Given the rising demand for diverse cell types in regenerative and transfusion medicines, such as human induced pluripotent stem cell-derived neurons (iPSC-Ns), human T/chimeric antigen receptor (CAR) T cells, and human natural killer (NK) cells, the ability to cryopreserve cells has become increasingly important. In regenerative medicine, iPSC-Ns are powerful tools for treating and modelling neurodegenerative diseases. Moreover, transplants/transfusions of T/CAR T cells or NK cells offer promising treatment for numerous types of tumors, such as leukemia and multiple myeloma. Cryopreservation of cells at sub-zero temperatures (-80 to -196 °C) allows for the development of master cell banks that can be used for clinical applications. Conventional cryoprotective agents (CPAs), such as dimethylsulfoxide (DMSO) and glycerol, are utilized to protect cells from cryoinjuries associated with the freezing process. However, the use of high concentrations of DMSO (i.e., 10 to 20%) has been shown to be accompanied with toxic effects on patients receiving cell therapies if it is not removed or diluted prior to transfusion. Moreover, DMSO does not prevent the occurrence of the cryoinjury associated with ice recrystallization, which is one of the major causes of cell death/damage during cryopreservation. As a result, there is a surge of attention toward developing new non-toxic cryo-additives that inhibit ice recrystallization during cryopreservation to permit future advancement in regenerative and transfusion medicines. Moreover, the use of ice recrystallization inhibitors (IRIs) as novel CPAs has become a promising strategy to improve cell viability and function post-thaw. The Ben laboratory heavily invested in synthesizing several classes of carbohydrate-based small molecule IRIs (i.e., O-linked alkyl and aryl glycosides, and N-aryl-D-gluconamides), and studying the correlation between their IRI activity and molecular properties, such as polar surface area to molecular surface area (PSA/MSA) ratio. Moreover, compounds that belong to the O-linked aryl glycosides and N-aryl-D-gluconamides classes of IRIs have been shown to enhance the viability and functionality of red blood cells (RBCs), hematopoietic stem cells (HSCs), and induced pluripotent stem cells (iPSCs) after thawing. Part of the research presented throughout this thesis focuses on structure-activity relationship (SAR) studies of alkyl pyranoses with modified alkyl chain lengths to explore any correlations between the IRI activity and the net polarity (i.e., PSA/MSA ratio) of the IRI candidates. O- and C-linked alkyl pyranose derivatives with different alkyl chain lengths were synthesized and their IRI activity was assessed using the modified splat cooling assay. While the IRI activity of the O- and C-linked alkyl glucosides did differ as the length of the alkyl chain increased, no correlation between the PSA/MSA ratios and their IRI activity was observed. In addition, this work allowed for investigation into the effect of the type of the glycosidic bond (i.e., C-O and C-C bonds) at the anomeric position, on the IRI activity of the different compounds. The O-linked alkyl glucosides appeared to be more IRI active than the C-linked compounds, suggesting the nature of the glycosidic bond is important for IRI activity. The second part of the research presented in this thesis focuses on examining the potential for IRIs to cryopreserve iPSC-Ns, T/CAR T cells, and NK cells. 2-fluorophenyl-D-gluconamides (2FA), which is one of the most active IRIs from the N-aryl-Dgluconamides, has shown promising results in maintaining a high number of viable and functional HSCs and iPSCs post-thaw, and therefore it was employed in the cryopreservation protocol of iPSC-Ns, human-derived T/CAR T cells, and human-derived NK cells. The efficacy of the cryopreservation protocol being constructed was evaluated by assessing the post-thaw viability and recovery rate, as well as the functionality of iPSCNs, T/CAR T cells, and NK cells post-thaw. These studies showed that protecting against ice recrystallization during cryopreservation with IRIs increases the number of viable and functional iPSC-Ns, and T/CAR T cells. It was also observed that employing IRI technology in the cryopreservation protocol of NK cells does not compromise their functionality compared to fresh, non-frozen NK cells. Overall, inhibition of ice recrystallization using IRIs appeared to enhance the cryopreservation outcomes of the different cell types, which will allow for the development of off-the-shelf cell therapy products and improvement of the delivery of efficacious cell products to clinics and hospitals.

<p dir="ltr">Hematopoietic stem cells (HSCs) originating from aorta-gonad-mesonephros (AGM) could self-renew and develop into various immune cells, such as T cells, neutrophil and natural killer (NK) cells, rendering them as a promising cell source for immunotherapy. NK cells belong to the family of the innate lymphoid cells, and are employed as one of immunotherapy to cure solid and hematological malignancies including leukemia. Neutrophils are one of the granulocytes, and they are emerging as a new therapeutic target in various cancers. Due to the lack of reliable sources for the amounts of HSCs and immune cells required for clinical infusions (~10⁹ cells/patient), it remains as a major challenge to realize their full potential in targeted cell and immunotherapy. While substantial efforts have been made to generate native cell-like HSPCs and immune cells from human pluripotent stem cells (hPSCs), intricate molecular process governing the differentiation of HSCs and immune cells remain elusive, preventing the development of robust strategies for HSC and immune cell productions.</p><p dir="ltr">In this study, we first demonstrated that critical role of temporally regulating Wnt signaling in initiating AGM-like hematopoiesis across 11 hPSC lines. By inhibiting TGFβ at the stage of aorta-like CD34+SOX17⁺ hemogenic endothelium, which led to the downregulation of Wnt signaling, we established a chemically defined, feeder-free culture system that efficiently produced robust AGM-like hematopoietic cells. Furthermore, we investigated how hypoxia affects the <i>in vitro</i> hPSC differentiation into HSPCs, which resulted in a hypoxia-enhanced HSPC differentiation platform.</p><p dir="ltr">Next, the temporal roles of transcription factors (TFs), including <i>NFIL3</i>, <i>ID2</i>,<i> </i>and <i>SPI1</i>, in regulating and promoting NK cell differentiation from hPSCs are determined. <i>NFIL3</i> and <i>SPI1</i> have been reported to influence the early stages of NK cell development, while <i>ID2</i> has an impact on the generation of NK cells throughout the early and intermediate stage. We genetically modified hPSCs with doxycycline-inducible expression of <i>NFIL3</i>, <i>ID2</i>,<i> </i>and <i>SPI1</i>, and investigated their roles in NK cell induction from hPSCs. Among these three TFs, forced expression of <i>ID2</i> yielded the highest percentage of NK cells under a chemically defined, feeder-free monolayer culture condition, demonstrating that forced expression of NK-specific TFs improves the efficiency of NK cell differentiation from hPSCs.</p><p dir="ltr">Chimeric antigen receptor (CAR) is an artificial cell receptor expressed on immune T or NK cells that has been engineered to allow T or NK cells to re-target cancer cells by exclusively binding to a cancer-specific protein. CAR engineering has significantly improved the anti-tumor efficacy of NK cell therapy, resulting in 6 FDA-approved CAR-T therapies and many other ongoing clinical trials. Recently, a chlorotoxin (CLTX)-based CAR was developed and shown to specifically bind to a variety of heterogenous glioblastoma (GBM) cell lines. To test whether CLTX-CAR could improve the anti-tumor cytotoxicity of hPSC-derived NK cells, hPSCs were engineered with CLTX-CAR for stable and homogenous CAR expression via Cas9-mediated homologous recombination. The expression of CLTX-CAR did not affect the pluripotency and NK cell differentiation potential of hPSCs, and CLTX-CAR significantly improved the cytotoxicity of hPSC-derived NK cells against GBM cells.</p><p dir="ltr">Finally, we implemented a GBM-on-a-chip microfluidic model to interrogate the tumor microenvironment (TME). Microfluidics are an emerging device for investigating cancer biology with spatiotemporal control over signaling modulators by using a small volume. The interaction between hPSC-drived neutrophils and GBM was explored in this microfluidic device. GBM TME is very complex and involves many cell types, including neurons, microglia, immune T and NK cells. In the future, microfluidic models with isogenic cell components will be designed and implemented to better model GBM TME.</p><p dir="ltr">In summary, these discoveries confirm the pivotal role of Wnt signaling in guiding hPSCs towards hematopoietic lineages, while also highlighting <i>ID2</i> as a potent enhancer of NK cell differentiation from hPSC-derived hematopoietic progenitor cells. Additionally, CAR engineering enhances the anti-tumor capabilities of hPSC-derived NK cells. Furthermore, microfluidic models are employed to interrogate GBM TME.</p>

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Master of Science / Department of Animal Sciences and Industry / Duane L. Davis / Culturing stem cells is usually done on tissue-culture treated plastic. Over time the cells change their gene expression and start to differentiate. Porcine umbilical cord (PUC) stem cells express the embryonic transcription factors Oct4, Nanog and Sox2 and changes in their expression may be useful for to evaluating culture-induced changes in the cells. We developed an extract of porcine Wharton’s jelly matrix (JMX) that may provide some characteristics of the stem cell niche located in the umbilical cord. Our extract used whole cords and enzyme digestion to simplify preparation of the product. We compare cells cultured on plastic to those grown on thin and thick gels of JMX in four experiments. In Exp 1a and b, growing PUCs on a thick JMX coating for 3(1a) or 4(1b) d increased the number of cells at the end of culture (P < 0.05) with minimal effects on gene expression. In Exp 2 we compared PUCs grown on thin and thick layered JMX with added collagen (+C) and to control cells. The JMX layers caused the cells to adopt a small, round shape and to form clumps or colonies during culture. No differences (P > 0.10) were seen between thin10 +C and control wells for viable and total cell counts but thick layered +C resulted in decreased numbers of viable cells compared to thin + C (P < 0.10) and control wells (P < 0.05). In a follow up experiment (Exp. 3) growing the PUCs mixed within, rather than plating on top of, a thick layer of JMX + C caused marked morphological changes with dense 3-dimensional structures formed. Exp 4 compared JMX allowed to gel for 10 (Thin10 +C) or 60 (Thin60 +C) min before the non-gelled fraction was removed. There were no effects on cell numbers at the end of culture (P > 0.10) but Sox2 expression was increased in Thin60 +C compared to controls on plastic (P < 0.05) and Thin10 +C (P < 0.10). In summary, JMX extracts change cell morphology and in some formats increased cell proliferation and may increase Sox2 expression. Further investigation is needed to fully understand the effects of JMX on PUCs.

Background Hematopoietic stem cells located in the bone marrow interact with a specific microenvironment referred to as the stem cell niche. Data derived from ex vivo co-culture systems using mesenchymal stromal cells as a feeder cell layer suggest that cell-to-cell contact has a significant impact on the expansion, migratory potential and ‘stemness’ of hematopoietic stem cells. Here we investigated in detail the spatial relationship between hematopoietic stem cells and mesenchymal stromal cells during ex vivo expansion. Design and Methods In the co-culture system, we defined three distinct localizations of hematopoietic stem cells relative to the mesenchymal stromal cell layer: (i) those in supernatant (non-adherent cells); (ii) those adhering to the surface of mesenchymal stromal cells (phase-bright cells) and (iii) those beneath the mesenchymal stromal cells (phase-dim cells). Cell cycle, proliferation, cell division and immunophenotype of these three cell fractions were evaluated from day 1 to 7. Results Phase-bright cells contained the highest proportion of cycling progenitors during co-culture. In contrast, phase-dim cells divided much more slowly and retained a more immature phenotype compared to the other cell fractions. The phase-dim compartment was soon enriched for CD34+/CD38− cells. Migration beneath the mesenchymal stromal cell layer could be hampered by inhibiting integrin β1 or CXCR4. Conclusions Our data suggest that the mesenchymal stromal cell surface is the predominant site of proliferation of hematopoietic stem cells, whereas the compartment beneath the mesenchymal stromal cell layer seems to mimic the stem cell niche for more immature cells. The SDF-1/CXCR4 interaction and integrin-mediated cell adhesion play important roles in the distribution of hematopoietic stem cells in the co-culture system.

Master of Science / Department of Animal Sciences and Industry / Duane L. Davis / The three transcription factors, Nanog, Oct-4 and Sox-2, are central regulators of pluripotency in embryonic stem cells. Porcine umbilical cord (PUC) matrix stem cells also express these transcription factors. Wharton’s jelly is composed of an extracellular matrix high in hyaluronic acid and various collagens and serves as a reservoir for several growth factors and cytokines. We expect that Wharton’s jelly includes a stem cell niche that provides a microenvironment that maintains and supports the stem-cell characteristics of PUCs. The mechanisms by which the PUCs remain primitive within the Wharton’s jelly are unknown. We developed methods for producing an extracellular matrix product extracted from porcine Wharton’s jelly that we named Pormatrix (PMX). When PMX is incubated at 37[degrees]C, it becomes a matrical gel that provides a matrix allowing PUC attachment and growth. Concentrating the protein in PMX by filtration provides a low molecular weight by-product which we refer to as flow through (FT). In Experiment 1, PUCs were seeded on Pormatrix, Matrigel or plastic substrates in the presence or absence of FT. PUCs cultured on Matrigel, Matrigel+FT, Plastic+FT and PMX had higher expression of Nanog compared to PUCs cultured on PMX+FT (P-value <0.05). In Experiment 2, the PMX and Matrigel were diluted to low protein concentrations (1.2-1.5 mg/ml protein) so that gelling did not occur. Adding FT to PMX, Matrigel and plastic increased gene expression of Nanog 2.78 fold compared to treatments without FT (P =0.10). Sox-2 expression was increased by adding FT to Matrigel but adding FT to the other matrix proteins had no effect resulting in a tendency for a matrix*FT interaction(P=0.10). The transcription factor Oct-4 remained unchanged regardless of treatment. To evaluate the effects of in vitro maintenance on Nanog, Oct-4 and Sox-2 we measured the relative gene expression in PUCs over the first six passages in vitro. Nanog, Oct-4 and Sox-2 did not differ over these passages. This may indicate that during the first six passages in vitro, PUCs remain relatively primitive. In summary, we prepared an extract from Wharton’s jelly from porcine umbilical cords. The extract supported PUC attachment and growth and appeared to regulate gene expression. Perhaps with further investigation the interactions of PUCs with their in vivo environment can be elucidated.

Die Entdeckung adulter dentaler Stammzellen eröffnete ein neues Forschungsfeld im Hinblick auf die Regeneration dentaler Gewebe. Bisher liegen nur wenige Studien vor, in denen das Genexpressionsprofil dentaler Stammzellen im Vergleich zu den Knochenmarkstammzellen analysiert wurde. Diese Untersuchungen wurden vorwiegend an Mischkulturen vorgenommen. Im Gegensatz dazu war es daher das Ziel der vorliegenden Arbeit, das Genexpressionsprofil einer bestimmten Stammzell-Population, nämlich der Stro1-positiven pulpalen mesenchymalen Zahnkeimstammzellen (Stro1+ZK) im Vergleich zu Stro1-positiven mesenchymalen Knochenmarkstammzellen (Stro1+BK), zu untersuchen. Die Genexpression beider Zelltypen wurde anhand von Microarrays ermittelt. Insgesamt gingen 22.454 Gene in die Auswertung ein, wovon bei einem konservativ festgesetzten Schwellenwert einer FDR≤1% 2730 Gene eine hochsignifikant differentielle Expression zeigten. Die Analyse dieser differentiell exprimierten Gene mithilfe der Programme „DAVID“ und „Ingenuity“ ergab, dass in den Stro1+ZK vermehrt Gene heraufreguliert sind, die mit Zellfunktionen wie beispielsweise Proliferationsregulation, der Zell-zu-Zell-Signalleitung und der Organisation des Zytoskeletts verknüpft sind. Die Stro1+BK hingegen exprimieren verstärkt Gene, die mit der Organisation der extrazellulären Knochenmatrix und Zell-Adhäsion assoziiert sind. Des Weiteren findet sich in diesen Zellen eine verstärkte Expression von Genen, die mit der Struktur- und Formgebung des Skeletts in Verbindung stehen. Trotz identischem Stammzellmarker-Typus (Stro1) weisen die untersuchten mesenchymalen Stammzelltypen stark unterschiedliche Hox-Gen-Signaturen auf. Dabei zeigt sich sowohl eine Variation in Anzahl und Art der Hox-Gene als auch in deren Expressionsmuster. Stro1+BK exprimieren verstärkter Hox-Gene der Cluster A bis D (HOXA-D), die Segment- und Positionsinformationen codieren. Hingegen sind in den Stro1+ZK die Hox-Gene BARX1, MSX1, MSX2, DLX1, DLX2, PAX9 und LEF1 hochreguliert, welche eine tragende Rolle in der Zahnentwicklung spielen. So ist z.B. bereits bekannt, dass Mutationen dieser Gene zu Fehlbildungen von Zähnen wie Aplasien oder Hypoplasien führen können. Die vorliegende Arbeit zeigt, dass insbesondere hinsichtlich der Hox-Gene signifikante Unterschiede zwischen den Stro1+ZK und Stro1+BK bestehen. Weiterführende Experimente zur Aufklärung der Funktionsweise von Genen, die in den Stro1+ZK von Bedeutung sein könnten, einschließlich deren Erforschung auf proteinbiochemischer und zellbiologischer Ebene, wären wünschenswert.

Amyotrophic Lateral Sclerosis (ALS) is an incurable late onset neurodegenerative disorder characterised by the specific loss of motor neurones (MNs). It has been recently demonstrated that Transactive response DNA-binding protein (TDP-43) is the dominant disease protein in both ALS and a sub-group of frontotemporal lobar degeneration (FTLDTDP). Moreover, the identification of TARDBP mutations in familial ALS confirms a mechanistic link between the observed mis-accumulation of TDP-43 and neurodegeneration but also provides an opportunity to establish an in vitro platform to model these diseases, based on patient-derived induced pluripotent stem cells (iPSCs). This study presents the optimization of an iPSC-based platform to study the consequences of TDP-43 M337V mutation in human functional populations of MNs and astrocytes in isolation as well as in co-culture. To develop this platform, two protocols to differentiate patient-derived iPSCs into functional MNs and astrocytes were first optimized, and the obtained cellular populations were then used to characterize the behaviour of mutant TDP-43 and its effect on the different cell types. This study show that it is possible to use iPSC-based platforms to recapitulate in vitro key aspects of TDP-43 proteinopathies such as MN cell autonomous toxicity and TDP-43 accumulation, but they can also be used to highlight previously unrecognised disease specific mechanisms and to test novel therapeutic approaches. Moreover, by performing co-culture experiments it was possible to evaluate the effects of M337V astrocytes on the survival of wild-type and M337V TDP-43 motor neurons, showing that mutant TDP-43 astrocytes do not adversely affect survival of co-cultured neurons. This iPSC-based platform represents an in vitro model to study both the effect of somatic mutations on isolated patient-specific cultures, but also to investigate cellular autonomy and neurodegeneration in the context of TDP-43 proteinopathies.

DNA methylation refers to an addition of a methyl group to the 5 position of the cytosine pyrimidine ring. As the best characterized epigenetic mark, DNA methylation plays an important role in a plethora of biological functions, including gene repression, genomic imprinting, silencing of retro-transposons and X chromosome inactivation. Genomic imprinting refers to the mono-allelic expression of certain genes according to their parent-of-origin. In mammals, the expression of imprinted genes is controlled by the cis-acting regulatory elements, termed imprinted control regions (ICRs). ICRs are marked by parent-of-origin-specific DNA methylation and loss of DNA methylation at ICRs also causes aberrant expression of imprinted genes. Therefore it is believed that the genomic imprinting is a DNA methylation-associated epigenetic phenomenon. As accurate expression of imprinted genes is essential for normal embryonic growth, energy homeostasis, development of the brain and behaviour and abnormal expression of imprinted genes leads to numerous clinical phenotype and human disorders, it is important to investigate how the imprinted DNA methylation is stably maintained in mammals. DNA methyltransferases (DNMTs) are the main enzymes that play a in the establishment and maintenance of imprinted DNA methylation. In primordial germ cells (PGCs), DNMT3A and DNMT3L are involved in the establishment of imprinted DNA methylation. Whereas once established, the imprinted DNA methylation is maintained by DNMT1, DNMT3A and DNMT3B, but mainly by DNMT1. In addition, some other enzymes and DNA binding proteins also play a role in this process. One of the best examples is ZFP57, which forms a complex with KAP1 and SETDB1. ZFP57 maintains imprinted DNA methylation by recognizing a methylated hexa-nucleotide and recruits DNMTs to the ICRs in mammalian embryonic stem (ES) cells. Interestingly, DNA methylation analysis combined with promoter microarrays carried out in our lab suggested that imprinted DNA methylation is absent from some of the maternal ICRs in ES cells genetically null for G9a, a histone H3 lysine 9 methylase. This indicates that G9a might also play a role in the maintenance of imprinted DNA methylation. In my work, I found that the repressive H3K9me2 and imprinted DNA methylation are absent from several analysed ICRs in embryonic stem (ES) cells genetically null for either G9a or its partner histone methyltransferase GLP. A knockdown of G9a in ES cells reproduced these observations suggesting that G9a/GLP complex is required for the maintenance of imprinted DNA methylation. I also found that neither wild type nor catalytically inactive G9a can restore the loss of imprinted DNA methylation in G9a-/- ES cells. Chromatin immunoprecipitation (ChIP) combined with bisulfite DNA sequencing showed that imprinted DNA methylation was present on the H3K9me2-marked allele indicating a direct role for G9a in maintenance of genomic imprinting. Using a pharmacological inhibitor of G9a and mutagenesis analyses, I found that G9a maintains the imprinted DNA methylation independently of its catalytic activity and recruits DNMTs to the ICRs via its ankyrin repeat domain. Dimerization of G9a with GLP is also essential for the maintenance of genomic imprinting in ES cells. In summary, in addition to establish H3K9me2, histone methyltransferases G9a and GLP also play an essential role in the maintenance of genomic methylation imprints in ES cells.