No description available.

Neurons in the central nervous system are typically not replaced and must therefore maintain their choice of fate and their synaptic connections throughout the life of an organism. I have used Drosophila genetics to analyze genes that prevent neurons from switching fates and allow them to form synapses onto target neurons. The Drosophila fly eye is composed of approximately 750 ommatidia, each comprising eight photoreceptor neurons (R1-R8) surrounded by non-neuronal accessory cells. These photoreceptor neurons undergo a well-defined developmental specification process and form synapses at defined locations in the brain. I have taken advantage of this system to investigate two questions: 1) how do neurons maintain their fate after specification? and 2) how do neurons form stable synapses? For the first half of my dissertation, I have focused my research on a gene, Sce, that I have shown is essential to prevent R7 neurons from undergoing a late switch in cell fate. Sce is an integral component of the Polycomb Group (PcG) complex that is essential for maintaining repression of multiple genes throughout the genome. I found that PcGs are required to prevent R7s from derepression of the R8-specific transcription factor Senseless. For the second half of my dissertation, I focused on the gene syd-1 that was identified to be required for proper presynaptic formation of R7 neurons. Previous studies in Caenorhabditis elegans suggested that Syd-1 acts upstream of Liprin-α and that Liprin-α promotes presynaptic development by binding the kinesin Kif1a to promote axon transport. I used live image analysis to show that, unlike Liprin-α, Syd-1 is not necessary to promote axon transport. Instead, we show that in R7s, Syd-1 acts upstream of Trio, and our results suggest that Syd-1's function is to promote Trio activity. This dissertation includes both my previously published and co-authored materials. / 10000-01-01

The adoption and subsequent retention of distinct cellular fates upon cell division is a critical phenomenon in the development of multicellular organisms. A well-studied example of this process is stem cell divisions; stem cells must possess the capacity to self-renew in order to maintain a stem cell population, as well as to generate differentiated daughters for tissue growth and repair. Drosophila neuroblasts are the neural stem cells of the central nervous system and have emerged as an important model for stem cell divisions and the genetic control of daughter cell identities. Neuroblasts divide asymmetrically to generate daughters with distinct fates; one retains a neuroblast identity and the other, a ganglion mother cell, divides only once more to generate differentiated neurons and glia. Perturbing the asymmetry of neuroblast divisions can result in the failure to self-renew and the loss of the neural stem cell population; alternatively, ectopic self-renewal can occur, resulting in excessive neuroblast proliferation and tumorigenesis. Several genetic lesions have been characterized which cause extensive ectopic self-renewal, resulting in brains composed of neuroblasts at the expense of differentiated cells. This contrasts with wild type brains, which are composed mostly of differentiated cells and only a small pool of neuroblasts. We made use of these mutants by performing a series of microarray experiments comparing mutant brains (consisting mostly of neuroblasts) to wild type brains (which are mostly neurons). Using this approach, we generated lists of over 1000 putatively neuroblast-expressed genes and over 1000 neuronal genes; in addition, we were able to compare the transcriptional output of different mutants to infer the neuroblast subtype specificity of some of the transcripts. Finally, we verified the self-renewal function of a subset of the neuroblast genes using an RNAi-based screen, resulting in the identification of 84 putative self-renewal regulators. We went on to show that one of these genes, midlife crisis (mammals: RNF113a), is a well-conserved RNA splicing regulator which is required in postmitotic neurons for the maintenance of their differentiated state. Our data suggest that the mammalian ortholog performs the same function, implicating RNF113a as an important regulator of neuronal differentiation in humans.

Development and the associated cellular differentiation are some of the most fundamental processes in biology. Since the early conception of the Waddington landscape, with cells portrayed as rolling down a landscape, understanding these processes has been at the forefront of biology. Progress in tissue regeneration, organoid culture, and cellular reprogramming relies on our ability to unfold cellular decision making and its dynamics. In this thesis, we ask to what extent development follows such landscape. Secondly, we address whether cellular branching points are discrete events. Given the recent surge in single-cell genomics data, we can now address these fundamental questions. To this end, we analyzed two large-scale single-cell RNAseq time course datasets from vertebrate embryogenesis in zebrafish. From the Waddington analogy, we expect the cell-to-cell correlation to increase across development as cells specialize. Our analysis does not show a linear trend, but rather, that cell-to-cell variability is lowest during gastrulation. Interestingly, the two different datasets from two different laboratories display a qualitatively similar trend, providing internal consistency of our analysis. To uncover the branchpoint dynamics, we extended our analysis to include computations of gene-to-gene correlations. It has been shown, using PCR data, that the transition index, the ratio between cell-to-cell and gene-to-gene correlations, displays a peak during such branchpoints, suggesting discrete transitions. To this end, we tracked individual developmental trajectories, and characterized both correlations, enabling computation of the transition index. However, the cell-to-cell correlation and gene-to-gene correlation did not follow a generic inverse relationship, as previously suggested. No unique signal corresponding to the branchpoints could, thus, be detected. Therefore, our analysis does not support the view that branchpoints during vertebrate embryogenesis are discrete, well-defined transition events. In conclusion, this first large-scale single-cell based analysis of time-resolved developmental data does not support a downhill rolling ball notion where cells decide their fate at discrete transition points. The temporal organization of an undulating developmental landscape appears to be more complex than initially conceptualized by Waddington. Therefore, it is of paramount interest to extend this type of analysis to other systems and to develop techniques to compute such landscape in a data-driven manner.

No description available.

No description available.

A complex regulatory framework underlies the generation of newborn neurons in the adult mammalian brain, including the lifelong maintenance of neural stem cell (NSC) quiescence and instructing NSC entry to and exit from quiescence. Future therapies targeting endogenous repair of the aging or afflicted brain, including neurodegenerative pathologies, rely on present efforts to define and characterize the mechanisms underlying the regulation of adult NSC fate. In this dissertation, we demonstrate a requirement for the Rb/E2F axis in the regulation of the molecular program instructing adult NSC quiescence and activation, with a potential role in the impaired hippocampal function observed in Alzheimer's disease pathology. While Rb plays a role in the production and survival of hippocampal newborn neurons, we identify a collective requirement for Rb family proteins — pRb, p107 and p130 — as well as their targets, E2F family transcriptional activators E2F1 and E2F3, in the regulation of NSC quiescence and activation. We further demonstrate that this is mediated through pivotal factors REST and ASCL1, identified as direct molecular targets of the Rb/E2F axis, and that REST inactivation can partially rescue NSC depletion following Rb family loss. We finally demonstrate impaired NSC activation and a return to quiescence in the 3xTG-AD model of Alzheimer's disease, with altered expression of Rb/E2F genes observed within cell population-specific defects. Ultimately, this work addresses the key issue of how transcriptional signatures of quiescence and activation among adult NSCs are co- ordinated with cell cycle control, and demonstrates that Rb family proteins serve as master regulators of the molecular program instructing adult NSC exit from and re-entry into quiescence.

<p>The divergence of distinct cell populations from multipotent progenitors is poorly understood, particularly <italic>in vivo</italic>. The gonad is an ideal place to study this process because it originates as a bipotential primordium where multiple distinct lineages acquire sex-specific fates as the organ differentiates as a testis or an ovary. The early gonad is composed of four lineages: supporting cells, interstitial/stromal cells, germ cells, and endothelial cells. Each lineage in the early gonad consists of bipotential progenitors capable of adopting either a male or female fate, which they do in a coordinated manner to form a functional testis or ovary. The supporting cell lineage is of particular interest because the decision of these cells to adopt the male or female fate dictates the fate of the gonad as a whole. </p><p><p>To gain a more detailed understanding of the process of gonadal differentiation at the level of the individual cell populations, we conducted microarrays on sorted cells of the four lineages from XX and XY mouse gonads at three time points spanning the period when the gonadal cells transition from sexually undifferentiated progenitors to their respective sex-specific fates. Our analysis identified genes specifically depleted and enriched in each lineage as it underwent sex-specific differentiation. We also determined that the sexually undifferentiated germ cell and supporting cell progenitors showed lineage priming. Multipotent progenitors that show lineage priming express markers of the various fates into which they can differentiate and subsequently silence genes associated with the fate not adopted as they differentiate. We found that germ cell progenitors were primed with a bias toward the male fate. In contrast, supporting cell progenitors were primed with a female bias. This yields new insights into the mechanisms by which different cell types in a single organ adopt their respective fates. </p><p><p>We also used a genetic approach to investigate how individual factors contribute to the adoption of the male supporting cell fate. We previously demonstrated that <italic>Fgf9</italic> and <italic>Wnt4</italic> act as mutually antagonistic factors to promote male or female development of the bipotential mammalian gonad. <italic>Fgf9</italic> is necessary to maintain <italic>Sox9</italic> expression, which drives male development. However, whether FGF9 acted directly on <italic>Sox9</italic> or indirectly through repression of <italic>Wnt4</italic>, was unknown. <italic>Wnt4</italic> is a female-primed gene, and is therefore repressed during male development. To determine how <italic>Fgf9</italic> functioned, we generated double <italic>Fgf9/Wnt4</italic> and <italic>Fgfr2/Wnt4</italic> mutants. While single XY <italic>Fgf9</italic> and <italic>Fgfr2</italic> mutants showed partial or complete male-to-female sex reversal, loss of <italic>Wnt4</italic> in an <italic>Fgf9</italic> or <italic>Fgfr2</italic> mutant background rescued normal testis development. We also found that <italic>Wnt4</italic> and another female-associated gene (<italic>Rspo1</italic>) were derepressed in <italic>Fgf9</italic> mutants prior to the down-regulation of <italic>Sox9</italic>. Thus, the primary function of <italic>Fgf9</italic> is the repression of female genes, including <italic>Wnt4</italic>. We also tested the reciprocal possibility: that de-repression of <italic>Fgf9</italic> was responsible for the aspects of male development observed in XX <italic>Wnt4</italic> mutants. However, we show that loss of <italic>Fgf9</italic> in XX <italic>Wnt4<super>-/-</super></italic> gonads does not rescue the partial female-to-male sex reversal. </p><p><p>Based on the <italic>Fgf9/Wnt4</italic> double mutant studies, we propose a two part model of male sex determination in which both the activation of male genes and repression of female genes is required. Also, this work demonstrates that the repression of the female-primed gene <italic>Wnt4</italic> is required for male development, and <italic>Fgf9</italic> is one factor that leads to the repression of female-primed genes.</p> / Dissertation

A l’état basal, les cellules souches musculaires sont quiescentes. Après blessure, ces cellules s’activent, s’amplifient et se différencient afin de réparer les myofibres lésées. Cependant, une petite population de ces cellules myogéniques activées ne va pas entrer dans la voie de la myogenèse, mais va retourner en quiescence par un phénomène appelé auto-renouvellement. Cette étape est cruciale afin de maintenir une réserve de cellules souches musculaires tout au long de la vie. Mais, les mécanismes cellulaires et moléculaires régulant ce phénomène sont peu décrits dans la littérature. La régénération musculaire est composée d’une série d’évènements complexes et bien orchestrés selon une cinétique précise. Le challenge de son étude est donc de pouvoir distinguer les évènements les uns des autres, tout en sachant qu’ils sont interconnectés. Bien que les cellules souches musculaires aient un fort potentiel de régénération, elles ont besoin d’interagir avec d’autres cellules au cours de la régénération, notamment avec les macrophages qui ont un rôle prépondérant dans ce processus. Après une blessure, les monocytes circulants sont recrutés sur le site de lésion et se différencient en macrophages inflammatoires. Ensuite, ces macrophages changent leur statut inflammatoire et acquièrent un profil anti-inflammatoire. Plusieurs études in vitro ont suggéré un rôle pour le métabolisme et son régulateur principal, la kinase activée par l’AMP (AMPK), dans la résolution de l’inflammation et dans le devenir des cellules souches adultes. Ainsi, j’ai étudié l’influence extrinsèque (via les macrophages) et intrinsèque du métabolisme sur le devenir des cellules souches musculaires au cours de la régénération. Pour cela, j’ai utilisé divers modèles déficients pour l’AMPK1 dans le macrophage, dans la cellule souche musculaire et dans la myofibre qui m’ont permis d’établir des cultures primaires de macrophages et de cellules musculaires. Dans un premier temps, grâce à ces outils, nous avons pu démontrer le rôle primordial de l’AMPK dans la résolution de l’inflammation au cours de la régénération musculaire et dans l’acquisition des fonctions anti-inflammatoires des macrophages. Dans ce contexte, l’activation de l’AMPK est dépendante de la kinase CAMKK et régule la phagocytose, principal phénomène cellulaire permettant le changement de statut inflammatoire des macrophages. Ce travail a été publié en 2013 dans le journal Cell Metabolism. Ensuite, j’ai mis en évidence un lien entre le métabolisme et le devenir des cellules souches musculaires. La suppression de l’AMPK dans les cellules souches musculaires augmente leur auto-renouvellement. Cette modification du devenir des cellules souches est due à un changement de métabolisme similaire à l’effet Warburg observé dans les cellules souches cancéreuses, qui s’effectue via la modulation de l’activité de l’enzyme Lactate Déshydrogénase, enzyme clé de la glycolyse. En conclusion, j’ai pu mettre en évidence deux nouveaux rôles de l’AMPK dans le devenir des cellules souches musculaires, établissant un lien de causalité entre métabolisme, inflammation et devenir des cellules souches. / During skeletal muscle regeneration, muscle stem cells activate and recapitulate the myogenic program to repair the damaged myofibers. A subset of these cells does not enter into the myogenesis program but self-renews to return into quiescence for further needs. Control of muscle stem cell fate choice is crucial to maintain homeostasis but molecular and cellular mechanisms controlling this step are poorly understood. A difficulty of understanding muscle stem cell self-renewal is that skeletal muscle regeneration is a coordinated and non-synchronized process. Various and dissociated molecular and cellular mechanisms regulate muscle stem cell fate. Indeed, skeletal muscle regeneration requires the interaction between myogenic cells and other cell types, among which the macrophages. Macrophages infiltrate the muscle and adopt distinct and sequential phenotypes. They act on the sequential phases of muscle regeneration and resolving the inflammation by skewing their inflammatory profile to an anti-inflammatory state. Some in vitro studies suggested a role for the metabolism and the AMP-activated protein Kinase (AMPK), the master metabolic regulator of cells, in both inflammation and stem cell fate. Thus, I investigated the role of metabolism on muscle stem cell fate within the muscle stem cells (cell autonomous regulations) and through the action of macrophages (non-cell autonomous regulations) during skeletal muscle regeneration. To analyze muscle stem cell fate, I used in vitro (macrophages and muscle stem cell primary cultures), ex vivo (isolated myofibers) and in vivo (using specific mice model deleted specifically for AMPK1 in the myeloid lineage, in muscle stem cells or in myofibers) experiments. First, I highlighted that macrophagic AMPK1is required for the resolution of inflammation during skeletal muscle regeneration and for the trophic functions of macrophages on muscle stem cell fate. Moreover, CAMKK-AMPK1 activation regulates phagocytosis, which is the main cellular mechanism inducing macrophage skewing. This work was published in 2013 in Cell Metabolism. Second, I demonstrated that depletion of myogenic AMPK1 tailors muscle stem cell metabolism in a LKB1 independent manner, orients their fate to the self-renewal by promoting metabolic switch from an oxidative to a glycolytic metabolism pathway, through the over activation of a new molecular target, which is a key enzyme for glycolysis: the Lactate Dehydrogenase. To conclude, during my thesis, I established two new crucial roles of AMPK1 in muscle stem cell fate choice, linking for the first time metabolism, inflammation and fate choice.

The maintenance of the airway/respiratory epithelium during adult homeostasis and repair and its construction during embryonic development require tightly regulated cell fate decisions. This regulation takes the form of complex transcription factor and signalling cascades, much of which are unknown, particularly in human lung development. Multiciliogenesis describes the process of specification/differentiation of airway epithelial progenitors/stem cells into mature multiciliated cells (MCCs). Here, I have identified 2 novel transcription factors, Fank1 and Jazf1 which form part of the transcription factor cascade regulating multiciliogenesis in adult and embryonic mouse tracheas. Mouse tracheal epithelium is representative of epithelium lining the entire human airway and it is possible that we will also be able to extrapolate these findings to the human airway. It is not until we fully understand the regulation of multiciliogenesis that it will be possible to look at ways of pushing basal cells towards a MCC fate for purposes of cell replacement therapy, for example in patients with mucociliary disease. As well as exploring cell fate decisions in the mouse upper airway epithelium using embryonic tracheal explants and mouse tracheal epithelial cell (MTEC) cultures, I have also explored the regulation of cell fate decisions in distal human lung epithelium at the pseudoglandular stage of development. At this stage SOX9+ distal tip cells are self-renewing and multipotent and give rise to SOX2+ stalk descendents, which differentiate into airway epithelium. The regulation of SOX9+ lung tip cell multipotency and migration of SOX2+ stalk descendents during human lung development is poorly understood. I have compared human tip (SOX9+) versus stalk (SOX2+) transcriptomes using gene ontology (GO), which has highlighted some key signalling pathways enriched in tip cells which could be important in maintaining distal tip cell multipotency. These pathways have been utilised in optimising conditions for propagating self-renewing tip-derived organoids. These organoids have the potential to be differentiated into bronchiolar and alveolar fates and as such are an invaluable research tool for studying human lung epithelial development, whilst minimising the use of human embryos and its associated ethical implications. I have also performed human tip versus mouse tip transcriptome GO analysis which highlights that although there are many similarities, there are also differences between human and mouse lung epithelium development, emphasising the need for research on human tissue.