The cerebral cortex develops through the coordinated generation of dozens of neuronal <p>subtypes, but the mechanisms involved remain unclear. Here we show that mouse embryonic <p>stem cells, cultured without any morphogen but in the presence of a sonic hedgehog inhibitor, <p>recapitulate in vitro the major milestones of cortical development, leading to the sequential <p>generation of a diverse repertoire of neurons that display most salient features of genuine <p>cortical pyramidal neurons. When grafted into the cerebral cortex, these neurons develop <p>patterns of axonal projections corresponding to a wide range of cortical layers, but also to <p>highly specific cortical areas, in particular visual and limbic areas, thereby demonstrating that <p>the identity of a cortical area can be specified without any influence from the brain. The <p>discovery of intrinsic corticogenesis sheds new light on the mechanisms of neuronal <p>specification, and opens new avenues for the modelling and treatment of brain diseases. <p>In a further attempt to prove the validity of this model, we have initiated the study of the <p>mechanism of action of FoxG1, a forkhead box transcription factor involved in the control of <p>cell fate decision in the developing cortex. / Doctorat en Sciences médicales / info:eu-repo/semantics/nonPublished

L’acétylation des histones est associée à une activation transcriptionnelle. Cette acétylation est mise en place par des histone acétyltransférases (HATs) qui sont le plus souvent les sous-unités catalytiques de complexes multiprotéiques. Mon travail concerne plus particulièrement deux complexes contenant l’acétyltransférase Mof, MSL et NSL, ainsi que le complexe HAT Tip60-p400 dans les cellules souches embryonnaires de souris (mESCs). Nos analyses de localistaion sur l’ensemble du génome par ChIP-seq indiquent que MSL, NSL et Tip60-p400 se lient aux gènes activement transcrits et agissent comme des co-activateurs transcriptionnels majeurs dans les mESCs. MSL, NSL et Tip60-p400 ont des rôles à la fois chevauchants mais aussi distincts dans la régulation transcriptionnelle dans les mESCs. Chaque complexe présent un profil distinct de liaison à la chromatine. NSL lie principalement des gènes de ménage. MSL et Tip60-p400 sont également présent les gènes impliqués dans le développement. MSL est directement impliqué dans l’augmentation de l’expression de ces gènes au cours de la différenciation des mESCs. / Histone acetylation is involved in transcriptional activation of genes and is carried out by histone acetyltransferases (HATs), which are part of molecular protein complexes. This study focuses on the genome-wide role of Mof-containing MSL and NSL complexes and the Tip60-p400 complex in mouse embryonic stem cells (mESCs). I have analysed these complexes by ChIP-seq, shRNA knockdown and biochemical approaches. The genome-wide binding studies show that NSL, MSL and Tip60-p400 have a global overlap at promoters, but also bind to specific gene sets. There distinct binding profiles propose distinct roles in transcriptional regulation. MSL is the main H4K16 acetylase in mESCs.NSL binds mainly to housekeeping genes, whereas MSL and Tip60 are also present at developmental genes. Importantly, these developmental genes are directly regulated by MSL during cellular differentiation.

La mutation LMNA H222P est responsable de dystrophie musculaire d’Emery Dreifuss autosomale dominante (DMED-AD). Les patients atteints de DMED-AD souffrent d’une dystrophie musculaire et de cardiomyopathie dilatée. Les mécanismes moléculaires impliqués dans cette pathologie sont encore peu connus. Dans mes travaux de thèse, je me suis servie de cellules souches pluripotentes murines ainsi que de souris portant la mutation LMNA H222P afin d’étudier une approche thérapeutique potentielle. L'échocardiographie des souris LMNA H222P in utero révèle une dilatation des cœurs embryonnaires dès E13.5, ce qui indique une origine développementale de la maladie. La différenciation cardiaque des cellules souches pluripotentes murines est altérée dès le stade mésoderme. Aussi, les niveaux d’expression de Mesp1, snail1 et twist, gènes impliqués dans la transition épithélio-mésenchymateuse (TEM) sont diminués dans les cellules mutées en comparaison avec les cellules sauvages en cours de différenciation. L'immunoprécipitation de la chromatine dans les cellules différenciées révèle une diminution spécifique de la marque d'histone H3K4me1 sur des régions régulatrices de Mesp1 et Twist. L'inhibition de LSD1, une déméthylase spécifique de H3K4me1 rétablit le taux de la marque H3K4me1 sur les régions génomiques étudiées dans les cellules mutées. De plus, la baisse de LSD1 améliore la contraction des cardiomyocytes différenciés obtenus à partir des cellules souches embryonnaires portant la mutation LMNA H222P. L'inhibiteur de LSD1, utilisé dans les essais cliniques en cancérologie, pourrait être une molécule thérapeutique potentielle pour le traitement des laminopathies à phénotype cardiaque. / The LMNA H222P missense mutation in autosomal dominant Emery-Dreifuss muscular dystrophy patients is responsible for a muscular dystrophy and dilated cardiomyopathy. The molecular mechanisms underlying the origin and development of the pathology are still unknown. Herein, we used mouse pluripotent stem cells as well as a mutant mouse, all harboring the LMNA H222P mutation, to investigate potential therapeutic approaches. Echocardiography of LMNA H222P mice in utero revealed dilatation of heart as early as E13.5, pointing to a developmental origin of the disease. Cardiac differentiation of mouse pluripotent stem cells was impaired as early as the mesodermal stage. Expression of Mesp1, a mesodermal cardiogenic gene as well as snail1 and twist, involved in epithelial-mesenchymal transition (EMT) of epiblast cells, was decreased in mutated cells when compared to wild type in the course of differentiation. In turn, cardiomyocyte differentiation was impaired. Chromatin immunoprecipitation assays of the H3K4me1 epigenetic mark in differentiating cells revealed a specific decrease of this histone mark on regulatory regions of MesP1 and Twist. Downregulation or inhibition of LSD1, that specifically demethylates H3K4me1, rescued the epigenetic landscape in mutated cells. In turn downregulation of LSD1 rescued contraction in cardiomyocytes differentiated from LMNA H222P pluripotent stem cells. Our data point to LSD1 inhibitor, used in clinical trials in cancerology, as potential therapeutic molecule for laminopathies with a cardiac phenotype.

O transplante de células-tronco hematopoéticas (CTHs) é o tipo mais bem-sucedido de terapia celular realizado até os dias atuais. No entanto, apesar do sucesso e da relevância clínica das CTHs isoladas a partir de fontes adultas, o uso destas células tem algumas limitações em relação à sua disponibilidade, compatibilidade imunológica e risco de contaminação. Desse modo, busca-se o desenvolvimento de soluções para as dificuldades apontadas para suprir a demanda de transplantes. Uma abordagem emergente para superar este problema é baseada na cultura e diferenciação de células-tronco embrionárias humanas (CTEhs). Estas são célulastronco pluripotentes e indiferenciadas com elevada capacidade de auto-renovação e diferenciação em todas as células derivadas dos três folhetos germinativos. No entanto, os métodos de diferenciação utilizados para a produção de CTHs a partir de células pluripotentes ainda não são eficientes. Os protocolos descritos até o momento têm gerado números variados e populações de células heterogêneas, e produz apenas CTHs muito primitivas e imaturas com baixa capacidade funcional in vivo. Parte desta dificuldade pode decorrer da ineficiência do microambiente de cultura para a diferenciação. Neste trabalho, nós demonstramos um eficiente protocolo de diferenciação hematopoética baseado em cocultivo de CTEhs com fibroblastos embrionários murinos com alto rendimento na geração de célulastronco/progenitoras hematopoéticas (CTPHs) que expressam os antígenos CD45, CD43, CD31 e CD34, e apresentam potencial clonogênico in vitro equivalente ao de células mononucleares isoladas de sangue de cordão umbilical. Nós fomos capazes de produzir todas as células das linhagens eritróide e mielóide em diferentes estágios de maturação, como também células positivas para marcadores linfóides. Demonstramos ainda que as células hematopoéticas surgem no sistema de cultura a partir de um endotélio-hemogênico constituído por células CD34+CD31+. No entanto, apesar das características maduras das CTPHs obtidas por tal método, os ensaios de reconstituição hematopoiética mostraram que estas células ainda possuem limitada capacidade funcional de enxertamento em camundongos imunocomprometidos quando transplantadas por via retro-orbital. / Hematopoietic stem cells (HSC) transplant is the most successful type of cell therapy carried out to date. However, despite the success and the clinical relevance of HSC isolated from adult sources, these cells have some limitations regarding its availability, immunological compatibility and risk of contamination. Thus, we seek to develop solutions to overcome these difficulties to supply the demand for transplants. An emerging approach to overcome this problem is based on human embryonic stem cells (hESCs) culture and differentiation. These are pluripotent and undifferentiated stem cells with high capacity for self-renewal and differentiation in all cells derived from the three embryonic germ layers. However, differentiation methods used for HSC production from pluripotent cells are not efficient yet. Protocols described so far have generated varying numbers and heterogeneous cell populations, and produce only very primitive and immature HSC with low in vivo functional capacity. Part of this difficulty may result from the inefficiency of the microenvironment of culture for differentiation. Here, we demonstrate an efficient protocol based on co-culture of hESCs with mouse embryonic fibroblasts for hematopoietic differentiation with high performance to generate in vitro hematopoietic stem/progenitor cells (HSPCs) that express CD45, CD43, CD31 and CD34 antigens with high purity of positive cells. We were able to produce all cells of erythroid and myeloid lineages at different stages of maturation. Lymphoid potential of hematopoietic cells was also evidenced. We demonstrated the primitive origin of hematopoietic cells through capillary-like structures constituted by hemogenic CD34+CD31+ cells. However, despite mature features of HSPCs obtained by our protocol, hematopoietic reconstitution assays showed that these cells have yet limited functional capacity for grafting into immunocompromised mice when exogenously transplanted by retro-orbital route.

Les cellules souches embryonnaires (cellules ES) constituent un excellent système modèle pour étudier les mécanismes épigénétiques contrôlant la transcription du génome mammifère. Un nombre important de membres de la famille des facteurs de remodelage de chromatine ATP-dépendants ont une fonction essentielle pour l’auto-renouvellement des cellules ES, ou au cours de la différentiation. On pense que ces facteurs exercent ces rôles essentiels en régulant l’accessibilité de la chromatine au niveau des éléments régulateurs de la transcription, en modulant la stabilité et le positionnement des nucléosome.Dans ce projet, nous avons conduit une étude génomique à grande échelle du rôle d’une dizaine des remodeleurs (Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Ep400, Brg1, Smarca3, Smarcad1, Smarca5, ATRX et Chd1l) dans les cellules ES. Une double stratégie expérimentale a été utilisée : Des expériences d’immunoprécipitation de la chromatine suivi par un séquençage à haute-débit (ChIP-seq) sur des cellules ES étiquetées pour les différents remodeleurs, pour étudier leur distribution sur le génome, et un approche transcriptomique sur des cellules déplétées de chaque remodeleur par traitement avec des vecteurs shRNA (knockdown). Nous avons établi les profils de liaison des remodeleurs sur des éléments régulateurs (promoteurs, enhancers et sites CTCF) sur le génome, et montré que ces facteurs occupent toutes les catégories d’éléments régulateurs du génome. La corrélation entre les données ChIP-seq et les données transcriptomiques nous a permis d’analyser le rôle des remodeleurs dans les réseaux de transcription essentiels des cellules ES. Nous avons notamment démontré l’importance particulière de certains remodeleurs comme Brg1, Chd4, Ep400 et Smarcad1 dans la régulation de la transcription chez les cellules ES. / The characteristics of embryonic stem cells (ES cells) make them one of the best models to study the epigenetic regulation exerted by different actors in order to control the transcription of the mammalian genome. Members of the Snf2 family of ATP-dependent chromatin remodeling factors were shown to be of specific importance for ES cell self-renewal and during differentiation. These factors are believed to play essential roles in modifying the chromatin landscape through their capacity to position nucleosomes and determine their occupancy throughout the genome, making the chromatin more or less accessible to DNA binding factors.In this project, a genome-wide analysis of the function of a number of ATP-dependent chromatin remodelers (Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1, Ep400, ATRX, Smarca3, Smarca5, Smarcad1 and Alc1) in mouse embryonic stem (ES) cells was conducted. This was done using a double experimental strategy. First, a ChIP-seq (Chromatin Immunoprecipitation followed by deep sequencing) strategy was done on ES cells tagged for each factor in the goal of revealing the genomic binding profiles of the remodeling factors. Second, loss-of-function studies followed by transcriptome analysis in ES cells were performed in order to understand the functional role of remodelers. Data from both studies were correlated to acquire a better understanding of the role of remodelers in the transcriptional network of ES cells. Specific binding profiles of remodelers on promoters, enhancers and CTCF binding sites were revealed by our study. Transcriptomic data analysis of the deregulated genes upon remodeler factor knockdown, revealed the essential role of Chd4, Ep400, Smarcad1 and Brg1 in the control of transcription of ES cell genes. Altogether, our data highlight how the distinct chromatin remodeling factors cooperate to control the ES cell state.

RNAs associate with chromatin through various ways and carry out diverse functions. One mechanism by which RNAs interact with chromatin is by the complementarity of RNA with DNA, forming a three-stranded nucleic acid structure named R-loop. R-loops have been shown to regulate transcription initiation, RNA modification, and immunoglobulin class switching. However, R-loops accumulated in the genome can be a major source of genome instability, meaning that they must be tightly regulated. This thesis aims to identify R-loop-binding proteins systemically and study their regulation of R-loops. Using immunoprecipitation of R-loops followed by mass spectrometry, with or without crosslinking, a total of 364 proteins were identified. Among them RNA-interacting proteins were prevalent, including some already known R-loop regulators. I found that a large fraction of the R-loop interactome consists of proteins localized to the nucleolus. By examining several DEAD-box helicases, I showed that they regulate rRNA processing and a shared set of mRNAs. Investigation of an R-loop-interacting protein named CEBPZ revealed its nucleolar localization, its depletion caused down-regulation of R-loops associated with rRNA and mRNA. Characterization of the genomic distribution of CEBPZ revealed its colocalization with insulator-regulator CTCF. When studying if CEBPZ recruits CTCF, I found that instead of regulating CTCF binding, CEBPZ depletion has a major effect on the performance of CUT&RUN, a technique for identifying DNA binding sites of proteins. How CEBPZ affects CUT&RUN is still under investigation, the study of which may help us understand the roles of CEBPZ in regulation of global chromatin structure and genome integrity.

Methylation of histone 3 (H3) at lysine 36 (K36) has been implicated in several biological processes, such as DNA replication, DNA repair, and transcription. To date, at least eight distinct mammalian enzymes have been described to methylate H3K36 in vitro and/or in vivo. In this work, Set2, Nsd1, and Nsd3 Venus tagged proteins were successfully expressed in mouse embryonic stem cells and, then, analyzed by confocal microscopy, mass spectrometry (MS), and chromatin immunoprecipitation sequencing (ChIP-seq). MS analysis revealed that Setd2, Nsd1, and Nsd3 do not associate in protein complexes with each other. Setd2 was associated with RNA polymerase II subunits and two transcription elongation factors (Supt5 and Supt6), whereas Nsd1 associated with the transcription factor Zfx. In contrast, Nsd3 interacted with multiple protein complexes including Kdm1b and Brd4 complexes. Interestingly, Nsd1 and Zfx seem to be bound to chromatin during cell division. ChIP-seq analysis of the H3K36 methyltransferases showed different binding profiles at transcribed genes: Nsd1 binds near the transcription start site (TSS), Setd2 loading starts near the TSS and spreads along the gene body, while, Nsd3 is preferentially enriched at the 5’ and 3’ gene regions. Sequential deletion of PWWP and zinger-finger like domains was achieved to study any possible changes in Nsd1 and Nsd3 function. Deletion of either PHD1-4 or PHD5/C5HCH domains decreased Nsd1 recruitment to chromatin. Particularly, the PHD5/C5HCH were identified as the protein-protein interface for Zfx interaction. In agreement, Zfx knockdown also decreased Nsd1 deposition at the Oct4 and Tcl1 promoter regions. Furthermore, Nsd1 depletion reduced bulk histone H3K36me2 and histone H3K36me3 loading at the coding regions of Oct4, Rif1, Brd2, and Ccnd1. In addition, Nsd1 knockdown led to an increased Zfx deposition at promoters. Our findings suggest Zfx recruits Nsd1 to its target loci, whereas Nsd1 regulates Zfx chromatin release and further contributes to transcription regulation through its H3K36 dimethylase activity. On the other hand, loss of Nsd3’s PHD5/C5HCH or PWWP domains decreased Nsd3 binding to DNA. In addition, we demonstrate that Nsd3 is recruited to target genes in a Brd4-dependent manner. Herein, we provided further insights on how H3K36 methyltransferases are regulated, and how they contribute to changes in the epigenetic landscape in mouse embryonic stem cells.fi

Les maladies cardiovasculaires sont souvent causées par des arythmies qui proviennent d'une obstruction du système de conduction cardiaque. L'intervenant clé de ce système est le nœud sinu-atrial (SA), qui est responsable de l’initiation de chaque battement cardiaque. L’activation électrique à intervalles réguliers, assurant que le rythme cardiaque est un rythme normal. Le dysfonctionnement du nœud SA entraînerait des instabilités électriques dans le cœur. Une maladie cardiaque acquise, comme la cardiopathie rhumatismale, ou un bloc de conduction ne sont que quelques-uns des nombreux cas qui nécessitent un stimulateur cardiaque électronique pour surveiller la fréquence cardiaque et générer une impulsion lorsqu'elle bat anormalement. Bien que le stimulateur cardiaque électrique soit considéré comme une thérapie fiable, il n'est pas sans limites. Ces limites comprennent les complications chirurgicales, l'infection au plomb ainsi que la durée de vie limitée de la batterie, qui doit être remplacée à intervalles de quelques années, ce qui alourdit le fardeau hospitalier. Plusieurs approches ont été adoptées pour développer une méthode thérapeutique plus adéquate. Une stratégie qui sera étudiée implique l'utilisation d'une greffe de cellules de stimulateur cardiaque, créant fondamentalement un stimulateur biologique. Les approches de thérapie cellulaire utilisent des cellules souches embryonnaires pour évoluer vers les lignées de cellules cardiaques, y compris les cellules stimulatrices cardiaques. Ces cellules de stimulation sont caractérisées par une dépolarisation spontanée qui crée les impulsions rythmiques dans le cœur et contrôle la fréquence cardiaque. Un élément important des cellules du stimulateur cardiaque qui donne lieu à la dépolarisation spontanée sont les canaux « hyperpolarization-activated and cyclic nucleotide-gated » qui sont activés pendant l’hyperpolarisation et conduisent le courant sous le nom de « funny current ». Ce courant augmente la perméabilité intérieure de la cellule aux courants de sodium et de potassium conduisant à la dépolarisation de la cellule. D'autre part, le taux de conduction est déterminé par la connexine 30.2 et la connexine 45, qui sont des protéines transmembranaires qui s’assemblent pour former des jonctions lacunaires. L'expression de HCN et l'expression de la connexine ont toutes deux étés liés au facteur T-box 3 (Tbx3) dans le développement des myocytes auriculaires. Une approche praticable pour moduler l'expression des gènes et par conséquent l'expression des protéines est l'utilisation du conditionnement chimique. Le Phorbol 12- myristate 13-acétate (PMA) est un activateur de Protéine Kinase C (PKC) lié à l'expression de Tbx3, et par conséquent à l'expression de HCN et de connexine, et entraînant une modification de l'activité spontanée. Les cellules souches embryonnaires de souris sont des cellules qui sont isolées de la masse cellulaire interne des embryons. Ces cellules ont la capacité de se différencier en tous les types de cellules somatiques. En combinant les facteurs de croissance, ces cellules peuvent se différencier en cardiomyocytes. Nous émettons l'hypothèse que le conditionnement chronique de cardiomyocytes de souris avec PMA entraîne une régulation à la hausse de l'expression de Tbx3 et par conséquent une régulation à la hausse de l'expression de HCN et de l'expression de connexine, favorisant ainsi le développement des cellules stimulatrices cardiaques dans la population des cardiomyocytes. Afin de vérifier notre hypothèse, nous avons acheté des cellules de la lignée cellulaire E14TG2A de souris. Ces cellules ont été cultivées dans des pétris et différenciées en cardiomyocytes à l'aide d'un protocole en trois étapes (voir la section Méthodes). Les cardiomyocytes sont ensuite exposés à la PMA à des concentrations variables (0.1 µM vs 1 µM) pendant 1h (exposition aiguë) ou 24 h (exposition chronique). Les résultats variaient d'un groupe expérimental à l'autre par rapport au groupe témoin. Dans toutes les conditions expérimentales, il semble y avoir une augmentation initiale de l'activité spontanée, mais elle s'inverse rapidement à la marque des 24 heures, où le rythme diminue. Différentes concentrations jouent un rôle dose-dépendant dans l'effet inhibiteur de longue durée sur la stimulation des cellules. / Cardiovascular diseases are often caused by arrhythmias that originate from an obstruction within the cardiac conduction system. The key player within that system is the sinoatrial (SA) node, which is responsible for initiation the electrical impulses at a regular interval, insuring the heartbeat at a normal pace. Dysfunction of the SA node would lead to electrical instabilities in the heart. An acquired heart disease, such as rheumatic heart disease, or a conduction block are just some of many cases that would require an electronic pacemaker to monitor the heart rate and generate an impulse when it beats abnormally. Although the electric pacemaker is considered as a reliable therapy, it is not without limitations. These limitations include surgery complication, lead infection as well as limited battery lifespan, which requires replacement every few years thus adding to the hospital burden. Several approaches have been taken to develop a more adequate therapeutic method. A strategy that will be investigated involves using a graft of pacemaker cells, fundamentally creating a biological pacemaker. Cell therapy approaches use embryonic stem cells to evolve into the cardiac cell lines, including pacemaker cells. These pacing cells are characterized by spontaneous depolarization that create the rhythmic impulses in the heart and control the heart rate. An important element of the pacemaker cells that give rise to the spontaneous depolarization are the hyperpolarization- activated and cyclic nucleotide-gated (HCN) channels that are activated during hyperpolarization and conduct the funny current by increasing the cell’s inward permeability to sodium-potassium currents. On the other hand, the conduction rate is determined by connexin 30.2 and connexin 45, which are transmembrane proteins that assemble to form gap junctions. Both HCN expression and connexin expression has been linked to T-box factor 3 (Tbx3) in the development of atrial myocytes. A practicable approach to modulate gene expression and consequently protein expression is using chemical conditioning. Phorbol 12-myristate 13-acetate (PMA) is a Protein Kinase C (PKC) activator that has linked to Tbx3 expression, and consequently HCN and connexin expression, and lead to a modification in spontaneous activity. Mouse embryonic stem cells (ESCs) are cells that are isolated from the inner cell mass of early embryos. These cells can differentiate into all somatic cell types. Given the proper combination of growth factors, these cells can differentiate into cardiomyocytes. We hypothesize that chronic conditioning of mice cardiomyocytes with PMA lead to an upregulation of Tbx3 expression and consequently an upregulation of HCN expression and connexin expression, therefore promoting the development of pacemaker cells within the cardiomyocyte population. In order to test our hypothesis, we purchased cells from the mouse E14TG2A cell line. These cells were cultured in glass bottom petri dishes and differentiated into cardiomyocytes using a three-step protocol (shown in Methods section). The cardiomyocytes are then exposed to PMA in varying concentration (0.1 µM vs 1 µM) for either 1h (acute exposure) or 24 h (chronic exposure). The results varied between the experimental groups compared to the control. In all experimental conditions there seems to be an initial increase in spontaneous activity, but this is quickly reversed at the 24 h mark, where pacing decreased. Different concentration plays a dose-dependent role in long-lasting inhibitory effect on the pacing of the cells

No description available.

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13464号 / 論医博第2251号 / 新制||医||1055(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 金子 新, 教授 江藤 浩之, 教授 髙折 晃史 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM