrane receptor in HEK293 cells. We discovered that low sulfation of the cell surface reduced non-specific binding of the pDNA:protein complex and permitted targeted binding via the E/Kcoil interaction. We demonstrate how to use recombinant pDNA-binding protein and the E/Kcoil system for targeted transgene delivery. This newly developed system provides a new transfection method, with reduced pDNA-binding protein quantities needed to achieve transgene expression.

A malária é uma das principais e a mais disseminada das parasitoses humanas. A falta de uma vacina eficaz e o problema da resistência aos fármacos tem contribuído para o adiamento da solução do controle desta infecção. A busca de novos alvos biológicos tem se concentrado, em parte, na compreensão de vias metabólicas. Em P. falciparum, identificamos a biossíntese das duas formas da vitamina K (filoquinona e menaquinona). Na via MEP foram caracterizadas duas importantes enzimas bifuncionais, a farnesil difosfato sintase/geranilgeranil difosfato sintase (FPPS/GGPPS) capaz de formar farnesil difosfato e geranilgeranil difosfato e octaprenil pirofosfato sintase/fitoeno sintase (OPP/PSY) responsável pela biossíntese da cadeia isoprênica que se liga ao anel da via de ubiquinona, como também forma o primeiro caroteno na via de carotenóides. Este projeto tem como objetivo caracterizar o gene MenA da biossíntese de MQ, determinar a localização de FPPS/GGPPS em P. falciparum e investigar a importância de OPP/PSY e de FPPS/GGPPS no ciclo intraeritrocítico de P. falciparum. / Malaria is one of the main widespread human parasites. The lack of an effective vaccine and the problem of drug resistance haves contributed to the delay of the control solution of this infection. The search for new biological targets has focused in part on the understanding of metabolic pathways. In P. falciparum, identified the biosynthesis of the two forms of vitamin K (phylloquinone and menaquinone). In the MEP pathway were characterized two important bifunctional enzyme, farnesyl diphosphate synthase/geranylgeranyl diphosphate synthase (FPPS/GGPPS) able to form farnesyl diphosphate and geranylgeranyl diphosphate and octaprenyl pyrophosphate synthase/phytoene synthase (OPP/PSY) responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, but also forms the first carotene in the carotenoid pathway. This project aims to characterize the MenA gene from the MQ biosynthesis, determine the localization of FPPS/GGPPS and investigate the importance of OPP/PSY and FPPS/GGPPS in intra-erythrocytic cycle of P. falciparum.

O uso de genes em terapias é um conceito originado em 1970 em consequência do crescimento exponencial de novas tecnologias para liberação de DNA, também pela capacidade de expressão de genes exógenos em células de mamíferos. Propomos, então, a síntese de polímeros catiônicos, em dois grupos, por meio da aminólise da poli(succinimida) (PSI): grupo 1An, polímeros catiônicos com arcabouço poli (ácido aspártico) com cadeias laterais contendo aminas protonáveis; grupo 2An, polímeros catiônicos anfifílicos, contenho o poli (ácido aspártico) como arcabouço, com aminas protonáveis e cadeias dodecilamina. Estudos de SEC mostraram que derivados dodecilados 2An tiveram tamanho menor que os polímeros do grupo 1An, não dodecilados. A capacidade tamponante para todos os polímeros sintetizados foi maior que o bPEI 25, e o grupo 2An apresentou as maiores capacidades tamponantes. Derivados 2An com as aminas A1 a A4 apresentaram menor CMC do que o grupo 1An. Citotoxicidade dos policátions foi dependente das suas concentrações e, entre todos os polímeros, aqueles com aminas A5 e A6 não foram citotóxicos. A presença da cadeia dodecilamina na PSI não diminuiu a viabilidade celular até 250 ?L-1, sugerindo que a porção hidrofóbica não é citotóxica na faixa de concentrações testada. A complexação do pEGFP-N3 com os derivados de PSI foi realizada, bem como a transfecção dos poliplexos em células HeLa. A expressão de GFP dos complexos obtidos com bPEI 25 foi quantificada e comparada com os poliplexos preparados com os derivados da PSI. Ensaios de transfecção mostraram que os derivados dodecilados da PSI apresentaram expressão negligenciável de GFP em células HeLa, sugerindo uma ligação forte entre plasmídeo e os derivados sintetizados e não-liberação do material genético nas células, ou dano celular causado pela cadeia hidrofóbica nas células. Os maiores valores de GFP quantificados foram encontrados nos poliplexos contendo polímeros não-dodecilados e com as aminas A3 e A4, nas razoes N:P 5 a 20 para A3 e N:P 5 para A4. Ambas as estruturas A3 e A4 fazem parte do core do bPEI 25. / Genes as drugs for human therapy is a concept originally conceived around 1970, a consequence of the exponential growth in knowledge of human gene function, the more effective technologies for DNA delivery, and the ability to transfer and express exogenous genes in mammalian cells. Here we propose synthesizing two small library groups of cationic polymers via aminolysis of poly(succinimide) (PSI) backbone: group 1An, polycationic polymers with a degradable amide of poly(aspartic) acid backbone, protonable oligoamine side chains into the main polymer structure, and group 2An, amphiphilic cationic polymers with a degradable amide of poly(aspartic) acid backbone, protonable oligoamine side chains into the main polymer structure and dodecyl side chain moieties. SEC showed that dodecylated derivatives 2An had lower size than 1An group, non-dodecylated polyelectrolytes. Buffering capacity of all synthesized polymers was higher than the standard bPEI 25, and the dodecylated 2An group had the highest buffering capacities values. 2An derivatives with amines A1 to A4 showed lower CMC than their non-dodecylated pairs. Cytotoxicity of all polycations was dependent on the concentrations, and among all polymers, those with amines A5 and A6 had lower cytotoxicity than bPEI 25. Moreover, the presence of the hydrophobic dodecyl side chain in the PSI backbone did not decrease the cell viability until 250 ?g mL-1 polymer concentration, thus suggesting the hydrophobic moiety is not cytotoxic in this range. Complexation of pEGFP-N3 plasmid with PSI derivatives grafted with amines A1 to A4 was performed, as well as the transfection of polyplexes into HeLa cells. GFP expression of bPEI25 polyplexes in different complex volumes was quantified and compared with PSI derivatives/pEGFP-N3 polyplexes. Transfection assays showed that dodecylated PSI derivatives had negligible or no GFP expression in HeLa cells, thus suggesting a strong interaction between polycations and pDNA or a cellular damage caused by the hydrophobic moiety, although cytotoxicity assay of polyplexes showed low cytotoxicity of polyplexes. The highest GFP expression values were found for polycations 1A3 and 1A4, both without the dodecylamine side chain, in the N:P ratios 5 to 20 for 1A3, and N:P ratio 5 for 1A4. Both amines A3 and A4 used for the PSI grafting are core structures of bPEI 25.

A malária é uma das principais e a mais disseminada das parasitoses humanas. A falta de uma vacina eficaz e o problema da resistência aos fármacos tem contribuído para o adiamento da solução do controle desta infecção. A busca de novos alvos biológicos tem se concentrado, em parte, na compreensão de vias metabólicas. Em P. falciparum, identificamos a biossíntese das duas formas da vitamina K (filoquinona e menaquinona). Na via MEP foram caracterizadas duas importantes enzimas bifuncionais, a farnesil difosfato sintase/geranilgeranil difosfato sintase (FPPS/GGPPS) capaz de formar farnesil difosfato e geranilgeranil difosfato e octaprenil pirofosfato sintase/fitoeno sintase (OPP/PSY) responsável pela biossíntese da cadeia isoprênica que se liga ao anel da via de ubiquinona, como também forma o primeiro caroteno na via de carotenóides. Este projeto tem como objetivo caracterizar o gene MenA da biossíntese de MQ, determinar a localização de FPPS/GGPPS em P. falciparum e investigar a importância de OPP/PSY e de FPPS/GGPPS no ciclo intraeritrocítico de P. falciparum. / Malaria is one of the main widespread human parasites. The lack of an effective vaccine and the problem of drug resistance haves contributed to the delay of the control solution of this infection. The search for new biological targets has focused in part on the understanding of metabolic pathways. In P. falciparum, identified the biosynthesis of the two forms of vitamin K (phylloquinone and menaquinone). In the MEP pathway were characterized two important bifunctional enzyme, farnesyl diphosphate synthase/geranylgeranyl diphosphate synthase (FPPS/GGPPS) able to form farnesyl diphosphate and geranylgeranyl diphosphate and octaprenyl pyrophosphate synthase/phytoene synthase (OPP/PSY) responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, but also forms the first carotene in the carotenoid pathway. This project aims to characterize the MenA gene from the MQ biosynthesis, determine the localization of FPPS/GGPPS and investigate the importance of OPP/PSY and FPPS/GGPPS in intra-erythrocytic cycle of P. falciparum.

O timo é um órgão linfóide primário, responsável pela indução da tolerância imunológica central. Histologicamente esse órgão é formado por um estroma composto por células tímicas epiteliais (TECs) além de outros tipos celulares. Dentre as TECs encontramos as células tímicas epiteliais corticais (cTECs) e as células tímicas epiteliais medulares (mTECs), as quais são responsáveis pela seleção positiva e seleção negativa dos timócitos em desenvolvimento, respectivamente. Durante seu desenvolvimento intra-tímico, os timócitos modulam da expressão de genes de marcadores de diferenciação, os chamados clusters de diferenciação (CDs) além de outros genes. Neste projeto nós nos interessamos por este aspecto, ou seja, o controle da expressão gênica durante a diferenciação dos timócitos. Como os microRNAs (miRNAs) são elementos essenciais de controle fino da expressão gênica, atuando ao nível pós-transcricional de RNAs mensageiros (mRNAs) de células eucarióticas, nosso interesse foi o de estudar este tipo de controle em timócitos. Dentre as centenas de miRNAs já descritos no camundongo, o miRNA 155 (miR-155) é o mais expresso no timo e no baço sendo que seu papel foi já foi demonstrado em células T maduras periféricas, mas ainda não se estudou seu possível papel em timócitos em desenvolvimento. A partir das evidências do papel do miR-155 nas células T maduras, nós elaboramos a hipótese de que esse miRNA também atua no desenvolvimento de timócitos. Para testar essa hipótese, nós utilizamos a estratégia de silenciamento do miR-155 por meio de eletroporação (eletrotransfecção) do antagonista Anti-miR-155 diretamente no timo de camundongos BALB/c. Os timócitos de camundongos controle e silenciados foram então separados por citometria de fluxo e amostras de RNA dessas células foram então analisadas por meio de qRT-PCR para nos certificarmos da eficiência do silenciamento do miR-155 e por hibridizações com microarrays de mRNAs para a análise do transcriptoma. Observamos que o silenciamento do miR-155 provoca a modulação de um grande conjunto de mRNAs, os quais foram analisados com auxílio do banco de dados do \"Immunogical Genome Project\" (ImmGen) quanto aos seus aspectos funcionais focando no desenvolvimento de timócitos. Os mRNAs modulados e envolvidos neste processo, foram ainda reanalisados quanto sua capacidade de interagir por hibridização com o miR-155 (hibridização miRNA-mRNA) por meio da ferramenta computacional RNA-Hybrid. Por meio destas estratégias, conseguimos repertoriar um conjunto de mRNAs que codificam proteínas importantes para o desenvolvimento de timócitos e que são potencialmente controlados por miR-155. / The thymus is a primary lymphoid organ responsible for the induction of central immune tolerance. Histologically this organ is formed by a thymic stroma composed of thymic epithelial cells (TECs) and other cell types. The TEC cells are subdivided into cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells (mTECs), which are responsible for positive selection and negative selection of developing thymocytes, respectively. During its intra-thymic development, thymocytes modulate the gene expression of differentiation markers, so-called clusters of differentiation (CD) and other genes. In this project we are interested in the control of gene expression during the differentiation of thymocytes. As microRNAs (miRNAs) are essential elements of fine control of gene expression, acting at the post-transcriptional level of messenger RNAs (mRNAs) of eukaryotic cells, our interest was to study this type of control in thymocytes. Among the hundreds of miRNAs been described in mice, miRNA 155 (miR-155) is strongly expressed in the thymus and spleen and its role was already demonstrated in peripheral mature T cells, but has not yet been studied during the thymocyte development. Taking into account the evidence for the role of miR-155 in mature T cells, we raise the hypothesis that this miRNA is also active in developing thymocytes. To test this, we use the miR-155 silencing strategy by using electroporation (electrotransfection) of anti-miR-155 antagonist directly into the thymus of BALB/c mice. The thymocytes of control or silenced mice were then separated by flow cytometry and RNA samples from these cells were initially analyzed by qRT-PCR to make sure of miR-155 silencing efficiency and then by hybridization with microarrays for mRNA transcriptomeanalysis. We note that miR- 155 silencing cause modulation of a large set of mRNAs, which were analyzed through \"Immunological Genome Project\" (ImmGen) database focusing on developing thymocytes. The modulated mRNAs that were involved in this process were also retested for their ability to interact with miR-155 (miRNA-mRNA hybridization) by means of RNA-Hybrid computational tool. Through these strategies we were able to found a set of mRNAs encoding proteins important for the development of thymocytes that are potentially controlled by miR-155.

A abordagem imunoterapêutica do câncer tem sido cada vez mais explorada. Entre os fatores que a tornam atraente, mas também a limitam, está o uso de material antigênico do próprio paciente. Assim, pretendeu-se estabelecer condições de extração e amplificação de mRNA tumoral, como fonte renovável de antígenos. Pretendeu-se avaliar também a eficácia da vacina, com o uso de monócitos transfectados com RNA tumoral total para mimetismo das células tumorais. Diferentes concentrações (0,1 mg a 10 mg) de RNA total de SK-BR-3 e diferentes tempos (12, 24 e 48 h) foram usados para transfecção. Na avaliação do potencial linfo-estimulador dos monócitos foi usado o ensaio de proliferação linfocitária e a secreção de citocinas durante a co-cultura. Como resultado viu-se que monócitos transfectados se tornaram mais ativados e foram capazes de induzir linfoproliferação. Esses resultados indicaram ser possível o desenvolvimento de um método para avaliação das respostas celulares induzidas contra células tumorais em pacientes com câncer que foram vacinados. / The cancer immunotherapeutic approach has been increasingly exploited. Among the factors that make it attractive, but also limited, is the use of patient antigenic material. Thus, we propose to establish conditions for extraction and amplification of mRNA tumor, as renewable source of antigens. It is also intended to assess the vaccine effectiveness, using monocytes transfection with total tumor RNA for mimicry the tumor cells. Different concentrations (0.1 to 10 mg) of SK-BR-3 total RNA and different times (12, 24 and 48 h) were used in transfection. To assess the lympho-stimulator potential of transfected monocytes was used the test of lymphocyte proliferation, and cytokines secretion during co-culture. The result was that transfected monocytes became more activated and were able to induce lymphoproliferation. These results indicated that the development of a method for evaluating cellular responses induced against tumor cells in cancer patients who were vaccinated is possible.