La première étape du cycle viral du virus de l'immunodéficience humaine se déroule grâce à l'interaction entre les glycoprotéines d'enveloppe gp120/gp41 et les récepteurs CD4 et CCR5/CXCR4. Les différentes fonctions activées par cette étape, incluant l'attachement, la pénétration et la signalisation cellulaire représentent des cibles potentielles pour le développement d'antirétroviraux. Dans ce travail, nous avons développé des approches permettant d'agir sur chacune de ces étapes à l'aide de peptides synthétiques, d'anticorps anti-peptide et d'inhibiteurs des voies de signalisation. Dans la première approche, nous nous sommes intéressé au développement d'analogues peptidiques de la région HRII en évitant les limitations, incluant courte demi-vie et émergence d'isolats de résistance, rencontrées lors de l'utilisation du peptide T-20 (Fuzeon). Nous avons synthétisé un peptide de 34 acides aminés modélisant la région HRII en incluant des acides aminés non naturels de série D uniquement au niveau de certains sites sensibles à la protéolyse ou dans la totalité de la séquence.Les résultats obtenus montrent que les modifications ponctuelles permettent de : i) maintenir la structure en hélice a du peptide, ii) maintenir sa capacité à interagir avec la région HRI, iii) d'augmenter sa demie-vie et iv) de conserver son activité antivirale. Dans la deuxième approche, nous avons testé la capacité des peptides analogues de la région HRII de VIH-1 et de la boucle V3 de SIV à induire la production d'anticorps neutralisants. Cette étude nous a permis d'aboutir à deux conclusions principales : i) les anticorps anti-HRII peuvent interférer avec l'activité antivirale du peptide administré lors du traitement antiviral, ii) contrairement aux anticorps anti-V3 du VIH-1, les anticorps anti-V3 de SIV sont incapables de neutraliser le virus SIV suggérant des fonctions différentes pour cette région chez HIV-1 et SIV. Dans la troisième partie, nous avons montré que l'attachement du virus VIH sur son récepteur s'accompagne de l'activation de la voie PKC dont l'isoforme PKC-d. L'inhibition de cet isoforme bloque totalement la réplication virale. Ce blocage semble s'opérer en interférant avec les étapes post-entrée du virus en inhibant la formation des pseudopodes et des filaments d'actine, structure nécessaire pour l'étape de la transcription inverse.

L'utilisation de la thérapie génique du cancer est limitée actuellement par la faible efficacité de transfection, la durée d'expression du gène et la toxicité des vecteurs. Ces difficultés ont guidé l'orientation de mes travaux dans 3 directions:<br />1/ Utilisation de gènes codant pour des glycoprotéines fusogeniques (FMG) comme gènes suicides à fort effet bystander. <br />2/ La vectorisation de siRNA in vivo par le vecteur polycationiques : polyethylenimine (PEI).<br />3/ La stabilisation de l'expression du transgène à long terme in vivo à l'aide du transposon Sleeping Beauty (SB).<br /><br /> Les résultats de ces travaux montrent que :<br /> 1/ La thérapie génique basée sur l'utilisation de FMG montre un fort intérêt thérapeutique sur des cellules de cancer du poumon humain in vitro et in vivo. En effet, ces protéines FMG ont i/ un fort effet cytotoxique qui passe essentiellement par la fusion entre la cellule transfectée et de nombreuses cellules voisines non-transfectées, ii/ la capacité d'induire une immunité antitumorale induite par la libération des vésicules immunogènes au cours de la mort des cellules fusionnées. Trois FMG ont été testées: GALV, HERV-W et RD. Dans les 3 cas nous avons montré que la transfection de ~1% des cellules in vitro conduit à la formation de large syncytia et à la mort de 25 à 80% des cellules en culture en moins de 5 jours. Le traitement des tumeurs sous-cutanées implantées chez des souris nudes induit une réduction du poids des tumeurs pouvant aller jusqu'à 70% alors que l'efficacité de transfection par injection directe des plasmides dans la tumeur est extrêmement faible (≤1%). Ces résultats démontrent que ces protéines FMG possèdent un potentiel intéressant pour la thérapie génique du cancer. Néanmoins, notre modèle de souris immunodéficient ne nous a pas permis de mesurer l'impact supplémentaire que nous pouvions attendre de la stimulation de la réponse antitumorale activée par la production de syncytiosomes. Cette étude est encore en cours. <br /> 2/ La vectorisation de polyplexes PEI/siRNA in vivo par voie intraveineuse, intrapéritonéale ou sous-cutané avec différentes formulations a montré des résultats faiblement positifs au mieux et souvent peu reproductibles. Nous avons étudié la biodistribution en temps réel de ces complexes en imagerie de fluorescence et mesuré leur capacité à inhiber l'expression d'un gène reporter ou d'un oncogène dans les poumons et/ou les tumeurs des souris. Globalement ces résultats démontrent que le PEI n'est pas un vecteur efficace pour les siRNA dans une approche systémique et que des modifications chimiques sur le PEI et/ou les siRNA devront être envisagées pour augmenter la stabilité et la performance de ces particules.<br /> 3/ L'insertion du transposon SB dans le plasmide vectorisé, complexé à du PEI et injecté en intraveineux, permet de stabiliser l'expression du transgène pendant plus de 4 mois dans les poumons. La mesure en cinétique à long terme du gène reporter dans les poumons montre en effet une forte expression du gène reporter codant pour la luciférase 1 jour après la transfection. Cette expression disparaît rapidement durant les 2 semaines suivantes jusqu'à devenir indétectable. De façon intéressante, le signal luciférase se rétablit ensuite progressivement pour atteindre un plateau 2 mois après la transfection. Le niveau d'intensité du signal de luciférase est alors d'environ 15% de celui mesuré le premier jour. Ces résultats suggèrent que le tansposon SB permet une insertion stable du transgène dans un nombre très restreint de cellules pulmonaires ayant la capacité de se multiplier. Ce résultat est prometteur et offrira une plate-forme d'intérêt qui permettra de vectoriser des gènes codant pour des protéines biologiquement actives, telles que celle codée par le gène CFTR (cystic fibrosis transmembrane conductance regulator) pour la thérapie de la mucoviscidose, ou le gène K-Ras pour l'analyse de l'oncogenèse ras-dépendante dans le cancer du poumon. Enfin, les cellules touchées par l'insertion stable du transposon ayant un pouvoir de régénération du poumon important, il semble que nous ayons un moyen de modifier génétiquement des cellules souches pulmonaires. Nous souhaitons donc maintenant les caractériser précisément car cela ouvre des perspectives thérapeutiques importantes.

Ce travail de thèse a permis d'établir la carte d'identité de nanoparticules développées au laboratoire, les nanocapsules lipidiques. En effet, nous avons caractérisé les nanocapsules lipidiques par diffusion dynamique de la lumière mais aussi par diffusion des neutrons aux petits angles : ces expériences nous ont permis de démontrer que ces particules possèdent une structure coeur-couronne ; le coeur étant composé de triglycérides et la couronne d'un mélange de tensio-actifs. Nous avons aussi démontré que la couronne est une monocouche mixte de tensio-actifs à l'interface huile/eau. A partir de cette structure, nous avons développé deux méthodes de modification post-formulation des nanoparticules initiales afin d'obtenir des nanocapsules lipidiques multifonctionnelles. La première méthode est la post-insertion, initialement développée sur les liposomes ; la deuxième méthode est basée sur une réaction de transacylation entre les tensio-actifs des nanocapsules lipidiques et des substrats d'intérêt pharmaceutique et technologique. Ensuite, nous avons démontré que ces nanocapsules lipidiques multifonctionnelles possédaient de nouvelles propriétés, comme la capacité à délivrer des principes actifs hydrophiles comme des petits ARN d'interférence (siRNA).

<p>In this thesis, chitosan, a biocompatible polysaccharide that has been approved as a food additive was selected as a platform for the development of safe, efficient non-viral gene delivery systems to mammalian cells. Previously, chitosan-based gene formulations had been generally associated with high molecular weight chitosans, which were poorly characterised in terms of molecular weight distribution and degree of acetylation. Therefore, in order to improve the properties of chitosan-based gene formulations, the research associated with this thesis focused on establishing the structure-property relationships of well-defined, low molecular weight chitosans (chitosan oligomers) as delivery systems for nucleic acids (pDNA and siRNA)<i> in vitro</i> and after lung administration <i>in vivo</i>. pDNA dissociated more easily from chitosan oligomers than from conventional high molecular weight chitosans, resulting in a faster onset and higher levels of<i> in vivo</i> gene expression, comparable to those mediated by polyethyleneimine (PEI), one of the most efficient non-viral delivery systems. Coupling of a trisaccharide branch to the chitosan oligomers so as to target extracellular lectins resulted in a significant improvement in transfection efficiency because of enhanced cellular uptake and colloidal stability. In contrast to pDNA, longer linear chitosan oligomers were required to form physically-stable nanoparticles with siRNA that mediated efficient, sustained gene silencing <i>in vitro</i>. Finally, the use of an optimised catheter device for the nebulisation of small volumes of pDNA formulations resulted in improved dose precision and lung distribution<i> in vivo</i> compared with conventional intratracheal instillation. In conclusion, chitosan oligomers are interesting and viable alternatives to other non-viral gene delivery systems.</p>

Sequence-specific small interfering RNA (siRNA) duplexes can be used for gene silencing in mammalian cells and as mechanistic probes for determining gene function. Transfection of siRNA for specificity protein 1 (Sp1) in MCF-7 or ZR-75 cells decreased Sp1 protein in nuclear extracts, and immunohistochemical analysis showed that Sp1 protein in transfected MCF-7 cells was barely detectable. Decreased Sp1 protein in MCF-7 was accompanied by a decrease in basal and estrogen-induced transactivation and cell cycle progression. These results clearly demonstrate the key role of Sp1 protein in regulating growth and gene expression of breast cancer cells. The aryl hydrocarbon (AhR) is a ligand-activated nuclear transcription factor. siRNA for the AhR decreased TCDD-induced CYP1A1 protein, CYP1A1dependent activity, and luciferase activity in cells transfected with an Ah-responsive construct. 17β-Estradiol (E2) induces proliferation of MCF-7 cells, and this response is inhibited in cells cotreated with E2 plus TCDD. The effects of TCDD on E2-induced cell cycle progression were partially blocked in MCF-7 cells transfected with siRNA for AhR. The decrease in AhR protein in MCF-7 cells was also accompanied by increased G0/G1 → S phase progression. Surprisingly, TCDD alone induced G0/G1 → S phase progression and exhibited estrogenic activity in MCF-7 cells transfected with siRNA for the AhR. In contrast, degradation of the AhR in HepG2 liver cancer cells resulted in decreased G0/G1 → S phase progression, and this was accompanied by decreased expression of cyclin D1, cyclin E, cdk2 and cdk4. In the absence of ligand, the AhR exhibits growth inhibitory (MCF-7) and growth promoting (HepG2) activity that is cell context-dependent. Sp family proteins play a complex role in regulation of pancreatic cancer cells growth and expression of genes required for growth, angiogenesis and apoptosis. Sp1, Sp3 and Sp4 cooperatively activate VEGF promoter constructs in these cells; however, only Sp3 regulates cell proliferation. siRNA for Sp3 inhibits phosphorylation of retinoblastoma protein, blocks G0/G1 → S phase progression of Panc-1 cells, and upregulates p27 protein/promoter activity. Thus, Sp3 plays a critical role in angiogenesis (VEGF upregulation) and the proliferation of Panc-1 cells by a novel mechanism of Sp3-dependent suppression of the cyclin-dependent kinase inhibitor p27.

In this thesis, chitosan, a biocompatible polysaccharide that has been approved as a food additive was selected as a platform for the development of safe, efficient non-viral gene delivery systems to mammalian cells. Previously, chitosan-based gene formulations had been generally associated with high molecular weight chitosans, which were poorly characterised in terms of molecular weight distribution and degree of acetylation. Therefore, in order to improve the properties of chitosan-based gene formulations, the research associated with this thesis focused on establishing the structure-property relationships of well-defined, low molecular weight chitosans (chitosan oligomers) as delivery systems for nucleic acids (pDNA and siRNA) in vitro and after lung administration in vivo. pDNA dissociated more easily from chitosan oligomers than from conventional high molecular weight chitosans, resulting in a faster onset and higher levels of in vivo gene expression, comparable to those mediated by polyethyleneimine (PEI), one of the most efficient non-viral delivery systems. Coupling of a trisaccharide branch to the chitosan oligomers so as to target extracellular lectins resulted in a significant improvement in transfection efficiency because of enhanced cellular uptake and colloidal stability. In contrast to pDNA, longer linear chitosan oligomers were required to form physically-stable nanoparticles with siRNA that mediated efficient, sustained gene silencing in vitro. Finally, the use of an optimised catheter device for the nebulisation of small volumes of pDNA formulations resulted in improved dose precision and lung distribution in vivo compared with conventional intratracheal instillation. In conclusion, chitosan oligomers are interesting and viable alternatives to other non-viral gene delivery systems.

RNA is a highly versatile molecule with functions that span from being a messenger in the transfer from DNA to protein, a catalytic molecule important for key processes in the cell to a regulator of gene expression. The post-genomic era and the use of new techniques to sequence RNAs have dramatically increased the number of regulatory RNAs during the last decade. Many of these are antisense RNAs, as for example the miRNA in eukaryotes and most sRNAs in bacteria. Antisense RNAs bind to specific targets by basepairing and thereby regulate their expression. A major step towards an understanding of the biological role of a miRNA or an sRNA is taken when one identifies which target it regulates. We have used RNA libraries to study the RNA interference pathway during development in the unicellular model organism Dictyostelium discoideum. We have also, by combining computational and experimental methods, discovered the first miRNAs in this organism and shown that they have different expression profiles during development. In parallel, we have developed a novel approach to predict targets for sRNAs in bacteria and used it to discover sRNA/target RNA interactions in the model organism Escherichia coli. We have found evidence for, and further characterized, three of these predicted sRNA/target interactions. For instance, the sRNA MicA is important for regulation of the outer membrane protein OmpA, the sRNAs OmrA and OmrB regulate the transcription factor CsgD, which is important in the sessile lifestyle of E. coli, and MicF regulates its own expression in a feed forward loop via the regulatory protein Lrp. In conclusion, we have discovered novel antisense RNAs, e.g. miRNAs in D. discoideum, developed an approach to identify targets for antisense RNAs, i.e. a target prediction program for sRNAs in bacteria, and verified and characterized some of the predicted antisense RNA interactions.

<p>Borane (BH<sub>3<sub>) chemistry offers unique chemical characteristics that enable boranophosphate (BP) oligonucleotides with potential to enhance RNA therapeutic applications such as RNA interference (RNAi) and RNA aptamers. Further, BP nucleotides are substrates for RNA polymerases which allow the enzymatic synthesis of stereoregular boranophosphate (BP)-RNA molecules of different lengths and properties. We expect that these BP-RNAs will interact in a novel way with the desired target molecules because they can coordinate with a diverse array of ligand sites in proteins or other RNA molecules. This is due to the distinct hydrophobicity, sterospecificity, and polarity properties imparted by the phosphorus-boron (P-B) chemical bond compared to the natural phosphorus-oxygen (P-O) bond. </p><p>The object of this dissertation is to explore the therapeutic applications of the BP-RNA such as siRNA, RNA aptamers, and in addition investigate the immunogenicity of this modification. We used mouse cells to determine if BP-RNA would activate toll-like receptor (TLR 7), which is involved in innate immune response to foreign single stranded RNA (ssRNA). This response is undesired when applied to oligonucleotide therapeutics such as siRNA and RNA aptamers. In terms of RNAi, it would be an advantage to have low immunogenicity and high downregulation activity by the siRNA. To determine the innate immune activation of the BP-RNA through the TLR 7 we used a known activator, the human immunodeficiency virus (HIV) derived single-stranded RNA (ssRNA40) and measured the production of cytokines as a function of the number of modified BP-linkages. The production of cytokines IL-6 and TNF&#945; was quantified after the boranophosphate (BP), phosphorothioate (PS) or natural ssRNA40 were transfected into murine macrophage Raw264.7 cells. Natural and phosphorothioate RNA (PS-RNA) have been shown to be activators of TLR 7 receptors. In contrast, we found that fully modified BP- ssRNA40 did not activate TLR 7. This is relevant in oligonucleotide applications such as siRNA and RNA aptamers where off-target effects such as immune activation after administration are not desired. </p><p>Subsequently, the low immune activation would be an advantage when coupled to RNAi activity of the oligonucleotide. Thus, we explored whether BP modified siRNA molecules would modulate gene expression and if there was an effect on downregulation activity when increasing the number of BH3 modifications on the phosphate backbone. Our therapeutic model was the multi-drug resistance 1 (MDR1) gene that expresses P-glycoprotein (P-gp), which has been notoriously difficult to modulate. The aberrant regulation of genes such as MDR1 in cancer cells are a major cause of chemotherapeutic treatment failure against human cancers. Hence, controlling the expression of cancer genes with antisense technology is a possible cancer therapy. Specifically, correcting the overexpression of p-glycoprotein using modified siRNAs that target and degrade the P-glycoprotein mRNA produced by the MDR1 gene. We found that there is a reduction of siRNA activity with an increasing number of BP-modifications. It appears that there is a fine balance between lack of immune response and gene downregulation when applied to BP-siRNA. </p><p>Finally, we compared the enrichment during the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method of two libraries, one BP-RNA (U&#945;B) compared to a doubly-modified RNA (2'FC & U&#945;B), against a human thrombin. Aptamers modulate protein activity and interfere with protein signaling by binding to the desired protein with high affinity and specificity leading to their use in therapeutic applications where protein activity needs to be controlled or it is anomalous. In the case of blood coagulation, thrombin plays a central role in coagulation signaling cascade and it is a good target to use to control blood coagulation in clinical settings. We attempted to optimize the selection of BP- RNA aptamers through 4-8 rounds of SELEX against the protein thrombin. We found that the selection conditions were not optimal for BP-RNA SELEX possibly due to non-specific binding to a bovine serum albumin (BSA) in the selection buffer.</p> / Dissertation

Tomato bushy stunt virus (TBSV) provides a good model system to investigate molecular virus-host interactions in plants. P22 and P19 proteins encoded by TBSV contribute to multiple invasion-associated functions. Green fluorescence-mediated visualization of TBSV invasion in this study suggests that virus exit from inoculated epidermal cells is a crucial event. Close examination of one P22 mutant showed that it had lost the capacity to move between epidermis and mesophyll which was possibly due to an altered subcellular localization. P19 is a potent suppressor of RNA interference (RNAi) in various systems by forming dimers that bind 21-nucleotide (nt) duplex siRNAs (short interfering RNAs), to affect the programming of the RNA-induced silencing complex (RISC). P19 is attractive for biotechnological and research purposes to prevent RNAi of certain value-added genes in plants. To obtain a good plant-based expression platform, a suppression-active mutant P19 was expressed in transgenic N. benthamiana lines. This is the first example of P19 accumulating to detectable levels in a transgenic plant and initial results suggest it is actively suppressing RNAi. Furthermore, to investigate the correlation between siRNA binding of P19 and its various biological roles, predicted siRNA-interacting sites of TBSV P19 were modified, and the corresponding TBSV mutants were used to inoculate plants. Substitutions on siRNA-contact sites on the central domain of P19 resulted in more severe symptoms in N. benthamiana compared to those affecting peripheral regions. All tested combinations of siRNA-binding mutations were associated with reduced accumulation of total TBSV-derived siRNAs, and loss of siRNA sequestration by P19. Additionally, some modifications were found to cause RNAi-mediated disappearance of viral and host materials in N. benthamiana but not in spinach. In conclusion, exit out of epidermal cells is a key host range determinant for TBSV and particular amino acids on P22 may influence this by regulating the proper subcellular localization. Mutant P19 transgenic plants were successfully established with minor physiological effects to be applied as a platform to study RNAi and to over-express proteins. Finally, a compromised P19-siRNA binding impacts symptom development, systemic invasion, integrity of virus plus host RNA and proteins, and that all in a hostdependent manner.

Resistance to anticancer drugs is a serious obstacle to cancer chemotherapy. A common form of multidrug resistance (MDR) is caused by the overexpression of transmembrane transporter proteins P-glycoprotein and MRP1, encoded by MDR1 and MRP1 genes, respectively. These proteins lead to reduced intracellular drug concentration and decreased cytotoxicity by means of their ability to pump the drugs out of the cells. Breast cancer tumor resistance is mainly associated with overexpression of P-gp/MDR1. Although some chemical MDR modulators aim to overcome MDR by impairing the function of P-gp, they exhibit severe toxicities limiting their clinical relevance. Consequently, selective blocking of the expression of P-gp/MDR1 specific mRNA through RNA interference strategy may be an efficient tool to reverse MDR phenotype and increase the success of chemotherapy. Aim of this study was re-sensitizing doxorubicin resistant breast cancer cells to anticancer agent doxorubicin by selective downregulation of P-gp/MDR1 mRNA. The effect of the selected MDR1 siRNA and MRP1 expression after MDR1 silencing was determined by qPCR analysis. XTT cell proliferation assay was performed to v determine the effect of MDR1 silencing on doxorubicin sensitivity.Intracellular drug accumulation and localization was investigated by confocal laser scanning microscopy after treatment with MDR1 siRNA or other MDR modulators / verapamil or promethazine. The role of P-gp in migration characteristics of resistant cells was evaluated by wound healing assay. The results demonstrated that approximately 90% gene silencing occurred by the selected siRNA targeting MDR1 mRNA. However the level of MRP1 mRNA did not change after MDR1 downregulation. Introduction of siRNA resulted in about 70% re-sensitization to doxorubicin. Silencing of P-gp encoding MDR1 gene resulted in almost complete restoration of the intracellular doxorubicin accumulation and re-localization of the drug to the nuclei. Despite the considerably high concentration of the modulators, verapamil and promethazine were not as effective as siRNA for reversal of the drug efflux. According to wound healing assay, MDR1 silencing did not have any effect on migration characteristics of resistant cells, that is, P-gp expression does not seem to affect the motility of the cells. Selected siRNA duplex was shown to effectively inhibit MDR1 gene expression, restore doxorubicin accumulation and localization, and enhance chemo-sensitivity of resistant cells, which makes it a suitable future candidate for therapeutic applications.