Down syndrome (DS) is caused by triplication of human chromosome 21 (HSA21) and is the most common genetic form of intellectual disability. It is unknown precisely how triplication of HSA21 results in the intellectual disability, but it is thought that the global transcriptional dysregulation caused by trisomy 21 perturbs multiple aspects of neurodevelopment that cumulatively contribute to its etiology. While the characteristics associated with DS can arise from any of the genes triplicated on HSA21, in this work we focus on oligodendrocyte transcription factor 2 (OLIG2). The progeny of neural progenitor cells (NPCs) expressing OLIG2 are likely to be involved in many of the cellular changes underlying the intellectual disability in DS. To explore the fate of OLIG2+ neural progenitors, we took advantage of two distinct models of DS, the Ts65Dn mouse model and induced pluripotent stem cells (iPSCs) derived from individuals with DS. Our results from these two systems identified multiple perturbations in development in the cellular progeny of OLIG2+ NPCs. In Ts65Dn, we identified alterations in neurons and glia derived from the OLIG2 expressing progenitor domain in the ventral spinal cord. There were significant differences in the number of motor neurons and interneurons present in the trisomic lumbar spinal cord depending on age of the animal pointing both to a neurodevelopment and a neurodegeneration phenotype in the Ts65Dn mice. Of particular note, we identified changes in oligodendrocyte (OL) maturation in the trisomic mice that are dependent on spatial location and developmental origin. In the dorsal corticospinal tract, there were significantly fewer mature OLs in the trisomic mice, and in the lateral funiculus we observed the opposite phenotype with more mature OLs being present in the trisomic animals. We then transitioned our studies into iPSCs where we were able to pattern OLIG2+ NPCs to either a spinal cord-like or a brain-like identity and study the OL lineage that differentiated from each progenitor pool. Similar to the region-specific dysregulation found in the Ts65Dn spinal cord, we identified perturbations in trisomic OLs that were dependent on whether the NPCs had been patterned to a brain-like or spinal cord-like fate. In the spinal cord-like NPCs, there was no difference in the proportion of cells expressing either OLIG2 or NKX2.2, the two transcription factors whose co-expression is essential for OL differentiation. Conversely, in the brain-like NPCs, there was a significant increase in OLIG2+ cells in the trisomic culture and a decrease in NKX2.2 mRNA expression. We identified a sonic hedgehog (SHH) signaling based mechanism underlying these changes in OLIG2 and NKX2.2 expression in the brain-like NPCs and normalized the proportion of trisomic cells expressing the transcription factors to euploid levels by modulating the activity of the SHH pathway. Finally, we continued the differentiation of the brain-like and spinal cord-like NPCs to committed OL precursor cells (OPCs) and allowed them to mature. We identified an increase in OPC production in the spinal cord-like trisomic culture which was not present in the brain-like OPCs. Conversely, we identified a maturation deficit in the brain-like trisomic OLs that was not present in the spinal cord-like OPCs. These results underscore the importance of regional patterning in characterizing changes in cell differentiation and fate in DS. Together, the findings presented in this work contribute to the understanding of the cellular and molecular etiology of the intellectual disability in DS and in particular the contribution of cells differentiated from OLIG2+ progenitors.

Alzheimer's disease (AD) leads to neurodegeneration resulting in cognitive and physical impairments. AD is denoted by accumulation of intracellular neurofibrillary tangles, known as tau, and extracellular plaques of the amyloid beta protein (Aβ). Aβ results from the proteolytic cleavage of the amyloid precursor protein (APP) by β- and gamma-secretases in the amyloidogenic pathway. Although, Aβ has been widely studied for neurodegeneration, the role of APP in both, the healthy and diseased conditions, has not yet been entirely understood. The function that APP has in neural stem cell (NSC) proliferation, differentiation, and migration during adult neurogenesis has been previously studied. Additionally, APP has be shown to be overexpressed after neural damage resulted from conditions, such as AD and traumatic brain injury (TBI). In this study, the role of APP in in vitro damaged neural tissue cells was further investigated by evaluating neural progenitor cell proliferation, migration, and differentiation after a scratch assay. For these purposes, induced pluripotent stem (iPS) cells from AD patients were differentiated into neural progenitor cells to model the disease conditions and later treated with Phenserine to reduce their levels of APP expression. The results suggested that APP may enhance neural progenitor cell proliferation and glial differentiation while inhibiting neural progenitor cell migration and neuronal cell specialization after neural tissue damage.

Cells in multicellular organisms are surrounded by a complex three-dimensional macromolecular extracellular matrix (ECM). This matrix, traditionally thought to uniquely serve a structural function providing support and strength to cells within tissues, is increasingly being recognized to have pleiotropic effects in neurogenesis and regeneration processes such as neocortex folding, stem cell niche maintenance, peripheral nerve regeneration, axonal growth, and many more. ECM mediates these processes via cell-ECM interactions which provide the cells with a wealth of signals including biophysical and mechanical cues in a spatiotemporal manner. Owing to the importance of the surrounding microenvironment, modern neural tissue engineering strategies have focused on the development of engineered biomaterials capable of finely instructing the neuronal response according to their physicochemical characteristics. Neurons and neural stem cells are in fact sensitive to their mechanical and topographical environment, and cell–substrate binding contributes to this sensitivity by activating specific signaling pathways for basic cell function. In addition, the advances in nanotechnology have opened the possibility of introducing decorative nano-motifs that interact with cells at the molecular level. Successful strategies in tissue engineering are driven by not only advances in the synthesis of highly instructive biomaterials but also greatly depend on the right selection of cell sources. As a matter of fact, advances in neural tissue engineering have been strongly hampered by the poor availability of cell sources, considering that primary neurons are the only type of cells that do not proliferate. The discovery of induced pluripotent stem cells (iPSCs) has addressed many of the cell-related limitations in neural tissue engineering, offering the possibility to consistently produce a wide range of neural cell lines. Advances in cell biology have led to the development of iPSCs-derived brain spheroid, which surely represent the most promising tools for several neural tissue engineering applications ranging from in vitro modelling of neurodegenerative diseases (i.e., Parkinson's, Huntington's and Alzheimer's), biomaterials testing and drug screening platforms. The overarching goal of my doctoral work was to engineer biomaterials with instructive physicochemical properties to elicit beneficial cellular responses that are suitable for different neural tissue engineering applications such as nerve regeneration and 3D in vitro modelling. In the first study (Chapter 2), I evaluated the compounded effects of surface stiffness and micro-topography on dorsal root ganglion and human bone-marrow mesenchymal stem cells behavior. To this end, arrays of parallel microchannels of different geometries were introduced on the surface of chitosan films by electrophoretic replica deposition. In addition, a novel chemical crosslinking with citric acid was performed to both enhance the long-term stability of the chitosan films and fine-tune the surface stiffness for the investigation of its role in cell behavior. In the second study (Chapter 3), I developed a novel nanocomposite consisting of a collagen hydrogel decorated with glycine-derived carbon nanodots (Gly-CNDs). After a comprehensive physicochemical characterization of the resulting nanocomposite, I evaluated the effects exerted on neuronal differentiation and electrophysiological maturation of mouse iPSCs-derived brain spheroid. In the third study (Chapter 4), I optimized an alignable collagen-based hydrogel characterized by anisotropically oriented fibers with potential applications in both peripheral and central nervous system repair. I established a protocol that encompasses the introduction in the collagen solution of biodegradable laminin-functionalized magnetic microbeads and the time-controlled application of an external magnetic field. The regenerative potential of the hydrogel was unveiled using mouse iPSCs-derived neural stem cells.

La dystrophie musculaire de Duchenne de Boulogne (DMD) est une myopathie héréditaire liée au chromosome X et causée par une mutation du gène de la dystrophine. Affectant un garçon sur 5000, cette maladie entraine une dégénérescence progressive des muscles striés squelettiques et cardiaques. A ce jour, la DMD demeure une maladie invalidante, incurable et les personnes atteintes ont une espérance de vie de 30 ans. Parmi les thérapies innovantes en cours de développement, la thérapie cellulaire est une stratégie prometteuse. Cependant elle présente plusieurs limitations notamment liées à l’efficacité des types cellulaires utilisés et le devenir des cellules après injection in vivo. Le premier objectif de cette thèse est le développement d’une méthode d’imagerie pour étudier à l’échelle de l’organisme et de façon non invasive la biodistribution et la survie des cellules suite à leur injection systémique dans un modèle préclinique pertinent, le chien GRMD (Golden Retriever Muscular Dystrophy), un modèle animal reproduisant fidèlement le phénotype DMD. Notre attention s’est portée sur l’utilisation du symporteur sodium iode (NIS) pour le suivi non invasif des cellules. Nous avons obtenu des cellules myogéniques exprimant le NIS, autorisant leur visualisation par scintigraphie grâce à la propriété d’absorption du technétium 99m conférée par ce symporteur. Nous avons montré in vitro que le NIS est fonctionnel pour la capture de radioactivité même après une différentiation avancée des cellules. En parallèle, nous nous sommes intéressés au type cellulaire. Les cellules primaires ayant une capacité de renouvellement limitée, cela restreint leur utilisation en thérapie et leur modification génomique. Afin de contourner cette limitation, plusieurs protocoles visant à obtenir des cellules souches pluripotentes induites (iPSCs) dérivées de cellules canines ont été utilisés. De plus, pour ne plus être dépendant de l’immunosuppression imposée par les greffes allogéniques, nous avons utilisé le système d’édition génomique CRISPR/Cas9 pour mettre au point une correction des cellules GRMD afin de permettre la réalisation de greffes autologues. Nous avons également utilisé le système CRISPR/Cas9 pour réaliser l’insertion ciblée du gène NIS dans un site précis du génome des cellules. Les résultats obtenus autorisent le développement de programmes comparant le potentiel thérapeutique de cellules dans un modèle préclinique de la DMD. / Duchenne muscular dystrophy (DMD), an X-linked recessive myopathy, is caused by mutations in the dystrophin gene. One boy out of 5000 is affected by this disease, which induces a progressive loss of skeletal striated and cardiac muscles. To date, DMD remains an invalidating disease and there is no cure for it. People suffering from DMD usually die in their 30’s. Among the innovative therapies currently under development, cell therapy is a promising strategy. However, it has some limitations related notably to a low efficiency of tested therapeutic cells and their tracking in vivo after injection. The first aim of this thesis is to develop an imaging method allowing non-invasive monitoring of biodistribution and survival of cells at the scale of a large organism, following systemic injection in the GRMD dog (Golden retriever muscular Dystrophy, a relevant animal model of DMD, as it replicates finely the DMD phenotype). We took interest in the sodium iodide symporter (NIS) as an imaging reporter. We induced the expression of the NIS in myogenic cells to allow visualization of the cells by scintigraphy thanks to its ability to uptake technetium 99m. We showed that NIS is functional in the cells and they maintain their ability to differentiate. Primary cells have a limited self-renewal capability restraining their use in human cell therapy and gene editing. To overcome this limitation, we used several protocols to derive induced pluripotent stem cells (iPSCs) from adult canine cells. Furthermore, to avoid immune suppression protocols, we used the CRISPR/Cas9 gene editing tools to design a correction strategy of the GRMD mutation for future autologous injections. We also used CRISPR/Cas9 to perform a targeted integration of the NIS gene in a safe harbor locus. Results allow us to develop protocols to compare the therapeutic potential of candidate cells in a preclinical model of DMD.

Em 2006, Takahashi e colaboradores demonstraram ser possível a obtenção de células-tronco pluripotentes por indução gênica (induced pluripotent stem cells ou iPSCs). Desde o surgimento desta tecnologia diversos modelos animais foram gerados, ampliando as possibilidades de seu uso na pesquisa, como por exemplo, na criação de modelos para doenças genéticas humanas como esclerose lateral amiotrófica, autismo, esquizofrenia, doença de Parkinson e Alzheimer, além do aprimoramento de características relevantes para produção animal. O modelo suíno é considerado vantajoso sobre os outros modelos animais principalmente pela criação já bem estabelecida e similaridades fisiológicas com os humanos. O intuito deste projeto foi reprogramar fibroblastos embrionários suínos através do sistema integrativo à iPSCs, para então diferenciá-las em células progenitoras neurais (neural progenitor cells, NPCs). Para isso, os fibroblastos foram transduzidos com vetores contendo sequencias humanas ou murinas dos genes OCT4, SOX2, c-Myc e KLF4 (hOSKM ou mOSKM) para formação das iPSCs. Estas foram caracterizadas quanto a morfologia, presença de fosfatase alcalina, a expressão dos genes exógenos e endógenos (OSKM, HS OCT4, OCT4, NANOG) através de imunofluorescência e RT-qPCR e formação de corpos embrióides. Então foram submetidas durante 14 dias ao meio de indução neural sob matriz extracelular comercial, gerando células potencialmente similares às NPCs. Estas foram caracterizadas morfologicamente, por imunofluorescência das proteínas NESTINA, BETA TUBULINA III e VIMENTINA, além da expressão de NESTINA e GFAP por RT-qPCR. Foram produzidas com sucesso 3 linhagens de iPSC em diferentes estágios de reprogramação e células positivas para todos os marcadores neurais testados. Os resultados apresentados deverão contribuir para a utilização do modelo suíno em futuros estudos voltados à medicina regenerativa e translacional. / In 2006, Takahashi and collaborators reported the induction into pluripotency of somatic cells (induced pluripotent stem cells, iPSCs). Since then, this technique has much been developed; many animal models have been created opening a new series of opportunities in research. They enable the creation of models for human genetic diseases, for example, amyotrophic lateral sclerosis, autism, schizophrenia, Parkinson´s disease, Alzheimer´s disease and the enhancement of relevant characteristics in agriculture. The swine model is considered to present many advantages over others, including the well-known production and maintenance and physiological similarities to humans. The aim of this project was to reprogram porcine embryonic fibroblasts (pEF) into iPSCs using the lentiviral integrative system, followed by its differentiation into neural progenitor cells (NPCs). The cells were reprogrammed using vector containing either the human sequences (hOSKM) or the mouse sequences (mOSKM) for the OCT4, SOX2, c-Myc and KLF4 genes to form the iPSCs. They were characterized regarding the presence of the Alkaline Phosphatase enzyme, expression of exogenous and endogenous genes (OSKM, HS OCT4, OCT4, NANOG) through immunofluorescence and RT-qPCR, and embryoid body formation. Then, the cells were cultured with neural induction media for 14 days in commercial extracellular matrix, generating cells potentially like NPCs. Those were characterized regarding their morphology, immunofluorescence for NESTINA, BETA TUBULIN III and VIMENTINA and gene expression of NESTINA and GFAP. iPSCs were successfully reprogramed, generating 3 cell lines at different stages of reprograming and cells positive for all the neural markers tested were produced. The results shown will contribute to the use of the porcine model in future regenerative and translational medicine research.

In adult CMs, ryanodine receptor 2 (RYR2) is an indispensable Ca2+ release channel that ensures the integrity of excitation-contraction (E-C) coupling, which is fundamental for every heartbeat. However, the role and importance of RYR2 during human embryonic cardiac development are still poorly understood. In this study, after the knockout of RYR2 gene (RYR2–/–), induced pluripotent stem cells (iPSCs) were able to differentiate into cardiomyocytes (CMs) with an efficiency similar to control iPSCs (Ctrl-iPSCs); however, the survival of iPSC-CMs was markedly affected by the lack of functional RYR2. While Ctrl-iPSC-CMs exhibited regular Ca2+ handling, significantly reduced frequency and intense abnormalities of Ca2+ transients were observed in RYR2–/–-iPSC-CMs. Ctrl-iPSC-CMs displayed sensitivity to extracellular calcium ([Ca2+]o) and caffeine in a concentration-dependent manner, while RYR2–/–-iPSC-CMs showed inconsistent reactions to [Ca2+]o and were insensitive to caffeine, indicating there is no RYR2-mediated Ca2+ release from the sarcoplasmic reticulum (SR). Instead, the compensatory mechanism for Ca2+ handling in RYR2–/–-iPSC-CMs is partially mediated by the Inositol 1,4,5-trisphosphate receptor (IP3R). Similar to Ctrl-iPSC-CMs, SR Ca2+ refilling in RYR2–/–-iPSC-CMs is mediated by sarcoplasmic/endoplasmic reticulum Ca2+-ATPase (SERCA). Additionally, RYR2–/–-iPSC-CMs showed a decreased beating rate and a reduced L-type Ca2+ current (ICaL) density. These findings demonstrate that RYR2 is not required for CM lineage commitment but is important for CM survival and contractile function. IP3R-mediated Ca2+ release is one of the major compensatory mechanisms for Ca2+ cycling in human CMs with the RYR2 deficiency. Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a life-threatening inherited arrhythmogenic disorder. RYR2 mutations are the genetic cause of CPVT Type 1. So far, the pathogenic mechanism of how RYR2 mutations remodel cardiac rhythm remains controversial, because all existing hypotheses cannot independently and universally represent the mechanism behind CPVT. Patient-specific iPSCs offer a unique opportunity for CPVT modeling and investigation in vitro. In this study, the effects of four different RYR2 mutations (R420W, A2254C, E4076K, and H4742Y) on cardiac Ca2+ handling were examined individually. The R420W mutation in CPVTa-iPSC-CMs showed no effect on the amplitude of paced Ca2+ transients but led to an increased Ca2+ leak and a decreased SR Ca2+ content. Moreover, CPVTa-iPSC-CMs presented an enhanced sensitivity to [Ca2+]o and caffeine but a lower ICaL density. Compared to Ctrl cells, CPVTb-iPSC-CMs carrying the A2254V mutation displayed Ca2+ transients with smaller amplitude and higher frequency. More importantly, CPVTb-iPSC-CMs showed remarkably severe Ca2+ leak and unaltered SR Ca2+ content. The A2254V mutation also enhanced the sensitivity of iPSC-CMs to [Ca2+]o and caffeine. Interestingly, the ICaL density was found higher in CPVTb-iPSC-CMs. As for the E4076K mutation, it caused a reduction in both amplitude and frequency of Ca2+ transients in CPVTc-iPSC-CMs. In addition, the sensitivity to [Ca2+]o was diminished in CPVTc-iPSC-CMs, while the caffeine sensitivity and ICaL density were not changed. Regarding the H4742Y mutation, it led to a reduction of Ca2+ transient amplitude. In addition, CPVTd-iPSC-CMs manifested unique SR Ca2+ leak, which was resistant to tetracaine, suggesting a conformational remodeling of the H4742Y-mutated RYR2. Furthermore, CPVTd-iPSC-CMs also showed enhanced sensitivity to [Ca2+]o and caffeine, although the ICaL density was comparable to Ctrl-iPSC-CMs. In summary, the A2254V variation presented a typical gain-of-function mutation, rendering the RYR2 hyperactive, while the E4076K variation was identified as a loss-of-function mutation, leading to hypoactive RYR2. R420W and H4742Y mutations did not enhance or suppress the activity of RYR2. However, by destabilizing the N-terminal domain (NTD) of RYR2, the R420W mutation caused Ca2+ leak via the mutant channel, which could be blocked by RYR2 inhibitor. As for the H4742Y mutation, it led to a consistent and inhibitor-resistant Ca2+ leak via RYR2, suggesting a structural remodeling of RYR2 that disturbs complete closure of the channel. These results confirmed the importance of RYR2 on the maintenance of Ca2+ handling and gained evidence for the theory that the underlying mechanisms of CPVT caused by mutations in RYR2 should be mutation-specific rather than unified. This study suggests hiPSC-CMs as a suitable platform for modeling cardiac arrhythmogenic disease, interpreting potential molecular and pathophysiological mechanisms, testing new therapeutic compounds, and guiding mechanism-specific therapy.:Abbreviations V List of figures VIII List of tables X 1 Introduction 1 1.1 Human induced pluripotent stem cells 1 1.1.1 Generation and characteristics of human induced pluripotent stem cells 1 1.1.2 Differentiation of hiPSCs into cardiomyocytes 3 1.1.3 Modeling of inherited cardiac disease with hiPSCs 4 1.2 Catecholaminergic polymorphic ventricular tachycardia 7 1.2.1 Clinical characteristics and diagnosis of CPVT 7 1.2.2 Genetic background of CPVT 8 1.2.3 Clinical descriptions of CPVT patients recruited in this study 10 1.2.4 Patient-specific iPSC-CMs recapitulate the phenotypes of CPVT in vitro 10 1.3 Cardiac excitation-contraction coupling 11 1.3.1 Cardiac action potential 12 1.3.2 Ca2+ homeostasis in cardiomyocytes 14 1.3.2.1 Ca2+ influx via L-type Ca2+ channel 14 1.3.2.2 Initiation and termination of SR Ca2+ release 15 1.3.2.3 Ca2+ removal from cytosol 17 1.3.3 Cardiomyocyte contraction 20 1.4 Cardiac ryanodine receptor 21 1.4.1 Distribution and classification of RYRs 22 1.4.2 Regulation of RYR2 23 1.4.2.1 Cytosolic Ca2+ 23 1.4.2.2 Luminal Ca2+ 24 1.4.2.3 Phosphorylation by PKA and CaMKII 25 1.4.2.4 Calmodulin 27 1.4.2.5 Caffeine 27 1.4.3 Pathophysiological mechanisms of CPVT associated with RYR2 mutations 28 2 Aims of this study 33 3 Materials and methods 34 3.1 Materials 34 3.1.1 Cells 34 3.1.2 Laboratory devices and experimental hardware 34 3.1.3 Disposable items 36 3.1.4 Chemicals, solutions, and buffers for physiological and molecular experiment 36 3.1.5 Antibodies 40 3.1.6 Primers 41 3.1.7 Chemicals, media and solutions used for cell culture 42 3.1.8 Software 44 3.2 Methods 44 3.2.1 Cell culture 44 3.2.1.1 Preparation of glass coverslips for cell culture 44 3.2.1.2 Coating of plates and dishes 44 3.2.1.3 Cultivation of iPSCs with feeder-free method 45 3.2.1.4 Cryopreservation and thawing of iPSCs 45 3.2.1.5 Spontaneous differentiation of iPSCs in vitro 45 3.2.1.6 Directed differentiation of iPSCs into cardiomyocytes 46 3.2.1.7 First digestion of iPSC-CMs 46 3.2.1.8 Cryopreservation and thawing of iPSC-CMs 46 3.2.1.9 Time-dependent proliferation analysis of iPSC-CMs 47 3.2.1.10 Second digestion of iPSC-CMs 47 3.2.1.11 Collection of cell pellets for molecular experiment 47 3.2.2 Cell viability assay 48 3.2.3 Gene expression analyses 48 3.2.3.1 RNA isolation 48 3.2.3.2 Reverse transcription reaction 48 3.2.3.3 Polymerase chain reaction 49 3.2.3.4 Agarose gel electrophoresis 49 3.2.4 Protein expression analyses 49 3.2.4.1 Western blot 49 3.2.4.1.1 Lysis of cultured cells 49 3.2.4.1.2 SDS-polyacrylamide gel electrophoresis 50 3.2.4.1.3 Transfer and detection of proteins 50 3.2.4.2 Flow cytometry 51 3.2.4.3 Immunofluorescence staining 51 3.2.5 Calcium imaging 51 3.2.5.1 Measurement of spontaneous Ca2+ transients 52 3.2.5.2 Evaluation of diastolic SR Ca2+ leak and SR Ca2+ content 52 3.2.5.3 Assessment of iPSC-CM sensitivity to [Ca2+]o 53 3.2.5.4 Quantification of iPSC-CM response to caffeine 53 3.2.6 Patch-clamp 53 3.2.6.1 Preparation of agar salt bridge 53 3.2.6.2 Assessment of liquid junction 53 3.2.6.3 Measurement of action potential and L-type calcium current 54 3.2.7 Statistical analysis 54 4 Results 55 4.1 IP3R-mediated SR Ca2+ release partially restores the impaired Ca2+ handling in iPSC-CMs with RYR2 deficiency 55 4.1.1 Loss of RYR2 does not alter the pluripotency of RYR2–/–-iPSCs 55 4.1.2 Loss of RYR2 leads to increased death of RYR2–/–-iPSC-CMs 56 4.1.3 Loss of RYR2 does not affect the expression of IP3R in iPSC-CMs 58 4.1.4 RYR2–/–-iPSC-CMs show abnormal Ca2+ transients 60 4.1.5 The sensitivity of RYR2–/–-iPSC-CMs to [Ca2+]o and caffeine is changed 62 4.1.6 IP3R is critical for the generation Ca2+ transients in RYR2–/–-iPSC-CMs 63 4.1.7 SERCA-mediated SR Ca2+ uptake is crucial for the Ca2+ handling in both Ctrl- and RYR2–/–-iPSC-CMs 65 4.1.8 RYR2–/–-iPSC-CMs display abnormal action potentials 66 4.2 Investigation of the impaired function of RYR2 in CPVTa-iPSC-CMs 69 4.2.1 The R420W mutation leads to increased SR Ca2+ leak and decreased SR Ca2+ content 69 4.2.2 The R420W mutation leads to an enhanced sensitivity of iPSC-CMs to [Ca2+]o 70 4.2.3 CPVTa-iPSC-CMs shows increased sensitivity to caffeine 71 4.2.4 CPVTa-iPSC-CMs show reduced ICaL density 72 4.3 Investigation of the impaired function of RYR2 in CPVTb-iPSC-CMs 74 4.3.1 CPVTb-iPSC-CMs show abnormal Ca2+ transients 74 4.3.2 The A2254V mutation intensifies the SR Ca2+ leak in iPSC-CMs 75 4.3.3 The A2254V mutation enhances the sensitivity of iPSC-CMs to [Ca2+]o 76 4.3.4 The A2254V mutation increases the sensitivity of iPSC-CMs to caffeine 78 4.3.5 CPVTb-iPSC-CMs show increased ICaL density 78 4.4 Investigation of the impaired function of RYR2 in CPVTc-iPSC-CMs 79 4.4.1 CPVTc-iPSC-CMs show abnormal Ca2+ transients 79 4.4.2 The E4076K mutation shows no effect on the SR Ca2+ leak and content 80 4.4.3 The E4076K mutation diminishes the sensitivity of iPSC-CMs to [Ca2+]o 81 4.4.4 The E4076K mutation shows almost no effect on the response of iPSC-CMs to caffeine 82 4.4.5 The E4076K mutation does not alter the ICaL density in iPSC-CMs 83 4.5 Investigation of the impaired function of RYR2 in CPVTd-iPSC-CMs 84 4.5.1 CPVTd-iPSC-CMs show abnormal Ca2+ transients 84 4.5.2 The H4742Y mutation leads to a tetracaine-resistant Ca2+ leak in iPSC-CMs 84 4.5.3 The H4742Y mutation improves the sensitivity of iPSC-CMs to [Ca2+]o 86 4.5.4 The H4742Y mutation enhances the response of iPSC-CMs to caffeine 87 4.5.5 The H4742Y mutation alters the gating properties of LTCC in iPSC-CMs 88 5 Discussion 90 5.1 IP3R-mediated compensatory mechanism for Ca2+ handling in iPSC-CMs with RYR2 deficiency 90 5.2 Pathophysiological mechanisms of RYR2 mutation-related CPVT are mutation-specific 93 5.2.1 Dysfunctional Ca2+ handling caused by RYR2-R420W mutation 94 5.2.2 Dysfunctional Ca2+ handling caused by RYR2-A2254V mutation 96 5.2.3 Dysfunctional Ca2+ handling caused by RYR2-E4076K mutation 99 5.2.4 Dysfunctional Ca2+ handling caused by RYR2-H4742Y mutation 101 5.3 Conclusions and future perspectives 104 6 Summary 106 7 Zusammenfassung 108 8 References 111 9 Acknowledgements 131 10 Declaration 132

Diabetes ist ein weltweites Problem, das durch den Verlust oder die Dysfunktion der Insulin-produzierenden β-Zellen des Pankreas verursacht wird. In seltenen Fällen entsteht Diabetes durch eine Mutation in einem einzigen Gen. Diese monogenetischen Formen des Diabetes können zur Identifizierung neuer Regulatoren der β-Zellen-Entwicklung und -Funktion beitragen. In der vorliegenden Arbeit habe ich neue putative Diabetes-assoziierte Gene untersucht, die zuvor durch „Next-Generation“ Sequenzierung in einer Gruppe von Kindern und Jugendlichen mit idiopathischem Diabetes festgestellt wurden. Insbesondere analysierte ich neuartige Mutationsvarianten in Genen kodierend für Histone deacetylase 4 (HDAC4), Glioma-associated oncogene homolog 1 (GLI1) und Glioma-associated oncogene homolog 2 (GLI2). Basierend auf den folgenden Kriterien wurden diese Transkriptionsregulatoren zur weiteren funktionellen Analyse priorisiert: Genetische Information, Patientenphänotyp und Expressionsprofil der Kandidaten Gene in Mauspankreas-Vorläuferzellen. Um die Rolle der Varianten während der pankreatischen Zelltypspezifizierung zu untersuchen, nutzte ich die CRISPR-Cas9 Methode in Kombination mit Stammzellendifferenzierung. Im Detail generierte ich diverse Stammzellen mittels CRISPR-Cas9, die die Mutationsvarianten der Patienten trugen und differenzierte diese zu β-ähnlichen Zellen. Weitere in vitro und Transkriptionsanalysen zeigten, dass die Variante c.C4661T in GLI2 die Entwicklung der β-ähnlichen Zellen beeinträchtigte, was für eine genetische Prädisposition zur Entwicklung von Diabetes verantwortlich sein kann. Zusätzlich nutzte ich diese Plattform, um neue extrinsische Faktoren zu untersuchen und zeigte, dass die fördernde Rolle von HC toxin (HDAC Inhibitor) und SLIT3 (ROBO Ligand) konserviert ist. Zusammenfassend habe ich eine Differenzierungsplattform etabliert, um die Rolle von genetischen und extrinsischen Faktoren für die Entwicklung des Pankreas und/oder β-Zellen zu untersuchen. / Diabetes is a worldwide health problem caused by the loss or dysfunction of the insulin-secreting β-cells in the pancreas. Unelucidated forms of monogenic diabetes, arising from rare mutations in one single gene, represent invaluable models for identifying new targets of β-cell development and function. In this study, I focused on putative disease-associated genes for diabetes that have been previously identified by next-generation sequencing of a cohort of patients with puberty-onset diabetes. In particular, I investigated unique mutant variants in genes coding for Histone deacetylase 4 (HDAC4), Glioma-associated oncogene homolog 1 (GLI1) and Glioma-associated oncogene homolog 2 (GLI2). These transcriptional regulators were prioritized for functional analysis based on patient phenotype, expression level in pancreas progenitor cells and available genetic information. To investigate the role of the genetic mutant variants in pancreatic cell fate decisions and cell function, I used the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 genome editing technology in combination with human induced pluripotent stem cell (iPSC)-directed β-cell differentiation. Employing these approaches, I established several patient-like iPSC lines carrying the identified heterozygous missense variants. Specifically, functional experiments and whole transcriptome analysis showed that the variant c.C4661T in GLI2 impairs human β-cell differentiation and β-cell function, which might be responsible for a genetic predisposition to develop diabetes. In addition, I used the same iPSC-based differentiation model system to study novel extrinsic factors, namely the HDAC inhibitor HC toxin and the ROBO ligand SLIT3 and uncovered their conserved role in enhancing human β-cell development. Taking together, I established a human iPSC differentiation platform to study critical genes and extrinsic factors that are necessary for human pancreas development and/or β-cells.

Amyotrophic Lateral Sclerosis (ALS) is an incurable late onset neurodegenerative disorder characterised by the specific loss of motor neurones (MNs). It has been recently demonstrated that Transactive response DNA-binding protein (TDP-43) is the dominant disease protein in both ALS and a sub-group of frontotemporal lobar degeneration (FTLDTDP). Moreover, the identification of TARDBP mutations in familial ALS confirms a mechanistic link between the observed mis-accumulation of TDP-43 and neurodegeneration but also provides an opportunity to establish an in vitro platform to model these diseases, based on patient-derived induced pluripotent stem cells (iPSCs). This study presents the optimization of an iPSC-based platform to study the consequences of TDP-43 M337V mutation in human functional populations of MNs and astrocytes in isolation as well as in co-culture. To develop this platform, two protocols to differentiate patient-derived iPSCs into functional MNs and astrocytes were first optimized, and the obtained cellular populations were then used to characterize the behaviour of mutant TDP-43 and its effect on the different cell types. This study show that it is possible to use iPSC-based platforms to recapitulate in vitro key aspects of TDP-43 proteinopathies such as MN cell autonomous toxicity and TDP-43 accumulation, but they can also be used to highlight previously unrecognised disease specific mechanisms and to test novel therapeutic approaches. Moreover, by performing co-culture experiments it was possible to evaluate the effects of M337V astrocytes on the survival of wild-type and M337V TDP-43 motor neurons, showing that mutant TDP-43 astrocytes do not adversely affect survival of co-cultured neurons. This iPSC-based platform represents an in vitro model to study both the effect of somatic mutations on isolated patient-specific cultures, but also to investigate cellular autonomy and neurodegeneration in the context of TDP-43 proteinopathies.

Submitted by PPG Medicina e Ci?ncias da Sa?de (medicina-pg@pucrs.br) on 2018-03-26T16:55:48Z No. of bitstreams: 1 RODRIGO_BRACCINI_MADEIRA_DA_SILVA_TES.pdf: 6388000 bytes, checksum: c5e864eb62bd553c3a29e7bad1b85fef (MD5) / Rejected by Tatiana Lopes (tatiana.lopes@pucrs.br), reason: Devolvido porque o pdf inserido no TEDE ? de outro aluno. on 2018-03-28T14:20:43Z (GMT) / Submitted by PPG Medicina e Ci?ncias da Sa?de (medicina-pg@pucrs.br) on 2018-03-28T14:24:15Z No. of bitstreams: 1 FERNANDA_MAJOLO_TES.pdf: 6002507 bytes, checksum: 764acb66fc06c518428a40b9eb5bdd26 (MD5) / Approved for entry into archive by Tatiana Lopes (tatiana.lopes@pucrs.br) on 2018-03-28T16:23:42Z (GMT) No. of bitstreams: 1 FERNANDA_MAJOLO_TES.pdf: 6002507 bytes, checksum: 764acb66fc06c518428a40b9eb5bdd26 (MD5) / Made available in DSpace on 2018-03-28T16:29:23Z (GMT). No. of bitstreams: 1 FERNANDA_MAJOLO_TES.pdf: 6002507 bytes, checksum: 764acb66fc06c518428a40b9eb5bdd26 (MD5) Previous issue date: 2018-01-11 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Malformations of cortical development (MDC) include a wide spectrum of Central Nervous System (CNS) disorders related to a complex process of cortex formation. Focal Cortical Dysplasia (FCD), a common type of MDC, is reported as the most frequent structural brain lesion found in children with refractory epilepsy to drug treatment undergoing surgery. Surgical treatment, with complete resection of the dysplastic lesion, is able to stop the seizure resistant to antiepileptic drugs, improving the individual's quality of life and reducing morbidity. FCD is characterized by multiple types of alterations both in cortical architecture and in cytologic abnormalities and it?s pathogenesis is still unknown. In 2004, Palmini et al. classified DCF according to white matter and cortical layer architecture. Taylor-type FCD is characterized by cortical laminar disorganization and dysplastic neurons, compromising the organization of the cortex into six-layered traditionally known. Understanding the mechanisms of action of neurological diseases has involved the use of animal models. However, in the case of brain development of epileptic syndromes, many decades of study have failed to provide a conclusive insight of their mechanisms. Modeling neurological diseases is especially attractive for the application of induced pluripotent stem cells (iPSCs), making possible to derive specific neurons for in vitro studies, contributing to the investigation of the disease. The aim of the present study was to investigate the possible differences in neurogenesis and neurodifferentiation of iPSCs from fibroblasts of individuals affected by Taylor-type FCD and normal individuals. iPSCs were generated from skin fibroblasts of two FCD individuals and two healthy individuals, to form the control group. The reprogramming was done through the fibroblasts exposure to viral vectors containing the OCT4, KLF4, SOX2, and c-MYC genes and the clones were characterized by immunohistochemistry. iPSCs were neurodifferentiated and analyzed at the 14th, 22nd and 35th days. We also analyzed the brain tissue, fibroblasts and iPSCs cells from the individuals. Through qRT-PCR, the expression of 14 genes involved in the neurodifferentiation process were quantified. These genes are associated to neural migration and differentiation, synaptic aspects and Notch signaling. Both individuals were diagnosed with Taylor-type FCD, more specifically, type IIb. In general, individuals with dysplasia presented alterations in the relative quantification in the most genes analyzed compared to control individuals in all processes and study groups (fibroblasts, brain tissue, iPSCs 8 and neurodifferentiated cells). The genes involved in the neural migration and differentiation processes, as well as synaptic aspects and Notch signaling presented quite altered expressions in dysplastic individuals, with the beginning of the majority processes early, before the physiologically typical period. From the found results, we can infer that during the embryonic period, in the neurogenesis and neurodifferentiation process, individuals affected by the disease, possibly presents neuroblasts more sensitive to stimulus, presenting differences in the development of the Nervous System. These changes may be directly related to dysplastic brain development. This work extends the understanding of embryonic neurodevelopment, open up opportunities to further investigations of the involvement and influence of each genes analyzed in the pathogenesis of FCD, as well as in each mechanism of action involved in the brain development. / As Malforma??es do Desenvolvimento Cortical (MDC) re?nem uma ampla gama de patologias do Sistema Nervoso Central (SNC) relacionadas a um complexo processo de forma??o do c?rtex. A Displasia Cortical Focal (DCF), tipo comum de MDC, ? relatada como a les?o cerebral estrutural mais frequente encontrada em crian?as com epilepsia refrat?ria ao tratamento medicamentoso submetidas ? cirurgia. O tratamento cir?rgico, com a ressec??o completa da les?o displ?sica, ? capaz de cessar a convuls?o resistente a drogas antiepil?ticas, melhorando a qualidade de vida do indiv?duo e diminuindo a morbidade. A DCF ? caracterizada por m?ltiplos tipos de altera??es tanto na arquitetura cortical quanto em anormalidades citol?gicas e sua patog?nese ainda ? desconhecida. Em 2004, Palmini e colaboradores classificaram as DCF de acordo com observa??es na subst?ncia branca e na arquitetura da camada cortical. A DCF do tipo Taylor ? caracterizada por uma desorganiza??o laminar e neur?nios displ?sicos, comprometendo a organiza??o do c?rtex em seis camadas histol?gicas tradicionalmente conhecidas. A compreens?o dos mecanismos de a??o das doen?as neurol?gicas tem envolvido o uso de modelos animais. Por?m, no caso do desenvolvimento cerebral das s?ndromes epil?pticas muitas d?cadas de estudo n?o conseguiram fornecer uma vis?o conclusiva sobre seus mecanismos. Modelar doen?as neurol?gicas ? especialmente atraente para aplica??o das c?lulas pluripotentes induzidas (iPSCs), possibilitando derivar neur?nios espec?ficos do pr?prio paciente para estudos in vitro, contribuindo para a investiga??o da doen?a. O objetivo do presente estudo foi investigar as poss?veis diferen?as na neurog?nese e neurodiferencia??o de iPSCs a partir de fibroblastos de indiv?duos acometidos pela DCF do tipo Taylor e indiv?duos normais. As iPSCs foram geradas a partir de fibroblastos de pele de dois indiv?duos displ?sicos e dois indiv?duos saud?veis, para compor o grupo controle. A reprograma??o se deu atrav?s da exposi??o dos fibroblastos a vetores virais contendo os genes OCT4, KLF4, SOX2, e c-MYC e os clones gerados foram caracterizados por imunohistoqu?mica. As c?lulas iPSCs foram neurodiferenciadas e analisadas nos per?odos de 14, 22 e 35 dias. Tamb?m foram analisados o tecido cerebral, fibroblastos e c?lulas iPSCs dos indiv?duos. Atrav?s de qRT-PCR, a express?o de 14 genes envolvidos no processo de neurodiferencia??o foram quantificados. Estes genes est?o associados a migra??o e diferencia??o neural, 6 aspectos sin?pticos e sinaliza??o Notch. Ambos os indiv?duos foram diagnosticados com DCF do tipo Taylor, mais especificadamente, do tipo IIb. No geral, os indiv?duos displ?sicos apresentaram altera??es na quantifica??o relativa na maioria dos genes analisados comparados aos indiv?duos controle, em todos os processos e grupos de estudo (fibroblastos, tecido cerebral, iPSCs e c?lulas neurodiferenciadas). Os genes envolvidos nos processos de migra??o e diferencia??o neural, aspectos sin?pticos e sinaliza??o Notch apresentaram express?es bastante alteradas nos indiv?duos displ?sicos, com o in?cio da maioria dos processos precoces, antes do per?odo fisiologicamente t?pico. A partir dos resultados encontrados, podemos inferir que durante o per?odo embrion?rio, no processo de neurog?nese e neurodiferencia??o, indiv?duos acometidos pela doen?a, possivelmente possuem neuroblastos mais sens?veis a est?mulos, apresentando diferen?as no desenvolvimento do Sistema Nervoso. Essas altera??es podem estar diretamente relacionadas com a forma??o do c?rebro displ?sico. Este trabalho amplia a compreens?o do neurodesenvolvimento embrion?rio, abrindo portas para futuras investiga??es de forma mais aprofundada sobre o envolvimento e influ?ncia de cada um dos genes analisados na patog?nese da DCF, bem como em cada mecanismo de a??o envolvido na forma??o do c?rebro.

Schizophrenia is a major psychiatric disorder that affects 1% of the world population and is among the 10 leading worldwide causes of disability. Disrupted-In- Schizophrenia (DISC1) is one of the most studied risk genes for mental illness and is disrupted by a balanced translocation between chromosomes 1 and 11 that co-segregates with major mental illness in a single large Scottish family. DISC1 is a scaffold protein with numerous interactors and has been shown to hold key roles in neuronal progenitor proliferation, migration, cells signalling and synapse formation and maintenance. The studies herein provide the platform in order to investigate the molecular and cellular consequences of the t(1;11) translocation using induced pluripotent stem cells (iPSCs)-derived neural precursor cells and neurons from within-family carriers and controls. Towards this end, several iPSC lines have been converted into neural progenitor cells (NPCs) and differentiated into physiologically active forebrain neurons following well-characterised protocols. These cells were characterised in terms of basic marker expression at each developmental stage. Inter-line variation was observed in all subsequent experiments but overall t(1;11) lines did not generate less neuronal or less proliferating cells compared to control lines. Furthermore, the expression pattern of genes disrupted by the t(1;11) translocation was investigated by RT-qPCR. DISC1 was reduced by ~50% in the translocation lines, both neural precursors and neurons. This observation corresponds to previous findings in lymphoblastoid cell lines (LBCs) derived from members of the same family. Moreover, DISC1 expression was found to increase as neural precursors differentiation to neurons. Two other genes are disrupted by the t(1;11) translocation;DISC2 and DISC1FP1. Their expression was detectable, but below the threshold of quantification. Similarly, DISC1/DISC1FP1 chimeric transcripts corresponding to such transcripts previously identifies in LBCs from the family were detectable, but not quantifiable. A fourth gene, TSNAX, was also investigated because it is located in close proximity to, and undergoes intergenic splicing with, DISC1. Interestingly, TSNAX was found to be altered in some but not all time points studied, in the translocation carriers compared to control lines. In addition to breakpoint gene expression profiling, iPSC-derived material was used to investigate neuronal differentiation. There seemed to be attenuation in BIII-TUBULIN expression at two weeks post-differentiation, while NESTIN, MAP2 and GFAP expression was similar between translocation carrier and control lines at all time points studied. I also had access to targeted mice designed to mimic the derived chromosome 1 of the t(1;11) balanced translocation. Using RT-qPCR Disc1 expression was found to be 50% lower in heterozygous mice compared to wild types, and I detected a similar profile of chimeric transcript expression as detected in translocation carrier-derived LBCs. These observations support my gene expression studies of the human cells and indicate that the iPSC-derived neural precursors and neurons can be studied in parallel with the genome edited mice to obtain meaningful insights into the mechanism by which the t(1;11) translocation confers substantially elevated risk of major mental illness. In conclusion, the studies described in this thesis provide an experimental platform for investigation of the effects of the t(1;11) translocation upon function and gene and protein expression in material derived from translocation carriers and in brain tissue from a corresponding mouse model.