Neurons in the spinal cord do not spontaneously regenerate, which often leads to debilitating injuries. One method proposed to promote axonal regeneration is the injection of viruses carrying genes for growth factors into the injured spinal cord. One such virus, the adeno-associated virus (AAV), has shown promise in gene therapy medical research. However, injecting AAV into rhesus macaques with C7 spinal cord hemisection lesions actually leads to motor neuron loss in the gray matter of the spinal cord, rather than contributing to the preservation or regeneration of axons. This unexpected result highlights the necessity of further testing with therapeutic approaches for axon regeneration in nonhuman primate models before moving into clinical trials. It is possible that an immune-related T cell response to the AAV-transfected cells causes this motor neuron loss. T cells are white blood cells that play a role in attacking cells infected with viruses. It is unknown whether such a response of the immune system to respond with an up-regulation of T cells may be taking place over a relatively short period (weeks) or over many months. This question was tested here: T cells were stained in spinal cord sections caudal (below) the lesion in the spinal cord and near AAV injection sites to determine whether there was a greater quantity of T cells in these areas compared to the subject’s baseline levels. Subjects that had AAV therapeutic injections and that were examined 6 months after the injection were found to have greater quantities of T cells than those who did not have injections containing AAV. It was also found that the AAV-injected subjects examined only 6 weeks post injection did not have greater quantities of T cells than control subjects. These results suggest that there may be a delayed immune response to the AAV injections in nonhuman primates with spinal cord injury, which occurs over a period of months. Pinpointing the mechanism that causes this cell death would allow researchers to create a safer therapeutic that could promote axonal growth in people with spinal cord injuries.

Upon consultation with NPS faculty, the School has determined that this thesis may be released to the public, its distribution is unlimited effective August 25, 2011. / One result of the break-up of the Soviet Union is that the DOD has been forced to reevaluate the roles of each of the Armed Services based on the declining resource pool. From the Marine Corps' evaluation of itself came the Combined Arms Regiment (CAR) concept. The objective of this study was to develop an estimate of the Life Cycle Cost (LCC) of the two possible vehicles used with the CAR and the CAR's components. Standard cost factors are used to cost out the various organizations involved. Two supporting analyses done in this study are: an evaluation of the Marine Corps' role in national security and how the CAR could be used to support that security role, and a comparison of the vehicle option operating characteristics which was done to enrich the dimensions under which the CAR could be evaluated. The results of the study are a tool which can help Marine Corps planners make more informed decisions in regards to the CAR concept. The final conclusion, based on the assumption that any CAR would act as a follow-on element of the MAGTF, was that although the CAR(LAV) was a workable option, the CAR using upgraded AAVs was the better, more cost effective option.

GM2 gangliosidoses are a family of lysosomal storage disorders that include both Tay-Sachs and Sandhoff diseases. These disorders result from deficiencies in the lysosomal enzyme β-N-acetylhexosaminidase (HexA). Impairment of HexA leads to accumulation of its substrate, GM2 ganglioside, in cells resulting in cellular dysfunction and death. There is currently no treatment for GM2 gangliosidoses. Patients primarily present with neurological dysfunction and degeneration. Here we developed a central nervous system gene therapy through direct injection that leads to long-term survival in the Sandhoff disease mouse model. We deliver an equal mixture of AAVrh8 vectors that encode for the two subunits (α and β) of HexA into the thalami and lateral ventricle. This strategy has also been shown to be safe and effective in treating the cat model of Sandhoff disease. We tested the feasibility and safety of this therapy in non-human primates, which unexpectedly lead to neurotoxicity in the thalami. We hypothesized that toxicity was due to high overexpression of HexA, which dose reduction of vector could not compensate for. In order to maintain AAV dose, and therefore widespread HexA distribution in the brain, six new vector designs were screened for toxicity in nude mice. The top three vectors that showed reduction of HexA expression with low toxicity were chosen and tested for safety in non-human primates. A final formulation was chosen from the primate screen that showed overexpression of HexA with minimal to no toxicity. Therapeutic efficacy studies were performed in Sandhoff disease mice to define the minimum effective dose.

Many steps go into developing a clinical viral gene therapy. The course starts with appropriate disease selection and moves through the many hurdles of in-vitro testing, animal model validation and proof-of-concept studies, all the way through pre-clinical large animal studies. In this thesis, I propose to outline the process of developing a translation pathway for a gene therapy using recombinant adeno-associated virus (rAAV). I will expand on this outline using data that I have generated during the course of my Ph.D. that ranges from animal model validation all the way through pre-clinical vector stability studies. Two disease models will be discussed throughout this thesis, Cockayne Syndrome (CS) and Alpha-1 Antitrypsin Deficiency (AATD). Cockayne Syndrome is a rare autosomal recessive genetic disorder involving mutations in either the CSA or CSB gene, leading to defects in DNA repair. Clinically this presents as progressive degeneration of the central nervous system, retina, cardiovascular system, and cochlea, which leads to mental retardation, post-natal growth defects, ocular abnormalities, and shortened life expectancy. Alpha-1 antitrypsin is a serine protease inhibitor largely produced in the liver that mainly functions to inhibit neutrophil elastase within the lung. AATD leads to an increased risk of emphysema, with shortened life expectancy, and also results in accumulations of mutant AAT polymers in the liver, sometimes leading to liver failure. Using these two disease models I will outline the upstream and downstream pre-clinical work as well as the transition to clinical trials of a rAAV based gene therapy.

Les maladies cardiovasculaires (MCV) constituent la première cause de mortalité dans le monde. Des efforts significatifs ont été menés pour améliorer la prévention des MCV et ont abouti à une réduction du taux de mortalité. Cependant, un ralentissement considérable du taux de réduction des MCV a été observé à partir de 2011 malgré les nouvelles avancées thérapeutiques. Ces taux alarmants justifient le besoin de découvrir de nouvelles thérapies afin d’améliorer la prévention des MCV dans la population générale. Des taux élevés de cholestérol total et transporté par les lipoprotéines de basse densité (LDL) sont fortement liés aux MCV athérosclérotiques. Ainsi, les thérapies hypolipémiantes sont les thérapies les plus utilisées pour prévenir les MCV. Nos résultats antérieurs ont identifié Golgi glycoprotein 1 (GLG1) comme étant une nouvelle protéine impliquée dans le métabolisme lipidique. Par conséquent, notre étude actuelle vise à démontrer l'effet de GLG1 sur le développement de l'athérosclérose. Pour étudier cet effet, nous avons réduit l'expression de GLG1 (silençage génique ou knockdown) dans le foie de souris hypercholestérolémiques Apoe-/- en utilisant un virus adéno-associé de type 8 (AAV8) véhiculant un petit ARN en épingle à cheveux (shRNA) ciblant GLG1. Deux semaines post-injection, les souris ont été nourries par un régime occidental pendant 12 semaines. L'étude a révélé que le knockdown de GLG1 réduit significativement les taux plasmatiques de cholestérol total, de lipoprotéines de très basse densité (VLDL), de LDL et diminue les lésions athérosclérotiques au niveau du sinus aortique. Cependant, nos résultats ont démontré que le knockdown de GLG1 à l’aide du système AAV8 n'était pas stable pendant toute l'étude, le rendant inefficace au-delà de 2 mois. En résumé, nos résultats montrent que le knockdown de GLG1 réduit les taux de cholestérol plasmatique ainsi que la progression de l'athérosclérose chez les souris Apoe-/-. Cette réduction s'est produite en dépit de la perte progressive du knockdown de GLG1 et est probablement liée à la réduction de la sécrétion d'apolipoprotéines B100. Ces résultats montrent que GLG1 est une cible thérapeutique prometteuse pour abaisser les taux de cholestérol plasmatique, en particulier les VLDL et LDL, et prévenir le développement de l'athérosclérose. / Cardiovascular diseases (CVD) are the leading cause of death worldwide. Significant efforts have been made to prevent CVD and have resulted in a reduced mortality rate. However, a considerable slowdown in the reduction rate of CVD has been observed starting in 2011 despite new therapeutic advances. These alarming rates justify the need to discover new therapies to improve the prevention of CVD in the general population. High levels of total cholesterol and low-density lipoprotein cholesterol (LDL-C) are strongly linked to atherosclerotic cardiovascular diseases. Thus, lipid-lowering therapies are the most used therapies to prevent CVDs. Our previous study identified Golgi glycoprotein 1 (GLG1) as a new protein involved in lipid metabolism. Therefore, our current study aims to demonstrate the effect of GLG1 on the development of atherosclerosis. To study the effect of GLG1 on atherosclerosis, we reduced GLG1 expression in hypercholesterolemic Apoe-/- mice livers using an adeno-associated virus coding for a short hairpin RNA (shRNA) targeting GLG1 then 2 weeks post-injection mice were fed a Western diet for 12 weeks. The study revealed that GLG1 knockdown significantly reduced plasma total cholesterol levels, especially very low-density lipoprotein (VLDL)- and LDL-C, and atherosclerotic lesions in the aortic root. However, our results showed that AAV-mediated GLG1 knockdown was not stable during the entire study, making it ineffective in lowering plasma cholesterol levels beyond 2 months. In summary, our results show that lowering GLG1 expression reduces plasma cholesterol levels as well as atherosclerosis progression in Apoe-/- mice. Remarkably, the reduction in atherosclerosis occurred in spite of the gradual loss of GLG1 AAV-mediated knockdown and is likely related to the reduced apolipoptotein B100 secretion. These findings demonstrate that GLG1 is a promising therapeutic target for lowering plasma cholesterol levels, particularly VLDL- and LDL-C, and preventing atherosclerosis development.

Les dysferlinopathies sont des dystrophies musculaires qui se manifestent par la dystrophie musculaire des ceintures de type 2B (LGMD2B) ou la myopathie de Miyoshi (MM). Elles sont causées par des mutations dans le gène dysferline. La dysferline est une protéine membranaire exprimée dans le muscle squelettique, responsable de la réparation des microlésions du sarcolemme. L’absence d’une telle réparation de la membrane entraîne une atrophie musculaire progressive. Ce travail de thèse explore le potentiel thérapeutique d'une stratégie de modulation d'épissage pour le traitement de la LGMD2B causée par la mutation faux-sens c4022T>C dans l'exon 38 du gène dysferline. Des oligonucléotides et des petits ARN U7 délivrés par un vecteur viral de type adéno-associé ont été utilisés comme outils antisens pour induire un saut d'exon in vitro et in vivo. Ce projet de thèse étudie également la capacité de la dysferline tronquée à se localiser de façon appropriée à la membrane et ainsi la réparer. / Dysferlinopathy is a muscular dystrophy that manifests as two major phenotypes: limb-girdle muscular dystrophy type 2B (LGMD2B) or Miyoshi myopathy (MM). It is caused by mutations in the dysferlin gene. Dysferlin is a membrane protein expressed in skeletal muscle. It is responsible for the repair of sarcolemma microlesions produced by muscle contractions. A compromised membrane repair leads to slowly progressing muscle wasting. This thesis explores the therapeutic potential of an antisense mediated splice switching strategy in LGMD2B caused by the missense mutation c4022T>C in the exon 38 of the dysferlin gene. Antisense oligonucleotides and U7 snRNAs delivered by an adeno-associated viral vector were used as antisense tools to trigger exon skipping in vitro and in vivo. The thesis investigates also if the truncated dysferlin maintainsa proper membrane localization and its membrane repair ability.

One of the major challenges facing medicine and drug discovery is the large number of genetic diseases caused by inherited mutations leading to a toxic gain-of-function, or loss-of-function of the disease protein. Microbiology offered a new glimpse of hope to address those disorders with the adaptation of the bacterial CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) defense system as a genome editing tool. Cas9 is a unique CRISPR-associated endonuclease protein that can be easily programmed with an RNA [a single-guide RNA (sgRNA)] that is complementary to nearly any DNA locus. Cas9 creates a double-stranded break (DSB) that can be exploited to knock out toxic genes or replenish therapeutic expression levels of essential proteins. In addition to a matching sgRNA sequence, Cas9 requires the presence of a short signature sequence [a protospacer adjacent motif (PAM)] flanking the target locus. Over the past few years, several Cas9-based therapeutic platforms have emerged to correct DNA mutations in a wide range of mammalian cell lines, ex vivo, and in vivo by adapting recombinant adeno-associated virus (rAAV). However, most of the applications of Cas9 in the field have been limited to Streptococcus pyogenes (SpyCas9), which, in its wild-type form, suffers from inaccurate editing at off-target sites. It is also difficult to deliver via an all-in-one (sgRNA+Cas9) rAAV approach due to its large size. In this thesis, I describe other Cas9 nucleases and their development as new AAV-based genome editing platforms for therapeutic editing in vivo in mouse disease models. In the first part of this thesis, I develop the all-in-one AAV strategy to deliver a Neisseria meningitidis Cas9 ortholog (Nme1Cas9) in mice to reduce the level of circulating cholesterol in blood. I also help characterize an enhanced Cas9 from another meningococcus strain (Nme2Cas9) and show that it is effective in performing editing not only in mammalian cell culture, but also in vivo by all-in-one AAV delivery. Additionally, I describe two AAV platforms that enable advanced editing modalities in vivo: 1) segmental DNA deletion by delivering two sgRNAs (along with Nme2Cas9) in one AAV, and 2) precise HDR-based repair by fitting Nme2Cas9, sgRNA and donor DNA within a single AAV capsid. Using these tools, we successfully treat two genetic disorders in mice, underscoring the importance of this powerful duo of AAV and Cas9 in gene therapy to advance novel treatment. Finally, I present preliminary data on how to use these AAV.Nme2Cas9 vectors to treat Alexander Disease, a rare progressive neurological disorder. These findings provide a platform for future application of gene editing in therapeutics.

Indiana University-Purdue University Indianapolis (IUPUI) / High-efficiency transduction of hematopoietic stem cells (HSCs) by recombinant adeno-associated virus serotype 2 (AAV2) vectors is limited by (i) inadequate expression of cellular receptor/co-receptors for AAV2; (ii) impaired intracellular trafficking and uncoating in the nucleus; (iii) failure of the genome to undergo second-strand DNA synthesis; and (iv) use of sub-optimal promoters. Systematic studies were undertaken to develop alternative strategies to achieve high-efficiency transduction of primary murine HSCs and lineage-restricted transgene expression in a bone marrow transplant model in vivo. These included the use of: (i) additional AAV serotype (AAV1, AAV7, AAV8, AAV10) vectors; (ii) self-complementary AAV (scAAV) vectors; and (iii) erythroid cell-specific promoters. scAAV1 and scAAV7 vectors containing an enhanced green-fluorescent protein (EGFP) reporter gene under the control of hematopoietic cell-specific enhancers/promoters allowed sustained transgene expression in an erythroid lineage-restricted manner in both primary and secondary transplant recipient mice. Self complementary AAV vectors containing an anti-sickling human beta-globin gene under the control of either the beta-globin gene promoter/enhancer, or the human parvovirus B19 promoter at map-unit 6 (B19p6) were tested for their efficacy in a human erythroid cell line (K562), and in primary murine hematopoietic progenitor cells (c-kit+, lin-). These studies revealed that (i) scAAV2-beta-globin vectors containing only the HS2 enhancer are more efficient than ssAAV2-beta-globin vectors containing the HS2+HS3+HS4 enhancers; (ii) scAAV-beta-globin vectors containing only the B19p6 promoter are more efficient than their counterparts containing the HS2 enhancer/beta-globin promoter; and (iii) scAAV2-B19p6-beta-globin vectors in K562 cells, and scAAV1-B19p6-beta-globin vectors in murine c-kit+, lin- cells, yield efficient expression of the beta-globin protein. These studies suggest that the combined use of scAAV serotype vectors and the B19p6 promoter may lead to expression of therapeutic levels of beta-globin gene in human erythroid cells, which has implications in the potential gene therapy of beta-thalassemia and sickle cell disease.

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