RNA epigenetics or Epitranscriptomics has emerged as a new field for understanding the post-transcriptional regulation of gene expression by RNA modifications. Among numerous types of RNA modifications, RNA cytosine-5 methylation (5-mrC) is recognized as an important epitranscriptomic mark that modulates mRNA transportation, stability and translation. In chapter 1, we summarize the currently available approaches to detect 5-mrC modification at global, transcriptome-wide and locus-specific levels, and compare the corresponding advantages and disadvantages of the techniques. We further focus on the bioinformatics data analysis of RNA bisulfite sequencing datasets by comparing existing packages with respect to key parameters for alignment and methylation calling and filtering of potentially false positive 5-mrC sites. To investigate the dynamic regulation of 5-mrC modification, as described in chapter 2, we adopt a widely used neuronal activity model, and perform RNA sequencing (RNA-seq) and RNA bisulfite sequencing (RNA BS-seq) to profile gene expression as well as transcriptome-wide 5-mrC modification. We have identified distinct gene expression profiles and differentially methylated 5-mrC sites (DMS) in neurons upon activation, and the genes with DMS sites are enriched with mitochondrial and synaptic functions. Moreover, it reveals a negative correlation between RNA methylation and mRNA expression in mouse cortical neurons during neuronal activity. Thus, these findings identify the dynamic regulation of 5-mrC modification during neuronal activity and reveal a potential link between RNA methylation and mRNA expression. In chapter 3, we investigate the effect of folate, a methyl-donor, on RNA cytosine-5 methylation (5-mrC) modification in adult mouse neural stem cells (NSCs). Compared to the control, NSCs cultured in folate deficiency or supplementation condition have shown no changes in mRNA expression, but significant changes in mRNA translation efficiency. RNA bisulfite sequencing of both total and polysome poly(A) RNA samples shows distinct 5-mrC profiles in NSCs treated with different concentrations of folic acid. It also shows consistent hypermethylation in polysome mRNAs than that in total mRNAs. This study presents the comprehensive influence of folate deficiency and supplementation on RNA cytosine-5 methylation and mRNA translation. / Doctor of Philosophy / RNA epigenetics, a collection of RNA modifications, has recently emerged as an exciting, new field for understanding post-transcriptional regulation of gene expression. RNA cytosine-5 methylation (5-mrC) is one of the most well-known RNA modifications that modulates mRNA export, stability and translation. In the first chapter, we summarize the currently available methods for the measurement of 5-mrC modification. We highlight one of the techniques, RNA bisulfite sequencing (RNA BS-seq) and focus on the bioinformatics data analysis of RNA BS-seq datasets. We have compared several existing tools in regard of the key parameters in data analysis. In the second chapter, we adopt a widely used neuronal activity model to study the dynamic regulation of RNA cytosine-5 methylation (5-mrC). We perform RNA-seq and RNA BS-seq in neurons in response to stimulation. We have identified numerous differentially expressed genes and differentially methylated 5-mrC sites in activated neurons and find that these DMS-related genes are associated with mitochondrial and synaptic functions. Furthermore, we identify a negative correlation between RNA methylation and mRNA expression, indicating a potential role of 5-mrC modification in the regulation of mRNA expression. In the third chapter, we investigate the influence of a nutrient supplement, folic acid, on 5-mrC modification in adult mouse neural stem cells. Compared to the control, NSCs cultured in folate deficiency or supplementation condition have shown no changes in mRNA expression, but significant changes in mRNA translation efficiency. We perform RNA bisulfite sequencing of both total poly(A) RNA samples and polysome poly(A) RNA samples. We identify distinct 5-mrC profiles in NSCs treated with different concentrations of folic acid. It shows consistent hypermethylation in polysome mRNAs than that in total mRNAs. This study presents the comprehensive influence of folate deficiency and supplementation on RNA cytosine-5 methylation and mRNA translation.

L'étude des cellules souches est l'un des champs de recherches les plus importants dans le domaine biomédical. La vision par ordinateur et le traitement d'images ont été fortement mis en avant dans ce domaine pour le développement de solutions automatiques de culture et d'observation de cellules. Ce travail de thèse propose une nouvelle méthodologie pour l'observation et la modélisation de la prolifération de cellule souche neuronale sous microscope à contraste de phase. À chaque observation réalisée par le microscope durant la prolifération, notre système extrait un modèle en trois dimensions de la structure de cellules observées. Cela est réalisé par une suite de processus d'analyse, synthèse et sélection. Premièrement, une analyse de la séquence d'images de contraste de phase permet la segmentation de la neurosphère et des cellules la constituant. À partir de ces informations, combinées avec des connaissances a priori sur les cellules et le protocole de culture, plusieurs modèles 3-D possibles sont générés. Ces modèles sont finalement évalués et sélectionnés par rapport à l¿image d¿observation, grâce à une méthode de recalage 3-D vers 2-D. A travers cette approche, nous présentons un outil automatique de visualisation et d'observation de la prolifération de cellule souche neuronale sous microscope à contraste de phase. / The study of stem cells is one of the most important fields of research in the biomedical field. Computer vision and image processing have been greatly emphasized in this area for the development of automated solutions for culture and observation of cells. This work proposes a new methodology for observing and modelling the proliferation of neural stem cell under a phase contrast microscope. At each time lapse observation performed by the microscope during the proliferation, the system determines a three-dimensional model of the structure formed by the observed cells. This is achieved by a framework combining analysis, synthesis and selection process. First, an analysis of the images from the microscope segments the neurosphere and the constituent cells. With this analysis, combined with prior knowledge about the cells and their culture protocol, several 3-D possible models are generated through a synthesis process. These models are finally selected and evaluated according to their likelihood with the microscope image using a 3-D to 2-D registration method. Through this approach, we present an automatic visualisation tool and observation of the proliferation of neural stem cell under a phase contrast microscope.

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Les cellules souches neurales quiescentes (CSN) sont le réservoir de la neurogenèse adulte, permettant de produire des nouveaux neurones tout au long de la vie. Cependant, la neurogenèse décroit au cours du vieillissement, provoquant des déclins cognitifs incurables. Afin de mieux comprendre les mécanismes qui contrôlent la prolifération des CSN, nous avons mis en place une méthode de tri par cytométrie en flux qui permet pour la première fois d’isoler les CSN quiescentes et leurs cellules filles dans la ZSV adulte murine. Cette technique nous a permis de prouver que le blocage de la voie GABAAR in vivo provoque l’entrée en cycle des CSN quiescentes. Ainsi, les signaux GABA produits par les neuroblastes dans la ZSV permettent de maintenir les CSN dans leur état de quiescence. Au cours du vieillissement, nous montrons que la production progressive de TGFβ1 par les cellules endothéliales de la niche allonge la phase G1 des CSN activées, diminuant sensiblement la production de nouveaux neurones, sans toutefois diminuer le stock de CSN. Nous mettons ainsi en évidence deux voies majeures contrôlant la prolifération des CSN in vivo, la voie du GABAAR et la voie TGF-β/Smad-3. En vue d’une application thérapeutique, nous prouvons que leur blocage pharmacologique permet de stimuler efficacement la neurogenèse in vivo. / Quiescent neural stem cells (NSCs) are considered the reservoir for adult neurogenesis, generating new neurons throughout life. However, neurogenesis decreases during aging, causing a progressive decline that is currently untreatable. To study the regulatory mechanisms of NSCs proliferation, we set up a new technique allowing the isolation of quiescent NSCs and their progeny. We show that GABAAR directly regulates NSCs quiescence in vivo as the depletion of GABA-producing neuroblasts or GABAAR pathway pharmacological blockade provoked NSCs cell cycle entry in the SVZ. During aging, the stock of NSCs is not perturbed, but we show that an over-production of TGFβ1 by brain endothelial cells directly lengthens activated NSCs G1 phase, strongly decreasing the production of new neurons. These findings highlight GABAAR and TGF-β/Smad-3 as two major pathways controlling NSCs proliferation. In line with a future therapeutic application, we also prove that their blocking stimulates endogenous neurogenesis in vivo.

Studies have shown that there is a strong correlation between aging and neurodegenerative diseases. Aging is considered the number one risk factor to develop neuropathologies such as memory loss, senile dementia, Alzheimer's disease (AD), and Parkinson's disease. Neurodegenerative diseases tend to start during adulthood, and aggravate over time, making them difficult to prevent and to treat. In the Unites States, demographic studies by U.S. Bureau of the Census have determined that our aging population of >65 years is expected to increase from the present 35 million to 78 million in 2030. This would result, not only to an increase of age-related chronic illness, and mental disability, but to a decrease of quality of life, and an elevation of medical cost. Thus, this dissertation has focused on investigating the molecular mechanisms during the process of aging and its correlation to chronic inflammation and cognitive impairments. The etiology of neurodegenerative diseases is not very well understood, but research has shown that the process of aging is a key factor, which involved oxidative stress, an over reactive microglia, and increased production of pro-inflammatory cytokines. All these factors are known to decrease cell proliferation, which limit neuroplasticity and they might lead the transition from normal aging to more severe cognitive dysfunction associated with neurodegenerative diseases. Previously, we have shown that natural compounds such as polyphenols from blueberry, and green tea, and amino acids like carnosine are high in antioxidant and anti-inflammatory activity that decreases the damaging effects of reactive oxygen species (ROS), in the blood, brain, and other tissues of the body. Therefore, we examined the hypothesis that the pro-inflammatory cytokine TNF-[U+F061] may be a critical factor that modulates classical conditioning behavior, the effects of NT-020 on adult neurogenesis, inflammatory markers of the CNS, and the effect of NT-020 on cognitive function as shown using spatial navigation task. The results show that in aged rats, endogenous production of pro-inflammatory cytokine TNF-α impairs the acquisition of learning and memory consolidation in the delay eyeblink classical conditioning task (EBC). It was shown that this effect can be replicated by infusing young rats with exogenous TNF-α prior to EBC. Using NT-020 as a dietary supplement for one month, it was found that NT-020 ameliorates the age-related impairments typically found in aged rats in the spatial navigation tasks Morris water maze and radial arm water maze. By looking at immunohistochemistry analysis, it was found a decreased number of OX6 MHC II positive cells, increased neurogenesis, and increased number of proliferating cells in the dentate gyrus (DG) of the hippocampus in the aged rats fed with NT-020 relative with their counterpart aged control. In the CNS, Inflammatory markers were analyzed, and it was found that aged rat fed with NT-020 supplemented diet has decrease levels of pro-inflammatory cytokines in compared with aged rats fed with NIH-31 control diet. In conclusion, TNF-α, a pro-inflammatory cytokine has shown to have a modulatory effect during classical conditioning. Moreover, NT-020 may promote a healthy CNS milieu, proliferation of neuronal progenitors, and maintenance of nature neurons in the aged rats and it might exert anti-inflammatory actions which promote a functional stem cell pool in the CNS of aged rats.

Traumatic brain injury (TBI) results in over 50,000 deaths and 80,000 disabilities each year. Current treatment strategies aim to alleviate acute disturbances, but are not able to address the chronic disorders associated with TBI. Neural transplantation is one potential treatment that will provide multifaceted sustained therapy to degenerating injured tissue. Transplantation of multipotent neural stem cells (NSCs) has been shown to enhance functional recovery in TBI models; however, poor cell survival and integration with host tissue potentially restrict the efficacy of such transplants. This limitation may be due to the absence of inherent NSC pro-survival cues (e.g., cell-ECM interactions). Furthermore, the neural injury environment presents cell death factors to transplanted NSCs. It is hypothesized that a 3-D scaffold presenting specific CNS adhesive moieties will enhance donor cell survival and promote differentiation and migration. This project encompassed material development and in vitro characterization. Results highlighted the importance of ligand tethering chemistry and density and also the mechanical integrity of cell scaffold systems. Furthermore, the developed scaffold provides a controlled microenvironment to assess the influence of LN on NSC survival, migration, and differentiation. Lastly, co-delivering NSC with the MC-LN tissue engineered scaffold into a mechanically injured neural co-culture test-bed or in vivo TBI model confirmed the importance of ECM cues for NSC survival and migration, respectively.

L'hypoxie périnatale entraîne une dégénérescence et un délai de maturation des oligodendrocytes et des neurones corticaux du cortex cerebral. Mon projet de thèse a d'abord consisté à étudier la contribution des cellules souche neurales de la zone sous-ventriculaire dorsale (dSVZ) à la tentative de régénération spontanée observée après la lésion. Dans un second temps, j'ai étudié la capacité de ces cellules souches à être manipulée en utilisant une approche pharmacologique.Mes résultats mettent en évidence une réponse spontanée et dynamique de la dSVZ qui produit des neurones et des oligodendrocytes corticaux en réponse à l'hypoxie. L'administration par voie intranasale d'un inhibiteur de Gsk3b, qui active la voie Wnt/b-caténine, petite molécule identifiée à l'aide d'une étude bio-informatique comme « dorsalisante », juste après la période d'hypoxie, potentialise cette réponse spontanée. En effet, mes résultats montrent que certains neurones corticaux issus de la dSVZ survivent avec le traitement alors qu'aucun ne semblent persister après 1 mois suivant l'hypoxie. De plus, le traitement accélère la maturation des oligodendrocytes corticaux et augmentent leur production et intégration à long terme. Enfin, le traitement a un effet à long terme sur les cellules souches de la dSVZ en augmentant la proportion de ces cellules qui sont actives. Pour conclure, la dSVZ participe à la récupération corticale spontanée qui suit l'hypoxie périnatale et cette réponse peut être potentialisée par l'administration d'une petite molécule identifiée par notre analyse bio-informatique, un inhibiteur de GSK3b / Perinatal hypoxia leads to degeneration and delayed maturation of oligodendrocytes and cortical glutamatergic neurons. My PhD project consists in assessing the contribution of neural stem cells (NSCs) of the dorsal subventricular zone (dSVZ, i.e. the largest germinal zone of the postnatal brain) to the spontaneous regenerative attempt observed following such injury as well as its amenability to pharmacological manipulation.The results I have obtained highlight a dynamic and lineage-specific response of NSCs of the dSVZ to hypoxia that results in de novo oligodendrogenesis and cortical neurogenesis. Newborn cortical neurons express appropriate cortical layer markers, supporting their appropriate specification. A pharmacogenomics analysis allowed us to identify small molecules boosting specificly dSVZ NSCs. Pharmacological activation of Wnt/ß-catenin signalling by intranasal GSK3ß inhibitor administration during the recovery period following hypoxia indeed potentiates dorsal SVZ participation to post-hypoxia repair. Gsk3b inhibitor CHIR99021 seems to promote survival of cortical neurons from the dSVZ produced in response to hypoxia. More interestingly, CHIR99021 promotes oligodendrocyte maturation and long term integration in the cortex as well as a long term increased activity of dSVZ NSCs.Altogether, my results highlighted a dynamic and lineage-specific response of dorsal NSCs cells to hypoxia and identify the early postnatal dorsal SVZ as a malleable source of stem cells for cortical repair following trauma that occur early in life. CHIR99021 (a Gsk3b inhibitor) intranasal administration promotes this cortical cellular repair with a long term activation of dSVZ NSCs which increased their production of oligodendrocytes migrating to the cortex and a short term improvement of their maturation, and might allow the integration of cortical neurons they produce

Le cerveau des mammifères abrite deux régions spécifiques où la neurogenèse adulte ne cesse pas après l'embryogenèse, mais persiste dans le cerveau postnatal et adulte. Ces deux régions sont la zone sous-granulaire du gyrus denté de l’hippocampe et la zone sous-ventriculaire (SVZ) des ventricules latéraux.Dans la SVZ, des cellules souches neurales génèrent des neuroblastes qui migrent jusqu’au bulbe olfactif (OB) pour coloniser les couches granulaires et glomérulaires et se différencier en différent types d’interneurones dont une petite fraction sont des interneurones dopaminergiques. La découverte de la neurogenèse postnatale et adultes a changé le point de vue de la plasticité du cerveau remarquable et ouvre de nouvelles perspectives pour la thérapie des maladies neurodégénératives. Etant donné que dans la maladie de Parkinson les symptômes moteurs principaux sont causés par la dénervation dopaminergique du striatum, la compréhension de la génération et de la différenciation des neurones dopaminergiques bulbaires a reçu une attention particulière au vu de leur intérêt potentiel pour la thérapie cellulaire. Dans ce contexte, le neuromédiateur dopamine lui-même a été suggéré d'influencer la neurogenèse olfactive et la spécification des interneurones dopaminergique.Dans ma thèse, j'ai analysé l’influence de l’innervation dopaminergique issue du mésencéphale sur la neurogenèse et le destin cellulaire des précurseurs de la SVZ. J'ai combiné un modèle 6-OHDA de dénervation dopaminergique chez la souris postnatale avec l’électroporation in vivo du ventricule latéral pour marquer spécifiquement les progéniteurs latéraux et dorsaux et suivre leur destin dans le OB. / In the postnatal and adult mammalian brain neurogenesis persists in the subgranular zone of the hippocampal dentate gyrus and the subventricular zone (SVZ). In the SVZ slowly dividing stem cells give rise to neuroblasts that migrate to the olfactory bulb (OB) where they reach the granule and glomerular cell layer of the OB and differentiate into different interneuron subtypes including a small fraction of dopaminergic interneurons. The discovery of postnatal and adult neurogenesis has changed the view of the plasticity of the brain remarkably and raised the hope for new therapeutical approaches in the field of neurodegenerative diseases. Since in Parkinson’s disease the main motor symptoms are caused by the dopaminergic denervation of the striatum adjacent to SVZ, the understanding of the generation and differentiation of OB dopaminergic neurons has received special attention. Interestingly, the neurotransmitter dopamine itself has been suggested to influence olfactory bulb neurogenesis via direct innervation of SVZ by midbrain dopaminergic neurons. However, data on this topic have been contradictory. In this study, I investigated how dopaminergic innervation influences SVZ neurogenesis and the fate of SVZ progenitors. I combined a 6-OHDA model of dopaminergic denervation in postnatal mice with in vivo forebrain electroporation to specifically label lateral and dorsal SVZ progenitors and to follow their fate in the olfactory bulb.

Actuellement, le procédé d’électrofilage également appelé electrospinning est une des voies les plus prometteuses permettant le design et le développement de nanofibres polymères poreuses. En effet, cette technique est simple d’utilisation, unique, modulable, à faible coût et est déjà couramment utilisée dans le milieu industriel. De part ces avantages, l’electrospinning fait l’objet d’un engouement grandissant de la recherche académique et industrielle dans plusieurs domaines d’applications tels que ceux de la filtration, la cosmétique, du textile, de l’ingénierie tissulaire et du domaine médical, notamment pour le relargage de molécules actives. De plus, cette technique est applicable sur de nombreux polymères synthétiques ou naturels et il est possible de contrôler de nombreux paramètres tels que la porosité, le diamètre des fibres ou encore la surface accessible. Un des premiers objectifs de cette thèse a été de développer des scaffolds pour le domaine de l’ingénierie des tissus neuronaux afin d’imiter les propriétés biologiques, physiques et mécaniques de la matrice extracellulaire native. Dans un premier temps, l’effet de l’alignement des fibres d’une matrice fluorée (PVDF) biocompatible a été étudié sur le comportement de cellules souches neurales de singe, en particulier les morphologies, l’adhésion cellulaire ainsi que leurs différentiations en cellules gliales ou neuronales. Dans un second temps, des scaffolds bioabsorbables composés de PLA et de PEG ont été synthétisés afin d’étudier l’influence de l’équilibre hydrophile-hydrophobe sur la culture de cellules souches neurales. Et dans une dernière partie, une véritable étude exploratoire a été réalisée afin de développer des textiles intelligents à base de PBAT contenant des curli, protéine bien connue pour sa capacité à chélater des métaux. / Currently, the electrospinning process is also one of the most promising routes for the design and development of polymer fibers. This technique is easy to use, unique, versatile, and low cost, which can be used to create fibers from a variety of starting materials. The structure, chemical and mechanical stability, functionality, and other properties of the fibers can be modified to match end applications. The first goal of this thesis was to develop scaffolds for the field of neural tissue engineering in order to mimic the biological, physical and mechanical properties of the native extracellular matrix. In the first time, the effect of fiber alignment of a biocompatible and fluorinated matrix denoted polyvinylidene fluoride (PVDF) was studied on the behavior of monkey neural stem cells particularly the morphology, cell adhesion and their differentiation in glial or neuronal cells. Secondly, bioabsorbable scaffolds composed of polylactide (PLA) and polyethylene glycol (PEG) polymers were synthesized to investigate the influence of the hydrophilic-hydrophobic balance on the culture of neural stem cells. Finally, an exploratory work was conducted to develop smart textiles based on poly(butylene adipate-co-terephthalate) (PBAT) containing curli as protein, well-known for its ability to chelate metals.