Submitted by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2018-09-27T14:19:27Z No. of bitstreams: 1 KELLEN ROCHA.pdf: 1430079 bytes, checksum: ba3882603d46f2a9824b73319d20cd73 (MD5) / Approved for entry into archive by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2018-09-27T14:19:44Z (GMT) No. of bitstreams: 1 KELLEN ROCHA.pdf: 1430079 bytes, checksum: ba3882603d46f2a9824b73319d20cd73 (MD5) / Made available in DSpace on 2018-09-27T14:19:44Z (GMT). No. of bitstreams: 1 KELLEN ROCHA.pdf: 1430079 bytes, checksum: ba3882603d46f2a9824b73319d20cd73 (MD5) Previous issue date: 2017-07-14 / A doença de Alzheimer (DA) é uma desordem neurodegenerativa crônica caracterizada clinicamente pela perda progressiva de função cognitiva, distúrbios neuropsiquiátricos e comportamentais. Patologicamente esta doença caracteriza-se pelo acúmulo anormal do peptídeo β-amilóide (Aβ) no córtex e no hipocampo, emaranhados neurofibrilares intracelulares formados por tau hiperfosforilada, disfunção progressiva sináptica e, posteriormente perda neuronal. As opções terapêuticas disponíveis melhoram os sintomas, mas não impedem a progressão da doença, portanto, ainda está faltando uma estratégia terapêutica efetiva para DA. Há estudos relacionados à utilização de terapia epigenética para o tratamento da DA, a terapêutica mais desenvolvida é a que envolve a classe dos inibidores das deacetilases (HDACs). Assim, este trabalho tem por objetivo investigar o efeito protetor do inibidor da HDAC ácido hidroxâmico de suberoilanilida (SAHA) em um modelo de DA em camundongos. Para isso, foram utilizados 50 camundongos Swiss adultos, pesando entre 30-35 g, divididos em dois experimentos. No primeiro, os camundongos foram divididos em 6 grupos que receberam uma injeção de Aβ1-42 via intracerebroventricular (i.c.v.) no início da experiência (exceto o grupo Sham que foi utilizado como controle) para investigar a atividade das histonas   acetiltransferase (HATs) e HDAC, determinação dos níveis do fator neurotrófico derivado do cérebro (BDNF), expressão do mRNA de BDNF e modulação da via (cAMP/PKA/CREB) em uma curva de tempo (6 horas, 1, 3, 7 e 21 dias). Ao final de cada tempo, os animais foram submetidos ao teste cognitivo e foram eutanasiados. O córtex pré-frontal e o hipocampo foram removidos para posteriores análises. No segundo experimento, os camundongos foram dividos em 4 grupos: Grupo Controle (sham+veículo); Grupo Aβ1-42 (Aβ1-42 + veículo); Grupo SAHA (25 mg/kg, via intraperitoneal) (sham + SAHA); Grupo Interação (Aβ1-42 + SAHA). O peptídeo Aβ1-42 ou o veículo foram infundidos por injeção i.c.v. e, um dia depois, iniciou-se o tratamento, por via i.p., durante 21 dias. Ao final do experimento os animais foram submetidos ao teste cognitivo, eutanásiados para retirada das estruturas cerebrais. As amostras foram utilizadas para a determinação dos níveis de BDNF, expressão do mRNA de BDNF, atividade enzimática das histonas (HDAC e HATs) e regulação da via cAMP/PKA/CREB. O presente estudo observou deficiências significativas causadas pela Aβ1-42 na memória (Labirinto Aquático de Morris), bem como causou desequilíbrio das enzimas HAT/HDAC, redução de cAMP, PKA e CREB e BDNF no córtex pré-frontal e hipocampo de camundongos. A inibição de HDAC, com SAHA demostrou neuroproteção nas alterações comportamentais e neuroquímicas induzidas por Aβ1-42. Estes dados mostram que a acetilação através da inibição do HDAC, desempenha um papel fundamental na mediação da memória e demonstra que SAHA poderá ser uma ferramenta médica promissora na abordagem terapêutica para o tratamento da DA. / Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized clinically by the progressive loss of cognitive function, neuropsychiatric and behavioral disorders. Pathologically this disease is characterized by the abnormal accumulation of β-amyloid peptide (Aβ) in the cortex and hippocampus, intracellular neurofibrillary tangles formed by hyperphosphorylated tau, progressive synaptic dysfunction and, later, neuronal loss. The available therapeutic options improve the symptoms, but they do not prevent the progression of the disease, therefore, an effective therapeutic strategy for AD is still lacking. There are studies related to the use of epigenetic therapy for the treatment of AD, the most developed therapy is that involving the class of deacetylase inhibitors (HDACs). Thus, this work aims to investigate the protective effect of the HDAC inhibitor hydroxamic acid suberoilanilide (SAHA) in an AD model in mice. For this, 50 Swiss adult mice weighing between 30-35 g were used, divided in two experiments. In the first, the mice were divided into 6 groups that received an injection of Aβ1-42 via the intracerebroventricular (i.c.v.) at the beginning of the experiment (except the Sham group that was used as control) to investigate histone activity acetyltransferase (HATs) and HDAC, determination of brain derived neurotrophic factor (BDNF) levels, expression of BDNF mRNA and modulation of the pathway (cAMP / PKA / CREB) in a time curve (6 hours, 1, 3, 7 and 21 days). At the end of each time, the animals were submitted to the cognitive test and were euthanized. The prefrontal cortex and hippocampus were removed for further analysis. In the second experiment, the mice were divided into 4 groups: Control Group (sham + vehicle); Group Aβ1-42 (Aβ1-42 + vehicle); SAHA group (25 mg / kg, intraperitoneal route) (sham + SAHA); Interaction Group (Aβ1-42 + SAHA). The Aβ1-42 peptide or vehicle was infused by i.c.v. and one day later the treatment was started i.p. for 21 days. At the end of the experiment the animals were submitted to the cognitive test, euthanasia for removal of the cerebral structures. The samples were used for the determination of BDNF levels, expression of BDNF mRNA, histone enzymatic activity (HDAC and HATs) and regulation of the cAMP / PKA / CREB pathway. The present study observed significant deficiencies caused by Aβ1-42 in memory (Morris Aquatic Labyrinth), as well as caused imbalance of HAT / HDAC enzymes, cAMP, PKA and CREB and BDNF reduction in the prefrontal cortex and hippocampus of mice. Inhibition of HDAC with SAHA demonstrated neuroprotection in behavioral and neurochemical changes induced by Aβ1-42. These data show that acetylation through inhibition of HDAC plays a key role in memory mediation and demonstrates that SAHA may be a promising medical tool in the therapeutic approach to AD.

O glioblastoma (GBM) é considerado um dos tumores mais agressivos do sistema nervoso central (SNC). Mesmo com o uso de protocolos modernos de tratamento o prognóstico se mantém bastante reservado, sendo que crianças com GBM apresentam uma sobrevida média de 12 a 15 meses. Mecanismos epigenéticos podem interferir no processo de carcinogênese, sendo que a acetilação do DNA pode modular a expressão de genes que atuam no controle do ciclo celular, contribuindo assim para o desenvolvimento e progressão de neoplasias. Estudos clínicos demonstram que inibidores de histonas deacetilases (HDACs), em monoterapia ou combinados a outros agentes antineoplásicos, são clinicamente ativos e bem tolerados no tratamento de uma ampla variedade de tumores. Estes inibidores podem sensibilizar a resposta celular à irradiação ionizante, possibilitando uma redução nas doses-padrão utilizadas, minimizando os efeitos colaterais a curto e longo prazo. A radiação ionizante induz dano no DNA e é geralmente aceito que quebras da dupla-fita (DSBs) é o tipo de lesão mais severa relacionada à sobrevivência celular e preservação da integridade genômica. No presente estudo, avaliamos o potencial efeito radiosensibilizante do PCI-24781, um novo e potente pan-inibidor de HDAC nas linhagens celulares de GBM pediátrico SF188 e KNS42. Foram comparadas as taxas de proliferação celular, clonogenicidade e apoptose das linhagens SF188 e KNS42 com ou sem tratamento com PCI-24781. Também foram comparadas as taxas de clonogenicidade das linhagens SF188 e KNS42 que foram irradiadas com ou sem tratamento prévio com PCI-24781. Adicionalmente, foram avaliados os efeitos do PCI-24781 na expressão de algumas das principais proteínas responsáveis pelo reparo de quebras da dupla-fita ocasionadas pela irradiação. Para os ensaios de proliferação celular foram utilizados os tempo de 24, 48, 72 e 96h, para apoptose, 48h e para capacidade clonogênica sem irradiação o tempo de 48h, em diferentes doses de PCI-24781 (0,25 - 16 M). O inibidor bloqueou significativamente a proliferação celular (p<0,05), induziu morte por apoptose (p<0,05) e reduziu a capacidade na formação de colônias (p<0,001) em ambas as linhagens. No ensaio para avaliação da radiosensibilidade, foram utilizadas as doses do IC30 11 de cada linhagem do ensaio clonogênico seguida de diferentes doses de irradiação. Ambas as linhagens apresentaram uma significativa (p<0,001) diminuição na formação de colônias em todas as doses de irradiação. A linhagem mais resistente à droga, SF188 foi escolhida para estudo do reparo de quebras da dupla-fita ocasionadas pela irradiação. As expressões da proteína Rad51, importante na via de reparo por recombinação homóloga (HR), e das proteínas DNA-PKcs, Ku70 e Ku86, importantes na via de reparo por união terminal não-homóloga (NHEJ) apresentaram uma maior diminuição quando a linhagem irradiada foi previamente tratada com PCI-24781 em comparação à radioterapia exclusiva. Estes achados demonstram que o inibidor de histona PCI-24781 apresenta um importante papel como agente radiosensibilizante, comprometendo o reparo das quebras de dupla-fita em células de GBM pediátrico tratadas com radioterapia. / Glioblastoma (GBM) is considered one of the most aggressive tumors to affect the central nervous system (CNS). Even employing modern treatment protocols the prognosis remains very poor, with children affected by GBM presenting a median survival rate of 12 to 15 months. Epigenetic mechanisms may interfere with the process of tumorigenesis, and DNA acetylation can modulate the expression of genes that contribute in cell cycle control and participate to the development and progression of cancer. Clinical studies demonstrate that histone deacetylase inhibitors (HDACs), alone or in combination with other antineoplastic agents, are clinically active and well tolerated in the treatment of a wide variety of tumors. These inhibitors may sensitize the cellular response to ionizing radiation, enabling the reduction in standard doses of radiation, ultimately minimizing both short and long-term side effects. Ionizing radiation induces DNA damage and it is generally accepted that the double-stranded breaks (DSBs) is the most severe type of injury related to cell survival and preservation of genomic integrity. In the present study, we evaluated the potential radiosensitizer effect of PCI-24781, a novel potent pan-HDAC inhibitor in the pediatric GBM cell lines SF188 and KNS42. We compared the cell proliferation rates, apoptosis of clonogenicity of KNS42 and SF188, with or without treatment with PCI-24781. Moreover, clonogenicity rates were compared between cell lines that were irradiated with or without prior treatment with PCI-24781 Additionally, we evaluated the effects of PCI-24781 in the expression of some of the major proteins responsible for the repair of double-stranded breaks caused by the irradiation. For the cell proliferation assays, the times of 24, 48, 72 and 96 hours were used, for apoptosis, the time of 48h and clonogenic capacity without irradiation, the time of 48h, and different doses of PCI-24781 (0,25 - 16 M). The inhibitor significantly blocked cell proliferation (p<0,05), inducing cell death by apoptosis (p<0,05) and reducing the colony forming ability (p<0,001) of both lineages. In the assays to evaluate the radiosensitivity , the IC30 doses of the clonogenic assays were used for each cell-line after different doses of irradiation. Both lineages showed a significant decrease (p<0,001) in colony formation at all doses of irradiation. The most resistant cell-line to the drug, SF188, was 13 chosen to study the double-strand breaks repair caused by irradiation. The Rad51 protein levels, critical for homologous recombination (HR), and the DNA-PKcs proteins Ku70 and Ku86, important for DNA repair through non-homologous end joining (NHEJ) showed significant decrease in expression when cell-line was treated with PCI-24781 prior to radiotherapy. These data demonstrates that the histone deacetylase inhibitor PCI-24781 plays an important role as a radiosensitizer agent, compromising the repair of double-strand breaks in pediatric GBM cells following irradiation.

The mammalian heart is a remarkable organ in that it must provide for the cardiovascular needs of the organism throughout life, without pausing. Yet, through developmental growth to adulthood and into ageing, the mammalian heart undergoes extensive physiological, morphological and biochemical remodelling. Pivotal to the age-associated alterations in cardiac phenotype is a decline in the proliferative capacity of cardiac myocytes (CMs), which is insufficient to compensate for the basal rate of CM death over time. The terminally differentiated nature of adult CMs also underlies the inability of the heart to repair itself after myocardial damage, such as infarction. As a consequence, existing CMs mount a compensatory hypertrophic response to sustain cardiac output. In parallel, the proliferation rate of resident cardiac fibroblasts, which comprise approximately 60% of total cardiac cells, increases, replacing healthy myocardium with fibrotic scar tissue. Together, CM hypertrophy and fibroblast hyperplasia progressively reduces cardiac function and the ability of the heart to adapt to environmental stressors or damage. Under continued stress or through natural ageing, the heart progresses to a failing state in which cardiac output can no longer meet the demands of the body. The societal impact of ageing-associated decline in cardiac function is great, with heart failure affecting around 8% of over 65s and consuming approximately 2% of the NHS budget. These statistics are set to rise with an ageing population. The substantial phenotypic alterations characteristic of ageing and disease-associated cardiac remodelling requires a wholesale reprogramming of the CM transcriptome. In many biological systems, although yet to be established in adult myocytes, epigenetic mechanisms underlie the transcriptome changes that arise. I hypothesised that alterations in the epigenetic landscape of CMs mediate the transcriptome remodelling that determines the phenotypic transformations that occur in cardiac ageing, hypertrophy and disease. To test this hypothesis, I examined CM-specific changes in DNA cytosine modifications, long non-coding RNA (lncRNA) expression and histone tail lysine methylation marks – epigenetic marks with central roles in transcriptional regulation in many biological systems. I examined how these changes correlate with alterations in the CM transcriptome during disease and ageing. Understanding how alterations in the transcriptome and epigenome contribute to phenotypic changes using whole tissue data is confounded by the heterogeneous nature of the heart, coupled with ageing and disease-associated changes in relative cellular composition. To overcome this, I validated a method to isolate CM nuclei specifically from post-mortem heart tissue. This method also has the advantage that it could be applied to frozen tissue, allowing access to archived material. LncRNAs are functional RNA transcripts longer than 200 bases are emerging as important regulators of gene expression. Common mechanisms of gene expression regulation by lncRNAs include by antisense suppression, as guide/co-factor molecules to direct chromatin modifying components or splicing factors to locations in the genome. Transcriptome profiling in healthy and failing human CMs identified an increase in expression of the lncRNA MALAT-1, which was consistently observed in rodent models of pathology and in ageing. Loss-of-function investigations revealed a potential anti-hypertrophic function for this lncRNA. Specifically, MALAT-1 knock down in vitro in CMs incited spontaneous hypertrophy with features reflecting pathological remodelling in the heart and hypertrophy induced by pro-hypertrophic mediators in vitro. ix In addition, novel uncharacterised transcripts were identified as differentially expressed in cardiovascular disease, including a lncRNA at 4q35.2, which was found significantly downregulated in CMs from human failing hearts. DNA methylation is a stable epigenetic modification and is generally associated with transcriptional repression. It is established by de novo DNA methyltransferases (DNMTs) in early development to determine and maintain differentiated cell states and is ‘copied’ to daughter strands in DNA synthesis by the maintenance DNMT1. Methylcytosine (MeC) can be subject to further processing to hydroxymethylcytosine (hMeC) through a TET protein-mediated oxidation reaction. This serves as a means to actively remove methylation marks as well as hMeC being a novel epigenetic modification in its own right. For the first time, I identified the cardiac myocyte genome as having a high global level of hMeC, comparable with that in neurones. I also discovered an age-associated increase in gene body hMeC that coincided with the loss of proliferative capacity and plasticity of CMs. In parallel, gene body DNA MeC levels decrease in CM ageing. Both these phenomena in gene bodies corresponded with a non-canonical upregulation in expression of genes particularly relevant to cardiac function. This relationship between gene body methylation and transcription rate is strengthened with age in CMs. Recent work in the laboratory had identified the pervasive loss of euchromatic lysine 9 dimethylation on histone 3 (H3K9me2) as a conserved feature of pathological hypertrophy and associated with re-expression of foetal genes. Concurrently, expression and activity of the enzymes responsible for depositing H3K9me2, euchromatic histone lysine methyltransferases 1 and 2 (EHMT1/GLP and EHMT2/G9a) were reduced. Consistently, microRNA-217-induced genetic or pharmacological inactivation of Ehmts was sufficient to promote pathological hypertrophy and foetal gene re-expression, while suppression of this pathway protected from pathological hypertrophy both in vitro and in mice. In summary, I provide new insight into CM-specific epigenetic changes and suggest the epigenome as an important mediator in the loss of plasticity and cardiac health in ageing and disease. Epigenetic mediators and pathways identified as responsible for this remodelling of the CM epigenome suggests opportunities for novel therapy approaches.

The important role of the central intermediary metabolite acetyl-coenzyme A (AcCoA)for several anabolic and catabolic pathways is well characterised. However, the role of AcCoA as the only known donor of acetyl groups for protein acetylation in regulation of enzyme activities, protein complex stability as well as epigenetic status off chromatin, is only recently emerging. Among multiple other pathways, the autophagy pathway has now been shown to be directly regulated by protein acetylation and deacetylation. Therefore, it was reasoned that the availability of AcCoA, via the modulation of AcCoA generating enzymes, may regulate autophagy. This study has focussed on the role of the acetate-mediated route to nuclear-cytosolic AcCoA synthesis, catalysed by AcCoA synthetase 2 (ACSS2), in the regulation of autophagy.

Regulation of gene expression is an essential process for all living organisms. Transcriptional regulation, associated with chromatin, is governed by: (1) DNA sequence, which creates regulatory sites (promoters, enhancers and silencers), where sequence motifs and features (e. g. CpG) can attract transcription factors (TFs) and influence chromatin structure or RNA polymerase II (Pol II) binding, initiation and elongation; (2) non-sequence, epigenetic factors - histone modifications, TF binding, chromatin remodelling (histone placement, eviction and reconstitution), and non-coding RNA regulation. These factors interact with each other, creating a complex network of interactions. In this thesis I describe computational studies of heterochromatin factors in regulation of gene and repeat expression, an analysis of active regulatory elements, and global analyses of big datasets in C. elegans. I first show that a team of heterochromatin factors - HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 - collaborates with piRNA and nuclear RNAi pathways to silence repetitive elements and protect the germline. I also found that the TACBGTA motif is particularly enriched on repeats and heterochromatin factors binding sites, and that repeat elements are derepressed in the soma during normal C. elegans ageing. I then describe the work on active regulatory regions. I show that CFP-1/CXXC1 binds CpG dense, nucleosome depleted promoters and, along SET-2, is required for H3K4me3 deposition at these loci. Using expression profiling I determined that the majority of CFP-1 binding targets are not significantly mis-regulated in cfp-1 mutants, but are weakly upregulated in bulk analyses. I also show that CFP-1 functionally interacts with the Sin3S/HDAC complex. In cfp-1 mutant I observed both loss and gain of SIN-3 binding, depending on chromatin context. Finally, I performed a data driven study on a large collection of ChIP-seq profiles using non-parametric sparse factor analyses (NSFA) and compared it to other, unsupervised machine learning algorithms. This study uncovered interactions and structure in genomic datasets. In addition, I present a collection of computational tools and methods I developed to facilitate processing, storage, retrieval, annotation, and analyses of large datasets in genomics.

Introdução: A formação da memória envolve mudanças na expressão de genes neuronais. Remodelações epigenéticas da cromatina e modificações pós-traducionais reversíveis no DNA ou nas proteínas histonas representam mecanismos centrais na regulação da expressão gênica durante o desenvolvimento do cérebro e a aprendizagem inicial ou recuperação da memória. Desequilíbrios nos níveis de acetilação de histonas estão associados à uma ampla variedade de desordens cerebrais. Histonas deacetilases (HDACs) desempenham um papel fundamental na homeostase da acetilação de histonas e na regulação de atividades celulares fundamentais como a transcrição, tornando-as um foco de estudo. Evidências mostram que a administração de inibidores de histonas deacetilases (HDACis) restauram a memória associada à regulação da expressão gênica e melhora a memória em ratos. Estudos em modelos animais têm mostrado que a formação da memória envolve uma série de alterações bioquímicas em várias áreas do sistema nervoso central, entre as quais se destacam o hipocampo e a amígdala basolateral (BLA). Neste contexto, fármacos experimentais, como a tricostatina A (TSA), que atuam sobre mecanismos epigenéticos, têm sido recentemente propostos como potenciais terapias para o tratamento de disfunção cognitiva e memória associados a doenças neurológicas e psiquiátricas. Objetivo: Neste trabalho objetivamos compreender e elucidar o papel da acetilação de histonas em processos envolvidos na modulação da memória utilizando o fármaco TSA e se baseia na hipótese de que a atividade de HDACs é essencial para a modulação das respostas de aprendizado na tarefa de esquiva inibitória (IA). Métodos: Ratos Wistar foram canulados bilateralmente na amígdala. Os efeitos das micro-infusões intra-amigdalares de TSA foram observados na consolidação e na extinção da memória após o treino na tarefa de esquiva inibitória e nos níveis do fator neurotrófico derivado do cérebro (BDNF) na BLA e no hipocampo referentes à consolidação da memória. Resultados: Os resultados demonstraram que a infusão intra-amigdalar de TSA 1.5 h, 3 h e 6 h após o treino na tarefa de esquiva inibitória resulta na melhora da memória de longa duração (LTM). TSA acelerou a extinção da memória quando infundido imediatamente pós-teste. Além disso, aumentou os níveis de BDNF no hipocampo. Conclusão: Estes resultados indicam que eventos epigenéticos possuem um papel importante no aprendizado e na memória através da atividade de HDACs. / Introduction: Memory formation involves changes in the expression of neuronal genes. Epigenetic remodeling of chromatin and reversible post-translational modifications in the DNA or in the histone proteins represent central mechanisms in the regulation of gene expression during brain development and early learning or memory retrieval. Imbalances in the levels of histone acetylation are associated with a wide variety of brain disorders. Histone deacetylases (HDACs) play a key role in homeostasis of histone acetylation and regulation of fundamental cellular activities, such as transcription, making them a focus of study. Evidences shows that the administration of histone deacetylases inhibitors (HDACis) restore the memory associated with the regulation of gene expression and improves memory in rats. Studies in animal models have shown that memory formation involves a series of biochemical changes in several areas of the central nervous system, which the hippocampus and basolateral amygdala (BLA) are the most highlighted. In this context, experimental drugs, such as trichostatin A (TSA), that act on epigenetic mechanisms, have recently been proposed as potential therapies for the treatment of memory and cognitive dysfunction associated with psychiatric and neurological disorders. Objective: In this work we aimed to understand and elucidate the role of histone acetylation in processes involved in memory modulation using the drug TSA and is based on the hypothesis that HDACs activity is essential for the modulation of learning answers in the inhibitory avoidance (IA) task. Methods: Wistar rats were cannulated bilaterally in the amygdala. The effects of TSA micro-infusions into the BLA were observed in the consolidation and extinction of memory after training in the inhibitory avoidance task and the levels of brain-derived neurotrophic factor (BDNF) in the BLA and hippocampus related to memory consolidation. Results: The results demonstrated that the TSA infusion into BLA 1.5 h , 3 h and 6 h posttraining in the inhibitory avoidance task results in improved long-term memory (LTM). TSA accelerated the extinction of memory when infused immediately post-test. In addition, increased levels of BDNF in the hippocampus. Conclusion: These results indicate that epigenetic events play an important role in learning and memory by HDAC activity.

Les qualités intrinsèques spermatiques (état de condensation de la chromatine, intégrité de l’ADN, contenu chromosomique, capacités fécondantes..) sont très variables d’un spermatozoïde à l’autre. Le pari aujourd’hui en assistance médicale à la procréation est de relier un aspect morphologique spermatique à ces qualités intrinsèques dans le but de mieux choisir le spermatozoïde vivant à injecter et d’améliorer les taux de grossesse. Depuis 2002, le MSOME (Motile Sperm Organelle Morphology Examination) permet d’observer les spermatozoïdes à fort grossissement, en contraste interférentiel de Nomarski et d’observer des structures qu’on appelle les « vacuoles ». L’injection intra-ovocytaire de spermatozoïdes sélectionnés en MSOME (IMSI) comme non porteurs de vacuoles céphaliques permettrait d’améliorer les taux de grossesses évolutives. Ici, nous avons montré que les vacuoles spermatiques correspondaient à des cratères nucléaires en lien avec une non-condensation chromatinienne (non remplacement des histones au cours de la spermiogenèse). Certaines atypies morphologiques spermatiques sont aussi en lien avec une non-condensation de la chromatine. De plus, spermatozoïdes vacuolés présentent parfois des taux de fragmentation élevés. Aucun lien n’a cependant été retrouvé entre un aspect morphologique spermatique d’une part et un contenu chromosomique ou des capacités fécondantes particulières d’autre part. De ces liens, nous avons pu dégager de nouvelles indications d’IMSI. Ainsi, nous avons avancé dans la description des critères de sélection du spermatozoïde humain vivant donnant le moins de risque d’échec d’implantation embryonnaire et/ou d’anomalies pour la descendance / Intrinsic sperm quality criteria (chromatin condensation, DNA fragmentation, chromosome content, fecundity, etc.) vary from one spermatozoon to another. It is critical to be able to link morphological aspects to these quality criteria, in order to improve the selection of high-quality, live spermatozoa and thus improve pregnancy and delivery rates. Since 2002, motile sperm organelle morphology examination has been used to screen for defects under high magnification and thus select vacuole-free spermatozoa (which are known to be associated with higher pregnancy rates in intracytoplasmic morphologically selected sperm injection (IMSI) programmes). Here, we demonstrate that sperm vacuoles are nuclear concavities associated with chromatin condensation failure (due to a lack of histone replacement during spermiogenesis). A number of other morphological abnormalities were found to be linked to chromatin condensation failure. In some cases, vacuolated spermatozoa were seen to be more DNA-fragmented than vacuole-free ones. In contrast, sperm morphology was not related to chromosomal content or fecundity characteristics. Our observations enabled us to identify new indications for IMSI and refine the criteria for selecting the best spermatozoon: the spermatozoon with the lowest risk of implantation failure or abnormalities in the offspring

Les éléments transposables (ET) et leur reliques sont des composants majeurs des génomes eucaryotes. Ils sont potentiellement hautement mutagéniques car leur prolifération peut engendrer des réarrangements chromosomiques, des interruptions de gènes ou affecter l’expression génique par interférence transcriptionnelle. Néanmoins, peu d’ET sont généralement mobiles dans les génomes grâce à l’action de mécanismes qui restreignent leur activité comme la méthylation de l’ADN chez les mammifères et les plantes. De fait, chez Arabidopsis thaliana, une perte sévère de méthylation de l’ADN causée par une mutation dans le gène codant la protéine remodeleuse de chromatine DDM1 (DECREASE IN DNA METHYLATION 1) engendre l’accumulation massive de transcrits correspondants à des séquences d’ET. En revanche, peu d’ET semblent être mobilisés suite à cette réactivation transcriptionnelle. Nous proposons ici de déterminer (1) l’étendue de la mobilisation des ET suite à la perte de méthylation de l’ADN, (2) la distribution des nouvelles insertions d’ET le long du génome d’Arabidopsis et (3) les conséquences des nouvelles insertions d’ET sur l’expression des gènes situés à proximité. Dans ce but, nous avons séquencé le génome d’une cinquantaine d’epiRIL (epigenetic Recombinant Inbred Lines) dérivées d’un croisement entre une plante sauvage et un mutant ddm1. Suite au croisement retour de la F1 avec une plante sauvage et sélection des individus F2 homozygotes pour l’allèle sauvage DDM1, les epiRIL ont été propagées au travers de 6 autofécondations successives. Les epiRIL permettent donc l’étude détaillée des évènements de transpositions juste après qu’ils aient eu lieu. Pour identifier les évènements de transpositions dans ces lignées nous avons mis au point TE-tracker, un programme basé sur les données issues du séquençage Illumina de banques maite-pair. Par cette approche, nous avons montré que les ET mobiles dans ddm1 et les epiRIL appartiennent à seulement une quinzaine environ des >300 familles identifiées dans le génome d’Arabidopsis. Qui plus est, on observe des variations importantes de fréquences et dynamiques de transpositions entre les différentes familles d’ET ce qui suggère l’existence de mécanismes additionnels contrôlant la transposition. Les analyses moléculaires réalisées sur un sous-ensemble des ET mobilisés appartenant à différentes familles ont notamment montré que ces différences sont dues en grande partie aux différentes modalités d’établissement du contrôle épigénétique sur les ET nouvellement insérés. D’autre part, nos analyses indiquent que la distribution des nouvelles insertions d’ET diffère grandement de celle des copies résidentes. Ce résultat suggère donc que la suraccumulation des séquences d’ET dans les régions péricentromériques du génome d’Arabidopsis n’est pas due à un ciblage spécifique des insertions dans ces régions, mais est plutôt la conséquence de leur élimination des bras chromosomiques. Enfin, nous avons cherché à déterminer dans quelle mesure la méthylation de l’ADN associée aux séquences répétées a un impact sur l’expression des gènes situés à proximité en étudiant des mutants affectés dans les différentes voies de la méthylation de l’ADN. Par des analyses phénotypiques et moléculaires nous avons montré que, même si la plupart des gènes d’Arabidopsis n’est pas affectée par l’état de méthylation des séquences répétées situées à proximité, deux voies de la méthylation de l’ADN agissent ensemble pour maintenir l’expression normale d’un petit nombre de gènes ayant des effets pléiotropes situés proximité de séquences répétées. La méthylation de l’ADN agit donc comme un double système de contrôle pour assurer l’expression normale d’un petit nombre de gènes clefs localisés a proximité de séquences répétées. / Transposable elements (TEs) and their relics are major components of eukaryotic genomes. TEs are potentially highly mutagenic as their proliferation can cause chromosomal rearrangements, disrupt genes or affect gene expression through transcriptional interference. However, few TEs are usually mobile within genomes at any one time thanks to potent mechanisms that restrain their activity, such as DNA methylation in mammals and plants. Thus, in the flowering plant Arabidopsis, severe loss of DNA methylation caused by mutations in the chromatin remodeler gene DDM1 triggers massive accumulation of transcripts corresponding to TEs. Yet, comparatively few TEs appear to be mobilized as a result. Here, we set out to determine (1) the extent to which DNA methylation prevents TE mobilization, (2) where do TEs insert following their reactivation and (3) what are the consequences of new TE insertions on the expression of neighboring genes. To this ends, we have sequenced the genome of over 50 epigenetic Recombinant Inbred Lines (epiRILs) that were derived from a cross between a wild type and an isogenic ddm1 mutant line. After backcrossing of the F1 and selection of the progeny homozygous for wild-type DDM1, the epiRILs were propagated through six rounds of selfing. The epiRILs therefore permit a detailed assessment of transposition events soon after they have occurred. In order to identify TE mobilization in the epiRILs we developed TE-tracker, a pipeline based on Illumina sequencing of mate pairs libraries. Using this approach, we could show that although both retroelements and DNA transposons are mobilized in ddm1 and the epiRILs, mobile TEs belong to only a dozen or so of the >300 TE families identified in the Arabidopsis genome. Furthermore the rate and dynamics of transposition vary dramatically between TE families, suggesting the existence of additional mechanisms controlling transposition. Molecular analysis performed on a subset of those mobile TEs belonging to distinct families show that these differences are greatly due to different modality of establishment of epigenetic control over newly inserted TEs. In addition, our analysis indicates that the distribution of new TE insertions differs dramatically from the one of resident copies. These findings provide compelling evidence that over accumulation of TE sequences in the pericentromeric regions of the Arabidopsis genome is not due to specific targeting of TEs, but rather to their elimination from chromosome arms. Finally, we assessed the extent to which repeat-associated DNA methylation impacts the expression of neighboring genes by studying mutants affected in different methylation pathways. Phenotypic and molecular analyses reveal that, even though most Arabidopsis genes are not detectably sensitive to the methylation status of neighboring repeats, two DNA methylation pathways act together to maintain the normal expression of only a very small number of genes near repeats and that these genes tend to have pleiotropic effects. Then, DNA methylation acts as a double-lock system to ensure the normal expression of a small number of key genes located near repeats.

Le génome humain est constamment la cible d'agents qui endommagent l'ADN. Ces dommages sont multiples et variés tels que les cassures simple et double brin (DSB). Les DSBs sont des lésions très toxiques dont l'origine peut être multiple. Les cellules de mammifères réparent les DSBs en utilisant deux mécanismes principaux, la recombinaison homologue (RH) qui est dépendante du cycle cellulaire et utilise la chromatide sœur comme matrice de réparation et la jonction des extrémités non homologues (NHEJ) qui est indépendante du cycle cellulaire et consiste en la ligation des extrémités d'ADN endommagées. Cette réparation a lieu dans un contexte chromatinien qui nécessite un dynamisme pour rendre accessible les sites lésés aux différentes machineries de réparation. Lors de mes travaux, j'ai étudié le remodeleur de la chromatine p400 ainsi que le variant d'histone H2A.Z qui sont deux protéines impliquées dans la dynamique de la chromatine, afin de comprendre leur rôle dans les mécanismes de réparation des DSBs et la stabilité du génome. p400, une ATPase de la famille SWI2/SNF2 participe à l'incorporation du variant d'histone H2A.Z dans la chromatine. Au cours de ma thèse, j'ai montré que la déplétion par siRNA du variant d'histone H2A.Z, dans la lignée d'ostéosarcome humain (U2OS) et dans des fibroblastes humains immortalisées, n'a pas d'effets sur la réparation des DSBs. Ces résultats sont corrélés avec une absence de recrutement de H2A.Z au niveau des cassures après étude par micro irradiation laser ou par immunoprécipitation de chromatine. Cependant, la déplétion de H2A.Z affecte la prolifération cellulaire en influençant l'efficacité de clonage et le cycle cellulaire. L'autre partie de mes travaux a mis en évidence que l'ATPase p400 est un frein à l'utilisation de la voie alternative de jonction des extrémités (alt-EJ) qui est un processus de réparation des DSBs très mutagène. L'augmentation des événements du NHEJ-Alternatif et la génération d'instabilité génétique observés lors de la déplétion de p400 par siRNA semblent tributaires de la résection des DSBs par CtIP. Ces résultats indiquent que p400 joue un rôle post-résection dans les étapes plus tardives de la RH. De plus, la déplétion de p400 conduit au recrutement de la polyADP ribose polymérase (PARP) et de l'ADN ligase 3 à la DSB, ce qui provoque la mort sélective de ces cellules lors d'un traitement par des inhibiteurs de PARP. Ces résultats montrent que P400 agit comme un frein pour empêcher l'utilisation du NHEJ-Alternatif et donc l'instabilité génétique. / The human genome is constantly targeted by DNA damaging agents. These damages are many and varied, such as single and double strand breaks (DSBs). The DSB are highly toxic lesions whose origin can be multiple. Mammalian cells mainly use two DNA repair pathways to repair DSB, homologous recombination (RH), which is dependent on the presence of the intact homologous copy (the sister chromatid) and on the cell cycle stage and the non-homologous end joining (NHEJ) pathway, which is cell cycle independent and performs direct ligation of the two DNA ends. The repair of DNA damage takes place in a chromatin context that needs to be remodeled to give access to damaged sites. During my work, I studied the chromatin remodeler p400 and the histone variant H2A.Z both involved in chromatin remodeling, to understand their role in DSB repair and genome stability. p400, an ATPase of the SWI2/SNF2 family is involved in the incorporation of H2A.Z in chromatin. I have shown that H2A.Z depletion in the osteosarcoma cell line U2OS and in immortalized human fibroblasts did not alter DSB repair. These results are correlated with the lack of H2A.Z recruitment at DSB observed after local laser irradiation or Chromatin Immunoprecipitation. However, H2A.Z depletion affects cell proliferation and the cell cycle distribution. In addition, I have shown that the chromatin remodeler p400 is a brake to the use of alternative End Joining (alt-EJ) which is a highly mutagenic repair process. The increase in alt-EJ events observed in p400-depleted cells is dependent on CtIP- mediated resection of DNA ends. Moreover, p400 depletion leads to the recruitment of poly(ADP) ribose polymerase (PARP) and DNA ligase 3 at DSB, leading to selective cell killing by PARP inhibitors. Altogether these results show that p400 acts as a brake to prevent alt-EJ dependent genetic instability and underline its potential value as a clinical marker.

Orientador: Willian Fernando Zambuzzi / Resumo: As células endoteliais (ECs) e células musculares lisas (AoSMCs) são os principais componentes celulares do endotélio. As interações entre estes tipos celulares desempenham funções na homeostase e na estrutura vascular. Como uma interface entre o sangue e a parede do vaso, as ECs ocupam um local único diretamente exposto ao shear stress (SS), a força mecânica de atrito lateral produzido pelo fluxo de sangue na membrana apical da célula endotelial, que pode influenciar o comportamento de ambas ECs e AoSMCs. Geralmente, AoSMCs não sofrem diretamente às forcas de cisalhamento, no entanto, estas são diretamente expostas ao fluxo sanguíneo quando ocorre alguma injúria vascular, como por exemplo em algumas lesões ateroscleróticas ou por técnicas invasivas, como a angioplastia. As forças hemodinâmicas influenciam as propriedades funcionais do endotélio, porém estas não são profundamente compreendidas quanto aos mecanismos bioquímicos de respostas de células endoteliais e de musculatura lisa. Assim, a proposta desta dissertação foi estabelecer um modelo de cultivo in vitro que mimetize as forças tensionais de cisalhamento (shear stress), buscando compreender mecanismos celulares, bioquímicos e epigenéticos. Cultura de células primárias endoteliais e de musculatura lisa humanas foram obtidas da empresa LONZA e mantidas conforme recomendações do fabricante. Estas células foram mantidas rotineiramente em condições convencionais em incubadora de CO2. Para mimetizar o fluxo sanguíneo, esta... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre