The derivation of embryonic stem cells (ESCs) has created an invaluable resource for scientific study and discovery. Further improvement in differentiation protocols is necessary to generate the large number of cells needed for clinical relevance. The goal of this work was to develop a method to incorporate biomaterial microparticles (MPs) within stem cell aggregates and to evaluate their use for local control of the cellular microenvironment for directed differentiation. The effects of unloaded MPs on ESC differentiation were first determined by controlled incorporation of poly(lactic-co-glycolic acid) (PLGA), agarose and gelatin MPs. Embryoid body (EB) formation, cell viability, and gross morphology were not affected by the presence of the MPs. Further analysis of gene expression and patterns of phenotypic marker expression revealed alterations in the differentiation profile in response to material incorporation. The ability of MPs to direct ESC differentiation was investigated by incorporation of growth factor loaded MPs within EBs. MPs were loaded with bone morphogenetic protein-4 (BMP-4). BMP-4 loaded MPs incorporated within EBs induced mesoderm gene expression while inhibiting expression of an ectoderm marker compared to untreated EBs. Finally, magnetic MPs (magMPs) were incorporated within EBs to induce magnetic sensitivity. The responsiveness of EBs to applied magnetic fields was controlled by the number of magMPs incorporated within the aggregates. Magnetic guidance was then used to control the precise location of single EBs or populations of EBs for bioreactor culture and for construction of heterogeneous cell constructs. Overall, the results indicated that PSC differentiation within spheroids is sensitive to various types of biomaterials. Incorporation of MPs within EBs can be used to direct ESC differentiation by control of the cellular environment from microscale interactions, by delivery of soluble factors, to macroscale interactions, by control of EB position in static and suspension cultures.

Precise control of stem cell fate is a fundamental issue in the use of human embryonic stem (hES) cells in the context of cell therapy We examined three ways in which the microenvironment can be controlled to alter hES cell behavior, providing insight into the best conditions for maintenance of pluripotency and neural differentiation in developmental and therapeutic studies. We first examined the effects of polydimethylsiloxane (PDMS) growth surfaces on hES cell survival and maintenance of pluripotency. Lightly cured, untreated PDMS was shown to be a poor growth surface for hES cells. Some of the adverse effects caused by PDMS could be mitigated with increased curing or UV treatment of the surface, but neither modification provided a growth surface that supported pluripotent hES cells as well as polystyrene. This work provides a basis for further optimizing PDMS for hES cell culture, moving towards the use of microdevices in establishing precise control over stem cell fate. The second study explored the use of an easily constructed diffusion-based device to grow hES cells in culture on a defined, physiologic oxygen (O₂) gradient. We observed greater hES cell survival and higher levels of pluripotency markers in the lower O₂ regions of the gradient. The greatest benefit was observed at O₂ levels below 5%, narrowing the potential optimal range of O₂ for the maintenance of pluripotent hES cells. Finally, we developed a small molecule-mediated adherent and feeder-free neural differentiation protocol that reduced the cost and time scale for in vitro differentiation of neural precursors and functional neurons from human pluripotent cells. hES cell-derived neural precursors transplanted into a murine model of focal ischemic stroke survived, improved neurogenesis, and differentiated into neurons. Transplant also led to a more consistent and measurable sensory recovery after stroke as compared to untransplanted controls. This protocol represents a potentially translatable method for the generation of CNS progenitors from human pluripotent stem cells.

No description available.

The amniotic membrane and the amniotic fluid are one of life's most complex and delicate tissues and fluids, respectively. What was known about this tissue and fluid prior to the 20th century was extremely limited scientifically, but was significantly defined by beliefs entrenched in mysticism, folklore, and superstitions. A comprehensive literature review of the amniotic membrane tissue and amniotic fluid reveals the many unique and complex characteristics and biological properties that been heavily investigated since the turn of the 20th century and continues to surge into the 21st century. The historical perspectives, evolution, derivation, histology, structure, and composition of the amniotic membrane; and historical perspectives, volume and regulation, and cellular and non-cellular composition of the amniotic fluid are discussed here and are coalesced for an easy and comprehensible resource. Lastly, future perspectives regarding research and application of the amniotic membrane and amniotic fluid, including stem cells are discussed.

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.

<p>Stem cell technologies hold great promise in solving problems within fields such as drug development, regenerative medicine, and disease modeling. Stem cell engineering provides a mechanism that will help stem cells achieve this promise. Currently, many applications within tissue engineering are limited by a lack of ability to create accurate micro-physiological structures that recapitulate multicellular tissue patterns <i>in vivo</i>. Precise control of spatial and temporal signaling is desired to perform concurrent differentiation to multiple cell types intentionally. The OptoWnt construct, a novel optogenetic system activating the Wnt signaling pathway, achieves precise spatiotemporal regulation, in pursuit of greater control in stem cell differentiation. We utilize OptoWnt, to differentiate stem cells into cardiovascular cells: endothelial progenitor cells and cardiomyocytes, valuable cell types for designing microtissues. Endothelial cells comprise the luminal lining of blood and lymphatic vessels, providing the integral structure for distribution within the body, separating mobile and stationary tissues. Cardiomyocytes provide the force required to pump blood throughout the human body and are a highly desired cell type in regenerative medicine.</p> <p>In this project, we have applied an optogenetic induced signaling pathway, OptoWnt, to differentiate human pluripotent stem cells (hPSCs) into cardiovascular cells via light-induced activation of Wnt signaling pathway. In the analysis of these cells and comparison to previous small molecule approaches to cardiovascular cell differentiation, we demonstrate the robustness of the optogenetic approach and similar efficiency that it has with the small molecule approach. In short, we have further demonstrated the utility and potential of optogenetic induction of developmental pathways, via the OptoWnt construct.</p>

Understanding which cells within a cancer are responsible for its initiation and propagation is vital if we are to achieve cure. If cancer stem cells are the only population able to sustain a tumour long term, designing therapeutic strategies to target this population will give medical science the best chance of long-term cure. Significant controversy remains over the existence of cancer stem cells, predominantly due to the lack of a sensitive human cancer stem cell assay. This thesis investigates whether two haematological malignancies, myelodysplastic syndromes (MDS) and chronic myelomonocytic leukaemia (CMML) can only be driven by rare and distinct cancer stem cells. We have demonstrated that low and intermediate-1 risk MDS is driven solely by the stem cell (Lin- CD34+ CD38- CD90+ CD45RA-) by developing a novel genetic approach, tracing all somatic mutations and karyotypic abnormalities back to this population. Prior to this study, very little was known about the clonal architecture of CMML. By performing detailed phenotypic, functional, molecular and genetic analysis of patients with CMML, we were able to demonstrate that the most likely candidate driver cell in these patients was also the stem cell rather than any of the down-stream progenitors. Currently, effective therapeutic strategies for MDS or CMML are very limited. Allogeneic stem cell transplantation is the only potential cure and not suitable for most patients. Cancer stem cells, including MDS stem cells are known to be highly quiescent and selectively resistant to therapy. Having demonstrated that both MDS and CMML were driven by stem cells, we developed a novel therapeutic targeting strategy. Using the thrombopoietin receptor agonist, Romiplostim, we were able to activate stem cells and enhance their subsequent sensitivity to chemotherapy dramatically. This approach may facilitate improved remission rates and prevent cancer stem cell driven relapse in many diseases.

During development, hematopoiesis develops in temporally distinct waves in the yolk sac (YS) and embryo proper, culminating in the emergence of definitive hematopoietic stem cells (HSCs) from the hemogenic endothelium (HE) of the dorsal aorta. The close association of this aortic endothelium with definitive hematopoiesis suggests a functional relationship between arteriogenesis and blood development, but this association is not fully understood. To gain insight into this relationship, we have chosen to study the role of the “arterial” marker, EphrinB2 (EfnB2) in hematopoietic specification. EfnB2 is a transmembrane protein critical for the development of the arterial vascular system. We find that EfnB2 is expressed in the VE-Cadh⁺CD41^- HE in Day 2 BL-CFC (blast-colony forming cell) culture and Day 6 EBs (embryoid bodies), and that EfnB2 expression in ES cell differentiation enriches for endothelial cells with greater hemogenic capacity. Knock-down experiments in ES cells showed that EfnB2 is not required for endothelial cell commitment and survival. It is also not required for early hematopoietic commitment and differentiation from EBs or BL-CFCs. However, we find that EfnB2 is required for the maturation of ES cells into CD41⁺/CD45⁺ hematopoietic cells in OP9 co-culture and for definitive hematopoietic colony formation in MethoCult3434 medium. This requirement for EfnB2 expression was confirmed by peptide-mediated blocking of EfnB2 binding to its cognate receptors and by forced expression of a phospho-tyrosine signaling-deficient EfnB2. These results provide evidence for an essential role of endothelial EfnB2 in hematopoiesis.

Embryonic stem cells (ESCs) are a special type of cell marked by two key properties: The capacity to create an unlimited number of identical copies of themselves (self-renewal) and the ability to give rise to differentiated progeny that can contribute to all tissues of the adult body (pluripotency). Decades of past research have identified many of the genetic determinants of the state of these cells, such as the transcription factors Pou5f1, Sox2 and Nanog. Many other transcription factors and, more recently, epigenetic determinants like histone modifications, have been implicated in the establishment, maintenance and loss of pluripotent stem cell identity. The study of these regulators has been boosted by technological advances in the field of high-throughput sequencing (HTS) that have made it possible to investigate the binding and modification of many proteins on a genome-wide level, resulting in an explosion of the amount of genomic data available to researchers. The challenge is now to effectively use these data and to integrate the manifold measurements into coherent and intelligible models that will actually help to better understand the way in which gene expression in stem cells is regulated to maintain their precarious identity. In this thesis, I first explore the potential of HTS by describing two pilot studies using the technology to investigate global differences in the transcriptional profiles of different cell populations. In both cases, I was able to identify a number of promising candidates that mark and, possibly, explain the phenotypic and functional differences between the cells studied. The pilot studies highlighted a strong requirement for specialised software to deal with the analysis of HTS data. I have developed GeneProf, a powerful computational framework for the integrated analysis of functional genomics experiments. This software platform solves many recurring data analysis challenges and streamlines, simplifies and standardises data analysis work flows promoting transparent and reproducible methodologies. The software offers a graphical, user-friendly interface and integrates expert knowledge to guide researchers through the analysis process. All primary analysis results are supplemented with a range of informative plots and summaries that ease the interpretation of the results. Behind the scenes, computationally demanding tasks are handled remotely on a distributed network of high-performance computers, removing rate-limiting requirements on local hardware set-up. A flexible and modular software design lays the foundations for a scalable and extensible framework that will be expanded to address an even wider range of data analysis tasks in future. Using GeneProf, billions of data points from over a hundred published studies have been re-analysed. The results of these analyses are stored in an web-accessible database as part of the GeneProf system, building up an accessible resource for all life scientists. All results, together with details about the analysis procedures used, can be browsed and examined in detail and all final and intermediate results are available and can instantly be reused and compared with new findings. In an attempt to elucidate the regulatory mechanisms of ESCs, I use this knowledge base to identify high-confidence candidate genes relevant to stem cell characteristics by comparing the transcriptional profiles of ESCs with those of other cell types. Doing so, I describe 229 genes with highly ESC-specific transcription. I then integrate the expression data for these ES-specific genes with genome-wide transcription factor binding and histone modification data. After investigating the global characteristics of these "regulatory inputs", I employ machine learning methods to first cluster subgroups of genes with ESC-specific expression patterns and then to define a "regulatory code" that marks one of the subgroups based on their regulatory signatures. The tightly co-regulated core cluster of genes identified in this analysis contains many known members of the transcriptional circuitry of ESCs and a number of novel candidates that I deem worthy of further investigations thanks to their similarity to their better known counterparts. Integrating these candidates and the regulatory code that drives them into our models of the workings of ESCs might eventually help to refine the ways in which we derive, culture and manipulate these cells - with all its prospective benefits to research and medicine.

Haematopoiesis is the process to produce haematopoietic stem cells (HSCs), haematopoietic progenitors (HPCs) and terminally differentiated cell types. In the adult, HSCs resided in bone marrow while in the embryo, haematopoiesis occurred sequentially in several niches including yolk sac, aorta-gonad-mesonephros (AGM) region, placenta and fetal liver. The AGM region is the first place where HSCs arise in vivo and therefore should provide important factors to induce haematopoiesis. The mouse embryonic stem cells (mESC) system is a powerful platform to mimic the development process in vitro and is widely utilized to study the underlying mechanisms because they are pluripotent and can be genetically manipulated. A novel co-culture system has been established by culturing differentiating mESCs with primary E10.5 AGM explants and a panel of clonal stromal cell lines derived from dorsal aorta and surrounding mesenchyme (AM) in AGM region. Results of these co-culture studies suggested that the AM-derived stromal cell lines could be a potent resource of signals to enhance haematopoiesis. Molecular mechanism involved in haematopoiesis is a key research direction for understanding the regulation network of haematopoiesis and for further clinical research. A series of studies have demonstrated involvement of the Notch signalling pathway in haematopoiesis during development but with controversial conclusions because of the difference of models concerning various time windows and manipulating populations. This project aimed to investigate the role of Notch signalling pathway during haematopoiesis in the AGM environment. We analyzed the expression of Notch ligands in AGM-derived stromal cells with or without haematopoietic enhancing ability. No correlation was observed between ligand expression and haematopoietic enhancing ability in stromal cell lines or between Notch activity in EBs and haematopoietic enhancing ability. We demonstrated that inhibition of the Notch signalling pathway using the γ-secretase inhibitor could abrogate Notch activity in both mES-derived cells and the haematopoietic enhancing AM stromal cell line. To better understand the involvement of the Notch signalling pathway in a more specific spatial-temporal environment, we established a co-culture system of haemangioblast like cells (Flk1+) with one of AM region derived stromal cell lines with haematopoietic enhancing ability . We found that the AM stromal cell line could enhance Flk1+ derived haematopoiesis as assessed by haematopoietic colony formation activity and production of CD41+cKit+ progenitor cells. Based on the issue that the inhibitor could potentially affect both the ES cells and stromal cells, we carried out genetic approaches to overexpress or knock down Notch signalling pathway in this Flk1+/AM co-culture system. Interestingly, it was found that when Notch activity was enhanced in Flk1+ cells, the production of haematopoietic progenitors was inhibited and the number of cells expressing the pan-haematopoietic marker CD45 was reduced. By using the inducible dominant negative MAML1 system to knock down Notch activity, it was found that the haematopoiesis in the Flk1+/AM co-culture system was not affected, which could be accounted for the low Notch activity in this system. These results supported the hypothesis that the Notch signalling pathway plays a role in modulating Flk1+ derived haematopoietic differentiation within the AGM microenvironment.