ABSTRACT Retinoic acid (RA) is a positive regulator of P19 EC cell differentiation. Pre-B cell leukemia transcription factors (PBXs) act in conjunction with homeobox genes during cell differentiation. PBX mRNA and protein levels are increased rapidly in P19 cells during RA-induced differentiation. However, silencing of PBX expression in P19 cells (AS cells) results in a failure of these cells to differentiate upon RA treatment. Chicken Ovalbumin Upstream Promoter Transcription Factor I (COUP-TFI) and Chicken Ovalbumin Upstream Promoter Transcription Factor II (COUP-TFII) are orphan members of the steroid-thyroid hormone superfamily. The mRNA and protein levels of both COUP-TFI and COUP-TFII are low in proliferating wild type P19 EC cells. However, when wild type P19 cells are induced to differentiate upon RA treatment, COUP-TFI and COUP-TFII mRNA and protein levels are dramatically increased while the levels of pluripotency associated gene products are strikingly reduced. Conversely, COUP-TFI and COUP-TFII mRNA levels fail to be elevated upon RA treatment in PBX AS P19 EC cells. Therefore it was hypothesized that COUP-TFs may be downstream targets of PBX and required factors mediating the RA-dependent differentiation cascade in P19 cells. To determine the role of COUP-TFI during differentiation of P19 cells, PBX AS cells that inducibly express V5 tagged COUP-TFI using the Tet-Off® Advanced Inducible Gene Expression system were prepared. Using this system, we demonstrate that exogenous COUP-TFI expression, in a dose-dependent fashion, leads to growth inhibition, modest cell cycle disruption and early apoptosis. Furthermore, using this cell model which inherently is incapable of undergoing RA-mediated differentiation due to blockage of PBX induction, we demonstrate that a supraphysiological level of COUP-TFI expression can overcome the blockage of RA-dependent differentiation in PBX AS cells. However, AS cells expressing a physiological level of COUP-TFI differentiate to endodermal cells only upon treatment with RA. Additionally, gene expression studies indicate that the reductions of pluripotency maintenance genes observed in the COUP-TFI expressing cells are similar to that of wild type P19 cells (upon RA treatment) suggesting that COUP-TFI expression is a driving force towards loss of pluripotency. Moreover, gene expression studies indicate COUP-TFI is involved in the regulatory modulation of at least two RA response genes, CYP26A1 and HoxA1, indicating that COUP-TFI may have some effect on either maintaining or reducing these genes expression levels when COUP-TFI becomes expressed. COUP-TFII is expressed as two distinct variants, Variant 1(V1) and Variant 2 (V2). V1 is the variant that functions as a classical nuclear receptor by binding target DNA sequences and affecting gene transcription whereas V2 is a truncated form of V1 lacking the ability to bind DNA. We therefore hypothesized that V2 could serve as a dominant negative receptor by limiting the amount of functional V1 in the cell. Unexpectedly, we found using P19 cells that overexpress V2 that RA-mediated differentiation proceeded normally suggesting V2 does not function as a dominant negative repressor. Taken together, these studies demonstrate for the first time (i) that COUP-TFI functions as a physiologically relevant regulator during RA-mediated endodermal differentiation of P19 cells and (ii) COUP-TFII V2 is endogenously expressed in P19 cells; however its role during RA-mediated differentiation remains unclear. / Biochemistry

No description available.

The anatomy of the cranial peripheral nervous system has been studied for over a century, yet surprisingly little is known about how the nerves are guided to their targets. The study of the development of these nerves has important implications for our understanding of craniofacial anomalies and possible treatments for both injury and genetic disorders of nerve development such as Goldenhar-Gorlin syndrome. We have discovered that retinoic acid (RA) may play a role in the development of the trigeminal nerve. Inhibition of retinoic acid receptors (RAR) results in trigeminal nerves that become unbundled or defasciculated in the eye region. To further understand how RA is affecting trigeminal development we searched for genes downregulated in response to RAR inhibition by the inhibitor BMS-453 and have identified neurotrophin-3 (NT-3), activated leukocyte cell adhesion molecule (ALCAM) and Semaphorin 4B (Sema4B). We have analyzed the expression patterns of Sema4B and NT-3 by in situ hybridization and have found NT-3 expression in the eye and Sema4B in the embryonic target of the trigeminal nerve, lens of the eye and in the pharyngeal arches. ALCAM has been analyzed via qRT-PCR and its transcription is downregulated just prior to the observed defasciculation phenotype. The pattern of expression of these genes combined with known expression of NT-3 receptors allows us to suggest a model whereby RA signaling regulates Sema4B, ALCAM and NT-3, which support the survival, guidance and fasciculation of the trigeminal nerve. This work has the potential to better understanding of the complex nature of cranial nervous system development.

The c-Myc transcription factor is a key player in cell homeostasis, being commonly deregulated in human carcinogenesis. In this PhD thesis we have addressed the question how regulatory mechanisms restrain the oncogenic activity of c-Myc and its impact on cell differentiation. In the first half, we report that PML promotes destabilization of c-Myc protein and re-activation of c-Myc-repressed target genes. The consequent re-expression of the cell cycle inhibitor CDKN1A/p21 mediates differentiation of leukemic cells. In the second half of the thesis we identified a novel mechanism of gene regulation by c-Myc, which is mediated through its interaction with DNA-bound RARα. In undifferentiated cells, c-Myc/Max dimers cooperate with RARα in the repression of genes required for differentiation. Upon phosphorylation of c-Myc by the previously identified Pak2, the complex switches from a repressive to an activating function by releasing Max and recruiting transcriptional coactivators. These findings add a new and at least partially Max-independent mechanism for transcriptional regulation by c-Myc and also discover an unexpected function of c-Myc in inhibiting and promoting cellular differentiation. Taken together, our results describe two new mechanisms that counteract the oncogenic activity of c-Myc. Both PML and Pak2 can be considered as tumor suppressors since they modulate c-Myc function in a way that ultimately promotes differentiation of leukemic cells. This knowledge provides the basis for novel approaches to be exploited for the development of c-Myc-targeted therapies. / El factor de transcripció c-Myc juga un paper clau en l’homeòstasi cel·lular, essent freqüentment desregulat en la carcinogènesi humana. En aquesta tesi s’ha estudiat com diferents mecanismes reguladors poden frenar l’activitat oncogènica de c-Myc i el subsegüent impacte en la diferenciació cel·lular. A la primera meitat de la tesi, es demostra que PML promou la desestabilització de la proteïna c-Myc i, en conseqüència, la reactivació dels genes diana reprimits per c-Myc. Entre aquests gens diana es troba l’inhibidor del cicle cel·lular CDKN1A/p21, la reexpressió del qual provoca la diferenciació de cèl·lules leucèmiques induïda per PML. En la segona meitat, s’identifica un nou mecanisme de regulació transcripcional per part de c-Myc a través de la interacció amb RARα, el qual està unit a l’ADN. En cèl·lules indiferenciades, els dimers c-Myc/Max cooperen amb RARα en la repressió de gens essencials per a la diferenciació. Un cop c-Myc és fosforil·lat per la kinasa Pak2, el complex de c-Myc amb RARα esdevé activador mitjançant la pèrdua de Max i el reclutament de coactivadors transcripcionals. Aquest descobriment suposa un nou mecanisme mitjançant el qual c-Myc pot exercicir la regulació gènica almenys en part independentment de Max, i també revela una funció desconeguda de c-Myc en la inhibició i promoció de la diferenciació cel·lular. En conjunt, aquests resultats descriuen dos nous mecanismes que contrarestren l’activitat oncogènica de c-Myc. PML i Pak2 poden ser considerats supressors de tumors ja que modulen la funció de c-Myc per a promoure la diferenciació de les cèl·lules leucèmiques. Aquests descobriments poden utilitzar-se com a base pel desenvolupament de noves teràpies anti-tumorals que tinguin com a diana la proteïna c-Myc.

Diss. (sammanfattning) Stockholm : Karol. inst., 2006. / Härtill 4 uppsatser.

L’acide rétinoïque (AR) est le dérivé actif majeur de la vitamine A et a de multiples rôles au niveau cellulaire ainsi que pendant le développement. L’AR agit via deux familles de récepteurs nucléaires : les Récepteurs de l’Acide Rétinoïque (RAR) et les Récepteurs X des Rétinoïdes (RXR). Ces récepteurs sont des facteurs de transcription dépendants du ligand et leur activité est régulée par des phosphorylations via des kinases activées par l’AR. Durant ma thèse, je me suis intéressé à l’étude fonctionnelle et évolutive de la voie de l’AR et de la phosphorylation des RAR chez le poisson-zèbre Danio rerio. En étudiant l’activité des différents sous-types de RAR chez le poisson-zèbre, nous avons mis en avant qu’il existe une activité transcriptionnelle propre à chaque sous-type dans un embryon précoce de poisson-zèbre. De plus, mes travaux ont montré qu’au cours de l’évolution, l’acquisition d’un site de phosphorylation chez RARα permet une régulation fine de son activité chez les mammifères. Enfin, en étudiant les mécanismes moléculaires à l’origine de la diversification de la denture chez les poissons, mes travaux mettent en avant un rôle de la voie de l’AR dans la genèse de nouveaux traits phénotypiques. / Retinoic acid (RA) is the main active metabolite of vitamin A and plays multiple roles in cellular processes but also during embryonic development. RA acts through two families of nuclear receptors: Retinoic Acid Receptors (RAR) and Retinoid X Receptors (RXR). Those receptors act as ligand-dependent transcription factors and their transcriptional activity is also regulated by phosphorylation processes through kinases activated by RA. During my PhD, I focused on the functional and evolutionary study of RA pathway and of the phosphorylation of RARs using zebrafish (Danio rerio). By studying the activity of the different RAR subtypes in zebrafish, we provide evidences that they can regulate gene expression in a subtype-specific fashion in the early zebrafish embryo. Furthermore, my work showed that during evolution, the acquisition of a phosphorylated residue in RARα promotes the fine-tuned regulation of its activity in mammals. Finally, aiming at deciphering the molecular mechanisms behind dentition diversification in fish, we propose a role for RA signaling in generating morphological novel traits during evolution.

Development and regeneration of the vertebrate eye are the result of complex interactions of regulatory networks and spatiotemporally controlled gene expression events. During embryonic retinal development, the coordination of cell signaling and transcriptional regulation allows for a relatively homogenous sheet of neuroepithelial cells to proliferate and differentiate in-to a multilayered, light sensitive retinal tissue. Following injury, the retinas of many cold-blooded vertebrates, such as the zebrafish, undergo a proliferative response that results not only in new retinal cells of the correct type in the correct location, but also functional integration of these cells and restoration of vision. In order for embryonic retinal neurogenesis to proceed correctly, systems must be in place that restrict subsets of progenitor cells from differentiation. Pools of actively proliferating retinal progenitor cells are maintained to fill the needs of developmental processes and normal growth of the retina. In addition, subsets of radial glia in the retina retain the ability to de-differentiate into proliferating progenitor cells to meet the demands of the regenerating retina. All of these processes rely on the tight coordination of extrinsic and intrinsic cues, as well as regulation of gene expression by transcription factors. Although a considerable amount of work has been conducted to identify key regulators of retinal development and regeneration, many gene regulatory networks which include both master signaling pathways as well as individual transcription factors remain poorly characterized. Some of these factors implicated in retinal development and regeneration are members of the Hairy/Enhancer of Split (Hes) superfamily of genes, including the Hairy-related (Her) factors Her4 and Her9. Her transcription factors are basic-helix-loop-helix-orange (bHLH-O) transcription factors that bind to palindromic E- and N-box canonical sequences in the promoters of target genes. Her factors have been previously shown to play roles in a diverse array of developmental and neurogenic processes, including neural tube closure, floor plate development, somitogenesis, and development of various components of the central nervous system as well as the cranial sensory placodes. The roles of her4 and her9 in retinogenesis, however, remain undefined. To determine the possible roles of her4 and her9 factors in the retina, I characterized the expression patterns of these factors during developmental retinal neurogenesis and/or regeneration, examined loss of function phenotypes, and identified signaling pathways that modulate expression of these factors. Chapter 1 of this dissertation provides an overview of vertebrate retina and retinal development, the known functions of her4 in other tissues, and the Notch-Delta signaling pathway. Chapter 2 provides evidence that her4 is a primary effector of the Notch pathway during retinal development, and examines the role of her4 expressing cells during regeneration of the mature zebrafish retina within the context of both chronic and acute photoreceptor damage paradigms. In addition, generation and validation of the transgenic her4:Kaede zebrafish which was used to identify the lineage of her4-expressing cells is described. Characterization of her9 during retinal development, identification of the retinoic acid signaling pathway as a regulator of her9 expression in the retina, and the role her9 plays during retinal vasculogenesis are discussed in Chapter 3. Chapter 4 discusses the generation of her9 knock-out zebrafish lines using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology and characterization of mutant phenotypes in mosaic her9 mutant F0 fish. In addition, in Chapter 4 I also discuss the screening processes used to identify and characterize genetic lesions in the her9 allele and establish various lines that stably transmit deleterious her9 alleles in the germline, and provide preliminary data of the her9 mutant phenotype. Finally, in Chapter 5 I discuss conclusions from the data generated from this dissertation, additional studies that would expand upon this work, and the implications of these results on the broader understanding of retinal development and regeneration. My dissertation incorporates reverse genetic analysis in zebrafish, biochemical analysis, transgenesis, and various molecular approaches to help better understand the roles of her4 and her9 during retinal neurogenesis. Moreover, these studies may also contribute to a better understanding of retinal development, and disease pathogenesis. It is my hope that this work could also ultimately contribute, even if in some small way, to the goal of enabling human patients who have suffered from vision loss a means by which a damaged retina could be regenerated and functional vision restored.

Smith-Magenis syndrome (SMS) is a complex mental retardation syndrome caused by deletion of 17p11.2 region or mutation of the RAI1 gene (retinoic acid induced 1). Individuals with SMS typically exhibit speech and motor delays, mental retardation, characteristic craniofacial and skeletal anomalies, and a distinct neurobehavioral phenotype that includes sleep disturbances, stereotypes, and maladaptive and self-injurious behaviors. RAI1 is thought to be a transcription factor modulating the expression of genes involved in a variety of cellular functions. Previous studies have shown the RAI1 gene being induced by retinoic acid (RA), a derivative of vitamin A. RA plays a significant role in many processes such as immune function, neurogenesis and reproduction, and deprivation of RA causes craniofacial defects. We hypothesized that RA could be inducing RAI1 which then acts as a transcription factor in modulating the expression of multiple genes. To understand the consequences of clinical variation of RAI1 gene, we performed mutation screening and identified the first case of SMS without mental retardation. Using a zebrafish model, full-length rai1 gene was cloned and spatial and temporal expression of rai1 by in-situ hybridization was evaluated and the effect of RA on rai1 expression was subsequently analyzed. The data show rai1 expression in forebrain (diencephalon) and midbrain. A rai1 antisense morpholino will eventually be created to perform knockdown studies and rescue experiments. These studies will help in determining the significance of the rai1 gene, and its interacting molecular pathways responsible for growth, development, and behavior.

Orofacial anomalies make up about a third of the 120,000 birth defects each year in the United States. Children born with these abnormalities must undergo immense physical and emotional strain in order to correct the defects. In fact, about $697 million is spent every year surgically treating children with cleft lip and/or cleft palate (2011). In countries where surgery is not an option, this abnormality causes immense difficulties in eating, hearing, speech, and psychosocial development. The causes of cleft lip/palate are extremely complex. Genetics play a role in the anomaly; however, 95% of cleft palate cases are non-syndromic and likely due to other factors. Vitamin deficiencies, lack of folic acid intake during pregnancy, exposure to cigarette smoke, anticonvulsant drugs, alcohol, and inappropriate amounts of retinoic acid have all been correlated to incidence of cleft palate and other orofacial defects (Weingartner, Lotz et al. 2007). Xenopus laevis, and the closely related Xenopus tropicalis, are excellent model systems for orofacial development studies. The ease of embryo collection and manipulation, in addition to the conservation of DNA sequence between the two species, makes them ideal for studying developmental processes. Further, tissue specific experiments are extremely feasible due to the size of Xenopus oocytes (approximately 1000 times larger than a human egg!), and their ability to develop outside of the mother (Lindeman, Winata et al. 2010; Liu 2011). Here, I show that molecules from both the folic acid and retinoic acid pathways are highly expressed in the developing face. I have found that inhibition of key enzymes that regulate these pathways induces similar orofacial malformations, including median clefts that extend into the developing palate. Further, disruption of these pathways induces severe abnormalities in the formation of the cartilages of the jaws and face. Thus, both folic acid and retinoic acid are key signaling molecules that regulate proper formation of the orofacial region.

Among the most prevalent and devastating types of human birth defects are those affecting the mouth and face, such as orofacial clefts. Children with malformed orofacial structures undergo multiple surgeries throughout their lifetime and struggle with facial disfigurements, speech, hearing, and eating problems. Therefore, facilitating new research in cranio- and orofacial development is paramount to prevention and treatment of these types of birth defects in humans. Xenopus laevis has emerged as a new tool for dissecting the mechanisms governing facial development. Thus, molecular analyses accompanied by quantitative assessment of morphological changes during orofacial development of this species could be very powerful for understanding how these defects arise. In this dissertation, I present such a study. I first establish a quantitative protocol to describe size and shape changes in facial morphology of wild-type Xenopus embryos. I then utilize this method on embryos in which retinoic acid signaling or folate metabolism have been disrupted to correlate morphological changes with their underlying mechanisms. Finally, I demonstrate the utility of Xenopus as a system for chemical genomics to uncover other regulators of orofacial development.