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Die Gentherapie hämatopoetischer Stammzellen (HSCs) besitzt das Potenzial, verschiedene erbliche, nur symptomatisch behandelbare, Erkrankungen dauerhaft zu heilen. Die Mehrheit der aktuell angewandten Verfahren dazu, basiert auf der Isolation von hämatopoetischen Stammzellen, der ex vivo Modifikation dieser Zellen durch retrovirale Vektoren und der Reinfusion der modifizierten Zellen in den immunsupprimierten Patienten. Dieser Ansatz ist mit einer Reihe von Nachteilen verbunden, unter anderem einem teilweisen Verlust des Rekonstitutionsvermögens der Stammzellen nach ex vivo Kultur oder der Gefahr der Transformation durch Integration des retroviralen Vektorgenoms. Darüber hinaus sind aktuelle Gentherapieansätze mit hohen Kosten und großem logistischem Aufwand verbunden, was den Zugang zu diesen Behandlungen für potentielle Patienten stark einschränkt. Die vorliegende Arbeit verfolgt einen neuen Ansatz zur Gentherapie von HSCs, der auf der Mobilisierung von Stammzellen aus dem Knochenmark in den peripheren Blutstrom und der Transduktion dieser Stammzellen mit adenoviralen Vektoren basiert. Hierbei codieren die Vektoren sowohl ein Transgen als auch eine Integrationsmaschinerie. Der erste Teil der Arbeit belegt in einem humanen CD46-transgenen Mausmodell, dass adenovirale Vektoren der ersten Generation in der Lage sind, mobilisierte HSCs im Blut zu transduzieren und dass es den so transduzierten Stammzellen möglich ist, zurück ins Knochenmark zu migrieren und dort das Transgen zu exprimieren. Allerdings wurde im Verlauf von zwei Wochen ein Rückgang der Transgenexpression beobachtet. Um dies zu umgehen, wurde ein adenovirales Vektorsystem der dritten Generation genutzt, das eine hochaktive Sleeping Beauty Transposase, zum Zweck der Transgenintegration, codiert. Dieses System ermöglichte die stabile Genmodifikation mobilisierter hämatopoetischer Stammzellen nach intravenöser Injektion. Die Expression des Transgens konnte über längere Zeitspannen (bis 12 Wochen) beobachtet werden. Die modifizeirten Stammzellen waren darüber hinaus in der Lage, genmodifizierte Kolonien in vitro zu bilden und das hämatopoetische System letal bestrahlter Mäuse nach Knochenmarkstransplantation zu rekonstituieren. Es wurde somit gezeigt, dass HSCs nach in vivo Modifikation weiterhin funktional waren. / The gene therapy of hematopoietic stem cells holds the potential for curative treatment of several otherwise incurable inherited diseases. The majority of current gene therapy treatments relies on the collection of hematopoietic stem cells, their ex vivo modification with retroviral vectors and their transplantation into a myeloconditioned patient. This approach entails several disadvantages, including a reduction of stem cell engraftment potential after ex vivo culture and the potential danger of integrational mutagenesis. In addition, the high costs and complex logistics of this approach limit the access of patients to gene therapeutic regimens. This work explores an alternative approach to hematopoietic stem cell (HSC) gene therapy, termed stem cell in vivo transduction. This approach is based on the mobilization of HSCs from the bone marrow into the peripheral blood and the transduction of the stem cells with adenoviral vectors delivering a transgene as well as a transgene integration machinery. In the first part of this work, it was shown that first-generation adenoviral vectors could be used for the transduction of mobilized HSCs in the periphery of human CD46-transgenic mice. Further, the transduced HSCs were able to home back to the bone marrow and express the transgene. However, over the course of 14 days, a loss of transgene expression in HSCs was observed. To ameliorate these shortcomings, helper-dependent adenoviral vectors encoding a hyperactive Sleeping Beauty transposase for transgene integration were used for stable gene modification of hematopoietic stem cells following intravenous vector administration in mobilized human CD46-transgenic mice. Using this improved vector platform, gene marking of bone marrow HSCs could be observed for extended periods of time (up to 12 weeks). Further, the functionality of the modified HSCs was demonstrated both in colony-forming progenitor assays as well as through the transplantation of gene-modified HSCs into lethally irradiated recipients. Transplantation of modified HSCsled to long-term multi-lineage reconstitution showing that gene-modified stem cells were fully functional. Subsequently the safety of systemic vector administration in mobilized hosts as well as of the Sleeping Beauty-mediated transgene integration was assessed in human CD46- transgenic mice. Lastly, the stem cell in vivo transduction approach was employed in NOG mice transplanted with human CD34+ cells, as well as in Macaca nemestrina non-human primates.

Gynecological cancers present a tremendous disease burden worldwide. Endometrial cancer, the most common gynecological malignancy, is predominantly a disease of deranged glandular function. The mechanisms by which known environmental risk factors influence the mutational profile of endometrial cancer are poorly understood. Non-HPV vulvar cancer, on the other hand, is a very rare gynecological malignancy of vulvar squamous cells with little known about its pathogenesis. Surgical resection of vulvar cancer is associated with high post-surgical morbidity. Pivotal to improving treatment and outcomes for patients with gynecological cancers is an understanding of the molecular drivers unique to each tumor type. To inform our understanding of endometrial gland regulation, I began my investigations with an assessment of normal endometrial adenogenesis in vivo and present the first evidence implicating the necessity of Sox17 in endometrial gland development. My data suggest Sox17 mediates adenogenesis via a non-cell autonomous mechanism from within the stromal compartment of the endometrium. I then interrogated the contribution of SOX17 to dysregulated glandular function in Type I endometrial adenocarcinoma in vitro. My findings reveal an oncogenic role of SOX17 in the Ishikawa Type 1 endometrial cancer cell line, with homozygous loss of SOX17 impairing cellular proliferation, blunting the cancer phenotype of these cells. The majority of cancers, including gynecological cancers, develop from the accumulation of genetic mutations that occur sporadically in cells over time. The complexity and heterogeneity of solid tumors, however, renders the identification of mutations responsible for driving tumorigenesis difficult. The Sleeping Beauty (SB) insertional mutagenesis system can be used to streamline sporadic tumor formation and driver mutation identification. I present results from an initial attempt to develop an SB model of endometrial cancer and discuss ways in which the SB system can be harnessed to evaluate tumorigenesis in a variety of tissue types and microenvironmental contexts. Finally, I present an SB model of metastatic vulvar cancer. Primary tumors from this model resulted in the identification of 76 novel candidate drivers of vulvar cancer, with the ubiquitin-specific peptidase, Usp9x, the most commonly disrupted gene in our screen. I show data suggesting that differential expression of Usp9x isoforms may underlie Usp9x-mediated tumorigenesis and preliminary data demonstrating the relevance of USP9X to human vulvar cancer. Taken as a whole, these data contribute to our scientific understanding of gynecological tissue homeostasis and cancers, lay the foundation for the development of an SB model of endometrial cancer, and describe the first reported model system for studying HPV-naive vulvar cancer in vivo.

Cystic fibrosis (CF) is the most common autosomal recessive genetic disease in Caucasian populations. CF affects multiple organ systems including pancreas, liver, intestines, sweat glands, and male reproductive organs, however the leading cause of morbidity and mortality in CF patients is chronic lung disease. CF is caused by a mutant cystic fibrosis transmembrane conductance regulator (CFTR) gene which leads to chloride (Cl-) and bicarbonate (HCO3-) anion dysregulation at the airway surface. Without adequate anion exchange, thick, viscous mucus accumulates at the airway surface allowing bacterial colonization to occur. Complementing CFTR in the appropriate airway cells restores the anion channel activity in CFTR-deficient cells. The ultimate goal for CF gene therapy is to design an integrating vector that would lead to persistent and efficient expression of CFTR in the airways. Performing gene therapy experiments is dependent upon a relevant animal model. The CF pig is a large animal model similar in size, anatomy, and physiology to humans. Importantly, the CF pig recapitulates human lung disease. From the CF pig, we have learned much about CF lung disease and have developed relevant assays to measure anion channel correction. We have learned that loss of CFTR leads to a decreased airway surface ASL pH, bacterial killing ability, and increased mucus viscosity. Standardized assays have been developed to evaluate the change in current by Ussing chambers, ASL pH, bacterial killing in vivo and ASL pH and viscosity on primary airway cultures in vitro. Ultimately, these metrics allow us to make conclusions about the efficiency of CFTR restoration. Viral vectors are promising candidates for CF gene therapy. Viral vectors such as adenovirus (Ad), adeno-associated virus (AAV), and pseudotyped lentiviral vectors such as feline immunodeficiency virus (FIV) or human immunodeficiency virus (HIV) can efficiently transduce airway cells and express CFTR. Ad and AAV have both been tested in CF clinical trials, but CFTR expression was transient, if detected at all. Understanding vector biology and overcoming barriers in the lung have allowed us to improve vector delivery to the airways. However, the next major hurdle was achieving persistent expression. Ad and AAV are both transiently expressing vectors, and vector readministration is implausible due to the presence of neutralizing antibodies that develop against the vector. Creating a hybrid nonviral/viral vector in which the integrating nonviral piggyBac transposon system is delivered by an Ad or AAV vector has allowed us to achieve persistent expression in mice. In a third integrating vector system, lentiviral vectors have historically been challenging to work with due to low titer levels. However, improvement in vector purification methods have allowed us to validate a lentiviral vector as a viable gene therapy option. In total, we have validated three integrating vector systems by restoring CFTR to CF pigs to correct the phenotypic defect.

Cancer is one of the leading causes of death in the world. Approximately one fifth of deaths in the western industrial nations are caused by cancer. Every year several hundreds of thousands of new patients are diagnosed with cancer and several thousands die of cancer. Scientists have been conducting research from different angles for effective prevention, diagnosis and cure of Cancer. Ever since the genetic basis of cancer has been demonstrated, a race has been ignited globally in the scientific community to identify potential oncogenes and tumor suppressor genes. The genetics of the tumors are complex in nature where combinations of loss of function mutations in tumor suppressor genes and gain of function mutations in oncogenes cause cancers. The identification of these genes is extremely important to devise effective therapies to treat cancer. Insertional mutagenesis systems such as sleeping beauty provide an elegant way to identify genes involved in cancers. More and more researchers are adopting the Sleeping Beauty system for their insertional mutagenesis experiments to identify potential cancer causing genes. Given next generation sequence technologies and the vast amount of data they generate requires novel bioinformatics techniques to process, analyze and meaningfully interpret the data. The goal of this project is to develop a publicly available system for researchers worldwide to analyze the sequence data resulting from insertional mutagenesis experiments. This system will identify and annotate all the insertion sites resulting from the sequencing of the experiment. It will also identify the Common Insertion sites (CIS) and genes with Common Insertion Sites (gCIS). The Common Insertion Sites being the regions in the genome that are targeted more often than by chance. The whole system is accessible as a web application for use by researchers worldwide performing insertional mutagenesis experiments.

Les éléments transposables (ET) ont un impact majeur sur le fonctionnement etla dynamique des génomes, à l’échelle de l’individu et de l’espèce. Le cilié Parameciumest un modèle original pour l’étude des ET. Chaque individu unicellulaire a un génomegerminal qui subit, lors des processus sexuels, des réarrangements massifs, comprenantl’élimination des ET et de leurs vestiges à copie unique, pour former un génome somatiqueoptimisé pour l’expression des gènes. La programmation épigénétique de cesréarrangements implique des petits ARN dans un processus complexe de soustractiongénomique.Au cours de ma thèse, j’ai effectué des analyses bioinformatiques et biostatistiques dedonnées hétérogènes à l’échelle du génome pour : (i) Identifier et analyser des propriétésintrinsèques, de dizaines de milliers de vestiges d’ET à copie unique, appelés "InternalEliminated Sequences" (IES). (ii) Comprendre le rôle de déterminants génétiques et dedifférents facteurs épigénétiques dans le ciblage et l’élimination des IES.L’ensemble de ces analyses met en lumière la co-Évolution des ET et des mécan-Ismes de défense de l’hôte. / Transposable elements (TE) have major impact on the function and dynamicsof genomes, both at the level of the individual and of the species. The ciliate Parameciumprovides an original model for studies of TE. Each individual unicell has a germlinegenome that undergoes massive rearrangements at each sexual generation including thephysical elimination of TE and their single copy remnants, yielding a somatic genomestreamlined for gene expression. The epigenetic programming of the rearrangementsinvolves small RNAs in a complex process of genomic subtraction.During my thesis, I carried out bioinformatic and biostatistical analyses of heteroge-Neous, genome-Scale datasets in order to : (i) Identifiy and study the intrinsic propertiesof tens of thousands of TE remnants know as "Internal Eliminated Sequences" (IES).(ii) Explore the roles of genetic determinants and epigenetic factors in the targeting andelimination of the IESs.Taken together, the studies illustrate the co-Evolution of TE and host defense mecha-Nisms.

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.

During mammalian post-implantation development, germ cells are induced from the somatic tissues of the embryo. Following their induction, primordial germ cells undergo a genome-wide erasure and de novo re-establishment of DNA methylation marks. This epigenetic reprogramming re-instates pluripotency and allows parental imprints to be deposited. In the male germ line, a unique RNAi pathway involving PIWI proteins and their associated small RNAs (piRNAs) is necessary for proper de novo methylation. PIWI mutant mice are infertile and display methylation defects over transposon sequences. Using a transgenic approach, we investigated the signals necessary for piRNA production. We show that artificial piRNAs can be produced from reprogrammed loci outside of their native context. We then studied the genome-wide impact of piRNA loss on germ cell methylation. Whereas most of the genome is properly methylated, only a small group of transposons transiently reactivated in primordial germ cells is affected. Also we identified important structural differences in de novo methylation profiles between human sperm and ES cells. Finally, we compared sperm methylation profiles between human and chimpanzee and showed that the genome and the epigenome can evolve independently. Taken together, our results highlight the surprising plasticity of genome and epigenome interactions during development and evolution

Bone marrow (BM)-derived mesenchymal stromal cells (MSCs) can be induced to express cardiac-specific markers by embryonic cardiomyocytes in vitro. To determine whether this phenomenon occurs in vivo, we have developed a cell transplantation system using zebrafish embryonic recipients. We were unable to isolate expandable zebrafish kidney stromal (ZKS) cells from the kidney, the human BM equivalent; hence, we analyzed the established ZKS1 cell line. We found that ZKS1 expresses stromal genes, but also expresses hematopoietic genes not normally expressed by MSCs. Furthermore, we were unable to differentiate ZKS1 cells into adipocytes, osteoblasts or cardiomyocytes in vitro. We created a transgenic ZKS1(CMV:eGFP) cell line which, after transplantation into zebrafish blastulae, was observed within the host heart, among other tissues. Finally, pT2/S2tnnt2-GM2 and pT2/S2tnnt2-DsRed transposons were generated to mark ZKS1 cardiac differentiation. The zebrafish model established here will be useful for studying the molecular mechanisms of exogenous MSC cardiac differentiation in vivo.

Bone marrow (BM)-derived mesenchymal stromal cells (MSCs) can be induced to express cardiac-specific markers by embryonic cardiomyocytes in vitro. To determine whether this phenomenon occurs in vivo, we have developed a cell transplantation system using zebrafish embryonic recipients. We were unable to isolate expandable zebrafish kidney stromal (ZKS) cells from the kidney, the human BM equivalent; hence, we analyzed the established ZKS1 cell line. We found that ZKS1 expresses stromal genes, but also expresses hematopoietic genes not normally expressed by MSCs. Furthermore, we were unable to differentiate ZKS1 cells into adipocytes, osteoblasts or cardiomyocytes in vitro. We created a transgenic ZKS1(CMV:eGFP) cell line which, after transplantation into zebrafish blastulae, was observed within the host heart, among other tissues. Finally, pT2/S2tnnt2-GM2 and pT2/S2tnnt2-DsRed transposons were generated to mark ZKS1 cardiac differentiation. The zebrafish model established here will be useful for studying the molecular mechanisms of exogenous MSC cardiac differentiation in vivo.