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Cancer is the second leading cause of death in America. In 2018, there were 9.5 million deaths due to cancer according to the International Agency for Research on Cancer (IARC), and this number is expected to grow to 16.3 million by 2040. Among the type of cancers, neuroblastoma and nerve tissue cancers have a 5-year survival rate of 33%, which is very low. One of the main issues linked to such situations is due to the lack of specificity in removing tumor cells. While clinical therapies work to reduce tumor mass as much as possible, they cannot always target all of them, and once some cancer cells are left behind, they regrow and spread. The work of this thesis seeks to enhance the treatment outcome by utilizing all-trans retinoic acid (ATRA), a metabolite of vitamin A, to induce differentiation of nerve tissue cancer cells and eliminate their ability to self-renew (reemerge). Differentiation therapy is currently utilized in select clinical applications but the utilization of ATRA is limited due to its poor solubility in the blood, low bioavailability, short half-life, and in vivo toxicity. In order to alleviate some of these issues, the ATRA molecule was engineered with a novel cell penetrating peptide and tested for its efficacy. Data and results presented herein report the differentiation induced by the CPP-conjugated ATRA may act as a viable method for neuroblastoma treatment. / Bioengineering

Liver transplantation is the only life-saving treatment for patients with end-stage liver disease; however, organ availability is insufficient to meet demands. Steatotic livers are extended criteria donor (ECD) organs that could be used for transplantation if not for an increased susceptibility ischemia reperfusion injury (IRI). Heme oxygenase-1 is a gene, that when upregulated has be shown to reduce IRI in animal models of transplantation. Increasing HO-1 activity in steatotic livers by delivery of a functional cell-penetrating HO-1 protein (through the use of cell-penetrating peptides) may provide protection against IRI, making these organs useful for transplantation. The purpose of this thesis was the generation and testing of a cell-penetrating HO-1 protein. HO-1 and EGFP gene sequences were cloned into the pET-28B(+) vector in frame with a CPP or TAT sequence. Resulting plasmids were cloned into E. coli, and protein expression was induced using IPTG. Proteins were purified using Ni-NTA affinity chromatography under denaturing and non-denaturing conditions. Non-denatured proteins were tested for HO-1 activity and the ability of both denatured and non-denatured proteins to transduce cells in vitro was tested by fluorescence microscopy. The cell-penetrating ability of nondenatured proteins was further tested in J774, HepG2 and HUVEC cells using immunofluorescence. Five HO-1 and two EGFP cell-penetrating proteins were generated expressed and purified successfully. Purified non-denatured HO-1 retains its enzymatic activity. Non-denatured CPP-EGFP and CPP-HO1 penetrated cells more effectively than their denatured counterparts. CPP-EGFP and CPP-HO1 proteins are able to penetrate multiple cell types in vitro. Successful generation and testing of a cell-penetrating HO-1 protein, for use in an animal model of steatotic liver transplantation. This protein demonstrates promise for use as a potential therapeutic agent in the field of liver transplantation.

Regulation of biological processes through the use of genetic elements is a central part of biological research and also holds great promise for future therapeutic applications. Oligonucleotides comprise a class of versatile biomolecules capable of modulating gene regulation. Gene therapy, the concept of introducing genetic elements in order to treat disease, presents a promising therapeutic strategy based on such macromolecular agents. Applications involving charged macromolecules such as nucleic acids require the development of the active pharmaceutical ingredient as well as efficient means of intracellular delivery. Cell-penetrating peptides are a promising class of drug delivery vehicles, capable of translocation across the cell membrane together with molecules otherwise unable to permeate cells, which has gained significant attention. In order to increase the effectiveness of cell-penetrating peptide-mediated delivery, further understanding of the mechanisms of uptake is needed in addition to improved design to make the cell-penetrating peptides more stable and, in some cases, targeted. This thesis encompasses four scientific studies aimed at investigating cell-penetrating peptide and oligonucleotide designs amenable to therapeutic applications as well as elucidating the mechanisms underlying uptake of cell-penetrating peptide:oligonucleotide nanoparticles. It also includes an example of a therapeutic application of cell-penetrating peptide-mediated delivery of oligonucleotides. Paper I presents a study evaluating a range of chemically modified anti-miRNAs for use in the design of therapeutic oligonucleotides. All varieties of oligonucleotides used in the study target miRNA-21 and are evaluated using a dual luciferase reporter system. Paper II introduces a novel cell-penetrating peptide, PepFect15, aiming at combining the desirable properties of improved peptide stability and efficient cellular uptake with a propensity for endosomal escape, to produce a delivery vector well suited for delivery of oligonucleotides. The performance of this new cell-penetrating peptide was evaluated based on its delivery capabilities pertaining to splice-correcting oligonucleotides and anti-miRNAs. Paper III investigates the involvement of scavenger receptor class A in the uptake of various cell-penetrating peptides together with their oligonucleotide cargo. Finally, paper IV aims at using cell-penetrating peptide-mediated delivery to improve the efficiency of telomerase inhibition by antisense oligonucleotides targeting the telomerase enzyme ribonucleotide component. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

La mucoviscidose est une maladie génétique létale induite par des mutations du canal ionique CFTR, provoquant une perte de sa fonctionnalité au niveau des tissus épithéliaux de divers organes. Le poumon est particulièrement touché et devient sujet à des infections bactériennes chroniques. Dans le but de traiter la maladie, nous avons développé des « stabilisateurs » de la protéine CFTR : il s’agit de peptides inhibant l’interaction de la protéine CFTR avec le médiateur-clé de sa demi-vie à la membrane apicale des cellules épithéliales, la protéine CAL. En particulier, le peptide iCAL36 a démontré une hausse de fonctionnalité de la protéine CFTR mutée. Le but de cette thèse a été de renforcer cet effet biologique en améliorant ses caractéristiques pharmacologiques : pénétration cellulaire (vectorisation), stabilité métabolique et affinité pour la protéine CAL.Le premier axe d’optimisation a été l’internalisation du peptide iCAL36 par 7 différents peptides vecteurs (CPP). Les conjugués correspondants ont été évalués suivant leur cytotoxicité, leur efficacité d’internalisation et leur capacité à maintenir cette efficacité en présence de sérum. Le mécanisme d’entrée des deux meilleurs conjugués a ensuite été étudié. Divers biais couramment rencontrés lors de l’analyse de l’efficacité d’internalisation de peptides vecteurs par des méthodes de fluorescence ont également été identifiés et expliqués. La séquence du peptide iCAL36 a ensuite été modulée par inclusion d’acides aminés non-naturels. Le criblage des interactions peptide/protéine a été réalisé par une procédure optimisée dans le cadre de cette thèse (méthode PIPEPLUS) et a permis d’identifier 32 analogues prometteurs de la séquence d’iCAL36 incluant différentes substitutions. En particulier, une des séquences identifiées (iCAL-Q27) a démontré une affinité 70 fois supérieure à celle du peptide iCAL36 pour la protéine CAL, indiquant une inhibition plus complète de l’interaction CAL/CFTR.Ces résultats majeurs permettent dans leur ensemble de développer des « stabilisateurs » peptidiques de seconde génération pouvant avoir un effet biologique accru dans le contexte de la mucoviscidose. / Cystic fibrosis is a lethal disease induced by genetic mutations of the CFTR chloride channel, leading to a loss of its function in the epithelial tissues of various organs. The lung is particularly affected and becomes a target for chronical bacterial infections. To cure the disease, we developed so-called CFTR “stabilizers”, which are peptides inhibiting the interaction between the CFTR protein and the key mediator of its half-life at the apical membrane of epithelial cells, the CAL protein. In particular, the iCAL36 peptide showed an increase of the functionality of the mutated CFTR protein. The aim of this thesis was to increase this biological effect by improving its pharmacological parameters: cellular internalization (vectorization), metabolic stability and affinity for the CAL protein.The first axis of optimization was the internalization of the iCAL36 peptide by 7 different cell-penetrating peptides (CPP). The corresponding conjugates were evaluated upon their cytotoxicity, their uptake efficiency and their capacity to maintain this efficiency in the presence of proteases. The mechanism of entry of the two best candidates was then studied. Various bias frequently encountered during the analysis of CPP uptake efficiency by fluorescence methods were also identified and explained. Afterwards, the iCAL36 sequence was modulated by inclusion of non-natural amino acids. The screening of the peptide/protein interactions was performed by a method optimized during this thesis (PIPEPLUS process) and allowed the identification of 32 promising analogues of the iCAL36 sequence including several substitutions. In particular, one of these sequences (iCAL-Q27) showed an affinity 70 times stronger for the CAL protein compared to iCAL36, hinting a more complete inhibition of the CAL/CFTR interaction.Overall, these major results grant the access to second-generation “stabilizers” potentially showing an improved biological effect in the context of cystic fibrosis.

L'interférence ARN est un processus biologique permettant la dégradation d'un ARN messager par un ARN double brin de courte taille spécifique de cet ARNm. Elle a un potentiel d'application en thérapie antivirale pour peu que les ARN interférents (ARNi) soient délivrés efficacement in vivo. Dans le genre Morbillivirus, on trouve des pathogènes importants en santé publique et vétérinaire tels que le virus de la rougeole et les virus de la peste des petits ruminants (PPR) et de la peste bovine. Il n'existe aucun traitement contre les infections à morbillivirus. L'objectif de ce travail était d'évaluer la possibilité d'administrer in vivo un ARNi actif contre le virus PPR in vitro. Une formulation basée sur des liposomes complexés avec des ARNi ou un adénovirus non réplicatif exprimant des ARN courts en tête d'épingle (shARN) ont été testés chez des chèvres dans un modèle d'épreuve infectieuse avec une souche virulente de PPR. Les différences observées n'étaient cependant pas significatives au plan statistique. Pour améliorer la délivrance par vecteur viral, nous avons comparé un autre vecteur de type baculovirus qui s'est avéré plus efficace in vitro que l'adénovirus précédent. Par ailleurs, nous avons testés in vitro également deux peptides capables de pénétrer dans les cellules. L'un d'entre eux, le Perfect 6 (PF6) a presque complètement inhibé l'expression du gène de la nucléoprotéine par le virus PPR. En revanche, l'autre (PF14) a été moins efficace mais a relativement mieux résisté à l'inhibition de son activité par la présence de fortes concentrations de sérum dans le milieu. Dans le but d'évaluer in vivo ces nouveaux systèmes de délivrance en s'affranchissant du modèle chèvre lourd et couteux à mettre en œuvre, nous avons initié une stratégie de mise au point d'un modèle non infectieux de suivi dynamique de l'interférence ARN chez la souris par imagerie in vivo. Dans ce travail, nous montrons qu'il est possible de mesurer et de standardiser l'expression d'un gène rapporteur comprenant une séquence du virus PPRV et ensuite de quantifier le niveau de dérégulation de l'expression induit par un ARNi dirigé contre le virus PPR. Après calibration, ce modèle est désormais pour tester différents systèmes de délivrance de siRNA chez la souris / RNA interference (RNAi) is the process of mRNA degradation that is induced by double-stranded RNA in a sequence-specific manner. RNAi has a potential of developing into an effective and specific antiviral therapy if small interfering RNAs (siRNAs) can be efficiently delivered in vivo. Morbillivirus genus includes important pathogens of humans and animals, which include measles virus, peste des petits ruminants virus (PPRV) and rinderpest virus. No treatment exists for morbillivirus diseases. The aim of this work was the in vivo delivery of siRNA against PPRV infection. The delivery of siRNA by a liposome and short hairpin RNA (shRNA) by means of a replication deficient adenovirus was tested in goats which were later challenged with PPRV. However, significant therapeutic effects were not obtained. To find more efficient vectors, the PPRV inhibition efficiency of recombinant replication deficient adenovirus and a baculovirus expressing shRNA against nucleoprotein of PPRV were compared in vitro. The baculoviral vector was found to be more efficient. Similarly, two cell penetrating peptides (CPPs) were also compared and PepFect6 (PF6) could deliver siRNA NPPRV1 effectively in vitro resulting in an almost complete inhibition of N gene expression by PPRV. Another CPP, the PF14 though with lower transfection efficiency in vitro, was found to be relatively serum resistant compared to PF6. A small animal model for PPRV infection does not exist. Due to economic, ethical, and biosecurity issues involved with use of small ruminants, a strategy based on the use of a non-infectious mouse model and a dynamic follow up of siRNA treatment by live imaging was developed. We show in this work that it is possible to measure and standardize the expression of a bioluminescent reporter gene containing a PPRV sequence and thus, to quantify a down-regulation of such gene by siRNA against PPRV. After some calibration, siRNA delivery can now be tested in this mouse model for comparing various delivery vectors in vivo.

L'utilisation des oligonucléotides antisens PMO ou PNA, pour corriger les erreurs d'épissage par blocage stérique, constitue une nouvelle stratégie prometteuse pour réguler l'expression génétique. Ces ON peuvent mener au traitement de maladies comme la β-thalassémie, la dystrophie musculaire de Duchenne (DMD) ou les cancers. Cependant leur développement clinique requiert un système de délivrance efficace. Les peptides cationiques (CPPs) sont caractérisés par leur capacité à s'internaliser dans les cellules eucaryotes. Cependant leur efficacité à promouvoir la délivrance cytoplasmique et nucléaire des ON est limitée par leur séquestration dans des vésicules d'endocytose, ce qui est à l'origine de la dégradation du matériel internalisé. Nous avons contribué à l'étude du trafic intracellulaire et de l'activité dans un essai de correction d'épissage de plusieurs familles de CPPs capables de délivrer efficacement des analogues d'ON à des doses non toxiques et en absence d'agents endosomolytiques. Nos études mécanistiques indiquent que ces constructions (covalentes ou non covalentes) CPP-ON sont endocytées par la voie clathrine, que la ségrégation dans les endosomes reste une limitation et qu'il existe une bonne corrélation entre leur activité biologique et leur capacité à déstabiliser les membranes endosomales. / The use of antisense oligonucleotides PMO or PNA to correct splicing errors by steric- block represents a new promising therapeutic strategy. These ONs lead to the treatment of diseases such as β-thalassemia, Duchenne muscular dystrophy (DMD) or cancers. However their functional success requires efficient delivery. Cationic cell penetrating peptides (CPPs) are characterized by their ability to be internalized in eukaryotic cells. However their efficiency in promoting cytoplasmic and nuclear delivery of ON has been hampered by endocytic sequestration and subsequent degradation of internalized material in endocytic vesicles, which is responsible for the degradation of internalized material. We have contributed to the study of intracellular trafficking and activity (using splicing correction assay) of several families of CPPs capable of delivering effective analogs ON at nontoxic doses and in the absence of agents endosomolytic. Our mechanistic studies indicate that these constructs (covalent or noncovalent) CPP-ON are internalized through clathrin, that segregation in endosomes remains a limitation and that there is good correlation between biological activity and their ability to destabilize endosomal membranes.

Le transport de substances dotées de propriétés pharmacologiques au travers de la membrane plasmique ainsi que leur accès aux divers compartiments intracellulaires, en particulier le compartiment cytoplasmique et nucléaire, demeure un obstacle pour la recherche biotechnologique et biomédicale et pour l'industrie pharmaceutique. Parmi les moyens actuellement connus pour introduire des substances dans les cellules, les peptides de translocation également dénommés CPPs (Cell- Penetrating-Peptides) qui représentent des vecteurs particulièrement intéressants. Dans le présent travail, nous avons utilisé trois CPPs, Tat, penétratine et un analogue de la maurocalcine (MCaAbu) pour la délivrance de la doxorubicine (Dox), une drogue utilisée en chimiothérapie anticancéreuse et dont son effet est limité par la résistance des cellules tumorales. Afin d'évaluer l'efficacité des trois complexes formés (Dox-CPPs), deux modèles cellulaires du cancer mammaire ont été utilisés; les cellules MDA-MB 231 et les cellules MCF7 qui présentent une sensibilité différente à la drogue seule. Notre étude nous a permis de monter en premier lieu que les trois CPPs utilisés représentent de puissants vecteurs pour l'entrée de la Dox à l'intérieur des cellules et que la conjugaison de la drogue a contourné la résistance des cellules MDA-MB 231 à la Dox. Nous avons également montré que la distribution de la Dox est plutôt nucléaire à l'état libre et cytoplasmique lorsqu'elle est couplée aux CPPs. Dans la deuxième partie de notre travail, nous avons montré que la Dox ainsi que les Dox-CPPs induisent l'apoptose des cellules MDA-MB 231 et que cet effet est observé en traitant les cellules avec une dose cinq fois plus faible de Dox-CPPs par rapport à la Dox. Cette mort est dépendante des caspases et implique la voie mitochondriale. De plus, l'apoptose induite par la Dox est médiée par les radicaux oxygénés (ROS). Ceux-ci sont en partie impliqués lors de l'apoptose induite par les Dox-CPPs puisque l'utilisation d'un inhibiteur de ROS inhibe partiellement l'apoptose induite par ces composés. Nous avons montré également que la surexpression de Bcl-2 protège l'apoptose induite par la Dox et partiellement par les Dox-CPPs, ce qui suggère qu'une autre voie est impliquée dans l'apoptose induite par les Dox-CPPs et qui expliquerait la plus forte toxicité de ces composés. Concernant cette deuxième voie nous avons pu montré que les récepteurs de mort TRAIL sont bien impliqués dans l'apoptose induite par les Dox-CPPs via la clustérisation membranaire des récepteurs de mort DR4 et DR5. Cette clustérisation modifie le taux d'expression de ces récepteurs membranaires et à l'origine d'une sensibilisation des cellules MDA-MB 231 au TRAIL endogène au cours de l'apoptose induite par les Dox-CPPs. Une telle sensibilisation au TRAIL est à l'origine de la génération de céramide, qui constitue une autre voie d'induction d'apoptose par les Dox-CPPs en plus de la voie mitochondriale. L'ensemble de ces résultats devraient nous permettre à valoriser la stratégie de couplage des CPPs à des agents antitumoraux afin d'améliorer leur effet et de mieux comprendre les voies de signalisation de la mort induite suite au couplage. Ceci pourrait à terme conduire à la conception de nouveaux analogues d'index thérapeutique plus élevé. Mots clés : Cell- Penetrating-Peptides, Doxorubicine, résistance cellulaire, apoptose, ROS, récepteurs de mort, céramide.

Development of chimeric, recombinant peptides, proteins and enzymes expands the availability of protein/enzyme–based tools for cellular analysis and new assay platforms. Ideal protein reagents for cellular analysis must translocate into a variety of cells with minimum cell damage, retain stability and biological activity within the cell during analysis, and provide a reliable, measurable signal. This work focused on development, characterization and utilization of chimeric recombinant peptide, protein and enzyme reagents for cellular analysis and immunoassays. A cell-penetrating, fluorescent protein substrate (PKAS) was developed to monitor intracellular protein kinase A activity in cells without the need for cellular transfection. PKAS translocated into HeLa cells, βTC-3 cells and pancreatic islets with minimal toxicity. Upon cellular loading, glucose dependent phosphorylation of PKAS was observed in both βTC-3 and pancreatic islets via capillary zone electrophoresis. In pancreatic islets, maximal PKAS phosphorylation (83 ± 6 %) was observed at 12 mM glucose, whereas maximal PKAS phosphorylation (86 ± 4 %) in βTC-3 cells was with 3 mM glucose indicating a left-shifted glucose sensitivity. A cell-penetrating luciferase chimera (Luc-TAT) and a cell-penetrating phospholipid nanoshell entrapped luciferase (Luc-PPN) was constructed to monitor dynamic changes in intracellular ATP levels in mammalian cells. Upon cellular loading, the activity of Luc-TAT and Luc-PPN was monitored with time. Luc-TAT lost approximately 50% activity within one hour, and decreased rapidly over time. In contrast Luc-PPNs retain approximately 95% activity in 1 hour and 77% after 12 hours showing longer biological lifetime. Luc-PPNs were able to detect dynamic ATP changes in intact HeLa cells in the presence of KCN and NaN3. The bioluminescence returned to background levels within 8-10 minutes after treatment with KCN, whereas NaN₃ showed ~ 40% reduction. Two novel recombinant human parathyroid hormone (hPTH) analogs hPTHEGFP and hPTH-Cys were prepared to develop immunoassays for PTH detection in clinical samples. Initial experiments show promise for these analogs for use in CZELIF based immunoassays. The analogs present a number of distinctive advantages for clinical assays and can be used to develop several immunoassay platforms.

Glioblastoma multiforme is the most aggressive form of malignant brain tumor with poor prognosis. The efficacy of brain cancer treatment by chemotherapeutics is limited by the blood-brain barrier (BBB) which allows less than 2% of the small molecules and blocks almost all the macromolecules to transport into the brain. Delivery of the large molecules such as proteins and nucleic acids across the BBB is a great challenge for brain-targeted drug delivery. To overcome this obstacle, cell-penetrating peptides (CPPs) were used as vectors for delivery of nucleic acids across the BBB targeting glioblastomas. The CPPs have shown such promising carriers to deliver various cargoes ranging from small molecules to large molecules into the cells. This thesis is focused on the development of glioblastoma-targeting vectors based on modifications of the CPPs and the targeting peptides. The peptide-based vectors were developed to improve the transport of the nucleic acids across the BBB and specifically target glioblastomas. In this thesis, a series of peptide-based vectors targeting glioblastomas were synthesized and modified with targeting peptides by either covalent conjugation or non-covalent complex formation. The delivery of plasmid DNA (pDNA) in the complex with the peptide-based vectors was studied in the in vitro model of the BBB. The role of receptors expressed on the BBB was investigated. Scavenger receptors class A and B were found to be expressed on the BBB, and they were involved in the delivery of the pDNA across the BBB model. Moreover, various targeting peptides were modified with hexaglutamate to form non-covalent complexes with the CPPs for small interfering RNA (siRNA) delivery to glioblastoma cells. The non-covalent complex of the CPP and the targeting peptide showed greater gene-silencing efficiency than the consecutively covalent conjugation of the CPP and the targeting peptide for siRNA delivery to glioblastoma cells. Lastly, a number of novel, amphipathic peptides were developed based on the model amphipathic peptide. The prediction of the biological effect of the designed peptides using quantitative structure-activity relationship model showed a correlation with the experimental data. Finally, the CPP-based nucleic acid delivery vectors with homing peptide strategy have a potential for the BBB shuttle and the future use as a glioblastoma-targeted drug carrier in the in vivo studies and the clinical applications. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>