Patterning, morphogenesis, and cell divisions are distinct processes during development yet are concurrent and likely highly integrated. However, it has been challenging to investigate them as a whole. Recent advances in imaging and labeling tools make it possible to observe live tissues with high coverage and resolution. In this dissertation work, we developed a novel imaging platform that allowed us to fully capture the early neural tube formation process in live zebrafish embryos at cellular resolution. Importantly, these datasets allow us to reliably track single neural progenitors. These tracks carry information on the history of cell movement, shape change, division, and gene expression all together. By comparing tracks of different progenitor fates, we found they show a spatially noisy response to Sonic hedgehog (Shh) and become specified in a positionally mixed manner, in surprising contrast to the "French Flag" morphogen patterning model. Both cell movement and division contribute to cell mixing. In addition, we decoupled the temporal and genetic regulatory network (GRN) noises in Shh interpretation using tracks that carry both Shh signaling and cell fate reporters. Our tracks suggest that, after specification, progenitors undergo sorting to self-assemble a sharp pattern. Consistent with this hypothesis, we found ectopically induced progenitors move to correct locations. Furthermore, we show that proper adhesion is required for cell sorting to happen (Chapters 2 and 3). In the cleavage stage embryos, the cells on the surface undergo shape changes followed by lineage separation and differentiation. We quantitatively measured this morphogenesis process and tracked cell divisions. By applying a mathematical model we uncover a predictive, and perhaps general link between cell division orientation, mechanical interaction, and the morphogenetic behavior of the whole surface layer (Chapter 4). Finally, we discuss the concepts and tools of cell tracking including a multi-color cell labeling method we developed by modifying the "Brainbow" system (Chapter 5). Together this dissertation showcases the importance and promise of live observation based, quantitative and integrated analysis in our understanding of complex multi-cellular developmental processes.

During optic cup morphogenesis, the neuroectodermal layers of the optic vesicle (OV) invaginate ventrally, and fuse at the choroid fissure (CF) along the proximo-distal axis such that the retina and retinal pigment epithelium (RPE) are confined within the cup. Failure of CF closure results in colobomas, which are characterized by the persistence of a cleft or hole at the back of the eye. While CF closure is a critical aspect of ocular development, the molecular and cellular mechanisms underlying this process are poorly understood. My research examined CF closure and colobomas using zebrafish as a model system. In the first study, I determined that early cell fate changes within the eye field could cause colobomas using the zebrafish mutant blowout. Colobomas in blowout resulted from defects in optic stalk morphogenesis whereby the optic stalk extended into the retina and impeded the edges of the CF from meeting and fusing. Positional cloning of blowout identified a nonsense mutation in patched1, a negative regulator of the Hedgehog pathway. Up-regulation of Hedgehog pathway activity causes disruption in the patterning of the OV into proximal and distal territories, revealing that cell fate determination, mediated by Hedgehog signaling, is intimately involved in regulating CF closure. In the second study, I examined Bcl6 function and regulation during zebrafish eye development. bcl6 encodes a transcriptional repressor expressed in the ventral retina during zebrafish eye development. Loss of Bcl6 function leads to colobomas along with up-regulation of p53, a previously known Bcl6 target, and an increase in the number of apoptotic cells in the retina, demonstrating that Bcl6 plays a critical role in preventing apoptosis in the retina during early eye development. I also showed that Vax1 and Vax2 act upstream of bcl6 in the ventral retina. Furthermore, I identified functional interactions between Bcl6, Bcor and Hdac1 during eye development, demonstrating that Bcl6 functions along with Bcor and Hdac1 to mediate cell survival by regulating p53 expression. Together my studies expand the gene regulatory network involved in cell fate determination and cell survival during CF closure and ventral retina formation, and provide mechanistic insight into coloboma formation. / text

Le morphogène Sonic hedgehog (Shh) est requis pour le guidage axonal des neurones commissuraux lors du développement de la moelle épinière, phénomène impliquant des événements de réorganisation du cytosquelette d’actine. Bien qu’il soit généralement admis que le cytosquelette d’actine soit régulé via les petites GTPases de la famille Rho, un effet de Shh sur ces protéines n’a jamais été observé dans aucun contexte physiologique. Nous démontrons que Shh active les petites GTPases Rac1 et Cdc42 et que cette activation est rapide et donc, compatible avec les effets de guidage induits par Shh sur les neurones commissuraux. En parallèle, nous avons étudié l’activation de la protéine Boc, qui est un récepteur de Shh requis pour le guidage axonal des neurones commissuraux. Ces résultats contribuent à raffiner notre compréhension de la transduction cellulaire induite par Shh lors du guidage axonal des neurones commissuraux. / Sonic hedgehog (Shh) is required for axon guidance of commissural neurons during spinal cord development, which involves reorganization of the actin cytoskeleton. Even if it is known that this process is regulated by small Rho GTPases, an effect of Shh on these proteins has not been clearly demonstrated. In this study, we show that Shh activates the small GTPases Rac1 and Cdc42. This activation occurs rapidly, which is compatible with the guidance effects of Shh on commissural neurons. In parallel, we characterized the Shh-dependent activation of Boc, which is a Shh receptor required for commissural axon guidance. Taken together, these results help refine our understanding of the signal transduction mediated by Shh during axon guidance of commissural neurons.

Dorsoventral patterning of the vertebrate nervous system is achieved by the combined activity of morphogenetic signals secreted from dorsal and ventral signalling centres. The Shh/Gli pathway plays a major role in patterning the ventral neural tube; however, the molecular mechanisms that limit target gene responses to specific progenitor domains remain unclear. Here, we show that Wnt1 and Wnt3a, by signalling through the canonical β-catenin/Tcf pathway, control expression of dorsal genes and suppression of the ventral programme, and thatthis role in DV patterning depends on Gli activity. Additionally, we show that Gli3 expression is controlled by Wnt activity. Identification and characterization of highly conserved non-coding DNA regions around the human Gli3 gene revealed the presence of transcriptionally active Tcf-binding sequences. These indicated that dorsal Gli3 expression might be directly regulated by canonical Wnt activity. In turn, Gli3, by acting as a transcriptional repressor, restricted graded Shh/Gli ventral activity to properly pattern the spinal cord.Additionally, the Wnt canonical pathway and Hedgehog signalling have been linked to cell proliferation in a variety of systems, however interaction of these pathways to control cell cycle progression have not been studied. In the developing vertebrate nervous system, although Shh and Wnt ligands are expressed at the opposite ventral and dorsal signalling centres, reports demonstrate that proliferation of neural progenitors require both activities throughout the dorsoventral axis. Here we demonstrate the integration of both pathways to control the length of G1 phase, and the absolute requirement of an upstream Hedgehog activity for the Wnt-mediated regulation of the key cell cycle activator CyclinD1 expression and for G1 progression. Although Wnt canonical activity appeared restricted to the control of G1 phase, Hedgehog activity additionally regulates the length of G2 phase through the regulation of ate cell cycle activators such as CyclinA2 and CyclinB2/3. These findings support a key role for Hedgehog in growth control, as a regulator of G1 and G2 phases of cell cycle and importantly as an upstream regulator of the canonical Wnt activity.KEY WORDS: SHH, WNT, Neural Tube, Patterning, CNS, Cell Cycle. / "La integración de las vías de señalización de Shh y Wnt controla la morfogénesis del SNC"TEXTO: La formación del patrón dorsoventral del sistema nervioso central en vertebrados está controlada por la acción de señales morfogenéticas. Estasseñales son secretadas por centros de señalización situados en el extremo dorsal, ectodermo y placa del techo, y ventral, notocorda y placa del suelo, del tubo neural. La vía de señalización de Shh/Gli juega un papel principal en el establecimiento temprano de la región ventral del tubo neural. Sin embargo, losmecanismos moleculares que restringen la expresión de los genes responsables de establecer este patrón a un dominio concreto no son del todo conocidos. En este trabajo mostramos que las señales morphogenéticas Wnt1y Wnt3a, activando la vía de señalización canónica mediada por β-catenina/Tcf, regulan la expresión de genes dorsales y reprimen el programa ventral, mediante un mecanismo que depende de la actividad Gli. Además, mostramosque la expresión de Gli3 está controlada por la vía de Wnt. La identificación y caracterización de regiones no codificantes altamente conservadas alrededor del locus de Gli3 humano revela que contienen sitios de unión consenso para los factores Tcf/Lef-1 activos. Esto indica que la expresión dorsal de Gli3 está controlada directamente por la actividad de la vía canónica de Wnt. A su vez, Gli3, actuando como un represor transcripcional, restringe la actividad del gradiente ventral Shh/Gli para establecer el patrón dorsoventral del tubo neural correctamente.Por otro lado, las vías canónicas de señalización celular de Wnt y Hedgehog regulan la proliferación celular en varios contextos de forma conjunta, Sin embargo, posiblesm interacciones de estas vías de señalización en el control del ciclo celular no han siso estudiadas. Durante el desarrollo del sistema nervioso de vertebrados, aunque las proteínas Shh y Wnts se expresan en extremos dorso-ventralmente opuestos del tubo neural, varios trabajos demuestran que la proliferación de los progenitores neuronales requiere ambas actividades a lo largo de todo el eje dorsoventral. En este trabajo, demostramos que esnecesaria la integración de ambas vías de señalización para controlar la duración de la fase G1 del ciclo celular. Además, mostramos el requerimiento de la actividad Hedgehog para la regulación mediada por Wnt de la expresión del activador de ciclo celular ciclina D1, componente clave para la progresión através de G1. Aunque la actividad de la vía canónica de Wnt se limita al control de la transición G1/S, adicionalmente, la actividad Hedgehog regula la duración de la fase G2 mediante la regulación de las ciclinas de fase G2 ciclina A2 y Ciclinas B2/B3. En conjunto, estos resultados proponen un papel fundamentalen el control del crecimiento para la actividad Shh/Gli como reguladora de las fases G1 y G2 del ciclo celular y además como reguladora por encima de la actividad canónica de Wnt.

Le bourgeon de membre est, dès son émergence dans le flanc de l'embryon, divisé en deux domaines distincts, l'un antérieur, l'autre postérieur. Nous analysons le rôle des gènes Msx dans cette polarisation. Chez la souris, les gènes Msx constituent une petite famille multigénique comprenant Msx1 et Msx2: ces gènes codent pour des facteurs de transcriptions à homéodomaine. Les souris mutantes pour Msx1 et Msx2 présentent également une surcroissance de la région antérieure du bourgeon de membre, associée à la perte d'un domaine apoptotique, qui conduit à des polydactylies antérieures. La projet vise à élucider les mécanismes par lesquels les Msx agissent sur la morphogenèse de cette région du membre. Au cours de cette investigation, nous avons fait d'intéressantes observations qui indiquent que les Msx interagissent avec Gli3, et nous avons obtenu d'intéressants résultats expérimentaux par co-immunoprécipitation des Msx et de Gli3 (co-IP) dans des cellules en culture transfectées, et par test de ligation de proximité (PLA) sur le bourgeon de membre in situ. La stratégie repose aussi sur l'analyse différentielle des transcriptome d'embryons doubles mutants pour Msx1 et Msx2 et d'embryons normaux, de façon à identifier les cibles qu'ils peuvent avoir en commun avec Gli3, ces dernières étant déjà décrites. Ces modèles devraient permettre de corréler le niveau d'apoptose avec la surcroissance du bourgeon et la polydactylie qui en résulte, apportant une importante contribution aux mécanismes de la morphogenèse qui sont encore très mal compris. / The vertebrate limb is a paradigmatic model for morphogenesis. The anteroposterior (AP) growth and patterning of the limb bud rely on an intricate regulatory genetic network involving many genetic players such Shh and Gli3. Shh is produced in the posterior region of the limb mesoderm and acts as a morphogen along the AP axis. It regulates both digit number and identity of different AP positions. As the main function of Shh is to prevent proteolysis of Gli3FL into Gli3R, Gli3R concentrates anteriorly which is also where apoptosis takes place. In the mouse, paradoxically, despite a quasi-symmetrical expression profile, Msx1/2 null mutants show systematic anterior defects with an overgrowth in the anterior limb domain, resulting in anterior polydactyly. Both Gli3 and Msx mutant limb defects are concentrated anteriorly in a similar fashion suggesting an interaction between these genes and a possible role of this interaction in AP patterning in the limb bud as well as dysregulation of apoptosis. Indeed, we demonstrate interactions between Msx and Gli3 genes and even proteins. Mutations of Msx and Gli3 result in anterior polydactylous phenotypes and a similar loss of anterior apoptosis. This morphological analysis is associated with a search for common Gli3 and Msx transcriptional targets and partners in an attempt to link gene activity with changes in cell physiology that underlie morphogenesis. We have performed a differential transcriptome (RNA-Seq) on whole limb buds of Msx1-/-Msx2 narrowing down on a number of potential common targets of Gli3 and Msx. We demonstrate that Msx and Gli3 work together in regulating the AP axis of limb development, independent of Shh.

Many signaling pathways which are classically understood for their roles in early development are also known to be involved in tissue maintenance and adult energy homeostasis. Furthermore, dysfunction of these signaling pathways results in human diseases such as cancer. An in depth understanding of how developmentally important signaling pathways function in the adult will provide mechanistic insights into disease and potential new therapeutic targets. Herein Chapter 1, the Wnt, fibroblast growth factor (FGF), and Hedgehog (Hh) signaling pathways are discussed and examples of their relevance in development, adult homeostasis, and disease are provided. Wnt signaling provides an example of this concept as it has well described roles during both development and adult metabolism.<div><br></div><div> Work included in Chapter 2, investigates the regulation of adult energy homeostasis by a member of the endocrine FGF family, FGF19. The three endocrine FGFs, FGF19 (FGF15 in mice), FGF21, and FGF23 have well described roles in the regulation of metabolic processes in adults. While FGF23 is primarily involved in the regulation of phosphate and vitamin D homeostasis,FGF19 and FGF21 have shown similar pharmacological effects on whole body metabolism. Here, the importance of adaptive thermogenesis for the pharmacological action of FGF19 is explored. UsingUCP1KO animals we show that whole-body thermogenesis is dispensable for body weight loss following FGF19 treatment.<br></div><div><br></div><div>Finally, the potential involvement of Hh signaling in mediating the hyperphagia driven obesity observed in certain ciliopathies is explored in Chapter 3. Emerging evidence suggests cilia play an important role in the regulation of feeding behavior. In mammals, the hedgehog pathway is dependent on the primary cilium as an organizing center and defects in hedgehog signaling share some clinical symptoms of ciliopathies. Here, we characterized the expression of core pathway components in the adult hypothalamus. We show that neurons within specific nuclei important for regulation of feeding behavior express Hh ligand and members of its signaling pathway. We also demonstrate that the Hh pathway is transcriptionally upregulated in response to an overnight fast. This work provides an important foundation for understanding the functional role of Hh signaling in regulation of energy homeostasis. In its entirety, this work highlights the emerging clinical relevance of developmentally critical pathways in diseases associated with dysfunction of adult tissue homeostasis, such as obesity.<br></div>

6 Abstract The development of the mouse tooth primordium is an important model for studying odontogenesis, as well as general organogenesis. The development of the mouse lower incisor is of remarkable interest. The epithelial anlage of the mouse lower incisor is interconnected with the vestibular anlage via the epithelial bridges. According to some authors, the epithelial bridges represent an area, where the transient rudimentary incisor germ appears. From a morphological point of view, the first sign of ongoing epithelial-mesenchymal interactions during early odontogenesis is the thickening of oral epithelium. From a molecular point of view, it is the expression of the Shh, Eda, Edar, Pitx2, Bmp2, Bmp4 and Dlx2 genes. Except for the transcription domain, representing the proper signalling centre of a developing prospective incisor, a transient transcription domain, localized anteriorly and superficially, appears in the odontogenic zone of the epithelium during early development. The anterior transcription domain originates in the area of epithelial bridges, and according to some authors, from an evolutionary point of view, it corresponds with the signalling centre of the rudimentary incisor germ. The aim of this diploma thesis was to compare the temporospatial dynamics of SHH and EDA protein expression in...

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Les neurones exprimant l'hormone de mélano-concentration (MCH) sont observés dans l'hypothalamus postérieur de tous les vertébrés, de la lamproie à l'Homme. Ces neurones sont impliqués dans diverses fonctions comme le cycle veille/sommeil ou la prise alimentaire. Ils forment une population non homogène et au moins deux sous-populations sont reconnues, chez le rat. La première sous-population est composée de neurones nés au 11ème jour de vie embryonnaire (E11) qui projettent massivement sur les régions les plus postérieures du système nerveux central. La seconde est générée à E12/E13 et les neurones la caractérisant projettent sur les régions les plus antérieures du cerveau et expriment le peptide CART (cocaine and amphetamine regulated transcript) et le récepteur NK3 (neurokinine). L'objectif de notre travail était de comprendre l'origine de ces deux sous-populations. Pour cela, nous avons utilisé des approches histologiques, moléculaires et in vitro. Les neurones à MCH sont parmi les premiers neurones à naître et à différencier leur phénotype chimique le long d'une région longitudinale définie par une prolifération intense, appelée " cell cords " par Keyser en 1972. Cette bande longitudinale est caractérisée par l'expression de gènes comme Sonic Hedgehog (Shh), Nkx2.1, Nkx2.2 et a été récemment renommée " diagonale intrahypothalamica " ou ID. La différenciation des neurones à MCH dépend de l'expression du facteur morphogène Shh et ces neurones expriment Nkx2.1 et Nkx2.2, facteurs de transcription régulés positivement par Shh. Les neurones de la première sous-population envoient des projections le long du premier tractus longitudinal à se mettre en place, le tractus postopticus (tpoc). Ceux issus de la deuxième sous-population se différencient concomitamment au développement des régions télencéphaliques et leurs projections changent de direction pour innerver les régions antérieures du cerveau sous la dépendance de protéines de guidage axonal, Nétrine1 et Slit2. Nétrine1 permet d'attirer les axones MCH exprimant le récepteur DCC précocement vers la moelle épinière et plus tardivement vers le télencéphale alors que Slit2 contraint les axones MCH exprimant Robo2 à sortir de l'hypothalamus. L'étude du modèle " MCH " permet de mettre en lumière un changement d'organisation précocement au cours du développement dans l'axe longitudinal du prosencéphale. La bande longitudinale d'expression des facteurs de transcription Shh, Nkx2.2 peut être perçue comme une extension rostrale de la colonne neurogénique médiane déjà décrite chez des espèces d'invertébrés possédant une symétrie bilatérale. Les neurones générés le long de cette colonne le sont très tôt au cours du développement. / Neurons expressing melanin-concentrating hormone (MCH) are observed in the vertebrate posterior hypothalamus, from lampreys to humans. These neurons are involved in various functions such as sleep/wake cycle or food intake. They form a non-homogeneous population and at least two sub-populations are indentified in the rat. The first sub-population is composed of neurons born on the 11th embryonic day (E11) that project heavily on posterior regions of the central nervous system. The second is characterized by neurons born at E12/E13, projecting in anterior regions of the brain and expressing the peptide CART (cocaine and amphetamine Regulated Transcript) and the NK 3 receptor (neurokinin). The aim of this study was to understand the origin of these two sub-populations. For this, we used histological, molecular and in vitro approaches. MCH neurons are among the first neurons to be born and to differentiate their chemical phenotype along a longitudinal region defined by intense proliferation and called " cell cord " by Keyser in 1972. This longitudinal band is characterized by the expression of genes such as Sonic Hedgehog (Shh), Nkx2.1, Nkx2.2 and was recently named " diagonal intrahypothalamica " or ID. Differenciation of MCH neurons depends on expression of the morphogenetic factor Shh and these neurons express Nkx2.1 and Nkx2.2, transcription factors upregulated by Shh. The neurons of the first sub-population send projections along the tractus postopticus (tpoc), which is the first longitudinal tract to develop. Neurons of the second sub-population differentiate concomitantly to the development of the basal forebrain and their projections innervate anterior brain regions. Our results obtained in vitro showed that Netrin1 attracts MCH axons and that this reponse is mediated by DCC. Slit2 repulses MCH axons and this reponse is mediated by the Robo2 receptor. Overall, our study of the development of the MCH system shed light on an organizational change in the longitudinal axis of the forebrain during early development : a primary longitudinal organization characterized by the longitudinal expression of Shh and Nkx2.2 and the path of the tractus postopticus in the diencephalon and mesencephalon. MCH neurons of the first sub-population develop during this stage. Then, as the basal telencephalon extends and expresses Netrin1, the medial forebrain bundle differentiates, inducing a change in the main axis of the forebrain ; meanwhile MCH neurons of the second sub-population appear. MCH sub-populations reflect distinct developmental stages of the forebrain.

The developing mouse dentition is a very useful tool to study molecular regulation of odontogenesis and also organogenesis. The embryonic mouse dentition comprises developing functional tooth primordia as well as rudimentary tooth primordia. These rudiments arrest their growth during development and either degenerate or become a part of a functional tooth. Mice with gene defects also allow elucidation of a function of genes, their products and signalling pathways. The protein ectodysplasin is essential for development of ectodermal derivatives - skin, hair, glands and teeth. The Tabby mice have a mutation in the Eda gene, which encodes the protein ectodysplasin, and they display a number of dentition anomalies. Early development of the lower jaw dentition in Tabby embryos has been already morphologically described. As a prerequisite for understanding regulatory mechanisms of odontogenesis in Tabby mice, it is also necessary to map the spatiotemporal dynamics of signalling centres that express Shh in both the rudimentary and functional tooth primordia. The aim of this thesis was to compare the signalling centres based on the Shh expression and its spatiotemporal dynamics in the lower jaw of Tabby and WT mouse embryos. Then the Shh data were correlated with known morphological data to clarify the...