DLX transcriptional targets have been implicated during retinal development. The Crx (Cone-Rod homeobox) gene is required for the differentiation and maintenance of cone and rod photoreceptors. Otx2 (Orthodenticle homeobox 2) is a key regulator of photoreceptor cell fate. The Dlx1/Dlx2 mutant mouse retina has a significant reduction of retinal ganglion cells with aberrant Crx expression in the neuroblastic layer and increased retinal Otx2 expression. We hypothesized that the Dlx homeobox genes directly repress Crx and Otx2 expression during retinal development. Expression of CRX demonstrates increased transcript and protein expression in the Dlx1/Dlx2 double knockout retina at E18.5, suggesting that these DLX transcription factors may repress CRX expression. OTX2 expression is increased in the Dlx1/Dlx2 knockout retina at E16.5 suggesting that DLX2 negatively regulates OTX2 expression. The Dlx1/Dlx2 knockout has aberrant and ectopic expression of CRX in the retina along with increased OTX2 expression. Our data suggests that both CRX and OTX2 are transcriptional targets directly repressed by the DLX1 and DLX2.

DLX transcriptional targets have been implicated during retinal development. The Crx (Cone-Rod homeobox) gene is required for the differentiation and maintenance of cone and rod photoreceptors. Otx2 (Orthodenticle homeobox 2) is a key regulator of photoreceptor cell fate. The Dlx1/Dlx2 mutant mouse retina has a significant reduction of retinal ganglion cells with aberrant Crx expression in the neuroblastic layer and increased retinal Otx2 expression. We hypothesized that the Dlx homeobox genes directly repress Crx and Otx2 expression during retinal development. Expression of CRX demonstrates increased transcript and protein expression in the Dlx1/Dlx2 double knockout retina at E18.5, suggesting that these DLX transcription factors may repress CRX expression. OTX2 expression is increased in the Dlx1/Dlx2 knockout retina at E16.5 suggesting that DLX2 negatively regulates OTX2 expression. The Dlx1/Dlx2 knockout has aberrant and ectopic expression of CRX in the retina along with increased OTX2 expression. Our data suggests that both CRX and OTX2 are transcriptional targets directly repressed by the DLX1 and DLX2.

Pour comprendre comment les gènes du développement exercent de multiples fonctions temporelles, nous prenons comme modèle le facteur de transcription Otx2. Celui-ci est impliqué dans la gastrulation, le développement de l’œil, du système olfactif, de la glande pinéale, du thalamus et de la région cranio-faciale. Dans la rétine adulte, deux tissus distincts expriment Otx2 : l’épithélium pigmenté (RPE) et la rétine neurale, contenant les photorécepteurs. L’ablation globale du gène Otx2 entraîne la dégénérescence exclusive des photorécepteurs alors qu’elle modifie l’expression de gènes surtout dans le RPE. Ces faits suggèrent un mécanisme non autonome, confirmé par des expériences de gain et perte de fonction restreintes au RPE. Pour approcher les fonctions de la protéine Otx2 dans la rétine neurale et le RPE, une étude à grande échelle de ses cibles génomiques a été menée. Les profils distincts d’occupation du génome du RPE et de la rétine neurale suggèrent des fonctions différentes d’Otx2. Dans la rétine neurale, ce profil est très proche de celui du facteur paralogue Crx, indiquant une redondance fonctionnelle entre Otx2 et Crx. Nous avons émis l’hypothèse qu’une combinatoire de partenaires protéiques différents permet de moduler l’action d’Otx2 en sélectionnant des cibles génomiques distinctes. Pour identifier cette combinatoire in vivo et la corréler aux fonctions exercées par Otx2, nous avons créé une lignée de souris exprimant une protéine de fusion Otx2-TAP-tag à un niveau physiologique. Cet outil permettra la purification des complexes protéiques Otx2 in vivo et leur identification par analyse protéomique. / In the present work, we study the Otx2 transcription factor as a model to understand how developmental genes achieve multiple functions throughout time. Otx2 is first implied in gastrulation, and then participates to the development of the eye, the olfactory system, the pineal gland, the thalamus and the craniofacial region. Otx2 is expressed in two distinct tissues: retinal pigmented epithelium (RPE) and neural retina including photoreceptors. Global Otx2 gene ablation leads to exclusive photoreceptor degeneration although most of the affected genes are RPE specific. These elements suggest a non-cell-autonomous mechanism, confirmed by RPE restricted gain and loss of function. To understand Otx2 functions in the neural retina and in the RPE, a large scale study of its genomic targets has been yielded. Genome occupancy profiles in RPE and neural retina suggest different Otx2 functions. In the neural retina, Otx2 genome occupancy profile is very close to the one of its paralogue Crx, indicating functional redundancy between both transcription factors. We hypothesized that a different combination of protein partners allows modulating Otx2 action by selecting distinct target genes. To identify Otx2 combinatory in vivo and correlate it to Otx2 functions, we produced a mouse line expressing an Otx2-TAP-tag fusion protein at physiological level. This tool will allow purification of Otx2 protein complexes in vivo and their identification by proteomic analysis.

Cette thèse s’intéresse aux mécanismes permettant d’expliquer plusieurs des fonctions de l’homéogène Otx2 au cours du développement. Une première partie étudie l’importance de la régulation de son expression dans la régionalisation du système nerveux central. A la fin de la gastrulation la frontière d’expression postérieure d’Otx2 déterminera la position de l’organiseur isthmique responsable de l’induction du mésencéphale et du métencéphale. Un modèle murin a été mis au point dans lequel cette frontière est abolie au profit d’une présence uniforme du gène. A l’encontre du modèle actuel, l’isthme est alors correctement induit, et est de plus déplacé antérieurement, signe qu’un seuil net de concentration d’Otx2 est nécessaire à sa fonction régionalisante. Une seconde partie étudie l’importance du contexte cellulaire dans les modalités d’action d’Otx2 au niveau de la rétine adulte. Otx2 est exprimé dans les deux tissus qui composent cet organe, la neurorétine et le RPE. Une étude par ChIP-seq dans ces deux tissus a pu montrer que l’homéogène y occupait des sites de fixation très différents, suggérant des fonctions distinctes. L’écrasante majorité des sites occupés par Otx2 dans la neurorétine l’était également par son paralogue Crx, indice d’une redondance fonctionnelle. Une nouvelle lignée de souris a permis l’analyse des partenaires protéiques d’Otx2 dans la neurorétine, et pu démontrer qu’Otx2 ne formait pas d’interactions avec les autres facteurs de ce tissu, faisant en fait de Crx l’acteur principal de la famille Otx. Cette analyse a également dévoilé une série de partenaires jusque-là inconnus d’Otx2, potentiellement associée à de nouvelles fonctions de la protéine. / The molecular mechanisms explaining several functions of the homeogene Otx2 during embryonic development are the focus of this work. In a first part the importance of the regulation of its expression in the regionalisation of the central nervous system is studied. At the end of gastrulation the posterior border of Otx2 expression will position the isthmic organizer responsible for the induction of the midbrain and hindbrain. A mouse model was developed where this border is replaced by an ubiquitous expression of the gene. Contrary to the predictions of the current model, the organizer then correctly arises, and is shifted anteriorly. A concentration threshold of Otx2 thus appears necessary to its regionalising function. In a second part the importance of the cellular context in Otx2 function in the adult retina is examined. Otx2 is expressed in both tissues of this organ, the neural retina and RPE. A ChIP-seq analysis performed on both tissues revealed that this homeogene occupies very different sets of binding sites, which suggests distinct functions of the transcription factor. Most Otx2-bound sites in the neural retina were also bound by its paralogue Crx, with which a functional redundancy may therefore exist. A new mouse line finally allowed the study of the complete Otx2 interactome in the neural retina; this analysis showed that Otx2 does not interact with other important transcription factors of this tissue, and that Crx may therefore be the main actor of the Otx family in neural retina function. It also led to the discovery of a series of previously unknown partners of Otx2, which could be associated to new functions of this homeogene.

Le facteur de transcription à homéodomaine Otx2 est essentiel au développement du système nerveux, et en particulier du cervelet, où il est exprimé dans les précurseurs des neurones granulaires (PCGs). Au cours du développement, les PCGs passent par des périodes prolifératives très intenses qui les exposent à la transformation tumorale. Ces cellules seraient ainsi à l’origine de la formation des cancers du cervelet, les médulloblastomes (MBs). Une altération génétique particulière est cependant retrouvée dans plus de 75% des MBs : la surexpression d’Otx2. Cette thèse vise à comprendre le rôle d’Otx2 dans le contrôle de la prolifération dans un contexte normal ou tumoral. D’abord, nous avons entrepris d’identifier et d’isoler ces précurseurs à partir de souriceaux, afin d’analyser leur caractéristiques prolifératives. Nos résultats ont montré que les cellules « Otx2+ » contiennent une fraction proliférative plus importante que les cellules « Otx2-». L’analyse du cycle cellulaire des cellules « Otx2+» montre également que ces dernières présentent des propriétés prolifératives distinctes. Ensuite, nous avons mis en oeuvre une approche de gain et de perte de fonction d’Otx2 dans une lignée de MBs exprimant Otx2 (HD-MB03). Nos résultats indiquent que la surexpression d’Otx2 stimule la prolifération de cette lignée, alors que sa perte de fonction la diminue. Enfin, Nous avons identifié par des analyses protéomiques par spectrométrie de masse des partenaires impliqués dans la régulation du cycle cellulaire, en particulier au niveau des phases S et G2M. Ces résultats suggèrent un mécanisme d’action unique d’Otx2 dans la régulation du cycle cellulaire dans le cervelet et les MBs / The homeobox transcription factor Otx2 is essential for the development of the central nervous system. During cerebellum development, Otx2 is expressed by granule cell precursors (GCPs), which have a high proliferation rate. Deregulation of GCPs proliferation may favor oncogenic processes, as seems to occur in medulloblastoma (MB), a malignant and invasive tumor of the cerebellum. A recurrent genetic alteration in medulloblastoma is the overexpression of Otx2 in 75% of the cases. The objective of this thesis is to study the role of Otx2 in the control of proliferation during normal and oncogenic development of the cerebellum. First, we investigated the role of Otx2 in the control of GCPs proliferation. Our results show that Otx2+ GCPs have an increased proliferation rate compared to «Otx2-» GCPs. In the second part of this work, we tested the oncogenic potential of Otx2 using the medulloblastoma cell line HD-MB03. We performed gain and loss of function experiments to analyze the effect of Otx2 expression on the proliferation of this cell line. Our results indicate that the overexpression of Otx2 increases the proliferation rate of HD-MB03 tumor cells. Conversely, Otx2 silencing significantly decreases it. Finally, to shed the light on the mechanism of action of Otx2 in the control of proliferation in cerebellum and medulloblastoma, we analyzed Otx2 protein partners in both cases by mass spectrometry analysis after immunoprecipating Otx2-protein complexes. We identified several protein partners that play an important role in cell cycle regulation, more specifically in S and G2M phases. Our project shows a pro-proliferative effect of Otx2 in cerebellum and medulloblastoma

Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is divided into 4 subtypes based on different genomic alterations and gene expression profiles. This extensive heterogeneity has made it difficult to assess the functional relevance of genes to malignant progression. For example, expression of the transcription factor, Orthodenticle homeobox2 (OTX2) is frequently upregulated in multiple MB variants; however, its role may be subtype-specific. We recently demonstrated that neural precursors derived from transformed human embryonic stem cells (trans-hENs), but not their normal counterparts (hENs), resemble Groups 3 and 4 MBs. These trans-hENs also have >10-fold expression of OTX2. Therefore, we hypothesize that OTX2 has cell context-dependent functions in MB and using both normal and trans-hENs, we can delineate its specific roles in MB progression. Parallel experiments with MB cells revealed that OTX2 exerts inhibitory effects on hEN and sonic hedgehog (SHH) MB cells by regulating growth, self-renewal and migration in vitro and tumor growth in vivo. Overexpression of OTX2 was accompanied by a decrease in expression of pluripotent genes such as SOX2. This was supported by exogenous introduction of SOX2 in OTX2+ SHH MB and hENs that rescued the OTX2 induced cellular deficits including self-renewal and cell migration. In contrast, OTX2 is oncogenic and promotes self-renewal of trans-hENs and Group 3 and 4 MBs by modulating expression of genes related to neurodevelopment and axonal guidance. OTX2 may play a central role in regulating the balance between self-renewal and differentiation in these aggressive MB cells. Our studies underscore the value of hESC derivatives as alternatives to cell lines and heterogeneous patient samples for investigating the contribution of key developmental regulators to MB progression. Using the neural derivatives of hESCs, we have demonstrated a novel role for OTX2 in self-renewal and migration of hENs and MB cells. Moreover, our results reveal a cell context-dependent link between OTX2 and pluripotent genes. The association between OTX2 and axonal guidance genes is important for its oncogenic role and may potentially be exploited for managing drug resistant stem cell and highly motile cellular populations in the most aggressive Group 3 and 4 MB subtypes. / February 2017

Nanog is a transcription factor that plays a central part in the gene regulatory network that maintains and induces pluripotency of embryonic stem cells (ESCs). However, the molecular basis by which Nanog achieves its functions is not fully understood. At the centre of C-terminal domain of Nanog a tryptophan repeat (WR) is located, comprising 10 penta-peptide repeats each starting with a tryptophan. A mutant form of Nanog (Nanog-W10A) in which all 10 tryptophan residues have been substituted by alanine has an impaired capacity to drive LIF-independent self-renewal and a reduced efficiency in reprogramming primed epiblast stem cells to naïve pluripotency. To understand how the WR contributes to Nanog function, Nanog-W10A-ERT2 was introduced into Nanog null cells. Upon hydroxytamoxifen addition, the Nanog-ERT2 fusion proteins were detected on chromatin within 1 hour, allowing a comparison of genome-wide transcriptional responses to Nanog and Nanog-W10A by microarray. When treated with LIF, Nanog-W10A can activate most of Nanog targets as efficiently as Nanog. In contrast, Nanog-W10A did not efficiently repress most Nanog targets, including Otx2 and Tcf15 that were previously suggested to prime ESCs for differentiation. The microarray experiments performed in the absence of LIF signalling showed that Nanog and LIF co-regulate an extensive list of targets, including Klf4 and Mras. When LIF is absent, wildtype Nanog can still activate pro-self-renewal factors, including Esrrb and repress differentiation-priming factor, such as Tcf15 and Otx2. In contrast, in the absence of LIF, the activation of pro-self-renewal factors Klf4 and Mras is reduced. In addition, activation of Esrrb by Nanog-W10A induction delays but does not prevent differentiation. These effects allow the de-repression of Otx2 and Tcf15 by Nanog-W10A to dominate. Therefore, the function of Nanog is not only mediated by the activation of pro-self-renewal genes, but also repression of pro-differentiation signals. The functional significance of the repression of Nanog targets was further exemplified by the robust capacity of Otx2 to dominate over the self-renewal signals and to drive differentiation. The Otx2 protein is a direct interacting partner of Nanog that binds the Nanog WR tryptophan residues. The previously identified Otx2 “tail domain” comprises two imperfectly aligned repeats and aromatic residues of each repeat align with aromatic residues of the Sox2 “SXS/TY” motif previously identified to mediate the interaction between Sox2 and Nanog. Aromatic residues of Otx2 were demonstrated to directly interact with both Nanog and Sox2. The interactions between Otx2, Nanog and Sox2 are essential for Otx2 functions in driving ESCs differentiation, as Otx2 mutants with alanine substitutions of the aromatic residues in both or either of the repeats have reduced efficiency to drive differentiation. As Nanog and Sox2 may co-occupy many loci important in maintaining ESC self-renewal, Otx2 may be able to “read” the Nanog/Sox2 co-binding sites to dissolve the pluripotent networks. In summary, the repression function of Nanog is located within the Nanog WR region and represents an important module of Nanog in fine-tuning the balance between self-renewal and differentiation. This module involving Nanog WR can also be recognised by differentiation-priming factor Otx2 and may represent an initial step during the exit of differentiation.

Unlike principal excitatory neurons, cortical interneurons comprise a diverse group of distinct subtypes. They can be classified by their morphology, molecular content, developmental origins, electrophysiological properties and specific connectivity patterns. The parvalbumin-positive \((PV^+)\), large basket interneuron has been implicated in two cortical functions: 1) the control and shaping of the excitatory response, and 2) the initiation of critical periods for plasticity. Disruptions in both phenomena have been implicated in the etiology of cognitive developmental disorders. Careful characterization of \(PV^+\) cell function and plasticity in response to their primary afferent, the thalamocortical synapse, is needed to directly relate their vital contribution at a synapse-specific or network level to whole animal behavior. Here, I used electrophysiological, anatomical and molecular genetic techniques in a novel slice preparation to elucidate \(PV^+\) circuit development and plasticity in mouse visual cortex. I found that GFP-positive \(PV^+\) cells in layer 4 undergo a rapid maturation after eye opening just prior to onset of the critical period. This development occurs across a number of intrinsic physiological properties that shape their precise, fast spiking. I further optimized and characterized a visual thalamocortical slice to examine the primary afferent input onto both pyramidal and \(PV^+\) cells. Thalamic input onto \(PV^+\) cells is larger, faster and again matures ahead of the critical period. Both the intrinsic and synaptic properties of \(PV^+\) cells are then maintained by a secreted homeoprotein, Otx2 (Sugiyama et al, 2008), which is mediated by an extracellular glycosaminoglycan recognition. Since the plasticity of fast-spiking, inhibitory neurons is dramatically distinct from their neighboring pyramidal neurons in vivo (Yazaki-Sugiyama et al. 2009), I directly examined the plasticity of thalamocortical synapses in vitro. After brief monocular deprivation, thalamic input specifically onto \(PV^+\) cells is reduced while remaining unaltered in pyramidal cells. Deprivations prior to critical period onset or in GAD65 knockout mice neither produce a shift of visual responsiveness in vivo (Hensch et al, 1998) nor reduce thalamocortical input onto \(PV^+\) cells. These results directly confirm that \(PV^+\) cells are uniquely sensitive to visual experience, which may drive further rewiring of the surrounding excitatory cortical network.

<p>Medulloblastoma is the most common malignant brain tumor in children. The understanding of the genetic alterations in this tumor is emergent, and many such genetic driver events have yet to be functionally-characterized. Our studies have sought to understand the causes and consequences of OTX2 dysregulation in established medulloblastomas and in its putative cellular origins. Using a tumor genetic approach, we have uncovered frequent OTX2 copy number gains driving expression of this oncogene in a subset of medulloblastomas. However, OTX2 is frequently expressed in medulloblastomas independent of genomic copy number gain, and we thus sought to understand the transcriptional regulation of this gene in these tumors. We have found that chromatin accessibility, promoter DNA methylation, and activity of a distal downstream enhancer is distinct between OTX2-expressing and -nonexpressing medulloblastomas. Notably, autoregulation serves to maintain OTX2 expression in some medulloblastomas, whereas DNA methylation actively suppresses OTX2 in tumors not expressing this gene. Finally, we describe the effect of expressing Otx2 (the mouse homolog of OTX2) aberrantly in the developing mouse hindbrain, revealing that Otx2 disrupts spatiotemporal restrictions of neuronal progenitor cell proliferation. The effect of Otx2 in vivo is transient, with ectopically-proliferating cells give way to differentiated neurons. We found that OTX2 expression was not able to give rise to high penetrance medulloblastoma when combined with P53 deletion or double heterozygosity for P53 and PTEN. Thus, although Otx2 alters migration and proliferation dynamics of hindbrain neuronal progenitor cells, further studies are needed to identify the genetic alterations that cooperate with this oncogene to give rise to medulloblastoma.</p> / Dissertation

La neurogenèse adulte permet la formation de nouveaux neurones dans les bulbes olfactifs de la souris. Les propriétés des cellules souches neurales situées dans la zone sous-ventriculaire (ZSV) et des précurseurs sont régulées par la niche contenant des cellules de support et une matrice extracellulaire (MEC). Des facteurs contenus dans le liquide cérébrospinal (LCS), produits par les plexus choroïdes (PC), contrôlent aussi la niche. L'homéoprotéine Otx2 est secrétée dans le LCS par les PC, et internalisée spécifiquement par certaines cellules du parenchyme cérébral. Otx2 est impliquée dans différentes étapes du développement du cerveau, dont celui des PC, et peut agir de manière non-cellulaire-autonome. Ma thèse vise à comprendre comment Otx2 régule les fonctions des PC et participe à la neurogenèse adulte. Grâce à des études génomiques d'un modèle murin knockdown (KD) d'Otx2 dans les PC adultes, nous avons montré que (i) les PC de différents ventricules présentent des profils d'expression différents (ii) le KD d'Otx2 modifie l'expression de gènes impliqués dans des fonctions importantes des PC (iii) la dérégulation de certains gènes après KD est spécifique d'un type de PC. Une étude protéomique suggère (iv) qu'Otx2 pourrait être impliquée à d'autres niveaux que la régulation transcriptionnelle. L'étude de la neurogenèse adulte dans des modèles murins KD d'Otx2 nous a permis de montrer que (i) l'expression d'Otx2 dans les PC régule la neurogenèse adulte (ii) Otx2 transfère dans les astrocytes de la ZSV (iii) le transfert d'Otx2 est suffisant pour réguler la neurogenèse (iv) le KD d'Otx2 dans les PC modifie l'expression de protéines de la MEC secrétées par les astrocytes. / Adult neurogenesis in mice involves neural stem cells in the subventricular zone (SVZ) whose progenitors integrate into the olfactory bulbs. The neurogenic niche, which contains supporting cells and extracellular matrix (ECM), regulates the properties (proliferation, migration and differentiation) of progenitor cells. This niche is influenced by factors from cerebrospinal fluid (CSF), which is produced by the choroid plexus (CP) in the brain ventricles. The Otx2 homeoprotein transcription factor is secreted into CSF by CP, and taken up by a specific subset of cells within the brain parenchyma. Otx2 is involved in various stages of brain development, including CP development, and has non-cell autonomous functions. The aim of my thesis is to understand how Otx2 regulates adult CP function and participates in adult SVZ neurogenesis. Through genomic studies, we investigated the consequence of Otx2 knockdown (KD) in adult CP and found: (i) adult CP from different ventricles exhibit different expression profiles; (ii) Otx2 KD alters the expression of genes with important CP functions; and (iii) deregulation of certain genes after Otx2 KD can be CP specific. Through proteomics studies, we found that (iv) adult Otx2 could be involved in functions beyond transcriptional regulation, such as RNA processing.To evaluate the role of Otx2 in SVZ neurogenesis, we also used Otx2 KD mouse models. We found that: (i) the expression of Otx2 in CP regulates adult neurogenesis; (ii) Otx2 transfers to astrocytes of the SVZ; (iii) Otx2 transfer is sufficient to regulate adult neurogenesis; and (iv) Otx2 KD in CP alters the expression of ECM proteins secreted by astrocytes in the neurogenic niche.