Current usage of human embryonic stem cells (hES) and induced pluripotent stem cells (iPS) in clinical therapies and personalized medicine are limited as a result of ethical, technical and medical problems that arise from isolation and generation of these cells. Isolation of hES cells faces ethical problems associated with their derivation from human pre-implantation embryos. The most controversial aspect of hES cell isolation targets the generation of autologous hES cell lines which requires the transfer of a somatic-cell nucleus from the patient to an enucleated oocyte. While already established embryonic stem cell lines from IVF embryos can be used in a similar manner, lack of genetic identity can cause therapy rejection from the host, and prevent their use in personalized medicine. Induced pluripotent stem cells on the other hand, are generated from somatic cells that have been reprogrammed in vitro to behave like stem cells. While these cells can potentially be used for personalized medicine without the risk of rejection by the host system, derivation methods prevent their therapeutic use. The most efficient method used to generate iPS cells involves usage of viral particles which can result in viral DNA being integrated in the host cell’s genome and render these cells non-compliant for clinical therapies. Other methods not involving viral particles exist as well, but the reprogramming efficiency is too low and technical problems with generating large enough numbers of cells prevent these methods from being feasible approaches for clinical therapies. Direct reprogramming of a differentiated cell into a developmentally more plastic cell would offer alternatives to applications in regenerative medicine that currently depend on either embryonic stem cells (ES), adult stem cells or iPS cells. We hypothesize that Xenopus laevis egg cytoplasmic extract contains critical factors needed for reprogramming that may allow for non-viral, chemically defined derivation of human induced pluripotent/multipotent cells which can be maintained by addition of exogenous FGF2. In this thesis we investigated a new method for generation of multipotent cells through determining the ability of select fractions of Xenopus laevis egg extract to induce multipotency in already differentiated cells. We were able to identify select fractions from the extract that in combination with exogenously added FGF2 can reprogram and maintain the reprogrammed cells in an undifferentiated state. The findings of this work also determined that Xenopus laevis egg extract mRNA is required for achieving full reprogramming. The body of work presented in this thesis showed the ability of FGF2 isoforms to bind and activate select FGF receptor tyrosine kinases, act as extracellular mitogenic factors to support growth of hES cells in an undifferentiated state as well bind to nuclear DNA and affect expression of endogenous genes. Moreover, we showed that all FGF2 isoforms can induce expression of stem cell specific proteins in human dermal fibroblasts as well as extend lifespan of human dermal fibroblasts in vitro. In this work we identified HECW1, the gene coding for E3 ubiquitin ligase NEDL1, as a novel nuclear target for all FGF2 isoforms and showed that overexpression of recombinant FGF2 isoforms in human dermal fibroblasts can down regulate expression of HECW1 gene.

The complexity of life exhibited in humans and other living creatures has drawn many to investigate the principles associated with organismal growth and development. A few broad questions: How do tissues develop into specified organs? How are these tissues maintained? Do they become different tissues? Scientific research has incessantly been seeking answers to these as well as a plethora of other questions. While on a quest to better understand developmental biology, investigators discovered unique populations of stem cells within a variety of tissues, which retain both varying degrees of developmental plasticity and their potential for self-regeneration. This thesis provides a brief review discussing the development and history of stem cells in medicine and associated research on these cells and their potential clinical applications. Substantial attention has been paid to pluripotent embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC) which are able to be recapitulate ESC properties through the in vitro reprogramming of somatic cells. While, the ethical and legal issues have greatly hindered the use of ESCs this has made the benefit of iPSCs so great. An interconnected network of pluripotency-associated genes, integrates external signals and exerts control to maintain the state of pluripotency. Recent research has proven the pluripotency regulatory network to be flexible such that the underlying principles promise unprecedented opportunities for scientific study and regenerative medicine. Additional topics reviewed here include vast clinical applications of stem cells as well as their notable limitations.

Mosaic, activating mutations in PIK3CA, the gene encoding the catalytic p110α subunit of class IA phosphatidylinositol 3-kinase (PI3K), are the cause of rare, developmental growth disorders collectively known as PIK3CA-Related Overgrowth Spectrum (PROS). Given the pressing need for targeted therapy and evidence for tissue- and cell lineage-specific distribution of PIK3CA mutations in PROS, developmental models of this disease will be a key asset for preclinical drug testing and for a better understanding of PIK3CA activation in development. This PhD project addressed the lack of human, developmental PROS models by establishing isogenic series of human induced pluripotent stem cells (iPSCs) with endogenously expressed, activating PIK3CA mutations. This involved the optimisation of a CRISPR/Cas9 protocol for efficient knockin of different PIK3CA variants into human iPSCs. An isogenic iPSC series was established with cells expressing either wild-type PIK3CA or PIK3CA-H1047R, knocked into either one or both endogenous alleles. In parallel, mosaic patient- derived fibroblast cultures were reprogrammed to obtain isogenic wild-type and heterozygous iPSCs expressing PIK3CA-E418K. The models were used in comprehensive signalling studies, providing new insights into PI3K signalling in human iPSCs and how it is perturbed by genetic p110α activation. PIK3CA-E418K, a rare variant in both PROS and cancer, caused minimal pathway activation, in contrast to the highly recurrent variant PIK3CA-H1047R which induced strong PI3K signalling in both heterozygous and homozygous iPSCs according to a graded pattern. Studies of clinically relevant PI3K pathway inhibitors provided proof-of-concept that stem cell-based PROS models can be used for preclinical drug testing, and demonstrated that p110α is likely to be the main catalytic isoform mediating canonical PI3K signalling in human iPSCs. Differentiation assays revealed allele dose-dependent effects of PIK3CA-H1047R on stemness, with homozygous iPSCs exhibiting widespread transcriptome remodelling affect- ing genes implicated in cancer and development. Accordingly, these cells showed increased expression of pluripotency genes such as NANOG and NODAL, resulting in self-sustained "stemness" in embryoid body and teratoma assays. In comparison, heterozygous mutants behaved similar to wild-type controls under all differentiation paradigms. Furthermore, evidence was obtained that strong activation of PI3K signalling is fully compatible with definitive endoderm formation, arguing against cell-autonomous differentiation defects as the cause of endoderm sparing in PROS. In summary, these studies demonstrate the utility of human stem cell-based models of PROS for preclinical drug testing and for improved understanding of class IA PI3K signalling in human development. They are also likely to be useful in efforts to obtain a better understanding of PIK3CA-H1047R in human cancer.

A anemia aplástica (AA) é uma doença hematológica rara caracterizada pela hipocelularidade da medula óssea, o que provoca pancitopenia. Esta pode ser de origem genética (associada a encurtamento telomérico) ou adquirida (não-associada a desgaste excessivo dos telômeros). Na forma adquirida, a ativação anormal de linfócitos T provoca a destruição das células hematopoéticas. O mecanismo que leva a essa destruição ainda não foi elucidado. Um dos tratamentos mais eficazes para repovoar a medula óssea hipocelular é o transplante com célulastronco hematopoéticas (CTHs). Porém, uma grande porcentagem de pacientes não se beneficia de nenhum tratamento, fazendo-se necessário o desenvolvimento de novas alternativas para terapia. A geração de células-tronco pluripotentes induzidas (iPSCs) a partir de células somáticas (reprogramação) representa uma ferramenta promissora para o estudo de doenças e para o desenvolvimento de possíveis terapias paciente-especificas, como transplantes autólogos. Neste trabalho, avaliamos a capacidade de reprogramação de fibroblastos e eritroblastos de pacientes com AA adquirida. Metodologias de reprogramação utilizando lentivírus ou plasmídeos epissomais não integrativos foram testadas em células de quatro pacientes e de um controle saudável. Eritroblastos dos quatro pacientes e do controle foram reprogramados utilizando os plasmídeos não integrativos. As iPSCs geradas apresentaram-se similares a células-tronco embrionárias quanto à morfologia, expressão dos marcadores de pluripotência OCT4, SOX2, NANOG, SSEA-4, Tra-1-60 e Tra-1-81, e capacidade de diferenciação in vitro em corpos embrioides (EBs). A dinâmica telomérica das células pré- e pós-reprogramação foi avaliada em diferentes passagens utilizando a técnica de flow-FISH. O comprimento telomérico foi aumentado nas iPSCs quando comparado às células parentais o que indica que a célula foi completamente reprogramada. No presente trabalho, células de pacientes com AA adquirida foram reprogramadas a um estado de pluripotência por meio de um método não integrativo. As iPSCs geradas serão essenciais para futuros ensaios de diferenciação hematopoética, o que poderá contribuir para o entendimento dos mecanismos envolvidos no desenvolvimento dessa doença. Além disso, a diferenciação dessas células livres de transgenes poderá servir como uma alternativa terapêutica para os pacientes com AA como, por exemplo, em transplantes autólogos / Aplastic anemia (AA) is a rare hematological disease characterized by bone marrow hypocellularity that leads to pancytopenia. Its origin can be genetic (associated with telomere shortening) or acquired (non-associated with telomere shortening). The acquired form exhibit T lymphocytes abnormal activation, which leads to hematopoietic cells destruction. The mechanisms behind this phenomenon are still unclear. One of the most effective treatments for hypocelullar bone marrow repopulation is hematopoietic stem cell (HSCs) transplantation. However, a large percentage of patients do not benefit from any of the available treatments. This highlights the need to develop new therapeutic strategies. The generation of induced pluripotent stem cells (iPSCs) from somatic cells (reprogramming) represents a powerful tool for disease modeling and for the development of patient-specific therapies such as autologous transplants. In this study, we evaluate the capacity of reprogramming acquired AA patients\' fibroblasts and erythroblasts. Reprogramming methods using lentivirus or non-integrative episomal plasmids were tested in four patients\' cells and in cells from one healthy donor. Erythroblasts from these four patients and healthy donor were reprogrammed using non-integrative plasmids. The iPSCs resembled human embryonic stem cells in morphology, in the expression of pluripotent markers such as OCT4, SOX2, NANOG, SSEA-4, Tra-1-60 and Tra-1-81, and in in vitro differentiation (capacity to form embryoid bodies). The telomere dynamics of the cells before and after reprogramming was assessed along passaging using flow-FISH. The telomere length in the iPSCs was increased when compared to the parental cells. Thus, acquire AA patients\' cells could be reprogrammed to a pluripotent state by a nonintegrative method. The iPSCs will be essential for future hematopoietic differentiation assays that could contribute to the understanding of the mechanisms involved in the disease development. Furthermore, the differentiation of transgene-free cells may serve as an alternative therapy for patients with AA such as autologous transplants

Amyotrophic lateral sclerosis (ALS) is a late onset neurodegenerative disorder characterised by selective loss of upper and lower motor neurons (MNs). Recently, the GGGGCC (G4C2) hexanucleotide repeat expansion in chromosome 9 open reading frame 72 (C9orf72) has been identified as the most common genetic cause of ALS, highlighting the importance of studying the pathogenic mechanisms underlying this mutation. Accumulating evidence implicates that ALS is a multisystem and multifactor disease. Specifically, non-neuronal cells, astrocytes in particular, are also affected by toxicity mediated by ALS-related mutations, and they can contribute to neurodegeneration, suggesting astrocytes as a key player in ALS pathogenesis. Here, a human induced pluripotent stem cells (iPSCs)-based in vitro model of ALS was established to investigate the impact of the C9orf72 mutation on astrocyte behaviour—both cell- and non-cell autonomous. Work in this study shows that patient iPSC-derived astrocytes recapitulate key pathological features associated with C9orf72-mediated ALS, such as formation of G4C2 repeat RNA foci, production of dipeptide repeat (DPR) proteins and reduced viability under basal conditions compared to controls. Moreover, C9orf72 mutant astrocytes in co-culture result in reduced viability and structural defects of human MNs. Importantly, correction of the G4C2 repeat expansion in mutant astrocytes through targeted gene editing reverses these phenotypes, strongly confirming that the C9orf72 mutation is responsible for the observed findings. Altogether, this iPSC-based in vitro model provides a valuable platform to gain better understandings of ALS pathophysiology and can be used for future exploration of potential therapeutic drugs.

Chemical modification of the cytosine base via the addition of a methyl group to form 5-­‐methylcytosine (5-­‐mC) is a well-­‐studied example of an epigenetic mark, which contributes to regulation of gene expression, chromatin organisation and other such cellular processes without affecting the underlying DNA sequence. In recent years it was shown that 5-­‐mC is not the only DNA modification found within the vertebrate genome. 5-­‐hydroxymethylcytosine (5-­‐hmC) was first described in 1952 although it wasn’t until 2009 when it was rediscovered in mammalian tissues that it sparked intense interest in the field. Research has found that unlike the 5-­‐mC base from which it is derived, 5-­‐hmC displays variable levels and patterns across a multitude of tissue and cell types. As such the patterns of these DNA modifications can act as an identifier of cell state. This thesis aims to characterize the methyl and hydroxymethyl profiles of induced pluripotent stem cells (iPSCs), derived from control mouse embryonic fibroblast cell line (p53-­‐/-­‐) as well as and methylation hypomorphic (p53-­‐/-­‐, Dnmt1 -­‐/-­‐) mutant cell lines. As such both somatic cells were subject to reprogramming with Yamanaka factors (Oct4, cMyc, Klf4 and Sox2) via the piggyback transposition technique. Successful reprogramming was confirmed by a number of techniques and outcomes, including the de novo expression of a number of key pluripotency related factors (Nanog, Sall4 and Gdf3). Reprogrammed cells were then analysed for transcriptomic changes as well as alterations to their methyl and hydroxymethyl landscapes that accompany reprogramming. Through this work I have shown that the reprogramming of MEF derived cell lines results in a global increase in 5-­‐hmC for both p53-­‐/-­‐ and (p53-­‐/-­‐, Dnmt1 -­‐/-­‐) hypomorphic mutant cell lines – possibly through the reactivation of an alternative form of DNMT1. I demonstrate by both antibody based dot blot assay and genome wide sequencing that the reprogramming of the (p53-­‐/-­‐, Dnmt1 -­‐/-­‐) somatic cells towards a pluripotent state brings about an increase in methylation levels within the cells. This latter observation may indicate that the reprogramming of the cells is driving them towards a more wild type phenotypic state. My studies suggest that lack of DNMT1 function is not a barrier to reprogramming of somatic cells.

Ten-Eleven-Translocation (TET) proteins form a family of enzymes responsible for active DNA demethylation by oxidation of 5-methylcytosine. TET proteins play a key role in genomic reprogramming in vitro and in vivo. Although TET proteins are expressed in embryonic stem cells (ESCs), their role in regulating pluripotency remains unclear. In addition, the mechanisms by which TET proteins are recruited to chromatin are largely unknown. To visualise TET protein dynamics during pluripotency and differentiation, the endogenous Tet1/2/3 alleles were fused to epitope tags in ESCs using CRISPR/Cas9. Characterisation of these cell lines showed that TET1 is the highest expressed TET protein in both naïve and primed pluripotent cells. In contrast, TET2 is expressed heterogeneously in ESCs and marks cells with a high self-renewal capacity. To assess the function of Tet genes in pluripotent stem cells, the endogenous Tet1/2/3 ORFs were removed using CRISPR/Cas9. Comparative analysis of single and combined Tet gene knockout ESC lines indicated that Tet1 and Tet2, but not Tet3, play redundant roles to promote loss of pluripotency. Furthermore, Tet-deficient cells retained a naïve morphology in differentiating conditions, suggestive of a LIF-independent self-renewal phenotype. To characterise physiological TET1 protein-protein interactions, TET1 protein partners were identified in ESCs by mass spectrometry and co-immuno-precipitations. This revealed that TET1 interacts with multiple epigenetic and pluripotency-related factors in ESCs. Moreover, detailed characterisation of the interaction between TET1 and NANOG identified three regions of TET1 involved in protein-protein interactions that are conserved in evolution. To investigate TET1 chromatin binding in ESCs, both at the molecular and cellular levels, TET1 was characterised by ChIP-seq analysis and live imaging experiments. Interestingly, TET1 is targeted to chromatin by two different mechanisms, involving distinct protein regions. The interaction with multiple protein partners, including NANOG, might enable TET1 to be targeted to specific chromosomal locations. Additionally, TET1 has the unusual ability to bind mitotic chromatin through its N-terminus, independently of its interaction with NANOG. Together these analyses provide a new understanding of the role of TET proteins in pluripotent cells, as well as a detailed map of TET1 residues involved in protein-protein interactions and mitotic chromatin binding.

Les précurseurs neuraux dérivés de cellules souches pluripotentes induites (iPS-NPCs) peuvent représenter la source cellulaire autologue idéale pour la thérapie cellulaire visant à promouvoir la remyélinisation et la neuroprotection des maladies de la myéline. Jusqu'à présent, le potentiel thérapeutique de ces cellules a été abordé dans des conditions néonatales. Cependant, l'efficacité de la réparation et de la sécurité de ces cellules dans le système nerveux central (SNC), une condition associée à une diminution de la plasticité cellulaire et effarouchement, reste à être bien traités. D'ailleurs, il reste à démontrer si le comportement de ces cellules ressemble à celle des NPCs du SNC. D'abord, j'ai comparé des iPS-NPCs de souris avec des cellules embryonnaires du SNC, in vitro et après greffe dans des modèles de démyélinisation de la moelle épinière de souris adulte. Nos données ont révélé la capacité de survie, intégration, migration et différenciation rapide des cellules greffées en oligodendrocytes matures. Les cellules greffées ont généré de la myéline compacte autour des axones, la restauration de n¿uds de Ranvier et la vitesse de conduction aussi efficacement que les précurseurs du SNC dérivés tandis supplantant cellules endogènes. Ensuite, pour valider la fonctionnalité des précurseurs gliaux humains dérivés des iPS-NPC, je les ai transplantés dans des modèles nouveau-nés et adultes de dys/démyélinisation. Mes données ont montré la migration généralisée, l'intégration et génération de oligodendrocytes fonctionnels, la formation de la myéline compacte tout en reconstruisant n¿uds de Ranvier dans chez les nouveau-nés et les adultes greffés. / Induced pluripotent stem cell-derived neural precursor cells (iPS-NPCs) may represent the ideal autologous cell source for cell-based therapy to promote remyelination and neuroprotection in myelin diseases and can serve as suitable tools to model myelin disorders or to test the potential of pharmacological compounds. So far the therapeutic potential of these cells was approached in neonatal conditions. However, the repair efficacy and safety of these cells in the demyelinated adult central nervous system (CNS), a condition associated with decreased cell plasticity and scaring, remains to be well addressed. Moreover, whether the therapeutic behavior of these pluripotent-derived cells resembles that of physiologically committed CNS-derived precursors remains elusive. First, I used mouse iPS-NPCs and compared them side-by-side to embryonic CNS-derived cells, in vitro and in vivo after engraftment in models of adult spinal cord demyelination. My data revealed the prominent capacity of survival, safe integration, migration and timely differentiation of the grafted cells into mature oligodendrocytes. Grafted cells generated compact myelin around host axons, restoring nodes of Ranvier and conduction velocity as efficiently as CNS-derived precursors while outcompeting endogenous cells. Second, to validate the functionality of human iPS-NPC-derived glial precursors, I transplanted them in newborn and adult models of dys/demyelination. My data showed widespread migration, integration and extensive generation of functional oligodendrocytes ensheathing host axons, forming compact myelin while reconstructing nodes of Ranvier both in newborn grafted and adult demyelination contexts.

Lin, Ka Yin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 108-122). / Abstracts in English and Chinese. / Abstract (In English) --- p.ii / Abstract (In Chinese) --- p.iii / Acknowledgment --- p.V / Abstracts of Publications --- p.vi / Abbreviations --- p.viii / List of Figures --- p.ix / List of Table --- p.X / Contents --- p.xi / Chapter Chapter I --- Introduction --- p.Page / Chapter 1.1 --- Pluripotent Stem Cell --- p.1 / Chapter 1.1.1 --- Characteristic of pluripotent stem cells --- p.1 / Chapter 1.1.2 --- Origin of pluripotent stem cells --- p.1 / Chapter 1.1.2.1 --- Embryonic carcinoma cells --- p.2 / Chapter 1.1.2.2 --- Embryonic stem cells --- p.2 / Chapter 1.1.2.3 --- Epiblast stem cells --- p.2 / Chapter 1.1.2.4 --- Embryonic germ cells and adult germline stem cells --- p.3 / Chapter 1.1.2.5 --- Induced pluripotent stem cells --- p.3 / Chapter 1.1.3 --- Pluripotency in Embryonic Stem Cells --- p.4 / Chapter 1.1.3.1 --- Extrinsic signal governing pluripotency --- p.5 / Chapter 1.1.3.1.1 --- LIF signaling --- p.5 / Chapter 1.1.3.1.2 --- BMP signaling --- p.6 / Chapter 1.1.3.1.3 --- Other signaling pathways --- p.6 / Chapter 1.1.3.2 --- Intrinsic sternness factors --- p.7 / Chapter 1.1.3.2.1 --- Oct4 Expression in Embryonic Stem cells --- p.7 / Chapter 1.1.3.2.2 --- Sox-2 Expression in Embryonic Stem Cells --- p.8 / Chapter 1.1.3.2.3 --- Nanog Expression in Embryonic Stem Cells --- p.9 / Chapter 1.1.3.2.4 --- "Transcriptional Regulation of Oct-4, Nanog and Sox-2 in Embryonic Stem Cells" --- p.10 / Chapter 1.1.3.2.5 --- Others pluripotent genes --- p.11 / Chapter 1.1.3.2.5.1 --- Utfl --- p.11 / Chapter 1.1.3.2.5.2 --- Rexl --- p.11 / Chapter 1.1.3.2.5.3 --- Esrrb --- p.12 / Chapter 1.1.3.2.5.4 --- Eras --- p.12 / Chapter 1.1.3.2.5.5 --- Tell --- p.12 / Chapter 1.1.3.2.5.6 --- Dnm3tl --- p.13 / Chapter 1.1.3.2.5.7 --- Dppa3 --- p.13 / Chapter 1.1.3.2.5.8 --- Dppa4 --- p.14 / Chapter 1.1.3.2.5.9 --- Dppa5 --- p.14 / Chapter 1.1.3.2.5.10 --- Klf2 --- p.15 / Chapter 1.2 --- Somatic cell reprogramming --- p.16 / Chapter 1.2.1 --- Definition of reprogramming --- p.16 / Chapter 1.2.2 --- The history of reprogramming --- p.16 / Chapter 1.2.2.1 --- Reprogramming by nuclear transfer --- p.17 / Chapter 1.2.2.2 --- Reprogramming by fusion with ES or EC cells --- p.18 / Chapter 1.2.2.3 --- Reprogramming with defined factor --- p.19 / Chapter 1.3 --- Induced pluripotent stem cells --- p.20 / Chapter 1.3.1 --- Transcription factor used for reprogramming to iPS cells --- p.20 / Chapter 1.3.1.1 --- Klf4 --- p.20 / Chapter 1.3.1.2 --- c-Myc --- p.21 / Chapter 1.3.2 --- Cornerstone of iPSC generation --- p.22 / Chapter 1.3.3 --- Major events in the reprogramming process --- p.23 / Chapter 1.3.4 --- Gene delivery systems for ips cell generation --- p.26 / Chapter 1.3.5 --- Culture system for embryonic stem cells and iPSC --- p.28 / Chapter 1.3.4.1 --- Feeder and serum used cell culture system --- p.28 / Chapter 1.3.4.2 --- Serum-free culture condition --- p.29 / Chapter 1.3.5 --- Differentiation potential of iPSC --- p.30 / Chapter 1.3.5.1 --- In vitro stringency tests --- p.30 / Chapter 1.3.5.2 --- In vivo stringency test --- p.30 / Chapter 1.3.5.3 --- In utero stringency test --- p.31 / Chapter 1.4 --- Mouse Lewis lung carcinoma-D 122 --- p.32 / Chapter 1.5 --- Dendritic cell vaccine in cancer immunotherapy --- p.33 / Chapter 1.5 --- Green Fluorescence protein Reporters --- p.35 / Chapter 1.5.1 --- GFP reporters in embryos and stem cell --- p.35 / Chapter 1.5.2 --- copGFP --- p.35 / Chapter 1.6 --- Aim of study --- p.36 / Chapter Chapter II --- Methods and Materials / Chapter 2.1 --- Materials --- p.37 / Chapter 2.1.1 --- Synthetic oligos used in polymerase chain reaction (PCR) --- p.37 / Chapter 2.1.2 --- DNA clones used in the study --- p.39 / Chapter 2.1.3 --- Materials for DNA manipulation --- p.39 / Chapter 2.1.4 --- Materials for RNA manipulation --- p.39 / Chapter 2.1.5 --- Antibodies --- p.40 / Chapter 2.1.6 --- Kits --- p.41 / Chapter 2.1.7 --- Bacteria strain and culture reagents 41 / Chapter 2.1.8 --- Culture media and reagents --- p.42 / Chapter 2.1.8.1 --- General culture media and reagents --- p.42 / Chapter 2.1.8.2 --- Traditional ES medium --- p.42 / Chapter 2.1.8.3 --- Feeder-free Serum-free ESGRO medium --- p.42 / Chapter 2.1.9 --- Cell lines used --- p.43 / Chapter 2.1.10 --- Instrumentation --- p.43 / Chapter 2.2 --- Methods --- p.44 / Chapter 2.2.1 --- Cell culture --- p.44 / Chapter 2.2.1.1 --- Routine cell culture --- p.44 / Chapter 2.2.1.2 --- Resuscitation and culture from frozen stock --- p.44 / Chapter 2.2.1.3 --- Passage of cells --- p.44 / Chapter 2.2.1.4 --- Cryopreservation of cells --- p.45 / Chapter 2.2.1.5 --- Mouse ES cells culture --- p.45 / Chapter 2.2.1.5.1 --- Passage and maintenance of SNL --- p.45 / Chapter 2.2.1.5.2 --- Inactivation and plating of SNLs (Feeder preparation) --- p.45 / Chapter 2.2.1.5.3 --- Cryopreservation (freezing) of SNLs --- p.46 / Chapter 2.2.1.6 --- Mouse ES cells culture in feeder-free culture conditions --- p.46 / Chapter 2.2.1.6.1 --- Preparation of gelatin coated plates --- p.46 / Chapter 2.2.1.6.2 --- Thawing mouse ES cells --- p.46 / Chapter 2.2.1.6.3 --- Passage of mouse ES cells --- p.47 / Chapter 2.2.1.6.4 --- Freezing mouse ES cells --- p.47 / Chapter 2.2.1.7 --- ES cells differentiation-Formation of embryoid bodies (EBs) --- p.47 / Chapter 2.2.1.8 --- Direct differentiation by retinoic acid --- p.48 / Chapter 2.2.1.9 --- Generation of iPS --- p.48 / Chapter 2.2.2 --- Cell transfections --- p.48 / Chapter 2.2.2.1 --- Lipofectamine 2000 transfection --- p.48 / Chapter 2.2.2.2 --- Nucleofection --- p.49 / Chapter 2.2.2.2.1 --- Optimization of nucleofection --- p.49 / Chapter 2.2.2.2.2 --- Nucleofection condition --- p.49 / Chapter 2.2.3 --- Nucleic acid --- p.49 / Chapter 2.2.3.1 --- Genomic DNA isolation --- p.49 / Chapter 2.2.3.2 --- Restriction Enzyme Digestion --- p.50 / Chapter 2.2.3.3 --- RNA and genomic DNA quantification --- p.50 / Chapter 2.2.3.4 --- Reversed transcription polymerase chain reaction (RT-PCR) --- p.50 / Chapter 2.2.3.4.1 --- RNA isolation and Reverse transcription (RT) --- p.50 / Chapter 2.2.3.4.2 --- Polymerase chain reaction (PCR) --- p.51 / Chapter 2.2.3.4.3 --- Real-time polymerase chain reaction (qRT- PCR) --- p.52 / Chapter 2.2.3.5 --- Agarose gel electrophoresis --- p.53 / Chapter 2.2.3.6 --- Genomic PCR for bisulfite sequencing --- p.53 / Chapter 2.2.4 --- Bacteria and Plasmid preparation --- p.54 / Chapter 2.2.4.1 --- Preparation of competent cells --- p.54 / Chapter 2.2.4.2 --- Heat-shock transformation --- p.54 / Chapter 2.2.4.3 --- Midi prep of plasmid --- p.54 / Chapter 2.2.5 --- Cell Staining --- p.55 / Chapter 2.2.5.1 --- Alkaline phosphatase staining --- p.55 / Chapter 2.2.5.2 --- Immunofluorescence --- p.55 / Chapter 2.2.6 --- Flow cytometry --- p.56 / Chapter 2.2.7 --- Animal Handling --- p.56 / Chapter Chapter III --- Results / Chapter 3.1 --- Generation of Nanog-reporter-GFP-D 122 --- p.57 / Chapter 3.2 --- Nucleofection optimization for D122 --- p.60 / Chapter 3.3 --- Generation ofD122-iPS --- p.65 / Chapter 3.3.1 --- Plasmid construct used in the study --- p.65 / Chapter 3.3.2 --- Protocol of D122-iPS generation --- p.67 / Chapter 3.3.3 --- Reprogramming Efficiency of D12´2ؤreNanog cells --- p.69 / Chapter 3.4 --- Expression of pluripotency markers upon reprogramming --- p.70 / Chapter 3.4.1 --- Alkaline Phosphatase staining --- p.70 / Chapter 3.4.2 --- Nanog-GFP expression --- p.72 / Chapter 3.4.3 --- Pluripotency gene expression upon reprogramming --- p.74 / Chapter 3.4.4 --- GFP positive D122 reNanog Colonies --- p.79 / Chapter 3.5 --- Characterization of the D122-iPS-lC --- p.80 / Chapter 3.5.1 --- Morphology of D122-iPS-lC --- p.80 / Chapter 3.5.2 --- Pluripotency gene expression --- p.82 / Chapter 3.5.3 --- Pluripotency markers SSEA-1 and Oct4 --- p.85 / Chapter 3.5.4 --- Bisulfite genomic sequencing --- p.88 / Chapter 3.5.5 --- Differentiation of the D122-iPS-lC --- p.90 / Chapter 3.5.5.1 --- Embryoid body formation by hanging drop --- p.90 / Chapter 3.5.5.2 --- Retinoic acid induced differentiation --- p.92 / Chapter Chapter IV --- Discussion / Chapter 4.1 --- General Discussion --- p.96 / Chapter 4.1.1 --- Cancer immunotherapy and dendritic cells --- p.96 / Chapter 4.1.2 --- Dendritic vaccine and tumor antigen --- p.97 / Chapter 4.1.3 --- Induced pluripotent stem cell technology and dendritic cells --- p.98 / Chapter 4.1.4 --- Tumor antigen presentation and dendritic cells --- p.98 / Chapter 4.1.5 --- D122 and cancer immunotherapy --- p.99 / Chapter 4.1.6 --- Method to introduce transcription factors for reprogramming --- p.100 / Chapter 4.1.7 --- Kinetics of reprogramming --- p.101 / Chapter 4.1.8 --- Culture condition for reprogramming D122_reNanog --- p.102 / Chapter 4.1.9 --- Reprogramming efficiency --- p.103 / Chapter 4.1.10 --- Establishment of D122-iPS-lC --- p.103 / Chapter 4.1.11 --- Differentiation of D122-iPS-1C --- p.104 / Chapter 4.2 --- Future Work --- p.106 / Chapter 4.3 --- Conclusion --- p.107 / Chapter Chapter V --- Bibliography --- p.108 / Appendix --- p.124

A esclerose lateral amiotrófica (ELA) é uma doença neurodegenerativa, progressiva de início tardio que afeta principalmente os neurônios motores (NM). As causas que levam os NM à morte são variadas e ainda sendo investigadas. A descoberta de alterações genéticas como uma possível causa de ELA deu início à uma nova era na investigação desta afecção. Atualmente existem mais de 30 genes associados com a doença, entre eles o FUS, um gene que frequentemente aparece mutado em casos familiais da doença. A proteína FUS normalmente se localiza predominantemente no núcleo, mas na maioria dos casos de mutações na FUS relacionadas à ELA, ela aparece retida no citoplasma. O presente estudo traz um paciente de ELA (P) portando a mutação p.R521H no gene FUS e três de seus irmãos (dos quais um é portador da mutação e não apresnta sinais clínicos de ELA, e os outros dois não apresentam mutações no FUS) dos quais foram obtidas amostras de sangue e biópsia de pele. O DNA extraído das amostras de sangue, foi submetido ao sequenciamento do tipo Sanger para verificar a presença, ou ausência, da mutação R521H na FUS. A partir dos fibroblastos dos participantes, foram derivadas linhagens de células tronco pluripotentes induzidas (iPSC). As iPSC produzidas passaram por ensaios a fim de indicar o estado de pluripotência e de indiferenciação destas linhagens. Nós investigamos a posição da proteína FUS nas linhagens de iPSC e de fibroblastos e há evidências que, assim como descrito na literatura, a proteína FUS aparece retida no citoplasma das linhagens do paciente e de seu irmão portador da mutação. Desta forma, o presente estudo associa dois irmãos com quadros clínicos discordantes mas que apresentam a mesma mutação e sinais moleculares patológicos semelhantes. As linhagens de iPSC obtidas são um rico material para o uso em pesquisas futuras sobre a ELA / Amyotrophic lateral sclerosis (ALS) is a late onset, progressive, neurodegenerative disease that primarily affects motor neurons (MNs). The causes behind motor neuron death are diverse and still under investigation. The discovery of genetic alterations as possible causes of ALS initiated a new era for ALS research. There are currently over 30 genes associated with the disease, among which is FUS, one of the most frequently mutated in familial cases. The FUS protein is predominantly located in the nucleus, but in most of the ALS-related FUS mutations this protein is dislocated to the cytoplasm. The present work investigates the molecular aspects of a specific FUS mutation, p.R521H. An ALS patient (P) harboring the mutation and three siblings (of which one is a non-affected carrier and two present no mutations in FUS) were analyzed using blood samples and skin biopsies. We extracted DNA from blood samples and submitted it to Sanger sequencing for confirmation of the presence, or absence, of the R521H FUS mutation. The fibroblasts obtained from these biopsies were used for iPSC derivation. Assays were performed to confirm the undifferentiated state and pluripotency for the four strains obtained. We investigated the FUS location in these strains, and there is evidence for FUS retention in the cytoplasm of cells harboring the mutation (as seen in recent literature). Thus, this work associates two siblings with the same pathogenic mutation, showing the same molecular pathological signal but with discording clinical phenotypes. The iPSC strains obtained here are a valuable resource for further ALS investigation