Embryonic stem cells (ESCs) are pluripotent cells derived from the early embryo and are able to differentiate into cells belonging to the three germ layers. They are a valuable tool in research and for clinical use, but their applications are limited by ethical and technical issues. In 2006 a breakthrough report described the generation of induced pluripotent stem cells (iPSCs). IPSCs are ESC-like cells generated from somatic cells by forcing the ectopic expression of specific transcription factors. This circumvents the ethical issues about the use of embryos in research and provides multiple opportunities to understand the mechanisms behind pluripotency. The aim of this project was to generate sheep iPSCs and characterise them. In order to learn the technique I initially repeated the original iPSC methodology: the putative mouse iPSCs I have generated display a morphology typical of ESCs, characterised by a high nuclear to cytoplasmic ratio, and form colonies with neat edges and smooth domes. These cells are positive to Nanog, a marker of pluripotency, and can give rise to cells belonging to the mesodermal and the ectodermal lineages when differentiated in vitro. Since the main aim of the thesis was the derivation of sheep pluripotent cells, once established the protocol in mouse, I then moved to the generation of ovine iPSC colonies. The cells I have generated have a morphology similar to that of mouse ESCs, express markers of pluripotency such as alkaline phosphatase and Nanog and can differentiate in vitro and in vivo into cells belonging to the three germ layers. Additionally, these ovine iPSCs can contribute to live born chimeric lambs, although at low level.

The liver is a multi-functional and highly regenerative organ. While resilient, the liver is susceptible to organ damage and failure. In both the acute and chronic settings liver disease has dire consequences for health. A common cause of liver damage is adverse reactions to drugs which can lead to drug induced liver injury (DILI). This creates major problems for patients, clinicians, the pharmaceutical industry and regulatory authorities. In the context of drug overdose or serious adverse reactions, liver failure can be acute and life threatening, and in some cases require orthotopic liver transplantation. While transplantation is highly successful, such an approach has limitations and justifies basic science attempts to develop better human models to study liver injury and to develop scalable intervention strategies. With this in mind, we have studied the importance of microRNAs (miRs) in regulating human drug metabolism in pluripotent stem cell – derived hepatocytes and their potential to reduce liver toxicity in response to toxic levels of paracetamol. miRs are small non-coding RNAs that are approximately 20 - 24 nucleotides long and their major function is to fine tune gene expression of their target genes. Recently, it has been demonstrated that microRNAs play a role in regulating the first phase of drug metabolism however the second phase of drug metabolism, drug conjugation, has not been studied in detail. Drug conjugation is a crucial stage in human drug metabolism, and any alterations in this process can lead to changes in compound pharmacology, including therapeutic dose and clearance from the body. To test the importance of miRs in regulating phase II drug metabolism we opted to study the metabolism of a common used analgesic, paracetamol. When taken in the appropriate amounts paracetamol is modified by sulfotransferases (SULTs) and UDP - glucuronosyltransferases (UGTs) and removed from the body without organ damage. However, when paracetamol is taken above the recommended dose it is metabolised by phase I enzymes to generate a toxic intermediate N-acetyl-p-benzoquinone imine (NAPQI), which if untreated can lead to massive hepatocyte cell death and liver failure, placing the patient in a life threatening situation. In order to promote non-toxic drug metabolism, in the context of drug overdose, we employed candidate miRs to regulate different parts of the paracetamol metabolism pathway. In summary, we have focused on studying human drug metabolism in the major metabolic cell type of the liver, the hepatocyte. We have identified a novel microRNA (called miR-324-5p) which regulates phase II drug metabolism and reduces cell cytotoxicity. Additionally, a supportive role of anti-microRNA- 324 in response to fulminant plasma collected from paracetamol overdose patients is also observed. The findings of this project are novel, provide proof of concept and exemplify the power of stem cell based models to identify new approaches to treating human liver damage.

L’amaurose congénitale de Leber (ACL) est une maladie génétique touchant la rétine. Les premiers symptômes apparaissent dès les premiers mois de la vie et mènent en quelques années à la cécité. A ce jour, des mutations dans 18 gènes ont été associées à la maladie. Cette hétérogénéité génétique rend difficile l’étude des mécanismes conduisant aux différents symptômes. Les modèles animaux utilisés en laboratoire, notamment les rongeurs, permettent d’étudier certains de ces mécanismes mais présentent des limites liées à l’espèce. Les cellules souches pluripotentes induites (iPSCs), qui proviennent de la reprogrammation de cellules somatiques issues de patients, constituent un nouvel outil pour étudier une maladie génétique dans un contexte humain naturel. Elles permettent d’obtenir tous les phénotypes cellulaires désirés sans limite quantitative ce qui ouvre la porte à des approches d’analyse à large échelle telle que l’analyse transcriptomique qui vise à explorer de manière systématique la modulation des gènes dans une maladie. L’objectif de mon projet de recherche a été de développer un modèle cellulaire humain naturellement porteur de l’ACL. Après avoir produit les iPSCs à partir de fibroblastes de patients, mes travaux ont consisté à les différencier en populations cellulaires homogènes et facilement amplifiables, les cellules souches neurales et les cellules de l’épithélium pigmentaire rétinien. Ces populations ont servi à mener des analyses transcriptomiques à large échelle qui ont permis d’identifier plusieurs gènes candidats, potentiellement impliqués dans le développement de la pathologie, parmi lesquels GSTT1 qui pourrait avoir un rôle dans le stress oxydatif. / Leber congenital amaurosis (LCA) is a genetic disease affecting the retina. The first symptoms appear in the first months of life and lead in few years to blindness. To date, mutations in 18 genes have been associated with the disease. This genetic heterogeneity makes it difficult to study mechanisms leading to different symptoms. Animal models, including rodents, are used to study some of these mechanisms but have limitations mostly related to the species. The induced pluripotent stem cells (iPSCs), which are reprogrammed somatic cells of patients, constitute a new tool for studying genetic diseases in a natural human context. They achieve all desired cell phenotypes without quantitative limits which opens the door to large-scale analysis approaches such as transcriptomic analysis that aims to systematically explore the modulation of genes in a disease. The aim of my research project was to develop a human cell model naturally carries the LCA. After producing the iPSCs from fibroblasts of patients, my work had consisted to differentiate them into homogeneous and easily amplifiable cell populations, neural stem cells and retinal pigment epithelial cells. These populations have served to conduct large-scale transcriptomic analyzes which have identified several candidate genes potentially involved in the development of the disease, including GSTT1 which might have a role in oxidative stress.

Genomic integrity in mouse embryonic and induced pluripotent stem cells can be compromised by factors such as extended time in culture and cellular reprogramming. Surprising, only a few studies have thus far examined the accumulation of chromosomal imbalances in mouse pluripotent populations upon prolonged propagation in vitro. It is presumed that specific recurring genetic changes can confer selective growth advantage and resistance to apoptosis and/or differentiation to the affected cells, although the genes that drive these processes remain elusive. The presence of these changes in published studies can confound the analysis of the data and hinder the reproducibility of the results. At the transcriptional level, aneuploidy manifests as large chromosomal regions of aberrant gene expression. This thesis presents a method to identify these regions in large-scale datasets and interrogate for recurrent patterns. The present analysis shows that over half of the 315 mouse pluripotent samples examined carry whole or partial-chromosome spanning clusters of aberrant transcription. Furthermore, there are common gene expression changes across samples with any type of predicted aneuploidy and samples with chromosome-specific aberrations. These transcriptional signatures have been used to train classification models which can predict aneuploid samples with over 90% accuracy. This is an important step towards the development of a low-cost and reliable transcriptional validation assay for the presence of aneuploidy.

The derivation of pluripotent stem cells (now termed induced pluripotent stem cells, iPSC) from mature somatic cells was a finding of seminal importance to fundamental cell biology. Thus established iPSC technology has been predicted to advance fields that previously relied on the ethically disputed use of embryonic stem cells. Being pluripotent (able to differentiate into every cell type present in the human body) and sharing most other characteristics with embryonic stem cells, but being much readier obtainable and their derivation free from ethical restraints, human induced pluripotent stem cells (hiPSC) provide access to cell types and insights into cell processes previously unattainable to researches. For this thesis, a hiPSC line was established from a skin biopsy donated by a Down’s syndrome patient. Most of what is known today about the molecular neurobiology behind this disease has been gathered from mice models or human post mortem studies, but this has a limited extrapolation potential to early human brain development in DS patients, as Down’s syndrome is an inherently human disease whose defining phenotype is established early during embryonic development. Having access to human pluripotent cells able to recapitulate the events of early neurogenesis is thus invaluable to the understanding of the mechanisms of this disorder. In parallel, work has been performed on optimizing iPSC reprogramming protocol. By exchanging one of the transcription factors used for reprogramming with a reporter gene, genomic integration of reprogramming factors has become possible to be traced visually, enabling more efficient selection of reprogrammed iPSC colonies.

No description available.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2009. / Title from PDF title page (viewed on Feb. 2, 2010). Includes bibliographical references.

The vascular endothelium is a dynamic cellular interface that displays a unique phenotypic plasticity. This plasticity is critical for vascular function and when dysregulated is pathogenic in several diseases. The development of new human endothelial genotype-phenotype studies, personalized vascular medicine efforts and cell based regenerative therapies are limited by the unavailability of patient-specific endothelial cells. Induced pluripotent stem cells (iPSC) offer great promise as a new personalized source of endothelium; however, the reproducibility, fidelity and functionality of iPSC-derived endothelial cells remains poorly understood. / Engineering and Applied Sciences

Human neurodegenerative disorders are among the most difficult to study. In particular, the inability to readily obtain the faulty cell types most relevant to these diseases has impeded progress for decades. Amyotrophic lateral sclerosis is a late onset neurodegenerative disease in which the upper and lower motor neurons degenerate, leading to paralysis and eventually death. Recent advances in pluripotent stem cell technology now grant access to significant quantities of disease pertinent neurons both with and without predisposing mutations. The two studies described in this thesis demonstrate the feasibility of using MNs, generated from pluripotent stem cell lines harboring known ALS mutations, to establish in-vitro models of the disease. Specifically, we first used gene targeting to establish genetically controlled systems, able to identify causal relationships between a familial ALS mutation and in vitro phenotypes. Next, using transcriptional profiling, we identified novel pathways altered by the mutation and demonstrated functional consequences of these pathways' misregulation. Furthermore, by monitoring the physiology of the pluripotent stem cell derived MNs, we discovered an increased firing rate in the mutant MNs, and identified an FDA-approved drug, retigabine, capable of rescuing this defect. Lastly, to aid in the discovery of additional therapeutic compounds, we combined gene targeting, transcriptional profiling, and a fluorescent reporter human embryonic stem cell line to establish a well-controlled in vitro system capable of identifying genetic modifiers of the phenotypes described herein.

Pluripotent stem cells (PSCs) can self-renew indefinitely in culture while maintaining their capacity to differentiate into any cell type of an organism, thus offering novel sources for drug screening, in vitro disease modelling, and cell replacement therapies. However, due to their sensitive nature, many PSC lines are still cultured using undefined components such as serum or serum-derived components, on either feeder cells or complex protein mixes such as Matrigel or gelatine. In order to fully realize the potential of these cells we need controlled, completely defined and xeno-free culturing conditions that maintain growth and survival of homogenous, non-differentiated colonies. This thesis focuses on the in vitro maintenance of both mouse and human PSCs, analysing the media and substrate requirements of these cells and linking them to the intracellular signalling pathways involved in the maintenance of pluripotency and self-renewal. Benchmarking of commercially available culture methods for PSCs has been performed, evaluating their capacity to maintain pluripotency and growth of undifferentiated PSCs over several passages and reporting new characteristics, like the tendency of mouse PSCs to grow as floating spheres in 2i medium, a novel media formulation that uses two inhibitors to hinder differentiation capacity and subsequently induce pure, undifferentiated cultures. The major finding in this thesis is the identification of Inter-α-Inhibitor (IαI) as a protein able to activate the previously described signal-transduction pathway Yes/YAP/TEAD in mouse PSCs and to induce transcription of the well-known stem cell transcription factors Nanog and Oct3/4. IαI is a serum protein found in high concentration in human serum that had been traditionally described as an extracellular matrix remodelling protein. For the first time, we describe IαI to have signalling capacity on PSCs. Moreover, IαI is demonstrated to induce attachment, growth and long-term survival of undifferentiated mouse and human PSCs when added to serum-free, chemically defined media. IαI is the first molecule described to date to induce attachment of human PSCs on uncoated, standard tissue-culture treated plastic, just by supplementation as a soluble molecule at the seeding step. Following this discovery, we evaluate a novel culture method using the completely defined, serum-free E8 medium supplemented with IαI (E8:IαI) for long-term propagation of four different human PSC lines and discover that IαI can indeed support long-term culture with maintained pluripotency, differentiation capacity, growth rate and genetic stability. Moreover, in contrast to the control culture method using a commercially available surface coating, IαI supplementation can support single cell passaging of human PSCs, and adapt feeder-dependent cultured human PSCs to E8:IαI with high efficiency. A mouse PSC line is also grown for over 20 passages in IαI with retained pluripotency, differentiation capacity and genetic stability. IαI is inexpensive to produce and derived from human plasma, and could therefore be produced in compliance with Good Manufacturing Practices. Ultimately, our group aims to develop and test large-scale, completely defined, xeno-free culturing methods for PSCs, suitable for pharmacological and medical applications.