Multiple research problems related to the lung involve a need to take into account the spatiotemporal dynamics of the underlying component cells. Two such problems involve better understanding the nature of the allergic inflammatory response to explore what might cause chronic inflammatory diseases such as asthma, and determining the rules underlying stem cells used to engraft decellularized lung scaffolds in the hopes of growing new lungs for transplantation. For both problems, we model the systems computationally using agent-based modeling, a tool that enables us to capture these spatiotemporal dynamics by modeling any biological system as a collection of agents (cells) interacting with each other and within their environment. This allows to test the most important pieces of biological systems together rather than in isolation, and thus rapidly derive biological insights from resulting complex behavior that could not have been predicted beforehand, which we can then use to guide wet lab experimentation. For the allergic response, we hypothesized that stimulation of the allergic response with antigen results in a response with formal similarity to a muscle twitch or an action potential, with an inflammatory phase followed by a resolution phase that returns the system to baseline. We prepared an agent-based model (ABM) of the allergic inflammatory response and determined that antigen stimulation indeed results in a twitch-like response. To determine what might cause chronic inflammatory diseases where the twitch presumably cannot resolve back to baseline, we then tested multiple potential defects to the model. We observed that while most of these potential changes lessen the magnitude of the response but do not affect its overall behavior, extending the lifespan of activated pro-inflammatory cells such as neutrophils and eosinophil results in a prolonged inflammatory response that does not resolve to baseline. Finally, we performed a series of experiments involving continual antigen stimulation in mice, determining that there is evidence in the cytokine, cellular and physiologic (mechanical) response consistent with our hypothesis of a finite twitch and an associated refractory period. For stem cells, we made a 3-D ABM of a decellularized scaffold section seeded with a generic stem cell type. We then programmed in different sets of rules that could conceivably underlie the cell's behavior, and observed the change in engraftment patterns in the scaffold over selected timepoints. We compared the change in those patterns against the change in experimental scaffold images seeded with C10 epithelial cells and mesenchymal stem cells, two cell types whose behaviors are not well understood, in order to determine which rulesets more closely match each cell type. Our model indicates that C10s are more likely to survive on regions of higher substrate while MSCs are more likely to proliferate on regions of higher substrate.

Master of Science / Biochemistry and Molecular Biophysics Interdepartmental Program / Anna Zolkiewska / Mitogen-activated protein kinase (MAPK) signaling plays an important role in the proliferation, survival, and therapy resistance of breast cancer cells. Two important protein kinases involved in the MAPK pathway are MEK and ERK. The MEK/ERK signaling cascade can be stimulated by activation of the epidermal growth factor receptor (EGFR) upon binding of EGF-like ligands, which are released from cells by ADAM proteases. EGFR is frequently overexpressed in triple-negative breast cancer (TNBC), a particularly aggressive form of breast cancer. Our analysis of clinical data revealed that high expression of ADAM12, but not other ADAMs, in TNBC is associated with poor patient survival. Thus, we hypothesized that ADAM12 plays a critical role in the progression of TNBC, possibly by stimulating MEK/ERK activity in an EGFR-dependent manner. To test this hypothesis, ADAM12 was knocked-down (KD) in SUM159PT TNBC cells, which express high levels of the endogenous ADAM12 protein. An antibody array assay indicated a significant decrease in the activation of the MAPK pathway in SUM159PT cells after ADAM12 KD. The decrease in MAPK activity was further confirmed by Western blotting using phospho-MEK and phospho-ERK specific antibodies. Additionally, conditioned media from ADAM12-deficient SUM159PT cells failed to support the survival of MCF10A cells, suggesting that ADAM12 KD reduced the release of pro-survival growth factors from SUM159PT cells. Based upon this data, we propose that ADAM12 is a novel regulator of the MAPK pathway and a potential therapeutic target in breast cancer.

Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) hold great promise in the fields of drug development and regenerative medicine. If iPSCs reprogrammed from patient cells replicate what is seen in vivo they may be used as a model of disease. A process that is disrupted in many neurodegenerative diseases is mitochondrial biogenesis. One of these diseases is amyotrophic lateral sclerosis (ALS), which is characterized by loss of motor neurons in the brain and spinal cord. Differentiation of hPSCs into motor neurons offers a way to study a previous unavailable cell type and may further our understanding of human motor neuron biology. The aims of the present study were to differentiate motor neurons from hESCs and iPSCs in low oxygen conditions and to explore mitochondrial biogenesis and electrical maturation during this process. After three weeks of treatment with retinoic acid and purmorphamine, a sonic hedgehog agonist, cells increased expression of post mitotic spinal motor neuron markers. One week later electrophysiological analysis revealed voltage-gated currents and action potential generation. Mitochondrial biogenesis signaling and expression of respiratory chain proteins increased with motor neuron differentiation. Respiration analysis revealed a decrease in glycolysis in motor neurons compared to neural stem cells. Interestingly, this was not accompanied by an increase in basal respiration or mitochondrial mass. These findings enhance our understanding of motor neuron mitochondrial biogenesis, a process impaired in ALS.

Several studies have shown cellular replacement therapy as a treatment strategy of myocardial infarction but results have been limited. Therefore, enhancing the therapeutic potential of stem cells injected into ischemic microenvironments by novel preconditioning (PC) techniques is critical for improving cellular therapy. Recent studies have shown that inhibition of phosphodiesterase-5 (PDE-5) is a powerful strategy to precondition the heart and cardiomyocytes against ischemia/reperfusion injury. We therefore tested the hypothesis that inhibition of PDE-5 with sildenafil (Viagra®) or selective knockdown with a silencing vector in adipose derived stem cells (ASCs) would improve their survival after ischemia/reoxygenation in vitro and enhance cardiac function following myocardial implantation in vivo. ASCs were treated with sildenafil or infected with PDE-5 silencing vector shRNA (shRNAPDE-5). The cells were subjected to simulated ischemia (SI) and reoxygenation (RO). Both sildenafil and shRNAPDE-5 significantly reduced cell injury, as shown by improved viability, decreased lactate dehydrogenase, and apoptosis. The preconditioned ASCs also demonstrated an increase in the release of growth factors including VEGF, b-FGF, and IGF. The protective effect against SI/RO injury was abolished by inhibition of protein kinase G (PKG) using both a pharmacological inhibitor and selective knockdown with shRNAPKG1α suggesting a PKG-mediated mechanism. To show the effect of preconditioned ASCs in vivo, adult male CD-1 mice underwent myocardial infarction (MI) by occlusion of the left descending coronary artery, followed by direct injection of PBS (control), non-preconditioned ASCs, or preconditioned ASCs (4x105) ASCs into the left ventricle (LV). Preconditioned ASC-treated hearts showed consistently superior cardiac function by all measures as compared with PBS and non-preconditioned ASCs after 4 weeks of treatment. Post-mortem histological analysis demonstrated that preconditioned ASC-treated mice had significantly reduced fibrosis, increased vascular density and reduced resident myocyte apoptosis as compared to mice receiving non-preconditioned ASCs or PBS. VEGF, b-FGF, and Ang-1 were also significantly elevated 4 weeks after cell therapy with preconditioned ASCs. Our data suggests that genetic or pharmacological inhibition of PDE-5 is a powerful new approach to improve stem cell therapy following myocardial infarction.

Optimizing culture conditions that reduce genomic instability in human pluripotent stem cells (hPSCs) is an unmet challenge in the field. Results from our lab and numerous research groups demonstrate that hPSCs are prone to genomic aberrations and single-cell passaging increases the rate of genomic alterations. However, single-cell based passaging maintains advantages for scale-up and standardizing differentiation protocols. In this study, we investigated the problem of genomic instability in hPSC cultures with the goal towards identifying and characterizing candidate genes that could contribute to generation and survival of abnormal hPSCs. Based on microarray analysis, we identify ARHGDIA, located on 17q25, as a candidate gene conferring selective advantage to trisomy 17 hPSCs. Using lentiviral approaches to overexpress ARHGDIA in hPSCs, [hPSC (Arg)], we functionally validate that in enzymatically passaged co-cultures, hPSC (Arg) lines exhibit competitive advantage against wild type hPSCs, [hPSC (WT)]. Additionally, hPSC (Arg) lines exhibit increased single-cell survival at low density plating. In co-cultures with hPSC (WT), ROCKi exposure attenuated the competitive advantage of hPSC (Arg) subpopulations. For the first time, this work demonstrates that increased expression of a gene on 17q25 confers selective advantage to hPSCs. In parallel studies, using medium devoid of bFGF containing LIF plus two inhibitors, MEK inhibitor (PD0325901) and p38 inhibitor (SB203580), we demonstrate that hPSCs are LIF responsive and can be stably maintained in naive pluripotent culture conditions. Based on their clonal viability, we propose that naive hPSCs are a more genetically stable population than primed hPSCs, when passaged as single- cells. These studies will aid the long-term goal of hPSC scale-up while promoting stable propagation of genomically normal hPSCs.

Central to the progression of all organisms is the maintenance of a stable genome despite continuous insults arising from genotoxic and environmental stresses. Embryonic stem cells show promise for treatment of a variety of diseases as well as for providing normal human tissue to conduct scientific research. A major obstacle for their application is that genomic instability arises in stem cells after prolonged cell culture. The most detrimental form of DNA damage is the DNA double-strand break (DSB), which is managed by cells through complex mechanisms, designated the DNA damage response. There are two major types of DSB repair; homologous recombination repair (HRR) and non-homologous end joining (NHEJ), both of which are regulated by members of the phosphatidyl-inositol-3’-kinase-related kinase (PIKK) family, including Ataxia Telangiectasia Mutated (ATM), Ataxia Telangiectasia Mutated and Rad3-related (ATR) and the DNA dependent protein kinase (DNA-PK). The aim of this study was to define the mechanisms and important proteins involved in repair of human embryonic stem cells. Here we have also described a system to differentiate hESCs into neural progenitors and astrocytes and were able to examine their DNA damage response. In both examining DNA repair markers and using a DNA repair reporter assay, this work shows that ATR is involved in DSB repair early in development, whereas ATM is essential in DSB repair in differentiated cells. We also show that HRR, a high fidelity form of repair, is used extensively by embryonic stem cells and HRR diminishes as cells differentiate. We also further defined the extent of NHEJ and the role of high fidelity NHEJ from the embryonic to differentiated state. These findings further the basic knowledge of repair fidelity in embryonic and mature human tissue. The data gives insight into what proteins maintain stem cell genomic stability and may be important to develop safe technologies for tissue engineering. Specifically, we have defined what DNA damage signaling pathways are used as embryologic cells progress to a mature, functional state.

A great need exists for an abundant, easily accessible source of patient-specific cells that will function for use in regenerative medicine. One promising source is the adult stem cell derived from adipose tissue (ASCs). Isolated from waste lipoaspiration, these cells could serve as a readily available source for the regeneration of damaged tissues. To further define the biology of ASCs, we have isolated multiple cell strains from different adipose tissue sources, indicating wide-spread distribution in the body. We find that a widely used set of cell surface markers fail to distinguish ASCs from normal fibroblasts. However, our ASC isolations are multipotent while fibroblasts show no differentiation potential. In further contrast to fibroblasts, these cells also show expression of genes associated with pluripotent cells, Oct-4, SOX2, and NANOG. Together, our data suggest that while the cell surface profile of ASCs do not distinguish them from normal fibroblasts and their lack of telomerase shows their limited proliferation capacity, the expression of genes closely linked to pluripotency and their differentiation capacity clearly define ASCs as multipotent stem cells. iPS cells are another promising cell type for tissue regeneration, due to their expression of hTERT and their capacity to differentiate into all three germ layers. Interestingly, telomerase is activated during the induction process, accomplished by the exogenous expression of four genes in normal, non-hTERT-expressing fibroblasts. To elucidate the mechanisms behind this activation, we examined the overexpression of these four factors in BJ fibroblasts and ASCs, which resulted in undetectable hTERT expression. We then demonstrated a lack of an acetylated histone H3K9 with the opposing di-methylation, indicative of a closed chromatin state at the hTERT promoter. Subsequent treatment of cells with TSA alone showed an upregulation of hTERT mRNA without telomerase activity. However, telomerase activity was found when ASCs, but not BJs were treated with TSA and all four factors, indicating differential regulation of hTERT in cells of similar mesenchymal origins. Our data suggest that while hTERT’s expression is universally dependent on the presence of a relaxed chromatin state and sufficient transactivating factors, other cell to cell differences can prevent its expression.

Cyclin Dependent Kinase-2 Associated Protein-1 (CDK2AP1) plays an important role in cell cycle regulation, by inhibiting CDK2 and by targeting it for proteolysis. It is also known to bind the DNA polymerase alpha-primase complex and regulate the initiation step of DNA synthesis. Its overexpression has been shown to inhibit growth, reduce invasion and increase apoptosis in a number of cancer cell lines. In studies in which mouse embryonic stem cells (mESCs) with targeted deletion of the Cdk2ap1 gene were used, Cdk2ap1 was shown to be required for epigenetic silencing of Oct4 during differentiation. The goal of this thesis was to examine the role of CDK2AP1 in somatic cells (primary human dermal fibroblasts (HDFs)) and human embryonic stem cells (hESCs) and specifically assess its impact on proliferation, self-renewal and differentiation. In the first part of this study, using a short-hairpin RNA (shRNA) approach, we investigated the effect of CDK2AP1 downregulation in HDFs. Outcomes indicated: (a) reduced proliferation, (b) premature senescence, (c) cell cycle alterations, (d) DNA damage, and (e) an increase in p53, p21, and the p53-responsive apoptotic genes BAX and PUMA. Simultaneous downregulation of p53 and CDK2AP1 in HDFs confirmed that observed phenotype was p53 dependent. In the second part of this study, using a shRNA approach, we investigated the role of CDK2AP1 on hESC fate associated with self-renewal and differentiation. We found that CDK2AP1 knockdown in hESCs resulted in: (a) reduced self-renewal (b) enhanced differentiation (c) cell cycle alterations and (d) increase in p53 expression. Results indicate that the knockdown of CDK2AP1 in hESCs enhances differentiation and favors it over a self-renewal fate. Thus, this study has successfully identified novel functions for CDK2AP1, as its knockdown has a significant impact on self-renewal, differentiation and senescence. Results obtained from this study could contribute to development of directed differentiation strategies for generating uniform populations of differentiated phenotypes from hESCs for clinical applications.

The goal of this research was to develop a system of injectable hydrogels to deliver stem cells to musculoskeletal defects, thereby allowing cells to remain at the treatment site and secrete soluble factors that will facilitate tissue regeneration. First, production parameters for encapsulating cells in microbeads were determined. This involved investigating the effects of osmolytes on alginate microbead properties, and the effects of alginate microbead cell density, alginate microbead density, and effects of osteogenic media on microencapsulated cells. Although cells remained viable in the microbeads, alginate does not readily degrade in vivo for six months. Therefore, a method to incorporate alginate lyase in microbeads was developed and optimized to achieve controlled release of viable cells. Effectiveness of this strategy was determined through cell release studies and measuring proteins and expression of genes that are characteristic of the cell’s phenotype. Lastly, in vivo studies were done to assess the ability of alginate microbeads to localize microencapsulated cells and support chondrogenesis and osteogenesis. This project will provide insight to the tissue engineering field regarding cell-based therapies and healing musculoskeletal defects.

Pancreaic stem cells are potent to differentiate into insulin producing -cells. Stem cells would be use for the cell therapy in the future. This diploma thesis is focused on this four transcription factors (LIF, noggin, TGF- a BMP-2) and their effects on the differentiation of the pancreatic stem cells into -cells. The results were analysed by evidential methods (RT-PCR, immunofluorescence and static incubation.