京都大学 / 0048 / 新制・論文博士 / 博士(医科学) / 乙第13332号 / 論医科博第5号 / 新制||医科||7(附属図書館) / 大阪大学大学院生命機能研究科生命機能専攻 / (主査)教授 河本 宏, 教授 濵﨑 洋子, 教授 髙折 晃史 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・論文博士 / 博士(医学) / 乙第13163号 / 論医博第2150号 / 新制||医||1029(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 林 康紀, 教授 渡邉 大, 教授 高橋 淳 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21454号 / 医博第4421号 / 新制||医||1033(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 渡邊 直樹, 教授 髙折 晃史, 教授 山下 潤 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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A anemia falciforme (AF) é uma doença monogênica de elevada mortalidade e morbidade, que afeta milhões de pessoas em todo o mundo. Não há tratamento definitivo que seja amplo, eficaz e seguro para a AF, de forma que os tratamentos paliativos são os mais utilizados. O tratamento definitivo disponível é transplante alogênico de células-tronco hematopoiéticas, porém com várias complicações envolvidas. O estabelecimento de um modelo in vitro permite uma melhor compreensão de como a doença ocorre, além de permitir o desenvolvimento de novos testes e tratamentos mais eficazes contra a doença. Neste contexto, a tecnologia das células-tronco pluripotentes induzidas (iPSC), que surgiu em 2006, é uma ferramenta poderosa na pesquisa básica, na pesquisa da diferenciação de tecidos e no modelamento de doenças, e uma promessa para futuras aplicações clínicas, na descoberta e triagem de novas drogas mais eficazes e seguras, além da possibilidade de utilização na medicina regenerativa, na produção de células paciente-específicas para terapia celular. Este trabalho teve como objetivo obter um modelo de estudo e tratamento da AF utilizando iPSC. Para isso, vetores epissomais foram utilizados para a reprogramação de células mononucleares de sangue periférico para obter iPSC livres de integração. Estas células foram coletadas de pacientes tratados com o medicamento hidroxiureia e sem tratamento, para avaliação do impacto da droga na reprogramação. As linhagens de iPSC PBscd geradas foram caracterizadas quanto ao potencial pluripotente e de diferenciação. Todas as linhagens geradas se mostraram pluripotentes com potencial de auto renovação e potencial de formar células e tecidos dos 3 folhetos germinativos. O rastreamento dos vetores utilizados na reprogramação mostrou que as células estão livres após cerca de 10 passagens em média, e que eles não se integram espontaneamente nas células. As linhagens de iPSC foram diferenciadas em progenitores hematopoiéticos através da agregação forçada associada à indução com citocinas específicas e um cultivo em suspensão. Dessa forma, nós obtivemos um protocolo dinâmico e eficiente de produção de células CD34+CD45+ com poucos dias de indução. Foram realizados experimentos iniciais de padronização da metodologia de CRISPR, para que essa metodologia possa ser utilizada no futuro para a correção da mutação da AF no gene da ?- globin. Além disso, a reação padronizada para o rastreamento da mutação no gene da ?-globin poderá ser usado em experimentos futuros de edição gênica para avaliar a correção da mutação. Em resumo, oferecemos uma ferramenta valiosa para uma melhor compreensão de como a AF ocorre, além de tornar possível o desenvolvimento de drogas e tratamentos mais eficazes e de fornecer um melhor entendimento dos tratamentos amplamente utilizados, como a hidroxiurea / Sickle cell anemia (SCA) is a monogenic disease of high mortality and morbidity, that affects millions of people worldwide. There is no definitive treatment that is broad, effective and safe for SCA, so the palliative treatments are the most used. The definitive treatment available is the allogeneic transplantation of hematopoietic stem cells, but with several complications involved. The establishment of an in vitro model allows better understanding of how the disease occurs, besides allowing the development of more effective new tests and treatments against the disease. In this context, the induced pluripotent stem cell (iPSC) technology, that emerged in 2006, is a powerful tool for basic research, tissue differentiation research and disease modeling, and a promise for future clinical applications, to find and screen new, more effective and safe drugs, besides the possibility of use in regenerative medicine, in the production of patient-specific cells for cell therapy. This work aimed to obtain a model for study and treatment of SCA using iPSC. For this, episomal vectors were used for reprogramming peripheral blood mononuclear cells to obtain integration-free iPSC. This cells were collected from patients treated with hydroxyurea and without treatment, for evaluation of the impact of the drug in reprogramming. The generated iPSC PBscd lines were characterized for pluripotent and differentiation potential. All the generated lines were shown to be pluripotent with potential for self-renewal and to form cells and tissues of the 3 germ layers. Screening of the vectors used for reprogramming showed that they are absent after about 10 passages, and that they do not integrate spontaneously into the cells. The iPSC lines were differentiated into hematopoietic progenitors through forced aggregation associated with induction with specific cytokines and culture in cell suspension. Thus, we obtained a dynamic and efficient protocol of CD34+CD45+ cells production with a few days of induction. Initial standardization experiments of CRISPR methodology was performed, so that this methodology can be used in the future to correct the ?-globin chain mutation of SCA. Also, the standardized reaction for the screening of ?-globin chain mutation can be used in future gene-editing experiments to evaluate the mutation correction. In summary, we offer a valuable tool for a better understanding of how SCA occurs, in addition to make possible the development of more effective drugs and treatments and providing better understanding of widely used treatments, such hydroxyrea

Les néoplasmes myéloprolifératifs (NMP) sont hémopathies malignes aboutissant à la surproduction d'une ou plusieurs lignées myéloïdes. Elles sont dues à l'acquisition de mutations sur l'axe de signalisation MPL/JAK2 incluant des mutations de JAK2V617F, de MPL et plus récemment de la calréticuline (CALR), dont les deux principales sont CALRdel52 et CALRins5. Ces mutations de signalisations peuvent être accompagnées de mutations de l'épigénétique, les plus importantes étant des mutations dans TET2. Le but de cette thèse était d'étudier le rôle des mutations de TET2 et de la calrdel52 dans les NMP grâce à une technologie de cellules souches induites à la pluripotence (IPSC). Dans la première partie j'ai pu démontrer que TET2 joue un rôle dans le processus de reprogrammation, vraisemblablement de manière indépendante de son activité catalytique. Dans la seconde partie, j'ai démontré que CALRdel52 joue un rôle dans les MPN en provoquant une hypersensibilité et une pousse indépendante de la TPO des progéniteurs mégakaryocytaires ainsi qu'une hyperprolifération des mégacaryocytes, liées à l'activation constitutive de stat3 et de ERK. J'ai également démontré une pousse indépendante du GCSF des granulocytes. Ce travail a donc permis de mettre en lumière le rôle du facteur épigénétique TET2 dans le processus de reprogrammation ainsi que le rôle de CALRdel52 dans les MPN dans un contexte d'expression endogène. / Myeloproliferative neoplasms (NMP) are hematological malignancies that lead to an ovrproduction of one or more myeloid lineages. They are driving by mutations in MPLl/jak2 signaling pathway, mainly JAK2V617F, MPL, and more recently calreticulin (CARL), with two main mutations being calrdel52 and calrins5. These signaling mutations are sometimes associated with epigenetic mutations, the major one being in tet2. The objective of my thesis was to study the role of TET2 and CALRdel52 in MPN thanks to an induced pluripotent stem cells (IPSC) model. In the first part i demonstrated the role of TET2 in reprogramming process, probably independently of the catalytic domain. In the second part i demonstrated that CALRdel52 induced a TPO hypersensitivity and a TPO indenpendant growth of the megakaryocytic progenitors as well as a hyperproliferation of the megakaryocytes. This phenotype is associated with a constitutive activation of stat3 and ERK. A G-CSF independent growth of the granulocyte was also demonstrated. In conclusion this work underline the role of an epegenetic factor, TET2, in the reprogramming process and demonstrate the role of CALRdel52in MPN with an endogenous expression model.

L'objectif général de ce travail de doctorat a été centré sur l'utilisation des cellules pluripotentes induites humaines dans la modélisation et l'évaluation thérapeutique des pathologies cardiaques. Depuis leur découverte en 2006, les iPSC offrent une opportunité pour le développement de modèles cellulaires humains et spécifiques de patients pour l'étude des mécanismes physiopathologiques, l'évaluation de réponses pharmacologiques et le génération de cellules redifférenciées (ici en cardiomyocytes) pour des applications thérapeutiques cellulaires. Dans ce travail nous avons démontré que la quantité mais aussi la qualité finale des cardiomyocytes dérivés d'iPSC dépend des conditions spatiales et pharmacologiques utilisées durant les différentes étapes de différenciation. L'utilisation d'un protocole de différentiation en monocouche avec blocage simultané et transitoire de l'ensemble des voies Wnt (canoniques et non canoniques) permet d'obtenir une maturation plus importante du sarcomère, étape essentielle pour la modélisation des sarcomèropathies La différenciation des iPSC en cardiomyocytes peut aussi être obtenue par une approche moléculaire ciblée visant à activer spécifiquement un programme cardiogénique. Celle-ci est obtenue via l'utilisation d'une protéine Cas9 mutée et couplée à un système transactivateur et permettant le ciblage simultané de 3 facteurs de transcription clés de la cardiogénèse (Gata4, Mef2c et Tbx5). Cette approche moléculaire est renforcée par la combinaison avec une stimulation pharmacologique ciblant la voie Wnt. / The general objective of this work was centered on the use of human induced pluripotent cells in modeling and therapeutic evaluation of cardiac pathologies. Since their discovery in 2006, the iPSC provide an opportunity for the development of human cellular models and specific patients for the study of pathophysiological mechanisms, evaluation of pharmacological responses and the generation redifférenciées cells (cardiomyocytes here) for applications cellular therapeutic. In this work we demonstrated that the quantity but also the final quality of cardiomyocytes derived from iPSC depends on the spatial and pharmacological conditions used during the various stages of differentiation. The use of a monolayer differentiation protocol with simultaneous and transient blocking of all Wnt pathways (canonical and noncanonical) allows to obtain a higher maturation of the sarcomere, an essential step for modeling sarcomeropathies IPSC differentiation into cardiomyocytes can also be obtained by targeted molecular approach to specifically activate cardiogenic program. This is achieved through the use of a mutated Cas9 protein and coupled with transactivator system. This allows simultaneous targeting of 3 key cardiogenesis transcription factors (Gata4, MEF2C and Tbx5). This molecular approach is enhanced by the combination with a pharmacological stimulation targeting the Wnt pathway. Beyond modeling of monogenic cardiac disease, cardiomyocytes derived from iPSC can reproduce more complex and multigenic diseases

En 2006 et 2007, les équipes de Yamanaka et Thomson réalisent la reprogrammation de cellules somatiques murines et humaines en cellules souches pluripotentes à partir de deux cocktails de gènes : OCT4, SOX2, KLF4, cMYC (OSKM) et OCT4, NANOG, SOX2, LIN28 (ONSL). Les cellules souches à pluripotence induite générées (iPS) partagent les propriétés fondamentales des cellules souches embryonnaires : l’auto-renouvèlement, le maintien de la pluripotence et la capacité de différenciation. Ces cellules laissent entrevoir des applications considérables tant en recherche fondamentale (compréhension des mécanismes de développement et de pathologies, développement de modèles) qu’en recherche appliquée (médecine régénérative, toxicologie prédictive, criblage de médicaments). L’avantage majeur de l’utilisation des iPS réside dans leur origine non embryonnaire. Les contraintes d’ordre éthique sont écartées et une grande diversité de types cellulaires à partir de n’importe quel donneur a priori est disponible pour une reprogrammation. L’établissement d’une banque d’hiPS issus de donneurs sains ou de patients, serait d’une grande utilité pour la communauté scientifique se consacrant à l’étude des mécanismes physiopathologiques ou de développement et une source considérable pour la dérivation à des fins de thérapie cellulaire. Dans le but de mettre en place une telle banque, nous avons développé avec la société Vectalys des rétrovirus de reprogrammation contenant les cassettes polycistroniques ONSL et OSKM. Dans un premier temps, nous avons établi un protocole de reprogrammation robuste à l’aide des rétrovirus RV-ONSL. Nous avons ensuite mis en évidence la synergie entre les facteurs ONSL et OSKM, la combinaison équimolaire de RV-ONSL et RV-OSKM permettant d’atteindre 2% d’efficacité de reprogrammation. Nous avons également entrepris la reprogrammation propre par transfections d’ARNm polycistroniques ONSL et OKM mettant à profit cette incroyable synergie. / In 2006 and 2007, Yamanaka and Thomson teams achieved the reprogramming of mouse and human somatic cells into pluripotent stem cells through the transfection of two cocktails of genes: OCT4, SOX2, KLF4, cMYC (OSKM) and OCT4, NANOG, SOX2, LIN28 (ONSL). The generated cells, called induced Pluripotent Stem Cells (iPSC) share the same fundamental properties of ESC : self-renewing, pluripotency maintenance and capacity of differentiation into the three germ layers and suggest the same application potential in basic research (developmental and epigenetic biology) as well as in therapy (regenerative medicine, disease modeling for drug development). One of the major advantages of iPSC lies in their non-embryonic origin. Indeed, the use of iPSC resolves the ethical constraints and offers the possibility to work with extensive cell types directly from the patient to treat. Stéphane Viville’s research team aims to develop a hiPSC bank from patient suffering from genetic or other diseases which will be available for the scientific community. We are experienced in human primary fibroblasts reprogramming especially with the use of two polycistronic cassettes: ONSL encoding Thomson’s cocktail and OSKM encoding Yamanaka’s cocktail separated with 2A peptides. Thanks to the combination of RV-ONSL and RV-OSKM retroviral vectors (developed with Vectalys) we are yielding more than 2% of reprogramming efficiency in a highly reproducible way. Indeed, we demonstrated the reprogramming synergy of ONSL and OSKM combination. We are now focusing our effort on non-integrative strategies (ie mRNA) which are more appropriate for clinical usage.

Novel technologies for genome analysis have provided almost unlimited opportunities to uncover structural gene variants behind human disorders. Whole exome sequencing (WES) is especially useful for understanding rare Mendelian conditions, because it reduces the requirements for a priori clinical data, and can be applied on a small number of patients. However, supporting functional data on the effect of specific gene variants are often required to power these findings. A variety of methods and biological model systems exists for this purpose. Among those, induced pluripotent stem cells (iPSCs), which are capable of self-renewal and differentiation, stand out as an alternative to animal models. In papers I and II we took advantage of WES to identify gene variants underlying autosomal recessive pure hair and nail ectodermal dysplasia (AR PHNED) as well as autosomal dominant familial visceral myopathy (FVM). We identified a homozygous variant c.821T>C (p.Phe274Ser) in the KRT74 gene as the causative mutation in AR PHNED, supported by the fact that Keratin-74 was undetectable in hair follicles of an affected family member. In a family segregating FVM we found a heterozygous tandem base substitution c.806_807delinsAA (p.(Gly269Glu)) in the ACTG2 gene in the affected members. This novel variant is associated with a broad range of visceral symptoms and a variable age of onset. In Paper III we explored the similarity between clonally derived iPSC lines originating from a single parental fibroblast line and we highlighted the necessity to use lines originating from various donors in disease modeling because of biological variation. Paper IV focused on how the genomic integrity of iPSCs is affected by the choice of reprogramming methods. We described several novel cytogenetic rearrangements in iPSCs and we identified a chromosome 5q duplication as a candidate aberration for growth advantage. In summary, this doctoral thesis brings novel findings on unreported disease-causing variants, as supported by extensive genetic analysis and functional data. A novel molecular mechanism behind AR PHNED is presented and the phenotypic spectrum associated with FVM is expanded. In addition, the thesis brings novel understanding of benefits and limitations of the iPSC technology to be considered for disease modeling.

Parkinson's disease (PD) is characterised by the loss of dopaminergic neurons in the Substantia Nigra pars compacta in the midbrain and the presence of intracellular aggregates, known as Lewy bodies (LBs), in the surviving neurons. The aetiology of PD is unknown but a causative role for α-Synuclein (SNCA) has been proposed. Although the function of αSyn is not well understood, a number of pathological mechanisms associated with αSyn toxicity have been proposed. In this study, nine induced pluripotent stem cells (iPSCs) lines from healthy individuals and PD patients carrying the A53T SNCA mutation or a triplication of SNCA were differentiated to dopaminergic neurons (iDAn). All iPSC lines differentiated with similar efficiency to iDAn, indicating that they could be used for phenotypic analysis. Quantification of αSyn expression showed increased αSyn intracellular staining and the novel detection of increased αSyn oligomerization in PD iDAn. Analysis of mitochondrial respiration found a decrease in basal respiration, maximal respiration, ATP production and spare capacity in PD iDAn, but not in undifferentiated iPSCs, indicating the cell-type specificity of these defects. Decreased phosphorylation of dynamin-1-like protein at Ser616 (DRP1^Ser616) and increased levels of Peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α) in A53T SNCA iDAn suggest a new pathological mechanism linking αSyn to the imbalance in mitochondria homeostasis. Markers of endoplasmic reticulum (ER) stress were found to be up-regulated, along with increased β- Glucocerebrosidase (GBA) activity, perturbation of autophagy and decreased expression of fatty acids binding protein 7 (FAPB7) in PD iDAn. Lastly, lentiviral vectors for RNAi-mediated knockdown of αSyn were developed and these reduced αSyn protein levels in iDAn, resulting in increased expression of FABP7. These results describe a novel functional link between αSyn and FABP7. This work demonstrates that iDAn are a promising and relevant in vitro cell model for studying cellular dysfunctions in PD pathology, and the phenotypic analysis of A53T SNCA and SNCA triplication iDAn enabled the detection of novel pathological mechanisms associated with PD.