Covalent histone modifications such as methylation, acetylation as well as differential incorporation of histone variants are shown to coincide with different chromatin compartments and mark active or repressed genes. Msc1 is one of the seven JmjC Domain Proteins (JDPs) in Fission Yeast. JDPs are known to function in chromatin and some act as histone demethylases. We found that Msc1 is a member of Swr1 Complex which is known to exchange histone H2A variant H2A.z in nucleosomes. We purified H2A.z as a member of Swr1 Complex and its interaction with Swr1 Complex depends on Swr1. We’ve shown that histone H4 Lysine 20 trimethylation (H4 K20 Me3) is lost in h2A.z and msc1 deletion strains and these strains are sensitive to UV. Deletion strain of h2A.z is sensitive to Camptothecin. Histones H3 and H4 are obtained in Msc1 and H2A.z purifications and we’ve shown that histone H4 from these purifications has low level of Lysine 16 acetylation (H4 K16 Ac). Deletion strains of h2A.z, swr1 and msc1 are shown to be sensitive to TSA, a histone deacetylase (HDAC) inhibitor suggesting that H2A.z cooperates with HDACs. TSA treatment of wild type cells cause an increase in H4 K16 Ac and a decrease in H4 K20 Me3. Gene expression profiles of h2A.z, swr1 and msc1 are significantly similar and upregulated genes in deletion strains localize at chromosome ends (a region of 160 kb for each end). The number of stress or meiotic inducible genes is increased in deletion strains suggesting that H2A.z has a role in regulation of inducible genes. We suggest that H2A.z, in cooperation with HDACs, functions in regulation of chromatin accessibility of inducible promoters.

La schistosomiase représente actuellement la seconde endémie parasitaire mondiale après le paludisme. Annuellement, cette pathologie est responsable de 280 000 décès et 700 millions d’individus y sont exposés dans 74 pays à travers le monde. Actuellement, le traitement de la schistosomiase repose sur l’utilisation d’un seul médicament, le Praziquantel®. Ainsi, le développement de nouveaux médicaments est devenu une priorité absolue pour l’OMS. Dans cette étude, notre objectif a été d’identifier de nouvelles cibles thérapeutiques afin de développer de nouveaux précurseurs de médicaments. Au cours de ce projet, nous avons focalisé nos recherches sur les enzymes impliquées dans la modification des histones et plus particulièrement sur les sirtuines, qui sont des lysines désacétylases NAD+ dépendantes.Dans une première partie, nous avons caractérisé 5 orthologues de sirtuines de mammifères chez Schistosoma mansoni (SmSirt1, 2, 5, 6 et 7). De plus, nous avons étudié le potentiel des sirtuines comme cibles thérapeutiques pour le traitement de la schistosomiase en évaluant la toxicité d’inhibiteurs génériques de sirtuines humaines sur des parasites maintenus en culture. Ainsi, nous avons montré que les inhibiteurs de sirtuines humaines affectent in vitro la viabilité des schistosomules ainsi que la stabilité de l’accouplement et la production d’oeufs des vers adultes. De plus, ces inhibiteurs induisent des changements morphologiques de l’appareil génital du ver femelle.Dans une seconde partie, nous avons entrepris d’étudier plus spécifiquement le rôle de SmSirt2 en tant que cible thérapeutique. Ainsi, l’expression de la protéine recombinante en bactérie E. coli (collaboration: C. Romier, IGBMC, Illkirch) ainsi que l’optimisation d’un dosage fluorimétrique nous ont permis de montrer que SmSirt2 présente une activité lysine désacétylase in vitro (collaboration: M. Jung, Université Albert-Ludwigs, Freibourg). De plus, l’utilisation de ce dosage nous a permis de mettre en place le criblage à haut débit d’une chimiothèque de plus de 80 000 composés afin d’identifier de nouvelles molécules inhibitrices de l’enzyme SmSirt2 (collaboration: J. Schultz, Kancera AB, Stockholm). Les composés les plus prometteurs, ont été testés in vitro sur des parasites en culture. Les résultats obtenus démontrent que les inhibiteurs de SmSirt2 affectent également la viabilité des schistosomules ainsi que la stabilité de l’accouplement et la production d’oeufs des vers adultes.Dans une dernière partie, nous avons mis en place un criblage d’une banque d’ADNc de vers adultes par la technique du double hybride en levure dans le but d’identifier les partenaires protéiques de Sirt1 chez S. mansoni. L’analyse partielle des résultats nous a permis de mettre en évidence que SmSirt1 interagit avec plusieurs protéines impliquées dans la régulation des gènes chez le schistosome. Au cours de ce projet, nous avons également développé et optimisé un protocole permettant d’étudier l’activité enzymatique de SmSirt1 par injection d’ARNm dans des ovocytes de Xénope. Ainsi, nous avons pu montrer que le sirtinol et la salermide, deux inhibiteurs de Sirt1 humaine, présentent également une activité inhibitrice sur l’enzyme du parasite (collaboration: K. Cailliau, Université des Sciences et Technologies, Lille).L’ensemble des résultats obtenus au cours de ce projet de thèse suggère que les sirtuines sont des cibles thérapeutiques potentielles dans le traitement de la schistosomiase. Parmi les 5 orthologues identifiés chez S. mansoni, SmSirt2 semble une cible prometteuse. De plus, le criblage à haut débit que nous avons réalisé sur l’enzyme recombinante a permis d’identifier des molécules qui, après bio-optimisation, pourront être des candidats médicaments. Pour finir, ces résultats participent à une meilleure compréhension du rôle biologique des sirtuines chez S. mansoni et plus particulièrement sur leur implication dans la survie et la reproduction du parasite. / Schistosomiasis is the second most important parasitic disease worldwide after malaria. It is responsible for about 280 000 deaths annually and 700 million people in 74 countries are exposed to infection. Treatment of schistosomiasis currently depends on the use of the only available drug, praziquantel, and for this reason the development of new drugs is a strategic priority of the W.H.O. In this study, our objective was to identify novel therapeutic targets in order to develop new lead molecules for drug development. During this project we have focused our research on enzymes involved in histone modification, and more particularly on sirtuines, which are NAD+-dependent lysine deacetylases.In the first part of the project, we have identified 5 homologues of mammalian sirtuins in Schistosoma mansoni (SmSirt1, 2, 5, 6 and 7). Moreover, we studied the potential of sirtuins as therapeutic targets for the treatment of schistosomiasis by evaluating the toxicity for parasites maintained in culture of generic inhibitors of human sirtuins. In this way we showed that these inhibitors affect the viability of schistosomula and the stability of pairing and egg production of adult worms. Moreover, these inhibitors caused major morphological changes, particularly to the female worm genital apparatus.A second part of our work was devoted to the more detailed study of SmSirt2 as a therapeutic target. Immunisation of mice with the recombinant protein allowed us to obtain specific antibodies and to show that SmSirt2 protein is expressed at all parasite developmental stages. Furthermore, the use of the recombinant SmSirt2 expressed in E. coli (collaboration: C. Romier, IGBMC, Illkirch) and the optimization of a fluorimetric assay allowed us to show that SmSirt2 possesses a lysine deacetylase activity (collaboration: M. Jung, University Albert-Ludwigs, Freibourg). Moreover, the use of this assay allowed the setting up of a high-throughput screen (collaboration: J. Schultz, Kancera AB, Stockholm) of more than 80 000 compounds in order to identify novel inhibitors. The most promising candidates were tested on parasites in culture and the results obtained showed that SmSirt2 inhibitors also affect the viability of schistosomula, as well as the stability of pairing and egg production of adult worms.In parallel, we have carried out screening of a yeast two-hybrid cDNA library in order to identify protein partners of Sirt1 in S. mansoni. The partial analysis of the results obtained shows that SmSirt1 interacts with several proteins involved in gene regulation. In the course of this project, using the enzyme expressed in Xenopus oocytes we were able to show that both sirtinol and salermide, inhibitors of human Sirt1, also inhibit the schistosome enzyme (Collaboration: K. Cailliau, University of Sciences and Technologies, Lille).Taken together, the results of this thesis project suggest that sirtuins are potential therapeutic targets for the treatment of schistosomiasis. Of the five orthologues of human sirtuins identified in S. mansoni, SmSirt2 seems to be a promising target. Moreover, high-throughput screening using the recombinant enzyme identified inhibitors that, after bio-guided optimization, could be drug candidates. Finally, these results contribute to a better understanding of the biological role of S. mansoni sirtuins and in particular their importance in parasite survival and reproduction.

A Leucemia Linfóide Aguda (LLA) é uma doença heterogênea em relação à biologia e ao prognóstico. Além de alterações genéticas, anormalidades epigenéticas, estão estreitamente relacionadas ao processo de carcinogênese e entre os mecanismos epigenéticos, a acetilação das histonas é um componente essencial para a regulação da estrutura da cromatina e atividade transcricional. Esse processo é mediado pelas histonas acetiltransferases (HATs). Por outro lado, a desacetilação, por meio das histonas desacetilases (HDACs), está relacionada à condensação da cromatina e repressão transcricional. A expressão anormal das HDACs tem sido associada ao processo de leucemogênese, revelando ser uma área promissora na caracterização de grupos de risco e tratamento do câncer. Os objetivos deste trabalho foram avaliar a expressão dos genes da classe I de HDACs (HDAC 1, 2, 3 e 8), correlacionar os resultados com as características clínicas e de prognóstico (idade, gênero, grupo de risco, contagem inicial de blastos, imunofenótipo, resposta ao tratamento, doença residual mínima nos dias 14 e 18 e a sobrevida livre de eventos) em 46 amostras consecutivas de medula óssea de crianças e adolescentes portadores de LLA; comparar e correlacionar a expressão dos genes estudados entre as amostras de pacientes portadores LLA e 10 amostras de medula óssea sem doença hematológica. A análise da expressão gênica foi realizada através da técnica de PCR em Tempo Real pelo método TaqMan®. Foi observado um aumento da expressão do gene HDAC1 nas amostras dos pacientes bons respondedores ao ix tratamento. O gene HDAC2 foi mais expresso no grupo de pacientes do gênero masculino (p=0,038). Esse gene também mostrou uma expressão aumentada nos pacientes de alto risco (p=0,060) e com sobrevida menor (p=0,065), entretanto os valores encontrados não foram estatisticamente significativos. Além disso, foi observada uma expressão aumentada dos genes HDAC2 (p=0,007), HDAC3 (p=0,014) e HDAC8 (p=0,002) em amostras de pacientes com LLA quando comparadas às amostras de medula óssea sem doença hematológica. Houve correlação entre a expressão de todos os genes de classe I das HDACs, exceto entre HDAC1 e HDAC8. Os resultados obtidos nesse trabalho sugerem que as HDACs de classe I, podem representar importantes alvos para futuros estudos em LLA, no entanto são necessários de testes funcionais para confirmar estes resultados. / Acute Lymphoblastic Leukemia (ALL) is a heterogeneous disease with distinct biologic and prognostic groups. In addition to genetic alterations, epigenetic processes play an important role in carcinogenesis, among which histone acetylation/deacetylation is crucial for chromatin modulation structure and transcriptional activity. Histone acetylation is regulated by the enzyme histone acetyl transferases (HATs). On the other hand, the deacetylation process is regulated by histone deacetylases (HDACs) enzymes, which is associated with the chromatin condensation and transcriptional repression. Abnormal expression of HDACs is a common feature of cancer and has revealed a promising field to stratify cancer treatment and risk classification. The investigation of these expression profiles may represent an important clinical factor for diagnosis and management of hematological malignances. The objectives of the present study were to analyze the expression profile of the class 1 HDACs (HDAC1, 2, 3 and 8) genes in bone marrow samples obtained from 46 childhood ALL samples, to correlate the results with prognostic and clinical features (age, gender, risk group, immunophenotype, treatment response, minimal residual disease and event free survival) of the patients; to evaluated differences in gene expression between ALL samples and 10 bone marrow samples without hematological disease and to verify the correlation of these genes. The gene expression analysis were made using xi TaqMan real-time polymerase chain reaction. A higher expression of HDAC1 in patients with better treatment response was observed. The HDAC2 showed a higher expression in male gender (p=0,038). HDAC2 also showed a higher expression for higher risk (p=0,060) and lower survival patients (p=0,065), however the statistical analysis did not show significant results. Furthermore, there was a higher expression of HDAC2 (p=0,007), HDAC3 (p=0,014) and HDAC8 (p=0,002) in ALL samples when compared to healthy donors. Class I HDACs showed correlation in gene expression, except for HDAC1 and HDAC8. These results suggest that class I HDACs can represent important targets for ALL research; however, it is necessary to perform functional investigation to confirm these results.

Wong Yue Hang Albert. / Thesis submitted in: December 2005. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 108-119). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.v / List of Figures --- p.x / List of Tables --- p.xi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.4 / Chapter 2.1 --- Nasopharyngeal Carcinoma (NPC) --- p.4 / Chapter 2.1.1 --- Anatomy of Nasopharynx --- p.4 / Chapter 2.1.2 --- Histopathology of Nasopharyngeal Carcinoma --- p.5 / Chapter 2.1.3 --- Epidemiology and Etiology of Nasopharyngeal Carcinoma --- p.5 / Chapter 2.1.3.1 --- Endemic Regions of Nasopharyngeal Carcinoma --- p.5 / Chapter 2.1.3.2 --- Gender and Age Bias --- p.6 / Chapter 2.1.3.3 --- Nasopharyngeal Carcinoma in Hong Kong --- p.6 / Chapter 2.1.3.4 --- Environmental Factors and Diet --- p.7 / Chapter 2.1.3.5 --- HLA Haplotypes and Nasopharyngeal Carcinoma --- p.9 / Chapter 2.1.4 --- Epstein-Barr Virus (EBV) and Nasopharyngeal Carcinoma --- p.10 / Chapter 2.1.4.1 --- EBV and Human Cacners --- p.10 / Chapter 2.1.4.2 --- EBV Infection --- p.10 / Chapter 2.1.4.3 --- "Latent, Clonal EBV Infection" --- p.11 / Chapter 2.1.4.4 --- EBV Latency Form --- p.11 / Chapter 2.1.4.5 --- Reactivation of EBV --- p.12 / Chapter 2.1.5 --- Molecular Pathogenesis of Nasopharyngeal Carcinoma --- p.13 / Chapter 2.1.5.1 --- Genetic Changes --- p.13 / Chapter 2.1.5.2 --- Epigenetic Changes --- p.13 / Chapter 2.1.6 --- Therapy of Nasopharyngeal Carcinoma and its Deficiency --- p.14 / Chapter 2.1.6.1 --- Radiotherapy --- p.14 / Chapter 2.1.6.2 --- Concurrent Chemoradiotherapy --- p.16 / Chapter 2.1.6.3 --- Adjuvant and Neo-adjuvant Chemotherapy --- p.17 / Chapter 2.1.6.4 --- Chemotherapy in Metastatic Nasopharyngeal Carcinoma --- p.18 / Chapter 2.1.6.5 --- Novel Therapeutic Agents and Approach --- p.19 / Chapter 2.2 --- Histone Modification and Cancer --- p.20 / Chapter 2.2.1 --- Histone Modification and Transcription Regulation --- p.20 / Chapter 2.2.2 --- Carcinogenic Effect of Aberrant HAT and HDAC Activities --- p.21 / Chapter 2.2.3 --- Structural Classes of HDAC Inhibitors --- p.24 / Chapter 2.2.4 --- Anti-Cancer Mechanisms of HDAC Inhibitors --- p.25 / Chapter 2.3 --- Suberoylanilide Hydroxamic Acid (SAHA) --- p.27 / Chapter 2.3.1 --- Anti-tumor Effect of SAHA in Various Cancer Cell Lines --- p.27 / Chapter 2.3.2 --- SAHA Mediated Non-apoptotic Programmed Cell Death --- p.29 / Chapter 2.3.3 --- Anti-tumor and Preventive Effect of SAHA in Animal Model --- p.29 / Chapter 2.3.4 --- Clinical Trials of SAHA --- p.30 / Chapter 2.4 --- FK228 (Depsipeptide or FR901228) --- p.31 / Chapter 2.4.1 --- Anti-malignancy mechanism of FK228 --- p.31 / Chapter 2.4.2 --- Anti-angiogenesis --- p.32 / Chapter 2.4.3 --- Drug Resistance and FK228 --- p.33 / Chapter 2.4.4 --- Studies of FK228 on Animal Models --- p.33 / Chapter 2.4.5 --- Clinical Trials --- p.34 / Chapter 2.5 --- Histone Modification and Nasopharyngeal Carcinoma --- p.34 / Chapter Chapter 3 --- Materials and Methods --- p.36 / Chapter 3.1 --- Cell Lines --- p.36 / Chapter 3.2 --- EBER ish Hybridization (EBER ISH) --- p.37 / Chapter 3.3 --- HDAC Inhibitors --- p.38 / Chapter 3.4 --- Cellular Sensitivity of NPC Cell Lines to HDAC Inhibitors --- p.38 / Chapter 3.4.1 --- Drug Treatment --- p.38 / Chapter 3.4.2 --- Determining Relative Amount of Survival Cells (WST-1 Assay) --- p.39 / Chapter 3.5 --- Flow Cytometry Analysis --- p.40 / Chapter 3.5.1 --- Collecting Cells and Fixation --- p.40 / Chapter 3.5.2 --- Staining --- p.41 / Chapter 3.5.3 --- Flow Cytometry Analysis --- p.41 / Chapter 3.6 --- Protein Extraction --- p.41 / Chapter 3.6.1 --- Harvesting Samples --- p.41 / Chapter 3.6.2 --- Protein Extraction --- p.42 / Chapter 3.6.3 --- Protein Quantification --- p.42 / Chapter 3.7 --- Western Blotting --- p.43 / Chapter 3.7.1 --- SDS-Polyarcylamide Gel Electrophoresis (PAGE) (SDS-PAGE) --- p.43 / Chapter 3.7.2 --- Wet Transfer of Proteins --- p.43 / Chapter 3.7.3 --- Immunoblotting --- p.44 / Chapter 3.7.4 --- Signal Detection --- p.44 / Chapter 3.8 --- CodeLin´kёØ Oligonucleotide Microarray --- p.45 / Chapter 3.8.1 --- HDAC Inhibitor Treatment --- p.45 / Chapter 3.8.2 --- RNA Extraction --- p.45 / Chapter 3.8.3 --- Quality and Quantity Assessment of Total RNA Extracted --- p.46 / Chapter 3.8.4 --- CodeLinkIM Expression Bioarray System --- p.46 / Chapter 3.8.5 --- Data Analysis --- p.48 / Chapter 3.9 --- Real-time Reverse Transcription PCR (Real-time RT-PCR) --- p.48 / Chapter Chapter 4 --- Results --- p.50 / Chapter 4.1 --- Presence of EBV --- p.50 / Chapter 4.2 --- Anti-prolirative Effect of HDAC Inhibitors --- p.52 / Chapter 4.3 --- Histone Acetylation --- p.56 / Chapter 4.4 --- Induction of p21 Expression in NPC Cell Lines --- p.58 / Chapter 4.5 --- HDAC Inhibitors Induced Cell Cycle Arrest and Polyploidy Formation --- p.60 / Chapter 4.5.1 --- Trichostatin A Induced G2/M Arrest --- p.60 / Chapter 4.5.2 --- Suberoylanilide Hydroxamic Acid Induced G1 Arrest --- p.62 / Chapter 4.5.3 --- FK228 Mediated G2/M Arrest --- p.64 / Chapter 4.6 --- HDAC Inhibitors Altered the Expression of Cell Cycle Regulatory Proteins --- p.66 / Chapter 4.6.1 --- TSA Down-regulated Cyclin A and B --- p.66 / Chapter 4.6.2 --- Suppressed Expression of Cyclin D1 and B by SAHA --- p.69 / Chapter 4.6.3 --- Effect of FK228 on Expression of Different Cyclins in NPC Cell Lines --- p.71 / Chapter 4.7 --- Effect of HDAC Inhibitors on EBV Proteins --- p.73 / Chapter 4.8 --- HDAC Inhibitors Modulated Gene Expression Profile --- p.76 / Chapter 4.8.1 --- SAHA and FK228-Induced Gene Expression Profile --- p.76 / Chapter 4.8.2 --- Validation of Expression Profile of Selected Genes by Real-time RT-PCR --- p.83 / Chapter Chapter 5 --- Discussion --- p.87 / Chapter 5.1 --- Anti-proliferative Effect of SAHA and FK228 on NPC Cell Lines --- p.88 / Chapter 5.2 --- Resistance of SAHA or FK228 in NPC --- p.93 / Chapter 5.3 --- Growth Inhibitory Mechanism of SAHA and FK228 in NPC Cells --- p.94 / Chapter 5.4 --- Induction of Polyploidy Cells in NPC Cell Lines --- p.98 / Chapter 5.5 --- Does EBV play a Role in HDAC Inhibiotrs Induced Growth Arrest in NPC Cell Lines? --- p.99 / Chapter 5.6 --- Transcriptional Signature of SAHA and FK228 in NPC Cell Lines --- p.100 / Chapter 5.7 --- Combining SAHA or FK228 with other Anti-tumor Agents --- p.104 / Chapter 5.8 --- Future Prospectus --- p.105 / Chapter Chapter 6 --- Summary --- p.106 / References --- p.108 / Appendix 1 --- p.120 / Appendix 2 --- p.121

abstract: Alzheimer’s disease (AD) is characterized by the degeneration of cholinergic basal forebrain (CBF) neurons in the nucleus basalis of Meynert (nbM), which provides the majority of cholinergic input to the cortical mantle and together form the basocortical cholinergic system. Histone deacetylase (HDAC) dysregulation in the temporal lobe has been associated with neuronal degeneration during AD progression. However, whether HDAC alterations play a role in cortical and cortically-projecting cholinergic nbM neuronal degeneration during AD onset is unknown. In an effort to characterize alterations in the basocortical epigenome semi-quantitative western blotting and immunohistochemistry were utilized to evaluate HDAC and sirtuin (SIRT) levels in individuals that died with a premortem clinical diagnosis of no cognitive impairment (NCI), mild cognitive impairment (MCI), mild/moderate AD (mAD), or severe AD (sAD). In the frontal cortex, immunoblots revealed significant increases in HDAC1 and HDAC3 in MCI and mAD, followed by a decrease in sAD. Cortical HDAC2 levels remained stable across clinical groups. HDAC4 was significantly increased in prodromal and mild AD compared to aged cognitively normal controls. HDAC6 significantly increased during disease progression, while SIRT1 decreased in MCI, mAD, and sAD compared to controls. Basal forebrain levels of HDAC1, 3, 4, 6 and SIRT1 were stable across disease progression, while HDAC2 levels were significantly decreased in sAD. Quantitative immunohistochemistry was used to identify HDAC2 protein levels in individual cholinergic nbM nuclei immunoreactive for the early phosphorylated tau marker AT8, the late-stage apoptotic tau marker TauC3, and Thioflavin-S, a marker of mature neurofibrillary tangles (NFTs). HDAC2 nuclear immunoreactivity was reduced in individual cholinergic nbM neurons across disease stages, and was exacerbated in tangle-bearing cholinergic nbM neurons. HDAC2 nuclear reactivity correlated with multiple cognitive domains and with NFT formation. These findings identify global HDAC and SIRT alterations in the cortex while HDAC2 dysregulation contributes to cholinergic nbM neuronal dysfunction and NFT pathology during the progression of AD. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2018

La schistosomiase est la deuxième endémie parasitaire mondiale après le paludisme; 200 millions d'individus sont infectés à travers le monde et la morbidité reste élevée (environ 200 000 morts par an) malgré l'utilisation du praziquantel, seule drogue disponible. Cinq espèces de schistosomes infectent l'Homme dont celle que nous étudions, Schistosoma mansoni. Ce parasite possède un cycle de vie complexe, comportant 4 stades de développement morphologiquement distincts et 2 hôtes successifs, un hôte intermédiaire, le mollusque Biomphalaria glabrata et un hôte définitif, l'Homme. Afin de déterminer les mécanismes mis en jeu dans le contrôle du développement du schistosome et de caractériser des cibles potentielles de nouveaux agents chimiothérapeutiques, nous nous intéressons à certains acteurs impliqués dans la régulation génique, et plus particulièrement, les histones déacétylases, ou HDACs. Les HDACs sont des enzymes bien conservées dans le règne du vivant. Elles contrôlent l'expression de 5 à 10% des gènes, majoritairement en réprimant la transcription via la déacétylation des histones. Elles sont réparties en 3 classes, les classes I et II sont composées d'enzymes dont le site catalytique comporte un ion de zinc ; tandis que la classe III est composée des sirtuines, dépendantes du NAD+. Chez le parasite, une partie de nos études porte sur les 3 enzymes de classe I que nous avons identifiées et caractérisées au niveau moléculaire, SmHDAC1, 3 et 8. Ensuite nous avons réalisé une étude fonctionnelle de SmHDAC1 et mis en évidence sa capacité de répression de la transcription en système hétérologue. Puis nous nous sommes intéressés à l'inhibition de l'activité HDAC chez le parasite, grâce à l'utilisation de différents inhibiteurs des classes 1 et 2 des HDACs. Nous avons montré que des parasites cultivés en présence de trichostatine A (TSA) mouraient de manière dose dépendante. Nous avons approfondi notre étude au niveau moléculaire et avons étudié la variation d'acétylation des histones des parasites en présence de TSA et d'acide valproique. Nous avons montré une augmentation de l'acétylation de manière dose-dépendante de l'histone H4. Le traitement par la TSA entraîne la mort de nombreux types cellulaires par apoptose et provoque une surexpression de certains gènes impliqués dans ce processus. Nous avons démontré que ce traitement induit l'apoptose chez des larves maintenues en culture, ainsi qu'une activation des Caspases 3/7. Ensuite, la caractérisation des ADNc des Caspases 3 et 7 nous a permis de montrer par RT-PCR en temps réelle que les transcrits correspondants sont surexprimés après traitement par la TSA, tandis que celle-ci n'a aucun effet sur la transcription de SmHDAC1 et 3. Par la suite, nous avons corrélé cette augmentation avec le taux d'acétylation de H4 sur le promoteur de caspase7. Cette étude sera poursuivie à l'avenir par l'investigation de la relation structure/fonction des HDACs afin de développer des inhibiteurs spécifiques. En parallèle, nous étudions une HDAC de classe III, SmSirt1, que nous avons identifiée et caractérisée. La présence d'une grande insertion dans son domaine catalytique présage des fonctions modifiées par rapport à ses orthologues chez d'autres espèces. Nous souhaitons nous focaliser sur les conséquences de cette insertion spécifique chez S. mansoni. En effet, elle semble être la cible de potentielles modifications post-traductionnelles (site de phosphorylation par PKB/Akt), que nous voulons mettre en évidence. De plus, l'une des fonctions de Sirt1 est l'interaction avec le facteur de transcription FoxO et la régulation de la voie de signalisation insuline dépendante (impliquant PKB/Akt). Par ce biais FoxO et Sirt1 contrôlent le métabolisme, des mécanismes de survie cellulaire et la longévité. Une modification de la fonction de SmSirt1 pourrait être à la base de la durée de vie anormalement longue de S. mansoni. Nous avons donc également réalisé la caractérisation moléculaire de SmFoxO, afin de mettre en évidence son interaction avec Sirt1 ainsi que l'implication de cette interaction dans le contrôle de la transcription de gènes cibles. Par la suite nous étudierons le rôle de Sirt1 et FoxO dans la régulation de la signalisation insuline dépendante sur des parasites en culture

The SRC gene encodes pp60c-Src, a 60 kDa non-receptor tyrosine kinase that is frequently activated and/or overexpressed in many cancers including colon cancer. In a subset of colon cancer cell lines, it has been shown, that the overexpression of c-Src can be explained, in part, by the transcriptional activation of the SRC gene. As a result, the general goal of this thesis was to further characterize how SRC is transcriptionally regulated in human cancer cell lines. Two highly dissimilar promoters, the housekeeping-like SRC1A promoter, as well as the HIF-1Ñ regulated tissue-specific SRC1Ñ promoter, regulate SRC expression. hnRNP K and the Sp family of factors regulate the SRC1A promoter; however, the true impact of Sp3 on SRC1A activity was not understood. In this thesis, a comprehensive analysis of the effect of Sp3 on SRC1A activity was performed. Physiologically, Sp3 exists as four translational isoforms that, in part, dictate the activation potential of Sp3. In general, the longer forms of Sp3 were modest transcriptional activators of the SRC1A promoter whereas the shorter forms were unable to activate the SRC1A promoter. An analysis of all Sp3 isoforms identified that the shorter Sp3 isoforms could be converted into transcriptional activators of SRC1A if the SUMOylation of a critical lysine residue within the inhibitory domain was prevented. Conversely, SUMOylation of the same isoform had little effect on the activation potential of the longer Sp3 isoforms at the SRC1A promoter. These results suggest that transcriptional activation by Sp3 is promoter context-, isoform- and modification-dependent.<p>SRC is transcriptionally repressed by histone deacetylase inhibitors (HDIs) and despite unsuccessful studies attempting to identify HDI-responsive elements within the SRC promoter regions none could be identified. This finding also suggests that histone deacetylases (HDACs) may be required for SRC expression. Historically, it was believed that HDIs act at the histone level to alter chromatin dynamics through the inactivation of HDACs to result in histone hyperacetylation and increased transcriptional activation. As such, a systematic investigation of the changes in histone H3 and H4 acetylation status at the transcriptionally repressed SRC promoter regions and the transcriptionally activated p21WAF1 promoter region was performed. The p21WAF1 promoter was used as control in this study as p21WAF1 is a classical example of a gene transcriptionally activated by HDIs. Interestingly, similar changes in histone acetylation at the p21WAF1 promoter and both SRC promoter regions were observed. Upon closer examination of acetylation changes at discreet histone residues, it was observed that in the rare case that a particular residue was differentially acetylated upon treatment at the promoter regions analyzed, the SRC1Ñ and p21WAF1 promoter regions demonstrated more similar changes in acetylation as compared to SRC1A. Taken together, these results suggest that histone acetylation status is not an accurate indicator of transcriptional activity following HDI treatment. To further investigate HDI-mediated SRC repression, RNA Pol. II occupancy at the promoter and regions downstream of the promoter were assessed. Despite the continued occupancy of RNA Pol. II at the promoter regions, RNA Pol. II was lost from the 3¡¦ UTR upon treatment with HDIs. These findings suggest that RNA Pol. II . may be sequestered at the promoter regions upon treatment with HDIs possibly as a result of impeded transcription initiation and/or elongation. Further analysis of the phosphorylation status of RNA Pol. II identified that transcriptional initiation was indeed occurring despite HDI treatment; however, productive transcriptional elongation could not be confirmed thus suggesting a role for abrogated elongation in HDI mediated SRC repression. Complimentary analysis of the effects of HDACs on SRC expression suggested that while class I HDACs abrogated SRC expression, class II HDACs were required for the maintenance of SRC transcript levels in a promoter-independent fashion. Together, these results provide the basis for a model whereby HDIs repress SRC transcriptional expression through the inhibition of class II HDAC activity to eventually result in curtailed SRC transcriptional elongation.

The SRC gene encodes pp60c-Src, a 60 kDa non-receptor tyrosine kinase that is frequently activated and/or overexpressed in many cancers including colon cancer. In a subset of colon cancer cell lines, it has been shown, that the overexpression of c-Src can be explained, in part, by the transcriptional activation of the SRC gene. As a result, the general goal of this thesis was to further characterize how SRC is transcriptionally regulated in human cancer cell lines. Two highly dissimilar promoters, the housekeeping-like SRC1A promoter, as well as the HIF-1Ñ regulated tissue-specific SRC1Ñ promoter, regulate SRC expression. hnRNP K and the Sp family of factors regulate the SRC1A promoter; however, the true impact of Sp3 on SRC1A activity was not understood. In this thesis, a comprehensive analysis of the effect of Sp3 on SRC1A activity was performed. Physiologically, Sp3 exists as four translational isoforms that, in part, dictate the activation potential of Sp3. In general, the longer forms of Sp3 were modest transcriptional activators of the SRC1A promoter whereas the shorter forms were unable to activate the SRC1A promoter. An analysis of all Sp3 isoforms identified that the shorter Sp3 isoforms could be converted into transcriptional activators of SRC1A if the SUMOylation of a critical lysine residue within the inhibitory domain was prevented. Conversely, SUMOylation of the same isoform had little effect on the activation potential of the longer Sp3 isoforms at the SRC1A promoter. These results suggest that transcriptional activation by Sp3 is promoter context-, isoform- and modification-dependent.<p>SRC is transcriptionally repressed by histone deacetylase inhibitors (HDIs) and despite unsuccessful studies attempting to identify HDI-responsive elements within the SRC promoter regions none could be identified. This finding also suggests that histone deacetylases (HDACs) may be required for SRC expression. Historically, it was believed that HDIs act at the histone level to alter chromatin dynamics through the inactivation of HDACs to result in histone hyperacetylation and increased transcriptional activation. As such, a systematic investigation of the changes in histone H3 and H4 acetylation status at the transcriptionally repressed SRC promoter regions and the transcriptionally activated p21WAF1 promoter region was performed. The p21WAF1 promoter was used as control in this study as p21WAF1 is a classical example of a gene transcriptionally activated by HDIs. Interestingly, similar changes in histone acetylation at the p21WAF1 promoter and both SRC promoter regions were observed. Upon closer examination of acetylation changes at discreet histone residues, it was observed that in the rare case that a particular residue was differentially acetylated upon treatment at the promoter regions analyzed, the SRC1Ñ and p21WAF1 promoter regions demonstrated more similar changes in acetylation as compared to SRC1A. Taken together, these results suggest that histone acetylation status is not an accurate indicator of transcriptional activity following HDI treatment. To further investigate HDI-mediated SRC repression, RNA Pol. II occupancy at the promoter and regions downstream of the promoter were assessed. Despite the continued occupancy of RNA Pol. II at the promoter regions, RNA Pol. II was lost from the 3¡¦ UTR upon treatment with HDIs. These findings suggest that RNA Pol. II . may be sequestered at the promoter regions upon treatment with HDIs possibly as a result of impeded transcription initiation and/or elongation. Further analysis of the phosphorylation status of RNA Pol. II identified that transcriptional initiation was indeed occurring despite HDI treatment; however, productive transcriptional elongation could not be confirmed thus suggesting a role for abrogated elongation in HDI mediated SRC repression. Complimentary analysis of the effects of HDACs on SRC expression suggested that while class I HDACs abrogated SRC expression, class II HDACs were required for the maintenance of SRC transcript levels in a promoter-independent fashion. Together, these results provide the basis for a model whereby HDIs repress SRC transcriptional expression through the inhibition of class II HDAC activity to eventually result in curtailed SRC transcriptional elongation.

Cancer represents the second leading cause of death in the United States. For many malignancies, currently available treatment options offer little long-lasting survival benefits to patients. However, recent studies have shown immunotherapeutic approaches to be an attractive strategy to cancer treatment. While many current immunotherapeutic strategies convey durable responses, such responses are only seen in a minority of patients. An increased understanding of the mechanisms governing tumor immunogenicity and the biology of immune responses is crucial to improving upon the efficacy of current and future cancer immunotherapies. Histone deacetylases (HDACs), enzymes classically associated with regulation of gene expression, have been therapeutic targets in various cancers for several years due to their involvement in cell growth. However, it has become increasingly clear that HDACs are intimately involved in regulating both the immunogenicity of tumor cells and immune response of leukocytes and lymphocytes. In order to expand upon this growing knowledge, the therapeutic efficacy of the pan-HDAC inhibitor LBH589 in the treatment of melanoma was studied. The results presented here demonstrate that LBH589 is a potent inhibitor of growth in a wide variety of melanomas through induction of cell cycle arrest and apoptosis. Additionally, LBH589 increases the immune visibility of melanoma cells by increasing expression of several immune associated cell surface markers (e.g. MHC I, MHC II, CD80, CD86) in addition to upregulating expression of melanoma differentiation antigens. Furthermore, LBH589 treatment of immune cells results in an enhanced pro-inflammatory phenotype of both APCs and T-cells. These combined effects result in better activation of T-cells and ultimately prolonged survival in LBH589 treated, melanoma-baring mice. To further the understanding of the role of individual HDACs in the T-cell response, the biology of the newest HDAC, HDAC11, was further assessed. To this end, it is shown that HDAC11 is differentially expressed in T-cell populations, and expression is rapidly decreased following activation. Utilizing an HDAC11 knockout (HDAC11KO) mouse strain, it is found that both CD4+ and CD8+ T-cells lacking HDAC11 have an enhanced type 1 effector function characterized by increased proliferation and secretion of IL-2, TNF and IFN-γ. Additionally, HDAC11KO CD8+ T-cells have increased expression of both granzyme B and perforin. HDAC11KO T-cells also demonstrate enhanced resistance to inhibition by Tregs and anergy formation. As a possible mechanism for the observed phenotype, it is also demonstrated that HDAC11KO T-cells produce elevated levels of the transcription factors Eomes and T-bet, both at the basal state and post-activation. In vivo, T-cells lacking HDAC11 have a more potent and robust ability to cause GvHD and mediate an enhanced anti-tumor response. Collectively, these results demonstrate that targeting of HDACs is a viable approach to cancer immunotherapy, and that targeting of specific HDACs may be an attractive strategy for optimizing immunotherapy efficacy while minimizing side effects.

Histone deacetylases (HDAC) 1 and 2 play crucial role in chromatin remodeling and gene expression regimes, as part of multiprotein corepressor complexes. Protein kinase CK2-driven phosphorylation of HDAC1 and 2 regulates their catalytic activities and is required to form the corepressor complexes. Phosphorylation-mediated differential distributions of HDAC1 and 2 complexes in regulatory and coding regions of transcribed genes catalyze the dynamic protein acetylation of histones and other proteins, thereby influence gene expression. During mitosis, highly phosphorylated HDAC1 and 2 heterodimers dissociate and displace from mitotic chromosomes. Our goal was to identify the kinase involved in mitotic phosphorylation of HDAC1 and 2. We postulated that CK2-mediated increased phosphorylation of HDAC1 and 2 leads to dissociation of the heterodimers, and, the mitotic chromosomal exclusions of HDAC1 and 2 are largely due to the displacement of HDAC-associated proteins and transcription factors, which recruit HDACs, from chromosomes during mitosis. We further explored the role of un- or monomodified HDAC1 and 2 complexes in immediate-early genes (IEGs), FOSL1 (FOS-like antigen-1) and MCL1 (Myeloid cell leukemia-1), regulation. Dynamic histone acetylation is an important regulator of these genes that are overexpressed in a number of diseases and cancers. We hypothesized that transcription dependent recruitment of HDAC1 and 2 complexes over the gene body regions plays a regulatory role in transcription and splicing regulation of these genes. We present evidence that CK2-catalyzed increased phosphorylation of HDAC1 and 2 regulates the formation of distinct corepressor complexes containing either HDAC1 or HDAC2 homodimers during mitosis, which might target cellular factors. Furthermore, the exclusion of HDAC-recruiting proteins is the major factor for their displacement from mitotic chromosomes. We further demonstrated that un- or monophosphorylated HDAC1 and 2 are associated with gene body of FOSL1 in a transcription dependent manner. However, HDAC inhibitors prevented FOSL1 activation independently of the nucleosome response pathway, which is required for IEG induction. Interestingly, our mass spectrometry results revealed that HDAC1 and 2 interact with a number of splicing proteins, in particular, with serine/arginine-rich splicing factor 1 (SRSF1). HDAC1 and 2 are co-occupied with SRSF1 over gene body regions of FOSL1 and MCL1, regardless of underlying splicing mechanisms. Using siRNA-mediated knockdown approaches and HDAC inhibitors, we demonstrated that alternative splicing of MCL1 is regulated by RNA-directed localized changes in the histone acetylation levels at the alternative exon. The change in histone acetylation levels correlates with the increased transcription elongation and results in change in MCL1 splicing by exon skipping mechanism. Taken together, our results contribute to further understanding of how the multi-faceted HDAC1 and 2 complexes can be regulated and function in various processes, including, but not limited to, transcription regulation and alternative splicing. This can be an exciting area of future research for therapeutic interventions.