Type I diabetes (T1D) is caused by autoimmune destruction of pancreatic β-cells. Immediate consequences of T1D are severe weight loss, ketoacidosis and death unless insulin is administered. The long-term consequences of T1D are dysregulation of metabolism leading to cardiovascular complications, neuropathy and kidney insufficiency. It is estimated that 3 million Americans have T1D, and its prevalence among young individuals is progressively rising. Islet transplantation is the most effective way to treat T1D. Unfortunately, there is a chronic shortage of cadaveric organ donors to treat all of the patients on the waiting list. Thus, an alternative source of insulin producing cells (IPCs) could significantly improve patient treatment. Our lab seeks to establish human induced pluripotent stem (iPS) cells as a novel source of IPCs that are patient tailored. The aim of this thesis was to 1) compare the differentiation of T1D and nondiabetic (ND) patient-derived iPS cells into IPCs, and 2) devise an effective protocol for differentiating skin fibroblast-derived T1D iPS cells into functional, glucose-responsive IPCs. Initially, T1D iPS cells were differentiated into IPCs. However, the yield was very poor. We hypothesized that epigenetic barriers were prevalent in T1D iPS cells, limiting their differentiation into IPCs. To address this problem, we utilized 5-aza-2’-deoxycytidine (5-aza-DC), a potent demethylating agent that inhibits the DNA methyltransferase (Dnmt). We reasoned that the use of a demethylation agent might induce a more labile, permissive state, allowing for greater cell responses to differentiation stimuli. Typically, after the differentiation of T1D iPS cells, several cell cluster types are obtained, namely compact cell clusters and hollow cysts. 5-aza-DC treatment appeared to convert all of the cell clusters into characteristic islet-like compact structures. In contrast, in untreated T1D IPC cultures, we observed the dominant presence of many hollow cysts with only a few tight spheroids. The hollow cysts stained negative for insulin whereas the rare solid spheroids highly expressed insulin. Flow cytometry analysis indicated a much greater percentage of Pdx1+ and insulin+ cells in 5-Aza-DC-treated cultures. These cells express markers typical of pancreatic β-cells, possessed insulin granules in similar quantities as islets, and were glucose-responsive. When transplanted in immunodeficient mice that had developed streptozotozin-induced diabetes, there was a dramatic decrease of hyperglycemia within 28 days. These mice effectively managed glucose challenge by recovering to normoglycemia, whereas nontransplanted mice did not. Altogether, our data for the first time reveal a very high yield of functional IPCs derived from human iPS cells derived from a patient with T1D, which presents a novel alternative source of IPCs that could be used to treat T1D.

The blood system consists of two main lineages: myeloid and lymphoid. The myeloid system consists of cells that are part of the innate immune response while the lymphoid system consist of cells that are part of humoral response. These responses protect our bodies from foreign pathogens. Thus, malignancies in these systems often cause complications and mortality. Scientists world wide have been researching alternatives to treat hematologic disorders and have explored induced pluripotent stem cells (iPSCs) and the conversion of one cell type to another. First, iPS cells were generated by overexpression of four transcription factors: Oct4, Sox2, Klf4 an cMyc. These cells closely resemble embryonic stem cells (ESCs) at the molecular and cellular level. However, the efficiency of cell conversion is less than 0.1%. In addition, many iPS colonies can arise from the same culture, but each has a different molecular signature and potential. Identifying the appropriate iPS cell lines to use for patient specific therapy is crucial. Here we demonstrate that our system is highly efficient in generating iPS cell lines, and cell lines with silent transgenes are most efficient in differentiating to different cell types . Second, we are interested in generating hematopoietic stem cells (HSCs) from fibroblasts directly, without going through the pluripotent state, to increase efficiency and to avoid complications associated with a stem cell intermediate. However, a robust hematopoietic reporter system remains elusive. There are multiple hematopoietic reporter candidates, but we demonstrate that the CD45 gene was the most promising. CD45 is expressed early during hematopoiesis on the surface of HSCs; and as HSCs differentiate CD45 levels increase. Furthermore, the CD45 reporter is only active in hematopoietic cells. We were able to confirm the utility of the CD45 reporter using an in vitro and an in vivo murine model. In conclusion, The goal of this research was to expand the knowledge of stem cell reprogramming, specifically the reprogramming of iPS cells. Furthermore, it is our desire that the CD45 reporter system will undergo further validation and find utility in clinical and cell therapy environments.

Induced pluripotent stem (iPS) cells generated from patients hold great promise for studying diseases that affect the central nervous system, as differentiation into the neuronal lineage creates a limitless supply of affected cells for disease study. Rett syndrome (RTT) is a neurodevelopmental autism spectrum disorder primarily caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene. Due to the inaccessibility of patient neurons, most of what is known about underlying phenotypes has been described using mouse models. iPS cells provide a potential solution, but reprogramming of patient cells is hampered by low efficiency, and early methods of identifying iPS cells involve transgenic techniques that are not translatable to human patient samples. The first part of this thesis describes the generation and characterization of a pluripotency reporter to address this issue. The EOS lentiviral reporter allows real-time observation of pluripotency changes during reprogramming, and is a useful tool for more efficient isolation of reprogrammed cell lines. Further, the EOS selection system can be used in a disease context to reproducibly mark and maintain disease-specific iPS cell lines for future use in disease modelling. Though iPS cells have been used to study RTT in vitro, extensive assessments of neuron function and electrophysiology have not yet been performed. In the second part of this thesis, iPS cell lines generated from a RTT mouse model were tested for their ability to model disease in vitro. Directed differentiation of multiple Mecp2-deficient and wild-type iPS cell lines to glutamatergic neurons revealed neurons that lack Mecp2 have a smaller soma size, diminished sodium currents, and are less excitable, firing fewer, prolonged action potentials that are smaller in magnitude. This deficiency in intrinsic excitability was accompanied by a dysfunction at excitatory glutamatergic synapses, which together recapitulate changes previously observed in the Mecp2-deficient mouse brain. Having accumulated counts and recordings from hundreds of neurons with consistent responses among lines, the iPS cell system is a representative model of the neuronal and synaptic defects in RTT. These results illustrate the requirement of MeCP2 in normal neuronal function, and suggest altered neuronal homeostasis or aberrant network circuitry may underlie RTT pathogenesis.

The discovery of resetting human somatic cells via introduction of four transcription factors into an embryonic stem cell-like state that enables the generation of any cell type of the human body has revolutionized the field of medical science. The generation of patient-derived iPSCs and the subsequent differentiation into the cells of interest has been, nowadays, widely used as model system for various inherited diseases. The aim of this thesis was to generate iPSCs and to subsequently derive NPCs which can be differentiated into neurons in order to model the two most common forms of the NCLs: LINCL which is caused by mutations within the TPP1 gene, encoding a lysosomal enzyme, and JNCL which is caused by mutations within the CLN3 gene, affecting a lysosomal transmembrane protein. It was shown that patient-derived fibroblasts can be successfully reprogrammed into iPSCs by using retroviral vectors that introduced the four transcription factors POU5F1, SOX2, KLF4 and MYC. The generated iPSCs were subsequently differentiated into expandable NPCs and finally into mature neurons. Phenotype analysis during the different stages, namely pluripotent iPSCs, multipotent NPCs and finally differentiated neurons, revealed a genotype-specific progression of the disease. The earliest events were observed in organelle disruption such as mitochondria, Golgi and ER which preceded the accumulation of subunit c of the mitochondrial ATPase complex that was only apparent in neurons. However, none of these events led to neurodegeneration in vitro. The established disease models recapitulate phenotypes reported in other NCL disease models such as mouse, dog and sheep model systems. More importantly, the hallmark of the NCLs, accumulation of subunit c in neurons, could be reproduced during the course of disease modeling which demonstrates the suitability of the established system. Moreover, the derived expandable NPC populations can be used for further applications in drug screenings. Their robust phenotypes such as low levels of TPP1 activity in LINCL patient-derived NPCs or cytoplasmic vacuoles, containing storage material, observed in CLN3 mutant NPCs, should serve as possible phenotypic read-outs.

No description available.

Spinal cord injuries result in permanent loss of motor function, leaving those affected with long term physical and financial burdens. Strategies for spinal cord injury repair must overcome unique challenges due to scar tissue that seals off the injury site, preventing regeneration. Tissue engineering can address these challenges with scaffolds that serve as cell- and drug-delivery tools, replacing damaged tissue while simultaneously addressing the inhibitory environment on a biochemical level. To advance this approach, the choice of cells, biomaterial matrix, and drug delivery system must be investigated and evaluated. This research seeks to evaluate (1) the behaviour of murine induced pluripotent stem cells in previously characterized 3D fibrin matrices; (2) the 3D fibrin matrix as a platform to support the differentiation of human induced pluripotent stem cells; and (3) the ability of an affinity-based drug delivery system to control the release of emerging spinal cord injury therapeutic, heat shock protein 70 from fibrin scaffolds. / Graduate / 0541 / amy.lynn.montgomery@gmail.com

Induced pluripotent stem (iPS) cells generated from patients hold great promise for studying diseases that affect the central nervous system, as differentiation into the neuronal lineage creates a limitless supply of affected cells for disease study. Rett syndrome (RTT) is a neurodevelopmental autism spectrum disorder primarily caused by mutations in the methyl-CpG-binding protein 2 (MECP2) gene. Due to the inaccessibility of patient neurons, most of what is known about underlying phenotypes has been described using mouse models. iPS cells provide a potential solution, but reprogramming of patient cells is hampered by low efficiency, and early methods of identifying iPS cells involve transgenic techniques that are not translatable to human patient samples. The first part of this thesis describes the generation and characterization of a pluripotency reporter to address this issue. The EOS lentiviral reporter allows real-time observation of pluripotency changes during reprogramming, and is a useful tool for more efficient isolation of reprogrammed cell lines. Further, the EOS selection system can be used in a disease context to reproducibly mark and maintain disease-specific iPS cell lines for future use in disease modelling. Though iPS cells have been used to study RTT in vitro, extensive assessments of neuron function and electrophysiology have not yet been performed. In the second part of this thesis, iPS cell lines generated from a RTT mouse model were tested for their ability to model disease in vitro. Directed differentiation of multiple Mecp2-deficient and wild-type iPS cell lines to glutamatergic neurons revealed neurons that lack Mecp2 have a smaller soma size, diminished sodium currents, and are less excitable, firing fewer, prolonged action potentials that are smaller in magnitude. This deficiency in intrinsic excitability was accompanied by a dysfunction at excitatory glutamatergic synapses, which together recapitulate changes previously observed in the Mecp2-deficient mouse brain. Having accumulated counts and recordings from hundreds of neurons with consistent responses among lines, the iPS cell system is a representative model of the neuronal and synaptic defects in RTT. These results illustrate the requirement of MeCP2 in normal neuronal function, and suggest altered neuronal homeostasis or aberrant network circuitry may underlie RTT pathogenesis.

There is a huge unmet clinical need to treat damaged articular cartilage such as that caused by osteoarthritis (OA) with an estimated 8.75 million people in the UK having sought treatment for OA (ARUK 2013). Embryonic stem cells (ESCs) offer a promising alternative therapeutic approach, potentially providing an unlimited source of chondrocytes capable of regenerating the damaged cartilage however this is limited by the efficiency of the chondrogenic differentiation protocol. An improved understanding of the posttranscriptional regulation of chondrogenesis by microRNAs (miRNAs) may enable us to improve hESC chondrogenesis. Also the recent discovery that miRNAs are selectively packaged into exosomes which can then be transferred to and be functionally active within neighbouring cells suggests they may have a role in cell-cell communication. This project investigated the regulation of miRNA expression in relation to the transcriptome during hESCs-directed chondrogenesis and the possible role for exosomes during differentiation and in stem cell maintenance of hESCs. Small RNA-seq and whole transcriptome sequencing was performed on distinct stages of hESC-directed chondrogenesis using the Directed Differentiation Protocol (DDP) developed in our lab. Also small RNA-seq was performed on exosomes isolated from hESCs and chondroprogenitors along with the donor cells that the exosomes originated from. This revealed significant changes in the expression of several miRNAs during hESC-directed chondrogenesis including: upregulation of miRNAs transcribed from the four Hox complexes, known cartilage associated miRNAs and the downregulation of pluripotency associated miRNAs. Overall miRome and transcriptome analysis revealed the two hESC lines exhibited slightly different miRome and transcriptome profiles during chondrogenesis, with Man7 displaying larger changes in miRNA and mRNA expression as it progressed through the DDP suggesting it may be more predisposed to undergo chondrogenesis. Integration of miRomes and transcriptomes generated during hESC-directed chondrogenesis identified four key functionally related clusters of co-expressed miRNAs and protein coding genes: pluripotency associated cluster, primitive streak cluster, limb development cluster and an extracellular matrix cluster. Further investigation of these gene/miRNA clusters allowed the identification of several potential novel regulators of hESC-directed chondrogenesis. In accordance with the reported literature the exosomal miRNAs from hESCs and hESC-chondroprogenitors were enriched with a guanine rich motif. Notably, several of these were enriched with targets associated with embryonic skeletal system development suggesting they may play a role in regulating differentiation. Preliminary functional experiments examining pluripotency-associated exosomes suggests they may have a role in regulating hESC stem cell maintenance. However the molecular mechanism by which this is achieved has not been investigated. This research identified main miRome and transcriptome changes during hESC-directed chondrogenesis leading to the identification of several potential novel regulators of chondrogenesis and pluripotency which can be further investigated. This project has also highlighted the potential of exosomal miRNAs to regulate hESC stem cell maintenance and differentiation.

No description available.

abstract: Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2013