Gene therapy is a fast growing technology that offers treatments for genetic diseases. The method is based on introducing genetic material into a patient to replace the disease-causing gene, using a vector. This report examines the potential of some viral vectors for gene therapy, to give Bio-Works Technologies a recommendation on what the future market demands. Oncolytic viruses, vaccines and gene editing are not treated in the report as a delimitation.  Viral vectors have different biological properties and require different purification methods, making them suitable for different applications in gene therapy. In the purification of the viruses it can be challenging to obtain a high purity and large-scale manufacturing. One major drawback with most purification methods is that they are not specific to just one virus, which leads to contaminants in the solution and lower purity. The viral vectors handled in the report are the adenovirus, adeno-associated virus, gammaretrovirus, lentivirus, alpharetrovirus, foamy virus, herpes simplex virus and baculovirus. These were chosen as they are relevant vectors for gene therapy and stay within the scope of the report. Lentiviral vectors (LVs) and adeno-associated viral vectors (AAVs) will dominate the gene therapy field in the coming years. This is based on the information that the use of AAVs and LVs in clinical trials have increased in recent years, while the other vectors mentioned above have slightly decreased or show no apparent change. However, challenges still remain in the purification processes. Ligands used in affinity chromatography for purification of AAVs are effective at removing most contaminants, but cannot distinguish between empty and loaded capsids, which can induce immune response when used clinically. This is the main challenge when purifying AAVs. The empty capsids can be removed with ion exchange chromatography, which results in higher purity but also lower recovery. There is no specific purifying method for LVs, therefore a lentivirus-specific affinity ligand, such as an antibody ligand, would be beneficial for the purification and manufacturing procedure.  In addition to AAVs and LVs, baculoviral vectors and foamy viral vectors show great potential in a long-term perspective but they only have been researched in preclinical studies. Moreover, herpes simplex viral vectors and adenoviral vectors show potential in cancer treatments or as vaccines rather than in augmentation gene therapy.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24505号 / 医博第4947号 / 新制||医||1064(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 渡邉 大, 教授 林 康紀, 教授 井上 治久 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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La myopathie myotubulaire est une maladie musculaire congénitale très sévère. Le laboratoire d’accueil a démontré que les échantillons de muscle de patients atteints de cette maladie ainsi que le modèle murin présentent une surexpression de DNM2, alors que sa réduction par croisement génétique améliore les signes cliniques et histologiques de la maladie. Le but de ce travail consistait à développer, tester et valider des composés injectables qui ciblent DNM2 et diminuent son niveau. Deux approches thérapeutiques ont été développées l’une basée sur l’utilisation de virus adéno-associés (AAV) exprimant des shRNA, l’autre sur les oligonucleotides antisens (ASO). L’injection des vecteurs AAV-shDnm2 ou bien les ASO-Dnm2 pouvait corriger les défauts histologiques et fonctionnels des muscles des souris myopathes.Les résultats obtenus montrent le potentiel thérapeutique de la réduction de DNM2, et présente une nouvelle approche pour le traitement de la myopathie myotubulaire. / Myotubular myopathy is a severe muscle disease. We previously have shown that muscle specimens of both patients and the mouse model presented an overexpression of DNM2, while its genetic reduction prevents the development of the muscle phenotypes. The aim of this work was to develop, test and validate deliverable compounds. Two therapeutic approaches were used. Injection of antisense oligonucleotide or adeno-associated virus expressing shRNA restores a normal lifespan with improved muscle structure and function of the myopathic mice. These results demonstrate that therapeutic potential of reduction of DNM2 level and provides an attractive therapeutic strategy that could be applied to treat myotubular myopathy.

L’expression d’un transgène grâce au vecteur AAV offre une perspective thérapeutique très prometteuse dans le traitement de maladies monogéniques. Malheureusement, il apparait souvent que des réponses immunes contre le vecteur et le transgène conduisent à un rejet des cellules transduites ainsi qu’à la mise en place d’une mémoire immunitaire spécifique empêchant un nouveau traitement ultérieur. Avec la perspective d’éviter tout rejet immun des cellules transduites, j’ai développé deux approches distinctes. D’une part, nous avons développé un système dans lequel l’expression du transgène est déstabilisée dans les cellules présentatrices de l’antigène grâce à l’ajout de cibles du miRNA 142.3p qui est spécifiquement exprimé dans le système hématopoïétique. Nous avons ainsi montré que la réponse immunitaire contre le transgène était favorisée par la transduction des cellules présentatrices de l’antigène par le vecteur, conduisant à la présentation directe du produit du transgène. En comparant l’initiation des réponses immunes contre plusieurs transgènes modèles, nous avons montré que la réponse immune dirigée contre le transgène pouvait être contrôlée mais que celle-ci dépendait étroitement de l’immunogénicité intrinsèque du transgène en question, c'est-à-dire de la présence d’épitopes reconnus par des lymphocytes T CD4 auxiliaires ainsi que par les lymphocytes B. Une autre approche a concerné l’utilisation de lymphocytes T régulateurs exprimant le facteur de transcription Foxp3 (Treg) et plus particulièrement l’étude de leur mode d’induction in vivo. La présence de Treg conférant une tolérance immunitaire spécifique du transgène a été décrite dans diverses situations et les Treg induits à partir de CD4+ matures (pTreg/iTreg) semblent avoir un potentiel thérapeutique important. Cependant, la population précise de lymphocytes CD4+ à même d’être convertie en Treg n’avait pas été identifiée auparavant. Au cours de mes travaux, analysant la capacité de conversion de cellules naïves, mémoires ou de récents émigrants thymiques, j’ai mis en évidence que le potentiel de conversion des lymphocytes CD4 naïfs issus de souris âgées était diminué et que ceci était dû à une caractéristique intrinsèque des lymphocytes T CD4+ provenant de telles souris. Enfin, nous avons montré que cette faible capacité de conversion des lymphocytes CD4 naïfs en Treg était associée à un rejet de greffe accru dans un modèle de transplantation de peau, montrant que la sénescence peut impacter négativement des protocoles d’induction de tolérance faisant appel à l’induction de Treg en périphérie. / Transgene expression through AAVvectors offers a very promising therapeutic perspective in the treatment of monogenic disorders. Unfortunately, it often appears that the immune responses against the transgene and the vector lead to the rejection of transduced cells and to an establishment of a specific immune memory preventing further processing. With a view to avoid immune rejection of transduced cells, I developed two distinct approaches.First, we have developed a system where the transgene expression is destabilized in the antigen presenting cells by addition of the target miRNA 142.3p which is specifically expressed in the hematopoietic system. We have shown that the immune response against the transgene was favored by transduction of antigen presenting cells with the vector, leading to the direct presentation of the transgene product. Comparing the initiation of immune responses against more transgenes models, we showed that the immune response against the transgene could be controlled but it depended greatly on the intrinsic immunogenicity of the transgène: the presence of epitopes recognized by T helper cells and CD4 by B lymphocytes. Another approach has involved the use of regulatory T cells expressing the transcription factor Foxp3 ( Treg ) and more specifically the study of their mode of induction in vivo. The presence of Treg conferring transgene -specific immune tolerance has been described in various situations and induced Treg from CD4 + mature ( pTreg / iTreg ) appear to have a significant therapeutic potential . However, the precise population of CD4 + lymphocytes capable of being converted into Treg was not identified previously. During my work, analyzing the conversion capacity naive, memory cells or thymic recent emigrants, I highlighted that the potential of conversion of naive CD4 lymphocytes from old mice was decreased and this was due to an intrinsic defect of CD4 + T cells from such mice. Finally, we showed that low conversion ability of CD4 naive Treg was associated with an increased graft rejection in a model of skin transplantation, showing that senescence may negatively impact protocols of tolerance induction using induction of Treg in the periphery.

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.

Mitochondria are dynamic organelles that function in a complex interconnected network within the cell. Neurons are sensitive and highly energy demanding cells in the brain which require a functioning mitochondrial network that is able to provide ATP and modulate calcium. Mitochondrial networks have yet to be explored which gives rise to the need for specific and efficient molecular tools. In this project, I designed and produced adeno-associated virus vectors carrying a fluorescent reporter gene for imaging mitochondrial networks under human synapsin 1 promoter to target neurons specifically. The design of each vector was conducted with careful consideration of the different components in the plasmid design that are important for optimal expression, which resulted in two constructs; one self-complementary adeno-associated virus vector that marks the mitochondria and one single-stranded that marks mitochondria and the membrane of neurons.  The modularity of viral vectors allows the usage of different serotypes which adapt the vector to the cell type and the model. For this project I chose the serotypes 1 for neurons in vitro and PHP.eB which suits in vivo models since it has better permeability to the blood brain barrier. The production was conducted in human embryonic kidney cells using the triple-plasmid transfection method, followed by extraction and purification. The existence of viral particles was verified through transmission electron microscopy and the DNA titer of the vector through quantitative polymerase chain reaction. The produced adeno-associated virus vectors were delivered into young brain organoids which were not able to express the reporter gene, probably due to not fully developed neurons. The fluorescent protein expression targeting specifically mitochondria and the membrane was however verified in the human embryonic kidney cells during the packaging stages.

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