Cell based therapy using stem cell derived cardiomyocytes, has emerged as a potential therapeutic approach for cardiac diseases such as myocardial infarction and heart failure. Induced pluripotent stem cells (iPS cells) could be an ideal source of cardiomyocytes (iPS-CM). Challenges facing cell therapy include the high number of viable cells needed to survive in pathological conditions. The Hippo signalling pathway has been described as a key pathway involved in regulating cardiomyocyte proliferation and survival in both embryonic and adult hearts. We hypothesise that modification of the Hippo pathway will enhance the efficiency of iPS-CM generation and will increase iPS-CM survival and viability in pathological conditions. Skin fibroblasts were reprogrammed to iPS cells and then differentiated to cardiomyocytes. The Hippo signalling pathway was modified by genetic ablation of MST1, a major upstream regulator of the Hippo pathway, or by overexpressing YAP, the main downstream effector of the pathway. Cell proliferation was analysed using an EdU incorporation assay and staining for cytokinesis markers Ki67 and phospho-histone H3. Cell death and viability were analysed by measuring caspase 3/7 and MTT activity and by trypan blue staining in both normal and hypoxic conditions (CoCl2 treatment). Analysis of cell proliferation shows that genetic ablation of Mst1 leads to significantly increased proliferation (+12±1.5% P < 0.001), survival and viability (+20±4.3% P < 0.001) of iPS cells in both normal and hypoxic (CoCl2 treatment) conditions compared to controls. In addition, overexpression of YAP, which is normally inhibited by upstream Hippo pathway components, and overexpression of mutated constitutively active form of YAP (S127A) increases cell proliferation in iPS-CM compared to control iPS-CM as shown with EdU assay (46±2.60% P < 0.01) and Ki67 staining (4.9±0.9% P < 0.001). Overexpression of YAP leads to up regulation of genes associated with inhibition of apoptosis and promotion of cell proliferation. Preliminary studies show mouse iPS-CM are retained in the myocardium following intra-cardiac injection and do not cause any adverse effects confirmed with histological, echocardiography and electrocardiogram analysis. In conclusion targeting the Hippo pathway in iPS cells and iPS-CM significantly increases proliferation and survival in both normal and hypoxic conditions. Therefore, modulation of the Hippo pathway could become a new strategy to enhance the therapeutic potential of iPS-CM.

Master of Science / Department of Grain Science and Industry / X. Susan Sun / Human induced pluripotent stem cells (hiPSCs) are generated from human somatic cells using defined transcription factors. These cells possess characteristics very similar to that of human embryonic stem cells including the ability to differentiate into cell types of all three germ layers. HiPSCs show great potential in clinical researches like drug screening and regenerative medicine, that all require large amount of cells cultured under well-defined conditions. The most common culture methods used for hiPSCs are 2D culture methods using Matrigel or vitronectin coated culture plates or flasks. 2D culture methods require large surface area to produce the same amount of cells compared to 3D methods. In addition, cells cultured in 2D culture environment are far from that in vivo. In this study, we developed a robust 3D culture condition based on hiPSC-qualified PGmatrix (PGmatrix-hiPSC) hydrogel. This 3D culture system provide hiPSCs with well-defined, more in vivo-like environment that encapsulate cells in liquid rich hydrogel with appropriate oxygen supply that resembles the hypoxia condition in vivo. Two hiPSC lines grown continuously in PGmatrix-hiPSC showed higher total population expansion and higher viability, with more consistency compared to the same cell lines grown in 2D on Matrigel or Vitronectin-XF. After grown in 3D PGmatrix-hiPSC for over 25 passages, major pluripotency markers, such as Oct4, Sox2, Nanog, and SSEA4 are expressed in most hiPSCs examined by flow cytometry. RT-qPCR also confirmed adequate expression levels of major pluripotency related genes. In addition, karyotype analysis of hiPSC after 37 passages in 3D PGmatrix-hiPSC was found normal. The same hiPSC lines cultured continuously in parallel in 2D and 3D showed differences in gene expression and surface marker TRA-1-81 expression. These results indicated the 3D PGmatrix-hiPSC system is likely superior in maintaining hiPSC growth as well as pluripotency. The findings also suggest that it is very important to study cells in 3D culture environment to better understand the mechanism of pluripotency maintenance.

Shimamoto R, Amano N, Ichisaka T, Watanabe A, Yamanaka S, et al. (2014) Generation and Characterization of Induced Pluripotent Stem Cells from Aid-Deficient Mice. PLoS ONE 9(4): e94735. doi:10.1371/journal.pone.0094735 / 京都大学 / 0048 / 新制・課程博士 / 博士(医科学) / 甲第18515号 / 医科博第56号 / 新制||医科||4(附属図書館) / 31401 / 京都大学大学院医学研究科医科学専攻 / (主査)教授 斎藤 通紀, 教授 平家 俊男, 教授 山田 泰広 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Systemic lupus erythematosus (SLE) develops when genetically susceptible individuals lose tolerance to autoantigens, likely as a result of an environmental insult. The list of identified genetic susceptibilities is expansive, however variants in the interferon regulatory factor 5 (IRF5) gene have consistently and convincingly been shown to be associated with an increased risk of developing SLE across all ethnic and racial groups examined. These genetic variants are hypothesized to produce a gain-of-function phenotype due to increased IRF5 mRNA and increased stability of the IRF5 protein; however, definitive functional studies examining these polymorphisms in primary human cells are not possible given the genetic variation from patient to patient. IRF5 is a transcription factor that is constitutively expressed in a number of immune cells including B cells and dendritic cells. IRF5 has cell type specific roles; in dendritic cells, it primarily controls a proinflammatory program which directs T cell polarization. Dysfunctional conventional dendritic cells (cDCs) have been implicated in the onset and development of SLE due to their high capacity to activate and interact with autoreactive lymphoid cells via a number of different pathways; the exact type of dysfunction and mechanisms underlying it are still debated. Study of primary cDCs either from SLE patients or healthy controls is complicated by the low frequency of cDCs in peripheral blood (<0.1%). To better evaluate the role IRF5 plays in cDC dysfunction in SLE, I developed a method for generating cDCs from induced pluripotent stem cells (iPSCs). The cDCs derived from this protocol are similar in many respects to primary human cDCs based on their gene expression profiles, cytokine production, and ability to act as antigen presenting cells to activate T cells. I also generated a library of iPSCs with and without the IRF5 risk haplotype to enable future studies to delineate the role of IRF5 polymorphisms in human cDCs. To facilitate these future studies, I also made an IRF5 deficient iPSC line which will be essential in discerning the role of IRF5 in cDC function. More broadly, we describe herein a platform to study gene function in an isogenic model of human conventional dendritic cells.

Induced pluripotent stem cells (iPSCs) can be differentiated into multiple cell types in the body while maintaining proliferative capabilities. The generation of human iPSC-derived hepatocytes (iPSC-Heps) has resulted in a new source for hepatic cells. The current available options for human hepatocytes are primary human hepatocytes (PHHs) and cell lines. PHHs isolated from healthy human donors are difficult to obtain, while cell lines exhibit reduced hepatotoxic sensitivity. iPSC-Heps are being investigated as an alternative option as they are derived from a continuous, stable source and are able to maintain their original donor genotype, which opens the door for patient-specific studies. iPSC-Heps show promise for utilization in tissue engineering, hepatotoxicity studies as well as screening for patient-specific therapeutics. Various reports have concluded that iPSC-Heps exhibit reduced hepatocyte function in comparison to PHHs. Prior reports on iPSC-Heps have focused on improving their adult phenotype functions through variations in differentiation protocols or by altering their in vitro culturing environment. This thesis focuses on incorporating hepatic non-parenchymal cells to more closely mimic the tissue and cell architecture found in the liver tissue. We designed and assembled a 3D iPSC-Hep model that integrates liver sinusoidal endothelial cells, with the goal of achieving functional maturity. Hepatotoxicants were administered to our models and various hepatic markers were measured to analyze the toxic response. This work demonstrates the need for the inclusion of hepatic non-parenchymal cells in iPSC-derived liver tissues, specifically for hepatotoxicity applications. / Master of Science / Induced pluripotent stem cells (iPSCs) can be differentiated into multiple cell types in the body while maintaining proliferative capabilities. The generation of human iPSC-derived hepatocytes (iPSC-Heps) has resulted in a new source for hepatic cells. The current available options for human hepatocytes are primary human hepatocytes (PHHs) and cell lines. PHHs originating from healthy human donors are difficult to obtain, while cell lines may exhibit reduced hepatotoxic sensitivity to chemicals. iPSC-Heps are being investigated as an alternative option since they are derived from a continuous source and are able to maintain their original donor genetic make-up, allowing for patient-specific studies. iPSC-Heps can be used in tissue engineering, hepatotoxicity studies as well as screening for patient-specific therapeutics. Various reports have concluded that iPSC-Heps exhibit reduced function in comparison to PHHs. Prior reports on iPSC-Heps have focused on improving their function through variations in differentiation procedures or by changing their culture environment. This thesis focuses on incorporating other hepatic cells to more closely mimic the tissue and cell architecture found in the liver tissue. We designed and assembled a 3D iPSC-Hep model that integrates liver sinusoidal endothelial cells, with the goal of improving hepatocyte function. Chemicals were administered to our models and various hepatic markers were measured to analyze the toxic response. This work demonstrates the need for the inclusion of additional hepatic cell types in iPSC-derived liver tissues, specifically for hepatotoxicity applications.

Here we describe some of the crucial steps to generate induced pluripotent stemcells (iPSCs) usingmRNA transfection. Our approach uses a V. virus-derived capping enzyme instead of a cap-analog, ensuring 100% proper cap orientation for in vitro transcribedmRNA. V. virus\' 2′-O-Methyltransferase enzymecreates a cap1 structure found in higher eukaryotes and has higher translation efficiency compared to other methods. Use of the polymeric transfection reagent polyethylenimine proved superior to other transfection methods. The mRNA created via this method did not trigger an intracellular immune response via human IFN-gamma (hIFN-γ) or alpha (hIFN-α) release, thus circumventing the use of suppressors. Resulting mRNA and protein were expressed at high levels for over 48 h, thus obviating daily transfections. Using this method, we demonstrated swift activation of pluripotency associated genes in human fibroblasts. Low oxygen conditions further facilitated colony formation. Differentiation into different germ layers was confirmed via teratoma assay. Reprogramming with non-synthetic mRNA holds great promise for safe generation of iPSCs of human origin. Using the protocols described herein we hope to make this method more accessible to other groups as a fast, inexpensive, and non-viral reprogramming approach.

Breast cancer is the most common cancer in Taiwanese women and the invasive ductal carcinoma (IDC) is the most common type. Increasing evidence shows that cancer stem cells (CSCs) have been implicated in tumorigenesis, tumor progression, and drug-resistance. In addition, four reprogramming factors (Octamer-binding Protein 4 (Oct4), Sex-determining Region Y (SRY)-related Box 2 (Sox2), Nanog and Lin28) employed to induce induced pluripotent stem (iPS) cells are associated with CSCs formation. The purpose of this study was to investigate the relationship of the protein expression levels of the reprogramming factors (Oct4, Sox2, Nanog and Lin28) with the tumorigenesis, clinicopathologic outcomes and prognosis of breast IDC patients. Immunohistochemistry (IHC) assay of tissue microarrays, made by 309 IDC and 20 breast fibrosis paraffin embedded samples, were used to examine the protein expression levels of Oct4, Sox2, Nanog and Lin28 in normal mammary ductal tissues, tumor adjacent normal mammary ductal tissues, ductal carcinoma in situ (DCIS), IDC and recurrence tissues. Our IHC results showed that Sox2 and Lin28 were expressed in half of breast IDC patients¡¦ tumor tissue (49.6% and 49.7%, respectively), but Oct4 and Nanog are less expressed (13.5% and 24.7%, respectively). The protein expression levels of the four proteins were positively correlated with each other. In addition, the expression levels of the four proteins were upregulated in tumor adjacent normal tissue as compared to breast fibrosis pateints¡¦ normal mammary ductal tissue. To compare the expression levels of the four proteins in different tissues; such as tumor adjacent normal, DCIS, IDC and recurrence tissues, the expression levels of the four protiens gradually decreased when tumor developed and progressed. However, their expression levels were comparable between IDC and recurrence tissues. Additionally, the high expression levels of four proteins were high in two good clinicopathological characteristics and a biomarker of breast cancer; such as nuclear Sox2 and Lin28 in those with pathology stage I; nucleus expression of the four proteins in those with well and moderate cell differentiation; and Sox2 in those with positive estrogen receptor. However, the four proteins¡¦ expression levels were not correlated with IDC patients¡¦ survival. In conclusion, the reprogramming factors: Oct4, Sox2, Nanog and Lin28 may play an important role in tumorigenesis of breast IDC, but their impacts on tumor progression were quite small.

Cellular fate, once established, is usually stable for the lifetime of the cell. However, the mechanisms that restrict the developmental potential of differentiated cells are in principle reversible, as demonstrated by the success of animal cloning from a somatic genome through somatic cell nuclear transfer (SCNT). An increased understanding of the molecular determinants of cell fate has also enabled the reprogramming of cell fate using defined transcription factors; recently, these efforts have culminated in the discovery of four genes that convert somatic cells into induced pluripotent stem cells (iPSCs), which resemble embryonic stem cells (ESCs) and can give rise to all the cell types in the body. As a first step toward generating clinically useful iPSCs, we identified a small molecule, RepSox, that potently and simultaneously replaces two of the four exogenous reprogramming factors, Sox2 and cMyc. This activity was mediated by the inhibition of the Transforming Growth Factor-\(\beta\) \((Tgf-\beta)\) signaling pathway in incompletely reprogrammed intermediate cells. By isolating these stable intermediates, we showed that RepSox acts on them to rapidly upregulate the endogenous pluripotency factor, Nanog, allowing full reprogramming to pluripotency in the absence of Sox2. We also explored lineage conversion as an alternative approach for producing a target cell type in a patient-specific manner, without first generating iPSCs. A combination of pro-neural as well as motor neuron-selective factors could convert fibroblasts directly into spinal motor neurons, the cells that control all voluntary movement. The induced motor neurons (iMNs) displayed molecular and functional characteristics of bona fide motor neurons, actuating muscle contraction in vitro and even engrafting in the developing chick spinal cord when transplanted. Importantly, functional iMNs could be produced from fibroblasts of adult patients with the fatal motor neuron disease, amyotrophic lateral sclerosis (ALS). Given the therapeutic value of generating patient-specific cell types on demand, defined-factor reprogramming is likely to serve as an important tool in regenerative medicine. It is hoped that the different approaches presented here can complement existing technologies to facilitate the study and treatment of intractable human disorders.

Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by over expression of the transcription factors OCT4, SOX2, KLF4 and c-MYC. Using serial live cell immunofluorescence imaging of human fibroblasts undergoing reprogramming, we traced the emergence of nascent iPS cell colonies among heterogeneous cell populations and defined the kinetics of marker expression. We identified distinct colony types that morphologically resemble embryonic stem (ES) cells yet differ in molecular phenotype and differentiation potential. By analyzing expression of pluripotency markers, methylation at the OCT4 and NANOG promoters, and differentiation into teratomas, we determined that only one colony type represented bona fide iPS cells, whereas the others represented reprogramming intermediates. Proviral silencing and expression of TRA-1-60, DNMT3B, and REX1 distinguished the fully reprogrammed state, whereas Alkaline Phosphatase, SSEA-4, GDF3, hTERT and NANOG proved insufficient as markers. Reprogramming in chemically defined medium favored formation of bona fide iPS cell colonies relative to partially reprogrammed colonies. These data highlight the need for rigorous characterization and standardization of putative iPS cells.

In addition to the well-characterized Induced Pluripotent Stem cells (iPSCs) that closely resemble Embryonic Stem cells (ESCs), a recent study has proven the existence of a stable state, resembling partially reprogrammed cells, termed F-class iPSCs. To study these distinct iPSC states, a reprogramming dataset has been generated, featuring the parallel analysis of multiple molecular platforms. MicroRNAs (miRNAs) are small RNA regulators of gene expression whose critical role in reprogramming is now being realized. In the present study, small RNA deep sequencing data from this novel reprogramming dataset was used to identify miRNAs that are likely to enhance reprogramming by detecting significantly up-regulated miRNAs in ESC-like iPSCs versus F-class iPSCs. These candidate miRNAs were cloned and overexpressed in reprogramming mouse embryonic fibroblasts and their effect on reprogramming efficiency was measured. miR-214 was discovered to increase iPSC generation efficiency, marking the first reprogramming-related role for this microRNA.