Myocardial Infarction (MI) is one of the most prevalent and deadliest diseases in the United States. Since the host myocardium becomes irreversibly damaged following MI, current research is focused on identification of novel, less invasive, and more effective treatment options for patients. Cellular cardiomyopathy, in which viable cells are transplanted into the necrotic tissue, has the potential to regenerate and integrate with the host myocardium. Stem cells, specifically pluripotent stem cells such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSC), are ideal candidates for this procedure because they are pluripotent; however, ESCs must be predifferentiated to avoid teratoma formation in vivo. In this dissertation, our goal was improve upon current protocols to direct differentiation of ESCs into cardiomyocytes using an embryoid body (EB) model. We immobilized pro-cardiomyogenic proteins, specifically Sonic Hedgehog (SHH) and Bone Morphogenetic Protein 4 (BMP4) to paramagnetic beads and delivered them in the interior of the EB. While lineage commitment was indiscriminate, the presence of the beads alone appeared to guide differentiation into cardiomyocytes: there were significantly more contracting areas in EBs containing beads than in the presence of SHH or BMP4. To take advantage of this result, we immobilized Arginine-Glycine-Aspartic Acid (RGD) peptides to the beads and magnetized them following incorporation into the EB. Magnetically mediated strain increased the expression of mechanochemical markers, and in combination with BMP4 increased the percentage of cardiomyocytes. Finally, PEGylated fibrin gels were used to investigate the effect of seeding method and fibrinogen concentration on cardiomyocyte behavior and maturation. Cells seeded on top of compliant hydrogels had the most contracting regions compared to stiffer PEGylated fibrin gels, whereas cardiomyocytes seeded within the hydrogels could not remodel the matrix or maintain contractility. As an alternative to 3D culture, we seeded cardiomyocytes within gel layers, which maintained viability as well as contractile activity. We observed that PEGylated fibrin gels can maintain ESC-derived cardiomyocytes; however, the ratio of cardiomyocytes and non-cardiomyocytes should be optimized to maintain contractile phenotypes. Therefore, this dissertation presents novel methods to differentiate ESCs into cardiomyocytes, and subsequently promote their maturation in vitro, for the treatment of MI. / text

Embryonic stem (ES) cells can be maintained indefinitely in culture while retaining the ability to give rise to cellular derivatives from the three germ layers. These unique characteristics hold great promise for regenerative medicine and underscore the importance of understanding the molecular mechanisms behind ES cell maintenance. The embryonic stem cell state is supported by a delicate equilibrium of mechanisms that maintain pluripotency, prevent differentiation, and promote proliferation and survival. We sought to find genes that could contribute to one or more of these processes in human ES cells by using a gain-of-function screen of over 8000 human open reading frames (ORFs). We identify Vestigial-like 4 (Vgll4), a co-transcriptional regulator with no previously known function in ES cells, as a positive regulator for survival of human ES cells. Specifically, Vgll4 protects human ES cells from dissociation stress, and enhances colony formation from single cells. These effects may be attributable in part to the ability of Vgll4 to decrease the activity of initiator and effector caspases. Based on global transcriptional analysis, we hypothesize that Vgll4 enhances survival of hES cells at clonal densities by regulating changes in the cytoskeleton, which may in turn regulate pathways known to result in hES cell death. This dissertation introduces a novel approach for studying hES cell survival in the context of cell dissociation and presents Vgll4 as a novel regulator of this process. We also propose that Vgll4 could have multiple functions in hES cells including possible roles in pluripotency, cell cycle dynamics, Hippo pathway regulation, and \(TGF\beta\) signaling. A direct regulator of survival in human embryonic stem cells could have important implications for facilitating the generation of transgenic cell lines and reporters, thus harnessing the therapeutic application of these cells.

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Epigenetic differences between maternally inherited and paternally inherited chromosomes, such as CpG methylation, render the maternal and paternal genome functionally inequivalent, a phenomenon called genomic imprinting. This functional inequivalence is exemplified with imprinted genes, whose expression is parent-of-origin specific. The dosage of imprinted gene expression is disrupted in cells with uniparental disomy (UPD), which is an unequal parental contribution to the genome. I have derived mouse embryonic stem (ES) cell sub-lines with maternal UPD (mUPD) for mouse chromosome 6 (MMU6) to characterize regulation and maintenance of imprinted gene expression. The main finding from this study is that maintenance of imprinting in mitotic UPD is extremely variable. Imprint maintenance was shown to vary from gene to gene, and to vary between ES cell lines depending on the mechanism of loss of heterozygosity (LOH) in that cell line. Certain genes analyzed, such as Peg10, Sgce, Peg1, and Mit1 showed abnormal expression in ES cell lines for which they were mUPD. These abnormal expression levels are similar to that observed in ES cells with meiotically-derived full genome mUPD (parthenogenetic ES cells). Imprinted CpG methylation at the Peg1 promoter was found to be abnormal in all sub-lines with mUPD for Peg1. Two cell sub-lines which incurred LOH through mitotic recombination showed hypermethylation of Peg1, consistent with the presence of two maternal alleles. Surprisingly, a cell sub-line which incurred LOH through full chromosome duplication/loss showed hypomethylation of Peg1. The levels of methylation observed in these sub-lines correlates with expression, as the first two sub-lines showed a near-consistent reduction of Peg1, while the latter showed Peg1 levels close to wild-type. Altogether these results suggest that certain imprinted genes, like Peg1 and Peg10, have stricter imprinting maintenance, and as a result show abnormal expression in UPD. This strict imprint maintenance is disrupted, however, in UPD incurred through full chromosome duplication/loss, possibly because of the trisomic intermediate stage which occurs in this mechanism.

Pluripotent stem cells provide the opportunity to study human cardiogenesis in vitro, and are a renewable source of tissue for drug testing and disease models, including replacement cardiomyocytes that may be a useful treatment for heart failure. Typically, differentiation is initiated by forming spherical cell aggregates wherein an extraembryonic endoderm (ExE) layer develops on the surface. Given that interactions between endoderm and mesoderm influence embryonic cardiogenesis, we examined the impact of human embryonic stem cell (hESC) aggregate size on endoderm and cardiac development. We first demonstrated aggregate size control by micropatterning hESC colonies at defined diameters and transferring the colonies to suspension. The ratio of endoderm (GATA-6) to neural (PAX6) gene and protein expression increased with decreasing colony size. Subsequently, maximum mesoderm and cardiac induction occurred in larger aggregates when initiated with endoderm-biased hESCs (high GATA-6:PAX6), and in smaller aggregates when initiated with neural-biased hESCs (low GATA-6:PAX6). Additionally, incorporating micropatterned aggregates in a stirred suspension bioreactor increased cell yields and contracting aggregate frequency. We next interrogated the relationship between aggregate size and endoderm and cardiac differentiation efficiency in size-controlled aggregates, generated using forced aggregation, in defined cardiogenic medium. An inverse relationship between endoderm cell frequency (FoxA2+ and GATA6+) and aggregate size was observed, and cardiogenesis was maximized in mid-size aggregates (1000 cells) based on frequency of cardiac progenitors (~50% KDRlow/C-KITneg) on day 5 and cardiomyocytes (~24% cTnT+) on day 16. To elucidate a relationship between endoderm frequency and cardiac differentiation efficiency, aggregates were initiated with varying frequencies of ExE progenitors (SOX7-overexpressing hESCs). Maximum cardiomyocyte frequencies (~27%) occurred in aggregates formed with 10 to 25% ExE progenitors. These findings suggest a geometric relationship between aggregate size and ExE differentiation efficiency subsequently impacts cardiomyocyte yield, elucidating a mechanism for endogenous control of cell fate through cell-cell interactions in the aggregate.

Pluripotent stem cells provide the opportunity to study human cardiogenesis in vitro, and are a renewable source of tissue for drug testing and disease models, including replacement cardiomyocytes that may be a useful treatment for heart failure. Typically, differentiation is initiated by forming spherical cell aggregates wherein an extraembryonic endoderm (ExE) layer develops on the surface. Given that interactions between endoderm and mesoderm influence embryonic cardiogenesis, we examined the impact of human embryonic stem cell (hESC) aggregate size on endoderm and cardiac development. We first demonstrated aggregate size control by micropatterning hESC colonies at defined diameters and transferring the colonies to suspension. The ratio of endoderm (GATA-6) to neural (PAX6) gene and protein expression increased with decreasing colony size. Subsequently, maximum mesoderm and cardiac induction occurred in larger aggregates when initiated with endoderm-biased hESCs (high GATA-6:PAX6), and in smaller aggregates when initiated with neural-biased hESCs (low GATA-6:PAX6). Additionally, incorporating micropatterned aggregates in a stirred suspension bioreactor increased cell yields and contracting aggregate frequency. We next interrogated the relationship between aggregate size and endoderm and cardiac differentiation efficiency in size-controlled aggregates, generated using forced aggregation, in defined cardiogenic medium. An inverse relationship between endoderm cell frequency (FoxA2+ and GATA6+) and aggregate size was observed, and cardiogenesis was maximized in mid-size aggregates (1000 cells) based on frequency of cardiac progenitors (~50% KDRlow/C-KITneg) on day 5 and cardiomyocytes (~24% cTnT+) on day 16. To elucidate a relationship between endoderm frequency and cardiac differentiation efficiency, aggregates were initiated with varying frequencies of ExE progenitors (SOX7-overexpressing hESCs). Maximum cardiomyocyte frequencies (~27%) occurred in aggregates formed with 10 to 25% ExE progenitors. These findings suggest a geometric relationship between aggregate size and ExE differentiation efficiency subsequently impacts cardiomyocyte yield, elucidating a mechanism for endogenous control of cell fate through cell-cell interactions in the aggregate.

Methylation of histone 3 (H3) at lysine 36 (K36) has been implicated in several biological processes, such as DNA replication, DNA repair, and transcription. To date, at least eight distinct mammalian enzymes have been described to methylate H3K36 in vitro and/or in vivo. In this work, Set2, Nsd1, and Nsd3 Venus tagged proteins were successfully expressed in mouse embryonic stem cells and, then, analyzed by confocal microscopy, mass spectrometry (MS), and chromatin immunoprecipitation sequencing (ChIP-seq). MS analysis revealed that Setd2, Nsd1, and Nsd3 do not associate in protein complexes with each other. Setd2 was associated with RNA polymerase II subunits and two transcription elongation factors (Supt5 and Supt6), whereas Nsd1 associated with the transcription factor Zfx. In contrast, Nsd3 interacted with multiple protein complexes including Kdm1b and Brd4 complexes. Interestingly, Nsd1 and Zfx seem to be bound to chromatin during cell division. ChIP-seq analysis of the H3K36 methyltransferases showed different binding profiles at transcribed genes: Nsd1 binds near the transcription start site (TSS), Setd2 loading starts near the TSS and spreads along the gene body, while, Nsd3 is preferentially enriched at the 5’ and 3’ gene regions. Sequential deletion of PWWP and zinger-finger like domains was achieved to study any possible changes in Nsd1 and Nsd3 function. Deletion of either PHD1-4 or PHD5/C5HCH domains decreased Nsd1 recruitment to chromatin. Particularly, the PHD5/C5HCH were identified as the protein-protein interface for Zfx interaction. In agreement, Zfx knockdown also decreased Nsd1 deposition at the Oct4 and Tcl1 promoter regions. Furthermore, Nsd1 depletion reduced bulk histone H3K36me2 and histone H3K36me3 loading at the coding regions of Oct4, Rif1, Brd2, and Ccnd1. In addition, Nsd1 knockdown led to an increased Zfx deposition at promoters. Our findings suggest Zfx recruits Nsd1 to its target loci, whereas Nsd1 regulates Zfx chromatin release and further contributes to transcription regulation through its H3K36 dimethylase activity. On the other hand, loss of Nsd3’s PHD5/C5HCH or PWWP domains decreased Nsd3 binding to DNA. In addition, we demonstrate that Nsd3 is recruited to target genes in a Brd4-dependent manner. Herein, we provided further insights on how H3K36 methyltransferases are regulated, and how they contribute to changes in the epigenetic landscape in mouse embryonic stem cells.fi

The Hedgehog (Hh) signalling pathway is one of the key signalling pathways orchestrating intricate organogenesis, including the development of neural tube, heart and skeletal muscle. Yet, insufficient mechanistic understanding of its diverse roles is available. Here, we show the molecular mechanisms regulating the neurogenic, cardiogenic and myogenic properties of Hh signalling, via effector protein Gli2, in embryonic and adult stem cells. In Chapter 2, we show that Gli2 induces neurogenesis, whereas a dominant-negative form of Gli2 delays neurogenesis in P19 embryonal carcinoma (EC) cells, a mouse embryonic stem (ES) cell model. Furthermore, we demonstrate that Gli2 associates with Ascl1/Mash1 gene elements in differentiating P19 cells and activates the Ascl1/Mash1 promoter in vitro. Thus, Gli2 mediates neurogenesis in P19 cells at least in part by directly regulating Ascl1/Mash1 expression. In Chapter 3, we demonstrate that Gli2 and MEF2C bind each other’s regulatory elements and regulate each other’s expression while enhancing cardiomyogenesis in P19 cells. Furthermore, dominant-negative Gli2 and MEF2C proteins downregulate each other’s expression while imparing cardiomyogenesis. Lastly, we show that Gli2 and MEF2C form a protein complex, which synergistically activates cardiac muscle related promoters. In Chapter 4, we illustrate that Gli2 associates with MyoD gene elements while enhancing skeletal myogenesis in P19 cells and activates the MyoD promoter in vitro. Furthermore, inhibition of Hh signalling in muscle satellite cells and in proliferating myoblasts leads to reduction in MyoD and MEF2C expression. Finally, we demonstrate that endogenous Hh signalling is important for MyoD transcriptional activity and that Gli2, MEF2C and MyoD form a protein complex capable of inducing skeletal muscle-specific gene expression. Thus, Gli2, MEF2C and MyoD participate in a regulatory loop and form a protein complex capable of inducing skeletal muscle-specific gene expression. Our results provide a link between the regulation of tissue-restricted factors like Mash1, MEF2C and MyoD, and a general signal-regulated Gli2 transcription factor. We therefore provide novel mechanistic insights into the neurogenic, cardiogenic and myogenic properties of Gli2 in vitro, and offer novel plausible explanations for its in vivo functions. These results may also be important for the development of stem cell therapy strategies.

Derivation of lung epithelial cells from stem cells remains a challenging task, due in part to a lack of understanding of the molecular mediators driving commitment of endoderm to an early lung lineage. Reciprocal signalling between the lung mesenchyme and epithelium is crucial for proper differentiation and branching morphogenesis to occur. We hypothesized that the combination of signalling pathways comprising early epithelial-mesenchymal interactions and the 3-D spatial environment are required for induction of embryonic and induced pluripotent stem cells (ESC and iPSC, respectively) into a lung cell phenotype with the hallmarks of the distal niche. Aggregating early lung mesenchyme with endoderm-induced ESC and iPSC resulted in differentiation to an NKX2.1 and pro-SFTPC positive lineage. The differentiating cells organized into tubular structures and became polarized epithelial cells. Ultrastructure analysis revealed precursors of lamellar bodies, and Sftpb mRNA expression was detected. Quantification of the differentiation using an Nkx2.1-reporter ESC line revealed that 80% were committed to an early lung lineage, a vast improvement over what has previously been published. The FGF growth factor family comprises well-known mediators of growth and differentiation during the development of many organs, including the lung. We found that FGF2 signalling through the FGFR2iiic receptor isoform was mediating the commitment of the stem cells to an early lung epithelial phenotype, as defined by NKX2.1/proSFTPC expression. FGF7 signalling through the FGFR2iiib receptor was found to be important for the maturation and morphogenesis of the NKX2.1/proSFTPC positive lineage, but did not play a role in the initial commitment. The addition of FGF2 to endoderm-induced ESC or iPSC in the absence of mesenchyme was able to commit the cells to an NKX2.1-positive lineage, but no proSFTPC was detected. Furthermore,the cells did not become polarized and no longer organized into tubular structures. These findings suggest that while FGF2 is important for initial commitment, additional mesenchyme components including matrix proteins, supporting cell lineages and other growth factors are crucial for an efficient differentiation to an early lung epithelial cell lineage.

No description available.