Friedreich ataxia (FRDA) is an autosomal recessive, neurodegenerative disorder with severely debilitating effects and no current cure. FRDA is mainly caused by the hyper-expansion of a GAA repeat present in intron 1 of the FXN gene, which results in decreased gene expression and consequently a deficiency of the mitochondrial protein frataxin. In the first instance, frataxin deficiency renders an impaired protection from oxidative stress. Antioxidant therapy with cannabinoids (CBD and THC) and CTMIO was investigated in GAA repeat FXN YAC transgenic mouse models of FRDA, but no significant improvements were detected on functional measurements such as rotarod performance and locomotor activity. Additionally such compounds failed to protect the brain of treated mice from oxidative insults. Therefore, the use of such antioxidant compounds cannot be advocated for FRDA therapy. Recent findings indicate that FXN silencing in FRDA may be mediated by repressive heterochromatin, suggesting the use of histone deacetylase inhibitors (HDACi) as FXN up-regulators. Therefore, therapy with a benzamide-type HDACi (106) was similarly investigated on the FXN YAC GAA mouse model. No significant improvements were detected by functional and histochemical analysis. However, significant changes were produced in global acetylation levels of H3 and H4 in the brain of treated mice, suggesting that the drug is capable of crossing the blood-brain barrier and producing an effect. Additionally, significant increases in frataxin expression were detected in the brain of treated mice. To identify further FRDA disease mechanisms, characterization of the FXN gene for the presence of the CCCTC-binding factor (CTCF) was also performed on FRDA patient cerebellum samples. Overall, lower levels of CTCF were detected in FRDA-associated FXN alleles, suggesting the potential involvement of CTCF in the regulation of FXN transcription.

Nous avons mis en place au cours de ce travail de thèse différentes stratégies permettant d’améliorer l’efficacité thérapeutique des adénovirus (Ad) oncolytiques contre différents types de tumeurs. Une première stratégie a été de combiner un inhibiteur d’histone-désacétylase, l’acide valproique (VPA) avec un Ad oncolytique à capside sauvage E1Δ24 (CRAd) dans le traitement de carcinomes côliques. Nous avons dans un premier temps démontré que la combinaison du CRAd et du VPA permettait une diminution plus importante de la survie des cellules cancéreuses côliques comparé au simple traitement basé sur le CRAd ou le VPA in vitro mais aussi in vivo.De plus, nous avons observé que cet effet n’était pas lié à une meilleure réplication du CRAd par le VPA. En effet, le VPA provoquait un ralentissement de la réplication virale à des temps précoces mais ne modifiait pas la production virale. Nous avons également découvert que le co-traitement CRAd+VPA conduisait à une forte inhibition de la croissance cellulaire mais aussi à une mort cellulaire non apoptotique. Par ailleurs, nous avons mis en évidence que les cellules co-traitées par le CRAd et le VPA affichaient une forte polyploïdie accompagnée d’une augmentation de la phosphorylation de l’histone H2AX, un marqueur de dommages à l’ADN. Une deuxième stratégie a été de fournir aux Ad oncolytiques de nouvelles voies d’entrée afin d’infecter et de détruire plus efficacement des cellules de carcinomes rénaux réfractaires à l’infection adénovirale. Nous avons démontré que les CRAd à hexon modifié porteurs d’un ligand CKS-17 (Ad-HCKS-17-E1Δ24) ou à fibre modifiée de sérotype 3 (AdF3-E1Δ24) étaient capables d’infecter et de tuer plus efficacement ces cellules qu’un CRAd à capside sauvage in vitro. Malheureusement in vivo, les modifications de capside n’ont permis ni d’améliorer l’entrée des CRAd dans les tumeurs rénales, ni d’améliorer leur efficacité anti-tumorale. Cependant, nous avons observé qu’après administration intra-tumorale, les Ad à capside modifiée présentaient un plus faible tropisme hépatique comparé à un Ad à capside sauvage. / During this thesis, we investigated different strategies to increase the therapeutic effects of oncolytic adenovirus (CRAd) to fight several kinds of tumors.The first strategy seeks to evaluate in human colon carcinomas the association of a CRAd bearing Δ24 deletion in E1A with valproic acid (VPA), a histone deacetylase inhibitor. Interestingly, this combination led to a dramatic reduction of cell survival both in vitro and in vivo compared to single treatment with CRAd or VPA. This effect did not stem from a better CRAd replication and production in the presence of VPA. Inhibition of cell proliferation and a non-apoptotic cell death were shown to be two mechanisms mediating the effects of the combined treatment. Interestingly, whereas cells treated only with CRAd displayed a > 4N population and polyploidy, this phenotype was strongly increased in cells treated with both CRAd and VPA. In addition, the increase in polyploidy triggered by a combined treatment with CRAd and VPA was associated with the enhancement of H2AX phosphorylation (γH2AX), a hallmark of DNA damage. The second strategy developed aimed to find new entry pathways allowing CRAd to better infect and kill renal tumor cells, known to be refractory of Ad infection. We demonstrated that CRAd with capsid modified (Ad-HCKS-17-E1Δ24 and AdF3-E1Δ24), containing respectively a ligand CKS-17 in hexon or a fiber of serotype 3, were more efficient to infect different renal cell carcinomas in vitro compared to a CRAd with a wild type capsid. However, these capsid-modified oncolytic adenovirus provoked, neither increase of the infection level, nor a better efficacy of growth inhibition in renal tumor xenografts bearing by nude mice. Nevertheless, both types of modifications reduce Ad ability to transduce hepatocytes after intratumoral injection.

En raison de l’efficience des traitements, le taux de survie globale à 5 ans des patients avec un cancer gastrique (CG) est d’environ 15%. A l’heure actuelle, il n’existe pas de stratifications des patients permettant de prescrire un protocole de traitements efficace. Durant ma thèse, j’ai établi le rôle de HDAC4 dans la sensibilité des cellules de CG au Cisplatine. J’ai montré que cette réponse semble dépendre du type de CG (intestinal ou diffus) et du statut p53 des cellules cancéreuses. J’ai souligné l’intérêt de combiner un inhibiteur des HDACs (SAHA) avec les chimiothérapies à base de dérivés de platine (PDC : Cisplatine, Oxaliplatine) afin de promouvoir leurs effets cytotoxiques. De manière intéressante, j’ai observé que la réponse aux traitements combinés est différente suivant le statut p53 des cellules cancéreuses. Ces résultats permettent d’ouvrir de nouvelles perspectives dans l’utilisation des traitements combinés PDC + SAHA dans la thérapie du CG. En particulier, le facteur p53 qui est souvent muté dans les CG, pourrait être un marqueur thérapeutique pour un tel protocole de traitement. / Due to the efficiency of treatments, the 5-year overall survival rate for patients with gastric cancer (GC) is approximately 15%. Currently, there is no stratification of patients to prescribe an effective treatment protocol.During my thesis, I established the role of HDAC4 in the sensitivity of GC cells to Cisplatin. I have shown that this response seems to depend on the type of GC (intestinal or diffuse) and the p53 status of cancer cells. I emphasized the interest of combining an HDAC inhibitor (SAHA) with platinum derivative chemotherapies (PDC: Cisplatin, Oxaliplatin) to promote their cytotoxic effects. Interestingly, I observed that the response to combination treatments is different depending on the p53 status of the cancer cells.These results open new perspectives in the use of PDC + SAHA combination therapies in GC. The p53 factor that is often mutated in GC could be a therapeutic marker for a such treatment protocol.

<p>Despite a largely static DNA sequence, our genomes are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome is accessed, transcribed, and replicated. However, how the dynamics of chromatin accessibility contribute to development, environmental response, and disease status has only begun to be appreciated. In this work we identified chromatin accessibility changes by DNase-seq in three diverse processes: in granule neurons of the developing cerebellum, with intestinal epithelial cells in the absence of a normal microbiota, and with myelogenous leukemia cells in response to histone deacetylase inhibitor treatments. In all cases, we coupled these analyses with RNA-seq assays to identify concurrent transcriptional changes. By mapping the changes to these genome-wide signals we defined the contribution of local chromatin structure to the transcriptional programs underlying these processes, and improved our understanding of their relation to other chromatin changes like histone modifications. Furthermore we demonstrated use of the strongest accessibility changes to identify transcription factors critical for these processes by finding enrichment of their binding motifs. For a few of these key factors, depletion or overexpression of the protein was sufficient to regulate the expression of predicted target genes or exert limited chromatin accessibility changes, demonstrating the functional significance of these proteins in these processes. Together these studies have informed our understanding of the role chromatin accessibility changes play in development and environmental responses while also proving their utility for key regulator identification.</p> / Dissertation

This study examined the mechanisms underlying the interactions between the natural polyphenol Resveratrol and HDAC inhibitors in both U937 myelomonocytic leukemia cell line and blood samples from AML patients and normal cord blood. Simultaneous exposure to Resveratrol and HDAC inhibitors (Vorinostat-SAHA or Panobinostat-LBH589) resulted in potentiating the lethality caused by any single agent of the combination, this interaction found to be synergistic at multiple concentrations. Exposing U937 cells to minimal toxic doses of Resveratrol and HDACIs results in release of mitochondrial pro-apoptotic proteins AIF and cytochrome c, pro-apoptotic caspase activation especially caspase-8, and induction of DNA damage. These events were associated with increase deacetylation of NF-κB and reactive oxygen species generation, as well as G0-G1 cell cycle arrest. Genetic knockdown of SIRT1 (a deacetylator of NF-κB that is upregulated by Resveratrol) resulted in significant increase in NF-κB acetylation and activity. However, SIRT1 knock down failed to protect U937 cells against combination-induced cell death, implying the possibility of the involvement of other mechanisms in inducing cell death rather than NF-κB deactivation only. Co-incubation of the antioxidant vi MnTBAP significantly reduced Resveratrol/HDACIs induced cell death, and resulted in a marked decrease in caspase-8, caspase-3, and PARP activation. Finally, the combined treatment of Resveratrol/HDACIs induce cell cycle changes possibly through Resveratrol action of blocking cell cycle in S phase exposing more cells to HDACIs lethality. Collectively, these finding indicate that the combined regimen of Resveratrol and HDAC inhibitors promote lethality in U937 cells and primary AML cells by a variety of mechanisms. The approved use of both agents in clinical setting make future clinical studies for development of this drug regimen a potential option in the battle with leukemia.

Histone deacetylase 6 (HDAC6) is a cytoplasmic enzyme that acetylates several proteins that are involved in the immune response. HDAC6 inhibition has been shown in various models to decrease inflammation by altering various proteins involved in the dysregulation of B and T cell responses. In our current studies we sought to determine if HDAC6 inhibition would decrease disease in lupus-prone mice using two murine mouse models of SLE: MRL/lpr mice and NZB/W F1 mice. Both mouse models were fed a rodent diet formulated with the selective HDAC6 inhibitor ACY-738 (N-hydroxy-2-(1-phenylcycloproylamino) pyrimidine-5-carboxamide). NZBW mice received 18 weeks of treatment starting at 16-weeks-of-age and had an average of 57.3 +/- 14.6 ng/mL of ACY-738 in the plasma. MRL/lpr mice received 7 weeks of treatment starting at 11-weeks-of-age and had an average of 78.5 +/- 17.3 ng/mL of ACY-738 in the plasma. Controls received either dexamethasone 5x a week or were left untreated. As the mice aged, body weight, urine protein, and blood sera was collected weekly. Spleen cells were isolated following euthanasia for flow cytometry and kidneys were also collected for histological analyses. We found that in both mouse models that mice treated with ACY-738 had reduced splenic weight and IgG immunoglobulin isotypes. MRL/lpr mice that were treated with ACY-738 had a reduction in the number of IL-17+, ROR-gamma-t TH17 cells. NZBW/ F1 mice that received ACY-738 treatment also had a reduction in the TH17 cells and we observed a significant reduction in kidney pathology. Selective HDAC6 targeting may warrant future investigations as a potential therapeutic target for the treatment of SLE. / Master of Science

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L’émergence et le développement des maladies métaboliques est sous le contrôle de multiples facteurs génétiques et environnementaux. Le diabète et la résistance à l’insuline sont des maladies métaboliques caractérisées par des défauts dans la sécrétion de l’insuline ou son utilisation périphérique, ou les deux. L’insuline est l’hormone clé de l’utilisation du glucose, et régule également transcriptionnellement et épigénétiquement l’expression des gènes.En travaillant sur le muscle, l’implication de l’épigénétique dans la régulation de l’expression des gènes de la voie de l’insuline a été mis en évidence. L’hexokinase 2 (HK2) est régulée par l’insuline et participe au métabolisme glucidique. Le rôle de l’épigénétique y est démontré avec l’augmentation de l’acétylation des histones autour du site d’initiation de la transcription (SIT) de HK2 et l’accumulation d’une isoforme permissive des histones, H2A.Z. Ces deux phénomènes sont le signe d’une transcription permissive.Nous avons ensuite étudié le rôle de l’acétylation des histones dans les régulations amenées par l’insuline dans les myotubes L6. Nous avons utilisé le butyrate, un inhibiteur des histones deacetylase (HDACi), dans un contexte d’insulino-résistance induite par une lipotoxicité. Le butyrate a en partie restauré la sensibilité à l’insuline visible au niveau des phosphorylations de la PKB (protein kinase B) et de la MAPK (Mitogen-activated protein kinase), inhibées par le traitement au palmitate. Le butyrate a augmenté l’expression de l’ARNm et de la protéine d’IRS1. La surexpression génique d’IRS1 est épigénétique-dépendante car liée à une augmentation de l’acétylation des histones au SIT d’IRS1.L’ensemble de ces résultats démontre l’existence d’un lien entre les modifications épigénétique et l’action de l’insuline. Cela suggère qu’une intervention pharmacologique sur la machinerie épigénétique pourrait être un moyen d’améliorer le métabolisme, et l’insulino-résistance / Diabetes and insulin resistance are metabolic diseases characterized by altered glucose homeostasis due to defects in insulin secretion, insulin action in peripheral organs, or both. Insulin is the key hormone for glucose utilization and regulates gene expression via transcriptional and epigenetic regulations.We determined the epigenetic implications in the regulation of expression of insulin signaling pathway genes. Hexokinase 2 (HK2) is known to be upregulated by insulin and directs glucose into the glycolytic pathway. In L6 myotubes, we demonstrated that insulin-induced HK2 gene expression rely on epigenetic changes on the HK2 gene, including an increase in histone acetylation around the transcriptional start site (TSS) of the gene and an increase in the incorporation of the histone H2A.Z isoform – a histone variant of transcriptionally active chromatin. Both are epigenetic modifications compatible with increased gene expression.To elucidate the role of histone acetylation in the regulation of insulin signaling and insulin-dependent transcriptional responses in L6 myotubes, we investigated the effects of butyrate, an histone deacetylase inhibitor (HDACi), in a model of insulin resistance induced by lipotoxicity. Butyrate partly alleviated palmitate-induced insulin resistance by ameliorating insulin-induced PKB (protein kinase B) and MAPK (Mitogen-activated protein kinase) phosphorylations, downregulated with exposure to palmitate. Butyrate induced an upregulation of IRS1 gene and protein expression. The transcriptional upregulation of IRS1 was proven to be epigenetically regulated, with butyrate promoting increased histone acetylation around the TSS of the IRS1 gene.These results support the idea of the existence of a link between epigenetic modifications and insulin action. Pharmacological targeting of the epigenetic machinery might be a new approach to improve metabolism, especially in the insulin resistant condition.Key words: Muscle, insulin resistance, epigenetic, chromatin, histone acetylation, histone deacetylase inhibitor (HDACi), butyrate, palmitate

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La récidive et la progression métastatique du cancer du sein ne sont toujours pas curables. Le concept des cellules souches cancéreuses (CSC) pourrait apporter une explication à ces échecs. Les CSC résisteraient aux thérapies conventionnelles (chimiothérapies, radiothérapie) et seraient responsables de la rechute et de la progression du cancer. L'élimination des CSC semble être un pré-requis indispensable pour le traitement des patientes. L'identité et le destin des cellules souches sont finement régulés par des acteurs épigénétiques. Les travaux de cette thèse se sont intéressés aux conséquences de la dérégulation de deux acteurs épigénétiques en particulier : les enzymes HDAC et le long ARN non-codant Xist. Nous avons montré que la modulation épigénétique via l'inhibition des HDAC (HDACi) permet d'éliminer les CSC en induisant leur différenciation. Nous présentons une nouvelle stratégie thérapeutique pour le cancer du sein : la thérapie différenciante. Nous avons déterminé Xist comme étant le biomarqueur prédictif de la réponse aux HDACi. Xist étant un partenaire clé de la plasticité cellulaire, les travaux de cette thèse se sont ensuite intéressés aux conséquences de la dérégulation de Xist dans l'initiation tumorale. Nous avons observé que l'inhibition de Xist favorise la division des cellules souches mammaires normales. Nous proposons un nouveau modèle de l'initiation tumorale où la dérégulation épigénétique est une modification précoce sans conséquence sur l'homéostasie tissulaire mais pourrait être la première étape de la transformation cancéreuse. / These last decades have allowed deciphering the biology of breast cancer and improving the therapeutic management. However, recurrence and metastatic progression of the disease are still not curable. The concept of cancer stem cells (CSC) could provide an explanation for these failures. CSC would resist conventional therapies (chemotherapy, radiotherapy) and would be responsible for both relapse and progression of cancer. The elimination of CSC seems to be an essential prerequisite for the treatment of patients. The identity and fate of stem cells are tightly regulated by epigenetic mechanisms. The work of this thesis investigated the consequences of deregulation of two epigenetic players: HDAC enzymes and long non-coding RNA Xist. We have shown that epigenetic modulation via HDAC inhibitor (HDACi) eliminates the CSC by inducing their differentiation. We present a new therapeutic strategy for breast cancer: differentiation therapy. We determined Xist as the predictive biomarker of response to HDACi. Xist is a key partner of cell plasticity, the work of this thesis therefore interested in the consequences of Xist deregulation in tumor initiation. We observed that Xist inhibition promotes division of normal breast stem cells. We propose a new model of tumor initiation: epigenetic deregulation is an early change without consequence on tissue homeostasis but could be the first step of the cancerous transformation.