Excitotoxicity, a major hallmark of neurodegeneration associated with cerebral ischemia, is a result of accumulation of extracellular glutamate. This excess glutamate leads to hyperactivation of glutamate receptors such as the N-methyl-D-asparate (NMDA) receptors (NMDARs) following the activation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor (AMPARs). Excessive activation of NMDARs causes an influx of calcium, which can eventually activate apoptotic pathways and lead to death of neurons. Regulation of NMDAR subunit composition, localization, surface expression, and activity can balance cell survival via activation of either pro-death or pro-survival pathways after a course of an ischemic insult. Specifically, phosphorylation of different NMDAR subunits defines their activity and downstream signaling pathways. NMDARs are phosphorylated by multiple kinases and dephosphorylated by different phosphatases. Besides phosphatases and kinases, per se, phosphorylation of synaptic proteins that regulate kinase or phosphatase targeting and activity also mediate NMDAR phosphorylation. Spinophilin, a major synaptic scaffolding and protein phosphatase 1 (PP1) targeting protein, mediates substrate phosphorylation via its ability to bind PP1. Our studies focus on delineating the role of spinophilin in the regulation of phosphorylation and function of the GluN2B subunit of the NMDA receptor as well as the role of spinophilin in modulating glutamate-induced neurotoxicity. Interestingly, our data demonstrate that spinophilin sequesters PP1 away from GluN2B thereby enhancing phosphorylation of GluN2B at Ser-1284. These changes impact GluN2B protein interactions, subcellular localization, and surface expression, leading to alterations in the amount of calcium entering the neuron via GluN2B-containing NMDARs. Our data show that spinophilin biphasically regulates GluN2B function. Specifically, Ser-1284 phosphorylation enhances calcium influx through GluN2B containing NMDA receptors, but spinophilin leads to dramatic decreases in the surface expression of the receptor independent of Ser-1284 phosphorylation. Moreover, in spinophilin knockout mice, we observe less PP1 binding to GluN2B and less phosphorylation of Ser-1284, but more surface expression of GluN2B and greater levels of caspase activity. Together, these observations suggest a potential neuroprotective role for spinophilin by decreasing GluN2B-containing NMDA receptor-dependent surface expression and thereby decreasing intracellular calcium and neuronal cell death.

<p>Transforming growth factor β-activated kinase 1 (TAK1), a hub kinase at the convergence of multiple signaling pathways, is critical to the development of the central nervous system and has been found to play a role in cell death and apoptosis. TAK1 may have the potential to elucidate mechanisms of cell cycle and neurodegeneration. The Belecky-Adams laboratory has aimed to study TAK1 and its potential roles in cell cycle by studying its role in chick retinal development as well as its possible implication in the progression of diabetic retinopathy (DR). Chapter 3 includes studies that explore TAK1 in a study in chick retinal development and TAK1 in in vitro studies in retinal microglia. Using the embryonic chick, immunohistochemistry for the activated form of TAK1 (pTAK1) showed localization of pTAK1 in differentiated and progenitor cells of the retina. Using an inhibitor or TAK1 activite, (5Z)-7-Oxozeaenol, in chick eye development showed an increase in progenitor cells and a decrease in differentiated cells. This study in chick suggests TAK1 may be a critical player in the regulation of the cell cycle during retinal development. Results from experimentation in chick led to studying the potential role of TAK1 in inflammation and neurodegeneration. TAK1 has previously been implicated in cell death and apoptosis suggesting that TAK1 may be a critical player in inflammatory pathways. TAK1 has been implicated in the regulation of inflammatory factors in different parts of the CNS but has not yet been studied specifically in retina or in specific retinal cells [3, 4]. Chapter 2 includes studies from the Belecky-Adams laboratory of in vitro work with retinal microglia. Retinal microglia were treated with activators and the translocation to the nucleus of a downstream factor of TAK1 was determined: NF-kB. Treatment of retinal microglia in the presence of activators with TAKinib, an inhibitor of TAK1 activation, revealed that TAK1 inhibition reduces the activation of downstream NF-kB. Together this data suggests that TAK1 may be implicated in various systems of the body and further studies on its mechanisms may help elucidate potential therapeutic roles of the kinase.</p>

Der induzierbare Kostimulator ICOS ist ein zu CD28 strukturell und funktionell verwandtes Molekül, das eine wichtige regulatorische Rolle bei der T-Zelleffektorfunktion spielt. Eine ICOS-Defizienz beim Mensch manifestiert sich in einer schweren Störung des humoralen Immunsystems. Eine murine ICOS-Defizienz führt ebenfalls zu einer Beeinträchtigung der T-Zell-abhängigen humoralen Immunantwort, bei der kleinere oder komplett fehlende Keimzentren zu beobachten sind. Vielfältige in vitro und in vivo Studien führten diese Phänomene auf die beeinträchtigte Regulation von Kommunikationsmolekülen der Zelloberfläche und der Zytokinexpression durch ICOS-defiziente T-Zellen zurück. Ein Ziel dieser Arbeit war es, mit Hilfe von ICOS KO Mäusen den Einfluss von ICOS auf die B-Zellentwicklung genauer zu untersuchen. Dabei konnte gezeigt werden, dass ICOS erst in der späten Phase der B-Zellentwicklung eine Rolle spielt, da der Interaktionspartner von ICOS erst auf transitionellen B-Zellen der Milz exprimiert wird. Durch die Etablierung eines in vivo adoptiven T-B Transfermodells konnte die Rolle von ICOS erstmalig bei der T-B Kooperation in den frühen Phasen der Immunantwort auf der Ebene Antigen-spezifischer T- und B-Zellen aufgeklärt werden. Dabei konnte beobachtet werden, dass eine ICOS-Defizienz einen dramatischen Einfluss auf die B-Zellexpansion und B-Zellproliferation hat. Zum ersten Mal konnte in vivo gezeigt werden, dass ICOS bei der T-B Kooperation eine entscheidende Rolle bei der Regulation diverser Oberflächenmarker der B-Zellen spielt, wodurch die B-Zellaktivierung, B-Zellproliferation und B-Zelldifferenzierung bei der Keimzentrums- und Plasmazellreaktion beeinflusst werden. Histologische Analysen zeigten, dass bei einer ICOS-Defizienz follikuläre T-Helferzellen nicht in die Keimzentrumsumgebung einwandern und daher keine T-Zellhilfe für die B-Zellen anbieten können. Dadurch kann die Keimzentrumsreaktion nicht weiter aufrechterhalten werden und eine Ausbildung von kleineren Keimzentren ist die Folge. Weiterhin konnte beobachtet werden, dass eine fehlende ICOS-Interaktion zwischen T- und B-Zellen zu einer Störung der Plasmazellgenerierung führt, wodurch auch die Mengen an messbaren Serumimmunglobulinen beeinflusst werden. Eine erhöhte Gabe von ICOS-defizienten T-Zellen kann diese Effekte nicht vollständig ausgleichen. Daher ist erkennbar, dass ICOS eine Vielzahl von zusätzlichen Faktoren beeinflusst, die für die ICOS-abhängigen B-Zelleffekte verantwortlich sind. / The inducible costimulator ICOS, structural and functional similar to CD28, plays an important regulatory role in T cell receptor function. The ICOS deficiency in humans is described as a severe dysfunction of the humoral immune response, resulting in dramatic reduced B cell numbers and impaired antibody response against pathogens. The murine ICOS-deficiency also leads to a disturbed T cell dependent immune response resulting in a reduced germinal center formation. Various in vitro and in vivo studies attributes this phenomenon to impaired upregulation of cell surface communication molecules and cytokine synthesis by ICOS-deficient T cells. In this work the investigations with ICOS KO mice should clarify the impact of ICOS in B cell development. As observed, ICOS can only play a role in the late phase B cell development, because the interaction partner is expressed on transitional B cells in the spleen. The establishment of an in vivo adoptive T-B transfer system could determine for the first time the role of ICOS in T-B cooperation in early immune response stages on antigen specific T and B cell levels. As shown, ICOS deficiency influences in a dramatic extend the B cell expansion and B cell proliferation. For the first time in vivo, we could demonstrate that ICOS plays a significant role by influencing the regulation of various B cell surface markers, which affects the B cell activation, B cell proliferation and B differentiation in germinal center or plasma cell reaction. Histological investigations revealed in the ICOS-deficiency that follicular T helper cells could not migrate into the germinal center microenvironment and therefore could not provide T cell help for B cells. As a result, the germinal center reaction could not maintained and therefore the formation of little germinal centers occurred. The missing interaction between T and B cells leads to a dysfunction in plasma cell generation and also influences the detectable amounts of serum immunglobulines. An administration of higher ICOS KO T cell numbers could not fully compensate these effects. Therefore, ICOS bias multitudes of additional factors, which are responsible for the ICOS dependent B cell effects.

Retinal ganglion cells (RGCs) serve as a vital connection between the eye and the brain with damage to their axons resulting in loss of vision and/or blindness. Retinal organoids are three-dimensional structures derived from human pluripotent stem cells (hPSCs) which recapitulate the spatial and temporal differentiation of the retina, providing a valuable model of RGC development in vitro. The working hypothesis of these studies is that hPSC-derived RGCs are capable of extensive outgrowth and display target specificity and pathfinding abilities. Initial efforts focused on characterizing RGC differentiation throughout early stages of organoid development, with a clearly defined RGC layer developing in a temporally-appropriate manner expressing a compliment of RGC-associated markers. Beyond studies of RGC development, retinal organoids may also prove useful to investigate and model the extensive axonal outgrowth necessary to reach post-synaptic targets. As such, additional efforts aimed to elucidate factors promoting axonal outgrowth. Results demonstrated significant enhancement of axonal outgrowth through modulation of both substrate composition and growth factor signaling. Furthermore, RGCs possessed guidance receptors that are essential in influencing outgrowth and pathfinding. Subsequently, to determine target specificity, aggregates of hPSC-derived RGCs were co-cultured with explants of mouse lateral geniculate nucleus (LGN), the primary post-synaptic target of RGCs. Axonal outgrowth was enhanced in the presence of LGN, and RGCs displayed recognition of appropriate targets, with the longest neurites projecting towards LGN explants compared to control explants or RGCs grown alone. Generated from the fusion of regionally-patterned organoids, assembloids model projections between distinct regions of the nervous system. Therefore, final efforts of these studies focused upon the generation of retinocortical assembloids in order to model the long-distance outgrowth characteristic of RGCs. RGCs displayed extensive axonal outgrowth into cortical organoids, with the ability to respond to environmental cues. Collectively, these results establish retinal organoids as a valuable tool for studies of RGC development, and demonstrate the utility of organoid-derived RGCs as an effective platform to study factors influencing outgrowth as well as modeling long-distance projections and pathfinding abilities.

The development of an organism and its adult homeostasis rely on regulatory mechanisms that control the underlying gene expression programs. In certain biological contexts, such as germ cell development, gene expression regulation is largely executed at the post-­‐transcriptional level. This relies on RNA-­‐binding proteins (RBPs), whose activity and expression are also heavily controlled. While the RNA-­‐binding potential of RBPs is currently of intense scrutiny, surprisingly little is known to date about the molecular mechanisms that control RNA-­‐binding proteins abundance in the context of germ cell development. This work identifies the molecular mechanisms that shape expression patterns of two evolutionarily conserved RNA-­‐binding proteins, CPB-­‐3 and GLD-­‐ 1, which belong to CPEB and STAR protein family, respectively. By focusing on their regulation in the C. elegans germ line, this work reveals an involvement of the proteasome in reducing levels of CPB-­‐3/CPEB and GLD-­‐1/STAR at the pachytene-­‐to-­‐diplotene transition during meiotic prophase I. Furthermore, it documents that CPB-­‐3 and GLD-­‐1 are targeted to proteasomal degradation by a conserved SCF ubiquitin ligase complex that utilises SEL-­‐10/Fbxw7 as a substrate recognition subunit. Importantly, destabilisation of both RBPs is likely triggered by their phosphorylation, which is regulated by the mitogen-­‐activated protein kinase, MPK-­‐1, and restricted to the meiotic timepoint of pachytene exit. Lastly, this work investigates the potential consequences of target mRNA regulation upon delayed RBP degradation. Altogether, the collected data characterise a molecular pathway of CPEB and STAR protein turnover, and suggest that MPK-­‐1 signaling may couple RBP-­‐mediated regulation of gene expression to progression through meiosis during oogenesis.

No description available.

<p>Skeletal muscle takes up nearly 40% of total body mass, is critical for daily function by</p> <p>providing balance, supports breathing, movement, and energy expenditure. Preserving</p> <p>skeletal muscle can also significantly improve one’s quality by maintaining balance, movement</p> <p>and improving metabolic health [1, 2]. This becomes more imperative with age, as skeletal muscle mass naturally declines, and further compounds decline in quality of life and health [1, 2]. Thus, it is critical to understand the physiology of skeletal muscle and the underlying cellular and</p> <p>molecular mechanisms that contribute to normal function. Using mouse models to further our</p> <p>understanding, this dissertation leverages single-cell RNA-sequencing (scRNA-seq) to dissect the</p> <p>cellular and molecular underpinnings of skeletal muscle injury and repair. Specifically, chapter 1</p> <p>provides an overview of skeletal muscle structure, muscle regeneration, and the current state of</p> <p>scRNA-seq literature in muscle regeneration. In chapter 2, I will discuss the large-scale scRNAseq of regenerating muscle which identified dynamic population of resident and infiltrating cells. In chapter 3, I will discuss the potential immunomodulatory role of MuSCs and leveraging scRNAseq data to understand the cellular mechanisms that govern successful muscle regeneration. Finally, in chapter 4 I will discuss the role of the transcription factor Sox11, which was identified by scRNA-seq and was specific to differentiating MuSCs. Thus, this dissertation spans the cellular and molecular components of muscle regeneration.</p>

<p dir="ltr">Lung cancer is the leading cause of cancer-related deaths, and although important therapy advancements have been achieved, ~1.6 million people die from lung cancer annually. Non-small cell lung cancer (NSCLC), which makes up ~85% of lung cancer cases, is mainly treated with radiotherapy, chemotherapies, and targeted agents. Targeted agents are selected based on the mutation spectrum of the tumor. In NSCLC the epidermal growth factor receptor (EGFR) is commonly mutated and, leads to increased proliferation and cell survival. The standard-of-care treatment for patients with activating mutations in EGFR is treatment with tyrosine kinase inhibitors (TKI), such as erlotinib. While tumors initially respond to TKIs, after 1-2 years most patients develop resistance. In ~60% of TKI resistant tumors, resistance is the result of a secondary mutation in EGFR, whereas in the remaining 20%, tumors turn on bypass track-signals to overcome inhibition of the EGFR pathway. However, 15-20% of the cases the mechanisms underlying resistance are unknown. Most studies focus on the gain of function of oncogenes as mediators of resistance; however, little is known about the role that tumor suppressors play in TKI resistance. Hence, we performed a genome-wide CRISPR Cas9 knock-out screen to identify genes that when knocked-out would drive erlotinib resistance, and KMT5C was identified as the top candidate. KMT5C is a histone methyltransferase that trimethylates H4K20 (H4K20me3), enabling the establishment of constitutive and facultative heterochromatin. Data from human samples suggests that the <i>KMT5C</i> transcript is globally downregulated in NSCLC and in tumor samples resistant to the third generation TKI osimertinib. Additionally, loss of the modification H4K20me3, influences prognosis of NSCLC, indicating that loss of KMT5C function is a crucial mechanism in carcinogenesis. Here we describe how loss of KMT5C leads to increased transcription of the oncogene MET, due to a loss in H4K20me3-mediated repression of a long non-coding RNA transcription (LINC01510) upstream of MET. This mechanism was found to be partially responsible in driving TKI resistance in EGFR mutant cells. Historically, KMT5C has been associated with generation of constitutive heterochromatin (cHC); however, recent reports, including our own, indicate that KMT5C also regulates transcription in regions outside of cHC. Our preliminary evidence suggests that deposition of H42K0me3 via KMT5C in regions outside of cHC, is less stable than in cHC regions. This novel finding led us to hypothesize that regulation of KMT5C and H42K0me3 at different regions of heterochromatin is a dynamic process.</p>

<p dir="ltr">Primary cilia are hair-like structures found on nearly all mammalian cell types, including cells in the developing and adult brain. Cilia establish a unique signaling compartment for cells. For example, a diverse set of receptors and signaling proteins localize within cilia to regulate many physiological and developmental pathways including the Hh pathway. Defects in cilia structure, protein localization, or cilia function lead to genetic disorders called ciliopathies, which present with various clinical features including several neurodevelopmental phenotypes and hyperphagia associated obesity. Despite their dysfunction being implicated in several disease states, understanding their roles in CNS development and signaling has proven challenging. I hypothesize that dynamic changes to ciliary protein composition contributes to this challenge and may reflect unrecognized diversity of CNS cilia. The proteins ARL13B and ADCY3 are established ciliary proteins in the brain and assessing their localization is often used in the field to visualize cilia. ARL13B is a regulatory GTPase important for regulating cilia structure, protein trafficking, and Hh signaling, while ADCY3 is a ciliary adenylyl cyclase thought to be involved in ciliary GPCR singaling. Here, I examine the ciliary localization of ARL13B and ADCY3 in the perinatal and adult mouse brain by defining changes in the proportion of cilia enriched for ARL13B and ADCY3 depending on brain region and age. Furthermore, I identify distinct lengths of cilia within specific brain regions of male and female mice. As mice age, ARL13B cilia become relatively rare in many brain regions, including the hypothalamic feeding centers, while ADCY3 becomes a prominent cilia marker. It is important to understand the endogenous localization patterns of these proteins throughout development and under different physiological conditions as these common cilia markers may be more dynamic than initially expected. Understanding regional and development associated cilia signatures and physiological condition cilia dynamic changes in the CNS may reveal molecular mechanisms associated with ciliopathy clinical features such as obesity.</p>

<p dir="ltr">Embryonic development relies on the complex interplay of epigenetic regulation, timely expression of genes, signal transduction pathways, and diverse morphological changes. The heart is the first organ to form during mammalian embryonic development. The proper development of the heart is critical to supply nutrients and oxygen to other cell types of the organism. Most cells that comprise the heart originate from the mesoderm post-gastrulation. Cardiomyocytes are the predominant cell type and confer function to the heart via contractile activity. The development and proliferation of cardiomyocytes ceases shortly after birth, where cardiomyocytes only nucleate and increase in size. Consequently, cardiomyocyte insufficiency underlies most cardiovascular diseases, a leading cause of death globally.</p><p dir="ltr">Vascular endothelial zinc finger 1 (VEZF1) is a transcription factor expressed predominantly in mesoderm during development. Previous studies from our lab show that the loss of VEZF1 impairs the differentiation of embryonic stem cells into endothelial cells, a cell type derived from mesoderm. Other published studies also show that Vezf1 loss impairs cardiomyocyte growth in Zebrafish and hematopoietic cell differentiation. Our work here describes a detailed investigation of the role of Vezf1 in the differentiation of mesoderm and cardiomyocytes using mouse embryonic stem cell (ESC) differentiation as a mammalian model system. We initially developed an efficient method, known as the Wnt Switch method, to differentiate ESCs into cardiomyocytes. Our technique relies on the treatment of differentiating ESCs with small molecule inhibitors: i) CHIR99021, which induces mesoderm development via the activation of Wnt signaling in the first 48 hours of differentiation, followed by ii) XAV939, which inhibits Wnt signaling and drives mesoderm cells toward cardiomyocyte differentiation pathway. The Wnt Switch method significantly increases the efficiency of cardiomyocyte derivation (86%) from ESC compared to published methods (56%).</p><p dir="ltr">Interestingly, the Wnt Switch method showed that despite the external stimulation of Wnt signaling, Vezf1 KO cells are unable to differentiate into cardiomyocytes and show reduced expression of mesodermal genes 48 hrs post-differentiation. To better understand the stage-specific role of Vezf1 in cardiomyocyte development, we generated doxycycline-inducible Vezf1 knockdown clones that significantly reduce Vezf1 protein levels upon treatment with doxycycline. We found that the knockdown of Vezf1 prior to mesoderm induction significantly impaired ESC differentiation but had no significant effect on cardiomyocyte development after mesoderm induction. These data indicate that Vezf1 expression is crucial for proper mesoderm and, thus, mesodermal lineage development. Further, FACS analysis showed reduced mesoderm cell populations derived from Vezf1 null post-differentiation. We used high throughput sequencing methods to determine genome-wide Vezf1 binding by ChIP-SEQ and compared gene expression in WT and Vezf1 null cells using RNA-SEQ. The data indicated that VEZF1 binds near the promoters of numerous Wnt signaling genes after differentiation and that the expression of Wnt pathway genes decreases when Vezf1 is lost. Interestingly, supplementing WNT3A protein in culture media of Vezf1 null cells rescues the expression of Wnt target genes necessary for mesoderm formation.</p><p dir="ltr">Differentiating Vezf1 KO cells to endothelial or cardiomyocyte lineages also resulted in massive cell death. The surviving cells interestingly stained positive for alkaline phosphatase (AP) staining, indicating retention of the pluripotency in Vezf1 KO cells. Whereas, re-culturing of WT ESC in LIF media, after differentiating them for five days in the absence of LIF, results in cell death, Vezf1 KO cells proliferate and form AP-positive and SSEA-positive colonies. We further show the retention of pluripotency gene expression post-differentiation using RNA sequencing and RT-qPCR. Moreover, we show that the continued expression of pluripotency genes post-differentiation was not a consequence of reduced global DNA methylation in Vezf1 KO cells.</p><p dir="ltr">Interestingly, our data show that Vezf1 is a transcriptional activator and binds to key pro-differentiation pathways like the MAPK signaling and WNT signaling pathways. The loss of Vezf1 correlates with reduced expression of genes in the pro-differentiation pathways. We show that CTCF, an insulator-binding protein, opportunistically binds to VEZF1 sites on genes in the pro-differentiation signaling pathways in VEZF1 KO cells. Therefore, we hypothesized that this opportunistic CTCF binding is the mechanism that drives the repression of pro-differentiation signaling genes or compensates for the loss of Vezf1 binding to support basal gene expression in the absence of VEZF1. Given the dire consequences of pluripotency in cancer stem cells, we investigated the expression of Vezf1 in cancers. We found that Vezf1 expression is reduced in many cancers and is correlated with poor prognosis. We also show that MAPK3, a prominent member of the MAPK signaling pathway, is reduced in these cancers, highlighting a strong correlation between Vezf1 expression and Mapk3 gene expression in cancers. The data extend our observation of pluripotency in ESCs to cancers. To gain further insights into the role of Vezf1 in cancer, we utilized F9 embryonic carcinoma cells. F9 cells have been reported to retain pluripotency expression post-differentiation. Interestingly, the ectopic and transient expression of Vezf1 in F9 cells significantly reduced the expression of pluripotency genes, suggesting that Vezf1 is sufficient to repress pluripotency gene expression in F9 carcinoma cells. These data highlight the significant role of Vezf1 in pluripotency gene repression and provide an excellent avenue for treating cancer relapse caused by the occurrence of cancer stem cells.</p><p dir="ltr">In conclusion, our research elucidates the critical role of Vezf1 in cardiomyocyte formation and pluripotency regulation during embryonic development. Understanding the molecular mechanisms underlying Vezf1-mediated pathways provides insights into developmental processes and holds promise for therapeutic interventions for cardiomyocyte regeneration and against cancers.</p>