Mouse epiblast stem cells (EpiSC) are pluripotent cells derived of the epiblast of post-implantation blastocysts that can self-renew indefinitely in culture, display lineage-restricted differentiation, and appear to closely resemble human embryonic stem cells (ESC). Despite significant advances in the last decade, the precise molecular mechanisms and many master regulator (MR) genes underlying stem cell self-renewal, pluripotency, interactions with surrounding cells, and lineage-specific differentiation still remain elusive. The goal of this thesis is to address these gaps of knowledge using a systematic approach to identify novel MR genes and functionally validate them using genetically modified mouse models.In order to elucidate MR genes that control understudied biological processes, previous work in the Shen lab have computationally reconstructed the regulatory network of EpiSC and interrogated the EpiSC interactome with pluripotency signatures of EpiSC lines. One MR gene of interest from the previous analysis is ZC3H13, which encodes a protein that has been previously shown to be a crucial for N6-methyladenosine modification in RNA (m⁶A). This suggests a novel connection between m⁶A epitranscriptional modifications and primed state pluripotency. In my thesis research, I have shown that Zc3h13 is essential for proper trophoblast lineage differentiation and the importance of m6A modifications in early embryonic development. Using two Zc3h13 knockout mouse lines, I have found that Zc3h13 null embryos are embryonic lethal at the peri-implantation stage due to a failure to implant into the uterus. In vitro outgrowth analysis revealed a lack of trophoblast giant cells in Zc3h13 null outgrowths, and the lack of enlarged nuclei in the Zc3h13 null outgrowth suggests a failure in endoreduplication. Immunofluorescence analysis of Zc3h13 null blastocysts showed that the trophectoderm cells of Zc3h13 null blastocyst expressed trophectoderm specific factors at abnormal levels, indicating a severe dysregulation of the trophectoderm regulatory network. To elucidate the effects of Zc3h13 knockout on pluripotency, I also performed a detailed immunofluorescence analysis of Zc3h13 null inner cell mass (ICM), which expressed pluripotency factors at normal levels. However, Zc3h13 null blastocysts were less efficient at generating ESC lines and the Zc3h13 KO ESC generated were morphologically abnormal. Dot blot and mass spectrometry analysis showed that Zc3h13 KO ESC had a dramatically lower level of m⁶A modification, suggesting a connection between m6A epitranscriptional modification and endoreduplication. Interestingly, chimera and teratoma analysis showed that while Zc3h13 KO ESC can contribute to derivatives of the three primary lineages, Zc3h13 KO ESC has a bias towards neuroectoderm differentiation. In this thesis, I have shown the importance of m6A transcriptional regulation in trophoblast giant cell differentiation. Taken together, my studies can help further the understanding of the biological functions of m⁶A modifications as well as the relationship between transcriptional regulation and cell fate transition. My work highlights another level of gene regulation through epitranscriptional modification and the importance of the epitranscriptomic landscape in cell fate transition and development.

Wolbachia is a vertically transmitted, obligate intracellular bacterium infecting ~40% of all known species of arthropods, as well as filarial nematodes. The nature of Wolbachia-host interactions ranges from reproductive parasitism to increased fecundity and pathogen protection. Wolbachia reduces the ability of mosquitoes to transmit human pathogens, which is being explored as a novel method for the control of vector-borne diseases like Dengue and Zika. The mechanisms of Wolbachia blocking the transmission of these diseases are not fully understood. There are studies indicating that Wolbachia-induced changes in the insect immunity could block the virus, however there is no consensus in the literature. A necessary step in the transmission of these diseases is the viral entry into the insect vector. This occurs trough the gut epithelium, highlighting the importance of understanding the interaction of this tissue with microorganisms. We have recently shown that Wolbachia colonizes the Drosophila gut epithelium and affects the gut microbiome composition. Wolbachia’s presence did not affect the gene expression of immune effector molecules from the main regulators of gut immunity, Imd and ROS pathways. Our understanding of the mechanisms of Wolbachia’s colonization of the gut epithelium and modulation of gut microbiome are still very limited. This work characterizes Wolbachia’s kinetics of colonization in Drosophila midguts. Imaging analysis revealed that Wolbachia colonizes adult and larval midguts in different patterns. We have also characterized a preferential colonization in specific adult midgut sub-regions. We observed that Wolbachia patches are confined to specific midgut subregions, in a pattern similar to the arrangement of intestinal stem cell (ISC) clones. These results led us to hypothesize that Wolbachia colonizes Drosophila midguts by infecting intestinal progenitor cells and spreading vertically to their progeny with limited lateral transmission between neighboring cells. We provide evidence to support this hypothesis by showing that Wolbachia is present in intestinal progenitor cells in all stages of the fly’s life cycle as well as by analyzing the infection status of ISC clones and differentiated cells surrounding ISCs. Finally, we found that ISC proliferation is reduced by the intracellular presence of Wolbachia, which also decreases ISC tumor incidence triggered by the downregulation of Notch signaling specifically in ISCs. These findings will aid in our understanding of Wolbachia tropisms and its phenotypic consequences. It has been shown that in the Wolbachia wMelPop strain excessive growth of intracellular bacteria leads to damage to the host cell, suggesting a mechanism of controlling intracellular growth in other strains. To better understand the molecular mechanisms behind Wolbachia-Drosophila interactions, we turned to the gonads, as Wolbachia colonization of these tissues has been well characterized. We chose to investigate the interplay between Reactive Oxygen Species (ROS) and Wolbachia, as intracellular ROS could regulate bacterial density but also be affected by Wolbachia and play a role in symbiont-related phenotypes. Using direct and indirect measurements of ROS, we show that the pathogenic strain wMelPop increases ROS in the germarium, while the symbiotic strains wMel and wMelCS reduce ROS in the terminal filaments. None of the Wolbachia strains tested affected ROS levels in the testes. In addition, genetically altering ROS levels in the germline or systemically in the fly did not affect Wolbachia levels in the ovaries. We conclude that ROS does not significantly affect Wolbachia in the fruit fly gonads.

Increasing evidence suggests that breast cancer is caused by cancer stem cells and the cure of breast cancer requires eradication of breast cancer stem cells. In this study, we established and characterized a sphere culture model derived from side population cells from the human breast cancer cell line MCF7. The sphere culture could be maintained long term and was enriched in cells expressing known breast cancer stem cell marker CD44+CD24 -. These sphere cells showed higher colony formation ability in vitro and higher tumorigenicity in vivo than MCF7 cells, suggesting the enrichment of breast cancer stem/progenitor cells. To identify compounds that preferentially inhibit the sphere cells, we performed a compound library screening. Two lead compounds, NSC24076 and NSC125034 and an analog of NSC125034, 8-quinolinol (8Q), were identified as having preferential activity against the sphere cells. 8Q showed some antitumor activity alone but had much better therapeutic effect and relapse prevention when combined with paclitaxel than either 8Q or paclitaxel alone in both MCF7 and MDA-MB-435 xenograft models. We propose that compounds selectively targeting cancer stem/progenitor cells when combined with standard chemotherapy drugs may produce an improved treatment of cancer without significant relapse.

Restoring blood flow, improving perfusion, reducing clinical symptoms, and augmenting ventricular function are the goals after acute myocardial infarction. Other than cardiac transplantation, no standard clinical procedure is available to restore damaged myocardium. Since we first reported cellular cardiomyoplasty in 1989, successful outcomes have been confirmed by experimental and clinical studies, but definitive long-term efficacy requires large-scale placebo-controlled double-blind randomized trials. On meta-analysis, stem cell-treated groups had significantly improved left ventricular ejection fraction, reduced infarct scar size, and decreased left ventricular end-systolic volume. Fewer myocardial infarctions, deaths, read-missions for heart failure, and repeat revascularizations were additional benefits. Encouraging clinical findings have been reported using satellite or bone marrow stem cells, but understanding of the benefit mechanisms demands additional studies. Adult mammalian ventricular myocardium lacks adequate regeneration capability, and cellular cardiomyoplasty offers a new way to overcome this; the poor retention and engraftment rate and high apoptotic rate of the implanted stem cells limit outcomes. The ideal type and number of cells, optimal timing of cell therapy, and ideal cell delivery method depend on determining the beneficial mechanisms. Cellular cardiomyoplasty has progressed rapidly in the last decade. A critical review may help us to better plan the future direction.

Surgical skin flaps are frequently used in plastic and reconstructive surgery to repair acquired or congenital defects. Necrosis is a common complication associated with these flaps postoperatively as a result of inadequate blood supply. Stem cells are precursor cells with the potential to differentiate into more specialized cells. Angiogenic factors act to direct cellular differentiation and organization to form new vascular elements. Our theory was that the combination of angiogenic growth factors with stem cells derived from the subject preoperatively would augment neovascularization, thereby increasing blood supply to the flap, which may ultimately improve flap survival. In phase I, 40 Lewis rats were randomized into 4 groups of 10. Random dorsal skin flaps were elevated and treated at the same time. The first group was injected with only medium, the second with stem cells, the third with stem cells and angiogenic factors, and the fourth with angiogenic growth factors. Millimetric measurements of flap viability at 7 and 14 days did not show any statistically significant differences between the studied groups. In phase II, 24 rats were also randomized into 4 groups of 6, but this time were treated 1 week before flap elevation. The viability measurements showed an increased rate of viability in the group in which stem cells and the angiogenic factors were administered simultaneously (84.5% ± 3.2%) as compared with the unmodified control group (62.6% ± 7.3%) or to the groups in which only precursor cells (60.4% ± 7.9%) or angiogenic factors (62.3% ± 10.1%). Increased blood supply brought by these manipulations is believed translated to increased tissue flap survival. Punch biopsies showed that "green fluorescent protein"-labeled precursor cells was noted to form luminal structures in the treated flaps. The vascular cast of all flaps was filled with Mercox plastic resin. After euthanasia, the soft tissues of the harvested flaps were dissolved and the remaining vascular cast was weighted. The weight-based ratio of the vascular composition was determined. The flaps injected with both stem cells and angiogenic factors showed higher values. We conclude that the administration of bone marrow stem cells with angiogenic factors 1 week before flap creation improves the survival of ischemic random skin flaps.

The pharyngeal foregut endoderm (PFE) gives rise to several important organs including the thyroid, thymus and parathyroid glands. In mice and humans, defects in the development of PFE can lead to thymic aplasia and aberrations in thymic epithelial cell (TEC) function can lead to immunodeficiency or autoimmune disease. Successful differentiation of pluripotent stem cells (PSCs) to PFE could provide a renewable cell source that enables the study of human diseases that originate in the PFE. Here, I identify signaling pathways that influence the differentiation of PSCs to PFE. Firstly, using a novel mouse reporter PSC line we develop a protocol that generates a Pax9 expressing population that is enriched for PFE markers and upon transplantation can form organized epithelial structures. However, since this protocol was inefficient for human PSCs, we subsequently identified additional signaling pathways required for the efficient generation of human PFE and determined a key role for retinoic acid. Upon transplantation, the human PFE gives rise to TECs, a ventral PFE derivative. Finally, to facilitate future investigation into the gene regulatory networks in PFE, we develop a CRISPR-effector system to modulate endogenous gene expression in PSCs. We demonstrate that developmentally relevant genes can be repressed or induced, thereby influencing the cellular state. These data present strategies to generate cells of the PFE lineage from PSCs, facilitating the production of cells for patient-specific disease modeling or cell replacement therapies, and a method to interrogate gene and regulatory element function in PFE and its derivatives.

Les mutations affectant la fonction d'enzymes impliquées dans le cycle des purines sont responsables d'une multitude de syndromes pédiatriques, caractérisés par des atteintes neurologiques et comportementales. A ce jour, aucune stratégie thérapeutique n'a été réellement efficace pour contrôler ces symptômes. La maladie de Lesch-Nyhan (MLN), associée à la perte de fonction de l'enzyme de recyclage HGPRT, constitue un bon modèle d'étude. Mon travail a consisté à utiliser la technologie des cellules souches induites à la pluripotence, reprogrammées à partir de fibroblastes de patients atteints des formes sévères de la MLN, pour identifier des phénotypes neuronaux associés à la perte de fonction de l'HGPRT. Ces marqueurs phénotypiques ont ensuite été utilisés pour identifier, par une approche de criblage à haut débit, de nouvelles molécules chimiques capables de corriger ces défauts. Plus de 3000 molécules ont été testées et 6 composés, tous dérivés de l'adénosine, ont pu être identifiés comme compensant le métabolisme par un mécanisme d'action indépendant de l'HGPRT. De manière intéressante, un des composés, la S-adenosylmethionine (SAM) a par le passé déjà démontré des effets bénéfiques sur les symptômes comportementaux typiques de la MLN dans plusieurs études de cas. Cela démontre que la stratégie abordée ici a permis l'identification de cibles thérapeutiques permettant d'améliorer les symptômes neurospychiatriques de cette pathologie et constitue un modèle réplicable pour différentes pathologies touchant le métabolisme cérébral. / Mutations in genes coding for enzymes involved in purine synthesis or recycling lead to dramatic neurological conditions with poor pharmacological options. Lesch–Nyhan disease (LND) is caused by deficiency of the salvage pathway enzyme HGPRT that compromises recycling of guanine and hypoxanthine into GMP and IMP. LND is characterized by severe neuropsychiatric symptoms that are out of reach of pharmacological treatments. Here we use human cortical neural stem cells and neurons derived from iPSC of children affected by severe forms of LND to identify neural phenotypes associated with HGPRT-deficiency and of interest to develop a target-agnostic based drug screening system. We screened more than 3000 molecules and identified 6 compounds, all possessing an adenosine moiety, that corrected LND related neuronal phenotypes by promoting metabolism compensations in a HGPRT-independent manner. One of these compound, S-adenosylmethionine (SAM), has already been reported as providing amelioration of behavioral symptoms in some LND cases, demonstrating that our screening allowed the identification of pathways that can be relevant therapeutic targets to ease the devastating neuropsychiatric symptoms associated with this pathology. Interestingly, these pathways can be activated in LND patients via simple food supplementation. This experimental paradigm can also be easily adapted to other purine associated neurological disorders affecting normal brain development.

Proper lung function relies on the precise balance of specialized epithelial cell types that coordinate to maintain homeostasis. The Hippo pathway has emerged as a critical regulator of cell fate both developmentally and in a regenerative setting. The work presented in this dissertation describes essential roles for the transcriptional effectors of Hippo pathway signaling, Yap and Taz, in maintaining lung epithelial homeostasis. The data presented here demonstrate that conditional deletion of Yap and Wwtr1/Taz in the lung epithelium of adult mice results in severe defects with consequent animal lethality. Phenotypes associated with Yap/Taz deletion include alveolar disorganization, a development of mucin hypersecretion throughout the airways, and ciliary disorganization. Through in vivo lineage tracing, analysis of mouse and human tissues, along with in vitro molecular experiments, these studies show that nuclear YAP/TAZ exert transcriptional control over club cell fate, while in multiciliated cells, they function within the cytoplasm to maintain ciliary structures. Within club cells, reduced YAP/TAZ activity promotes intrinsic goblet transdifferentiation of secretory airway epithelial cells. Global gene expression and ChIP-Seq analyses reveal that YAP/TAZ act through the TEAD family of transcription factors to suppress a goblet cell differentiation program in airway epithelial cells, including direct repression of the SPDEF gene, which encodes a transcription factor required for goblet cell identity. Further in vitro studies identify cooperation between YAP/TAZ-TEAD and the NuRD chromatin remodeling complex to inhibit SPDEF expression and that Hippo-regulated YAP/TAZ impinge on cytokine-induced goblet cell differentiation. Within multiciliated cells, we observe that phosphorylated Yap localizes in a planar polarized manner at the base of cilia and controls ciliary and basal body density. Lineage specific Yap/Taz deletion leads to reduced ciliary density and height due to a loss of apically basal bodies. Collectively, this work identifies YAP/TAZ as critical factors in lung epithelial homeostasis and offers new molecular insight into the mechanisms regulating the secretory and multiciliated cell lineages, which are frequently impaired in a broad range of lung diseases. / 2024-02-02T00:00:00Z

Indiana University-Purdue University Indianapolis (IUPUI) / The development and function of hematopoietic stem cells (HSCs) is regulated by numerous signaling pathways including Akt-mechanistic target of rapamycin complex1 (mTORC1) pathway. Dysregulation of this pathway results in impaired HSC function and contributes to the development of hematologic malignancies. Activated mTORC1 phosphorylates and subsequently activates ribosomal protein S6 kinase 1 (S6K1). To study the role of S6K1 in hematopoiesis as well as leukemogenesis, we used a genetic model of S6K1 deficient mice (S6K1-/-). We found that loss of S6K1 expression in HSCs results in reduction of absolute HSC number in bone marrow (BM). Following chemotherapy, cycling HSCs undergo apoptosis and quiescent HSCs are required to cycle to regenerate the hematopoietic system. S6K1 regulates the quiescence of HSCs and in the absence of S6K1, mice are more susceptible to repeated myeloablative stress. We also observed that loss of expression as well as gain of expression of S6K1 affects the self-renewal ability of HSCs. Interestingly, when we overexpressed S6K1, it also resulted in reduced self-renewal of HSCs. Next, we assessed the role of S6K1 in the propagation of acute myeloid leukemia (AML). The mixed-lineage leukemia (MLL) gene is required for the maintenance of adult HSCs. Translocations in MLL are detected in approximately 5-10% of adult acute leukemia patients and in approximately 70% of acute leukemias in infants. We expressed MLL-AF9 fusion oncoprotein in WT and S6K1-/- hematopoietic stem and progenitor cells (HSC/Ps) and performed serial transplantation. Upon secondary transplantation, recipients of S6K1 deficient AML cells survived significantly longer compared to controls. In vitro, pharmacological inhibition of S6K1 activity resulted in reduced growth of primary human cells expressing MLL-AF9. Both human and murine HSC/Ps expressing MLL-AF9 showed reduced mTORC1 activity upon inhibition of S6K1 suggesting that loss of S6K1 activity results in reduced Akt-mTORC1 activation both upstream and downstream of mTORC1. Overall, our studies establish a critical role of S6K1 activity in the maintenance of HSC function and in the propagation of leukemia.

Indiana University-Purdue University Indianapolis (IUPUI) / Mitochondria are the major ATP producing source within cells. There is increasing data supporting a direct involvement of mitochondria and mitochondrial function in regulating stem cell pluripotency. Mitochondria have also been shown to be important for hematopoietic stem and progenitor cell function. Hematopoietic stem cells have lower numbers of mitochondria (mass), lower mitochondrial membrane potential, and lower ATP levels as compared to other blood cell types. Mitochondria play an important role in hematopoietic stem and progenitor cells, thus we investigated the role of the chemokine, SDF-1/CXCL12, in mitochondrial function in hematopoietic stem and progenitor cells using an SDF-1/CXCL12 transgenic mouse model. We found increased mitochondrial mass is linked to CD34 surface expression in hematopoietic stem and progenitor cells, suggesting that mitochondrial biogenesis is linked to loss of pluripotency. Interestingly these hematopoietic progenitor cells have low mitochondrial membrane potential and these mitochondrial become active prior to leaving the progenitor cell compartment. We also tested the ability of SDF-1/CXL12 to modulate mitochondrial function in vitro by treating the human leukemia cell line, HL-60, and primary mouse lineage- bone marrow cells with SDF-1/CXCL12. We found significantly reduced mitochondrial function at two hours while mitochondrial function was significantly increased at 24 hours. This suggests that SDF1/CXCL12 regulates mitochondrial function in a biphasic manner in a model of hematopoietic progenitors and immature blood cells. This suggests SDF1/CXCL12 may play a role in regulating mitochondrial function in hematopoiesis. We also investigated STAT3 in hematopoietic stem and progenitor cells. Mitochondrial STAT3 plays an essential role in regulating mitochondrial function. By using a knockout (Stat3-/-) mouse model we found that Stat3-/- hematopoietic progenitor cells had reduced colony forming ability, slower cell cycling status, and loss of proliferation in response to multi-cytokine synergy. We also found mitochondrial dysfunction in Stat3-/- hematopoietic stem and progenitor cells. Our results suggest an essential role for mitochondria in HSC function and a novel role for SDF-1/CXCL12 and STAT3 in regulating mitochondrial function in hematopoietic stem and progenitor cells.