Transgenic manipulation of exogenous and endogenous gene expression in human embryonic stem cells (hESCs) is a powerful approach to decipher the genetic pathways dictating their developmental fate. Presently used genetic tools face limitations including leakiness in inducibility of expression, epigenetic silencing in long-term cell culture, low genomic integration efficiencies, small genetic cargo limit and lack of high-throughput cloning capabilities. To overcome these limitations, I have constructed R4-Integrase and piggyBac transposon genetic vector systems for stable transgene overexpression and knockdown in hESCs. Preliminary functional testing of the piggyBac vector system in HEK 293T and hESCs demonstrated vector inducibility as well as successful overexpression and knockdown of pluripotency factor OCT4. Concurrently, a cost-effective and high efficiency method for chemical transfection of hESCs was developed. Exogenous overexpression and knockdown of transcription factors in hESCs will aid in the elucidation of gene regulatory networks controlling pluripotency and developmental fate.

Transgenic manipulation of exogenous and endogenous gene expression in human embryonic stem cells (hESCs) is a powerful approach to decipher the genetic pathways dictating their developmental fate. Presently used genetic tools face limitations including leakiness in inducibility of expression, epigenetic silencing in long-term cell culture, low genomic integration efficiencies, small genetic cargo limit and lack of high-throughput cloning capabilities. To overcome these limitations, I have constructed R4-Integrase and piggyBac transposon genetic vector systems for stable transgene overexpression and knockdown in hESCs. Preliminary functional testing of the piggyBac vector system in HEK 293T and hESCs demonstrated vector inducibility as well as successful overexpression and knockdown of pluripotency factor OCT4. Concurrently, a cost-effective and high efficiency method for chemical transfection of hESCs was developed. Exogenous overexpression and knockdown of transcription factors in hESCs will aid in the elucidation of gene regulatory networks controlling pluripotency and developmental fate.

Early embryo development is one of the most sensitive stages to environmental chemicals during the whole life. Prenatal exposures to many environmental chemicals have been shown to impact fetal development and be associated with adverse health outcomes in later life stages. However, the effects of chemical mixture exposure on developing embryos, especially in early developmental stages, have yet to be fully studied. To fulfill this research gap, my thesis was divided into three data chapters and mainly aimed at investigating the effects of a chemical mixture on human early-stage embryo development. In Chapter 2, I chose methylmercury (MeHg) as the main study toxicant to establish procedures for embryotoxicity testing using human embryonic stem cells (hESCs). I then characterized the effects of low doses of MeHg on this stem cell model by screening a set of cell fate decision-related makers and found MeHg is embryotoxic, which is consistent with epidemiological and in vivo findings. In Chapter 3, I studied the embryotoxicity of a chemical mixture that consists of 23 individual environmental chemicals (including MeHg) detected from the maternal blood samples of pregnant women in Nunavik, labelled as Nunavik Contaminant Mixture (NCM), using the same cell model. The effects of NCM exposure on hESCs were compared to MeHg exposure alone. NCM exposure adversely affected cell viability and adhesion, induced apoptosis, disrupted the cell cycle, altered the expression of cytoskeleton and autophagy proteins, and changed the levels of lineage marker gene and protein expressions in a dose-dependent manner. Some distinct effects on hESCs between NCM exposure and MeHg alone exposure were noticed, and the potential interactions among the chemical components within a chemical mixture were indicated. In Chapter 4, I studied the effects of MeHg exposure during the formation of definitive endoderm (DE) cells from hESCs and compared that to MeHg's effects on undifferentiated hESCs. I found that cell specification towards endoderm could be affected by MeHg exposure, mainly through disrupting calcium homeostasis and over-generating reactive oxygen species, leading to increased ribosome biogenesis and protein synthesis. Moreover, MeHg effects are state-dependent; MeHg enhances pluripotency in undifferentiated hESCs, but it promotes differentiation during DE induction. Taken together, this thesis verifies the value of hESCs in testing the embryotoxicity and developmental toxicity of environmental chemicals, enriches the understanding of the toxicity of MeHg and NCM, emphasizes the necessity of evaluating the effects of chemical mixtures and provides new directions in studying environmental chemical toxicity using stem cells. Findings from my thesis could hopefully contribute to predicting the potential effects of prenatal environmental chemical exposures and aid in developing evidence-based public health policy.

Cardiovascular disease (CVD) affects more than 70 million Americans and is the number one cause of mortality in the United States. Because the regenerative capacity of adult tissues such as the heart is limited, human embryonic stem cells (hESC) have emerged as a source for potential cardiac therapies. However, despite the use of a variety of biochemical differentiation protocols, current yields of hESC-derived cardiomyocytes (CM) have been low. In the case of hESC-CM, which are inherently electromechanically active, additional forms of inducing a mature cardiac fate have not been fully explored. In order to non-invasively visualize and quantify biochemical, electrical, and mechanical stimulation on hESC-CM differentiation in future studies, a bioreactor imaging system has been developed and is described in this report. / text

Em fêmeas de mamíferos, um dos cromossomos X é inativado proporcionando compensação de dose entre os produtos gênicos de machos e fêmeas. A inativação do cromossomo X (ICX) ocorre no embrião em desenvolvimento, e se caracteriza pela aquisição de marcas heterocromáticas no cromossomo X inativado (Xi), que são mantidas nas células somáticas ao longo das divisões celulares. O melhor modelo para estudo do início da ICX são as células-tronco embrionárias femininas. Provenientes da massa celular interna de blastocistos, elas representam um embrião em desenvolvimento e possuem os dois X ativos; a diferenciação das células promove a ICX in vitro, o que permite a identificação dos fatores e mecanismos moleculares envolvidos. A derivação de linhagens de célulastronco embrionárias humanas (human embryonic stem cells - hESCs) em 1998 permitiu novas possibilidades de estudo da ICX, pois a maioria dos trabalhos procurou esclarecer o mecanismo da ICX no modelo murino. Tradicionalmente, a manutenção da ICX em humanos tem sido investigada em células somáticas híbridas ou transformadas; porém, sabe-se que estas não representam um contexto celular natural. Assim, o presente trabalho teve como objetivos principais explorar a potencialidade de hESCs no estudo do início da ICX, e ainda investigar a função de três fatores na manutenção da ICX em células humanas imortalizadas: DNMT1 (enzima responsável pela manutenção da metilação do DNA), SMCHD1 (proteína da família de coesinas/condensinas), e XIST (um RNA não-codificador que inicia o processo de heterocromatinização do futuro Xi) foram selecionados para este estudo, uma vez que todos participam da manutenção da ICX em camundongos. Até o momento foram derivadas em nosso laboratório quatro linhagens de hESCs, as primeiras da América Latina. A caracterização das linhagens mostrou que, apesar de se manterem indiferenciadas, as hESCs femininas encontram-se em estágio pós-ICX, pois mesmo indiferenciadas já apresentam um dos X inativado. Nossos dados indicam que, submetidas às atuais condições de cultivo, as hESCs não são bons modelos para o estudo do início da ICX, e é possível que a inativação de um cromossomo X durante o cultivo confira alguma vantagem seletiva às células. A estratégia utilizada no estudo da manutenção da ICX foi o silenciamento dos três genes por interferência de RNA (RNAi). Não foi possível diminuir significativamente a expressão dos genes XIST e SMCHD1. Porém, o silenciamento de DNMT1 foi expressivo, e em resposta foi observada reativação do gene MAOA, localizado no cromossomo X e submetido à inativação. Apesar de nossas análises mostrarem que os efeitos da diminuição de DNMT1 foram restritos ao gene MAOA, estes resultados sugerem a existência de diferentes hierarquias de controle epigenético dos genes submetidos à ICX em células humanas / In female mammals, one of the X chromosomes is inactivated to achieve dosage compensation between males and females. The X chromosome inactivation (XCI) occurs early during embryogenesis and is characterized by the acquisition of heterochromatic features on the inactive X (Xi), which are maintained during all the subsequent cell divisions. Embryonic stem cells are the most suitable cells to study the establishment of XCI. They are obtained from the inner cell mass (ICM) of blastocysts, and can represent a developing female embryo, possessing two active X-chromosomes; when differentiated, these cells recapitulate XCI in vitro, and thus one can identify XCI regulators and factors involved. The derivation of human embryonic stem cells (hESCs) in 1998 offered new possibilities to study XCI, since most of the mechanistic studies of XCI have so far been investigated in the mouse model system. Traditionally, maintenance of XCI in humans has been addressed in somatic cell hybrids or transformed cells; however, they do not represent a natural cellular context. The main goals of the present work were to verify the potential of hESCs as models of XCI, and also to study the function of three important factors in XCI maintenance in immortalized human cells. DNMT1 (DNA-methyltransferase 1), SMCHD1 (a cohesin/condensin protein family member) and the XIST gene (a non-coding RNA which triggers XCI and promotes X heterochromatin formation on the future Xi) were selected, as they are key factors in XCI maintenance in the mouse. Until now four hESCs lines were derived in our lab. Their characterization showed that, in spite of been undifferentiated, the female hESCs have already undergone XCI. Our data suggest that, under the actual culture conditions, hESCs are not good models to study XCI, and it is also possible that X inactivation confers selective advantage to hESCs. Knockdown by RNA interference was used to study the roles of three genes in XCI maintenance. We could not efficiently knockdown XIST or SMCHD1. However, the DNMT1 silencing was substantial, and led to the reactivation of MAOA, an X-linked gene subjected to XCI. Although the effect of DNMT1 silencing was restricted to MAOA, our data suggest that there are different epigenetic hierarchies to control the expression of the genes subjected to XCI in human cells.

Those who are very wealthy may also be extremely free. Independently wealthy philanthropists epitomize this type of freedom. They seem to be able to act in whichever way they please, as long as they respect the limits of the law. Their freedom also implies that they do not experience as much accountability as other funders. Considering philanthropists’ ambitions as policymakers, and given their imposition of performance demands on their grantees, their accountability is relevant to investigate. However, there are no comprehensive comparative studies of philanthropists’ accountability, and there is mainly anecdotal evidence of a lack of accountability being derived from their independent wealth. This dissertation is a study of philanthropists’ accountability. I compare their experienced and exhibited accountability to that of other funders within societies, and I also compare philanthropists’ accountability across societies. I investigate whether philanthropists’ independent wealth influences to whom they are accountable, for what they are accountable, and how they are accountable. To learn about these topics, I examine their accountability relationships, their accountability mechanisms, and how they justify their potentially controversial funding of human embryonic stem cell research. Across these dimensions, I study their legal, financial, hierarchical, peer, professional, political, and fiduciary/social accountability. Empirically, I make a cross-sectional comparison of philanthropists to other funders of human embryonic stem cell research within and across three welfare regimes - liberal California, social democratic Sweden, and statist South Korea. I compare the accountability of independently wealthy philanthropists to that of public agencies, corporations, and fundraising dependent nonprofits. The empirical materials include 101 structured interviews with open-ended questions covering 51 funding organizations, as well as questionnaires explored in ANOVA and social network analysis. The study indicates that philanthropists experience and exhibit less accountability than other funders in some ways, in some contexts. By developing and using a framework to analyze their accountability, I show that philanthropists’ accountability is patterned within the societies in which they fund, and it differs greatly across societies. In California, philanthropists enact themselves as free actors, whereas in Sweden they enact a moral identity as funders of science. In South Korea, there is no clear boundary between philanthropic and corporate accountability. My results point to the contextual limits of philanthropists’ accountability. By enacting their moral identity in a way that conforms to local norms, philanthropists simultaneously retain and enable their continued freedom. In terms of their accountability, philanthropists are free to conform, and they become free by conforming.

Em fêmeas de mamíferos, um dos cromossomos X é inativado proporcionando compensação de dose entre os produtos gênicos de machos e fêmeas. A inativação do cromossomo X (ICX) ocorre no embrião em desenvolvimento, e se caracteriza pela aquisição de marcas heterocromáticas no cromossomo X inativado (Xi), que são mantidas nas células somáticas ao longo das divisões celulares. O melhor modelo para estudo do início da ICX são as células-tronco embrionárias femininas. Provenientes da massa celular interna de blastocistos, elas representam um embrião em desenvolvimento e possuem os dois X ativos; a diferenciação das células promove a ICX in vitro, o que permite a identificação dos fatores e mecanismos moleculares envolvidos. A derivação de linhagens de célulastronco embrionárias humanas (human embryonic stem cells - hESCs) em 1998 permitiu novas possibilidades de estudo da ICX, pois a maioria dos trabalhos procurou esclarecer o mecanismo da ICX no modelo murino. Tradicionalmente, a manutenção da ICX em humanos tem sido investigada em células somáticas híbridas ou transformadas; porém, sabe-se que estas não representam um contexto celular natural. Assim, o presente trabalho teve como objetivos principais explorar a potencialidade de hESCs no estudo do início da ICX, e ainda investigar a função de três fatores na manutenção da ICX em células humanas imortalizadas: DNMT1 (enzima responsável pela manutenção da metilação do DNA), SMCHD1 (proteína da família de coesinas/condensinas), e XIST (um RNA não-codificador que inicia o processo de heterocromatinização do futuro Xi) foram selecionados para este estudo, uma vez que todos participam da manutenção da ICX em camundongos. Até o momento foram derivadas em nosso laboratório quatro linhagens de hESCs, as primeiras da América Latina. A caracterização das linhagens mostrou que, apesar de se manterem indiferenciadas, as hESCs femininas encontram-se em estágio pós-ICX, pois mesmo indiferenciadas já apresentam um dos X inativado. Nossos dados indicam que, submetidas às atuais condições de cultivo, as hESCs não são bons modelos para o estudo do início da ICX, e é possível que a inativação de um cromossomo X durante o cultivo confira alguma vantagem seletiva às células. A estratégia utilizada no estudo da manutenção da ICX foi o silenciamento dos três genes por interferência de RNA (RNAi). Não foi possível diminuir significativamente a expressão dos genes XIST e SMCHD1. Porém, o silenciamento de DNMT1 foi expressivo, e em resposta foi observada reativação do gene MAOA, localizado no cromossomo X e submetido à inativação. Apesar de nossas análises mostrarem que os efeitos da diminuição de DNMT1 foram restritos ao gene MAOA, estes resultados sugerem a existência de diferentes hierarquias de controle epigenético dos genes submetidos à ICX em células humanas / In female mammals, one of the X chromosomes is inactivated to achieve dosage compensation between males and females. The X chromosome inactivation (XCI) occurs early during embryogenesis and is characterized by the acquisition of heterochromatic features on the inactive X (Xi), which are maintained during all the subsequent cell divisions. Embryonic stem cells are the most suitable cells to study the establishment of XCI. They are obtained from the inner cell mass (ICM) of blastocysts, and can represent a developing female embryo, possessing two active X-chromosomes; when differentiated, these cells recapitulate XCI in vitro, and thus one can identify XCI regulators and factors involved. The derivation of human embryonic stem cells (hESCs) in 1998 offered new possibilities to study XCI, since most of the mechanistic studies of XCI have so far been investigated in the mouse model system. Traditionally, maintenance of XCI in humans has been addressed in somatic cell hybrids or transformed cells; however, they do not represent a natural cellular context. The main goals of the present work were to verify the potential of hESCs as models of XCI, and also to study the function of three important factors in XCI maintenance in immortalized human cells. DNMT1 (DNA-methyltransferase 1), SMCHD1 (a cohesin/condensin protein family member) and the XIST gene (a non-coding RNA which triggers XCI and promotes X heterochromatin formation on the future Xi) were selected, as they are key factors in XCI maintenance in the mouse. Until now four hESCs lines were derived in our lab. Their characterization showed that, in spite of been undifferentiated, the female hESCs have already undergone XCI. Our data suggest that, under the actual culture conditions, hESCs are not good models to study XCI, and it is also possible that X inactivation confers selective advantage to hESCs. Knockdown by RNA interference was used to study the roles of three genes in XCI maintenance. We could not efficiently knockdown XIST or SMCHD1. However, the DNMT1 silencing was substantial, and led to the reactivation of MAOA, an X-linked gene subjected to XCI. Although the effect of DNMT1 silencing was restricted to MAOA, our data suggest that there are different epigenetic hierarchies to control the expression of the genes subjected to XCI in human cells.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19568号 / 医博第4075号 / 新制||医||1013(附属図書館) / 32604 / 京都大学大学院医学研究科医学専攻 / (主査)教授 伊佐 正, 教授 渡邉 大, 教授 影山 龍一郎 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Final publication is available at http://www.sciencedirect.com/science/article/pii/S1873506115001191 / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19579号 / 医博第4086号 / 新制||医||1013(附属図書館) / 32615 / 京都大学大学院医学研究科医学専攻 / (主査)教授 井上 治久, 教授 髙橋 良輔, 教授 岩田 想 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

A hematopoese tem sido bem descrita em modelos murinos nas últimas décadas, contudo, trabalhos demonstrando os mecanismos da hematopoese em humanos ainda são escassos. A derivação da primeira linhagem de células-tronco embrionárias humanas (CTEhs) em 1998, gerou novas perspectivas tanto para o estudo da hematopoese na tentativa de mimetizar o que ocorre naturalmente durante o desenvolvimento embrionário, quanto para a aplicação clínica das células hematopoéticas obtidas a partir da diferenciação dessas células. Contudo, apesar de inúmeros trabalhos terem demonstradoa obtenção de células hematopoéticas a partir de CTEhs, os protocolos têm gerado quantidades variáveis de células, com baixa eficiência e com propriedades funcionais de células primitivas. Desse modo, este trabalho procurou estabelecer um modelo próprio de diferenciação de CTEhs-H1 em células progenitoras hematopoéticas para que estas pudessem ser melhor caracterizadas e obtidas de forma mais eficiente. Para isto, foi desenvolvido um sistema de diferenciação baseado no co-cultivo da linhagem de CTEh-H1 com fibroblastos de embrião de camundongo (MEFs), em meio de diferenciação suplementado soro fetal bovino (SFB) e citocinas e fatores de crescimento hematopoéticos em baixas concentrações. Como resultado, o desenvolvimento do presente trabalho permitiu o estabelecimento de um método para geração de populações mistas de células enriquecidas em CPHs positivas para o marcador CD45, o qual mostrou ser coexpresso com outros marcadores hematopoéticos (CD31, CD43, CD71 e CD38), e células hematopoéticas maduras positivas para marcadores mielóide-específicos (235a, CD14, CD15, CD16) e com características morfológicas típicas. Foi demonstrado que as células obtidas expressavam genes relativos ao sistema hematopoético (CD45, CD31, runx1, tal1, lmo2, prom1, CD34 e notch1), e possuíam potencial clonogênico in vitro da ordem de 1/574 células plaqueadas. Em adição, corroboramos os achados de que as células hematopoéticas apresentam duas origens distintas: a partir do endotelio hemogênico e a partir de células com propriedades hemangioblásticas independentes do endotélio hemogênico. / Hematopoiesis has been well described in murine models in recent decades, however, studies demonstrating the mechanisms of hematopoiesis in humans are still scarce. The first human embryonic stem cells line (hESCs) derived in 1998, has generated new perspectives about the study of hematopoiesis as in attempting to mimic what naturally occurs during embryonic development, as for clinical application of hematopoietic cells obtained from the differentiation of these cells. However, although numerous studies have shown the production of hematopoietic cells derived from hESCs, the protocols have generated varying quantities of cells with low efficiency and functional properties of primitive stem cells. Thus, this study sought to establish our own model for hESC-H1 differentiation in hematopoietic progenitor cells so that they could be better characterized and obtained more efficiently. For this way, we developed a differentiation system based on co-culture of hESC-H1 line with inactivated mouse embryonic fibroblasts (MEFs) in differentiation medium supplemented with fetal calf serum (FCS) and cytokines and hematopoietic growth factors in low concentrations. As a result, the development of this study allowed the establishment of a method for generation of mixed population of cells enriched in hematopoietic progenitor cells positive for the marker CD45, which proved to be co-expressed with other hematopoietic markers (CD31, CD43, CD71 and CD38), and mature hematopoietic cells positive for myeloid-specific markers (235a, CD14, CD15, CD16) and morphological characteristics typical. It was shown that these cells expressed genes related to the hematopoietic system (CD45, CD31, runx1, TAL1, LMO2, prom1, CD34 and NOTCH1), and had clonogenic potential in vitro of 1/574 plated cells. In addition, we corroborate the findings that hematopoietic cells have two distinct origins: they can arise as from an hemogenic endothelium as from cells with hemangioblastic properties by an hemogenic endothelium-independent way.