O carcinoma hepatocelular (HCC) é a 3ª causa de morte por neoplasias no mundo, sendo também o 5º tipo de neoplasia mais frequente. Seu tratamento limitado juntamente com o mau prognóstico tornam importante a adoção de medidas preventivas. A prevenção das etapas iniciais da hepatocarcinogênese pela administração de compostos bioativos de alimentos (CBAs) atualmente vem sendo observada em diversos estudos. Sugere-se que o processo de carcinogênese envolva alterações genéticas e epigenéticas, como a hipometilação do DNA e a desacetilação de histonas. Nesse sentido, o tratamento com ácido fólico (AF), precursor indireto de grupamento metil, e tributirina (TB), inibidora de enzimas desacetilases de histonas, quando em associação, poderia agir em adição potencializando os efeitos quimiopreventivos dos mesmos comparados às suas ações isoladas. A eventual atividade quimiopreventiva da TB (100mg/100g de peso corpóreo), do AF (0,08mg/100g de peso corpóreo), ambos com a metade da dose utilizada na literatura, e da associação entre os mesmos (AS) foi analisada durante a etapa de promoção da hepatocarcinogênese em ratos Wistar submetidos ao modelo do hepatócito resistente (HR). Para avaliação de GST-P, da proliferação celular, da apoptose, bem como a localização da histona H3K9 foi utilizada a técnica de imunohistoquímica; para a quantificação de H3K9, western blot. Em relação à análise macroscópica, os grupos tratados apresentaram menor número de nódulos em relação a MD (sem significância estatística), além de menor porcentagem de LPN menores do que 1mm nos grupos TB e AS. Na análise microscópica foi observado que os grupos TB, AF e AS apresentaram menor número de lesões pré neoplásicas persistentes (pLPN) em relação ao grupo controle isocalórico (MD, maltodextrina), assim como menor porcentagem de área ocupada por pLPN e por lesões em remodelação (rLPN). Quanto a proliferação celular, os grupos AF e AS apresentaram menor número de núcleos em fase S/mm2 quando comparados aos grupos MD e TB. Em relação à apoptose, os grupos TB e AS apresentaram maior número de hepatócitos em apoptose e corpúsculos apoptóticos/mm2 quando comparados aos grupos MD e AF. No resultado da metilação global do DNA não houve diferença entre os grupos. Em adição, os grupos AF e AS apresentaram maiores concentrações séricas de folato; o mesmo não ocorrendo para B12. No que diz respeito à acetilação de H3K9, os grupos TB e AS apresentaram maior porcentagem de acetilação quando comparados aos grupos N, MD e AF. Em conclusão, os grupos tratados com TB, AF e a associação entre eles apresentaram quimioprevenção pronunciada, sendo que o grupo AS apresentou mecanismos aditivos dos tratamentos isolados. / The hepatocellular carcinoma (HCC) is the third leading cause of death by cancer in the world, and the fifth most frequent type of neoplasm. Its limited treatment along with poor prognosis make it important to adopt preventive measures. The prevention of the initial stages of hepatocarcinogenesis by the administration of bioactive food compounds (BFCs) is currently being observed in several studies. It is suggested that the process of carcinogenesis involves genetic and epigenetic modifications, such as DNA hypomethylation and deacetylation of histones. Accordingly, treatment with folic acid (FA), indirect precursor of methyl grouping, and tributyrin (TB), a histone deacetylases inhibiting enzyme, when associated could act in addition to enhance the chemopreventive effects compared to their isolated actions. The possible chemopreventive activity of TB (100mg/100g body weight), FA (0.08 mg/100 g body weight) and the association between them (AS) were studied during the promotion stage of hepatocarcinogenesis in Wistar rats submitted to resistant hepatocyte model (RH).For evaluation of GST-P, cell proliferation, apoptosis, and the location of histone H3K9 was used immunohistochemistry, to quantify H3K9, western blot. Regarding the macroscopic analysis, the treated groups showed a lower number of nodules compared to MD (not statistically significant), and a lower percentage smaller than 1mm in groups TB and AS. Under microscopic examination the groups TB, FA and AS showed a lower number of persistent pre-neoplastic lesions (pLPN) compared to the isocaloric control group (MD, maltodextrin), as well as a lower percentage of the area occupied by pLPN and remodeling lesions (rLPN). As cell proliferation, FA and AS groups had fewer S phase nuclei/mm2 compared to MD and TB groups. Regarding apoptosis, TB and AS groups showed higher numbers of hepatocytes in apoptosis and apoptotic corpuscles/mm2 compared to MD and FA groups. Global DNA methylation did not differ between groups. In addition, AF and AS groups had higher serum concentrations of folate, which did not occur for B12.Concerning the H3K9 acetylation, the groups TB and AS showed higher percentage of acetylation when compared with the groups N, MD and FA. In conclusion, the groups treated with TB, FA and the association of both showed pronounced chemoprevention, and the AS group showed additive mechanisms compared with isolated treatments.

Fatores dietéticos como o selênio (Se) são apontados como importantes moduladores do risco de desenvolvimento do câncer de mama. Essa neoplasia pode apresentar sua origem no início do desenvolvimento e, assim, a alimentação materna poderia ter importantes repercussões na programação fetal da doença. A fim de verificar se diferentes concentração de selênio na dieta materna poderiam programar o risco da progênie feminina ao câncer de mama, ratas foram alimentadas com ração contendo 0,15 (CO), 1,0 (SUP) ou 0,05 (DEF) ppm de Se durante a gestação e sua progênie feminina iniciada com DMBA. A progênie do grupo SUP apresentou menor suscetibilidade à carcinogênese, indicado pelo menor número médio e multiplicidade de adenocarcinomas mamários (p< 0,05), enquanto a do grupo DEF apresentou maior suscetibilidade à carcinogênese, indicado pela maior incidência dos mesmos (p< 0,05). Mães do grupo DEF apresentaram menor concentração de Se no sangue (p< 0,05) e sua prole apresentou menor atividade da enzima GPx1 (p< 0,05). Além disso, observou-se na glândula mamária da progênie de 50 dias menor expressão (western blot e qPCR) de ER&#945;, Her-2, EGFR e Ras no grupo SUP em comparação aos grupos CO e DEF (p< 0,05). Analisou-se, ainda, o padrão de metilação global do DNA (HPLC-DAD), expressão das enzimas DNMT1, 3a e 3b (qPCR), o padrão global de modificações pós traducionais em histonas (western blot) e o padrão de metilação da região promotora do gene Er&#945; (modificação com bissulfito e pirossequenciamento) na glândula mamária da progênie de 50 dias. Não houve diferença no padrão de metilação global do DNA e expressão das enzimas DNMTs (p>0,05). Houve aumento na expressão de H4K16 acetilada nos grupos SUP e DEF (p< 0,05). Finalmente, em comparação a progênie do grupo DEF, a do grupo SUP apresentou região promotora de Er&#945; com aumento marginal (p=0,07) na metilação de dois dinucleotídeos CpG. Conclui-se que o consumo de diferentes concentrações de Se na dieta materna tem impacto sobre a suscetibilidade da progênie ao câncer de mama na vida adulta através da modulação da expressão de receptores e oncogenes relacionados ao desenvolvimeto dessa neoplasia, além da influência em processos epigenéticos. Tais resultados apontam para a existência de uma \"janela de programação\" no início do desenvolvimento sensível a ação do Se, resultando em diminuição do risco de câncer de mama quando suplementado na dieta materna e o inverso quando de sua deficiencia. / Based on epidemiological studies and animal models, the essential micronutrient selenium has been highlighted as a promising dietary factor associated to breast cancer risk reduction. Breast cancer may have its origin in early development and thus the maternal diet could have important implications in the fetal programming of the disease. In order to ascertain whether differences in selenium concentration in maternal diet could modulate the susceptibility of female offspring to breast cancer, a biological assay was conducted in which female rats were fed a diet with 0.15 (CO), 1.0 (SUP) or 0.05 (DEF) ppm of selenium during gestational period and the female offspring subjected to a mammary carcinogenesis model induced by DMBA. SUP group offspring presented decreased susceptibility to mammary carcinogenesis, as indicated by lower (p< 0,05) average number and multiplicity od adenocarcinomas, while the DEF group offspring had a greater susceptibility, as indicated by the increase (p< 0,05) in adenocarcinomas incidency. Mothers of the DEF group pesented lower (p< 0,05) Se blood concetrations and their offspring presented lower (p<0,05).GPx1 activity. In addition, there was a decrease (p< 0,05) in ER&#945;, Her-2, EGFR and Ras expression (western blot and qPCR) in the mammary gland of 7 weeks old female SUP group offspring when compared to CO and DEF groups offspring. DNA global methylation pattern (HPLC-DAD), DNMT1, 3a e 3b expression (qPCR), global pattern of post-translational modification in histones (western blot) and methylation status of Er&#945; promoter region (bisulfite modification and pyrosequencing) were also evaluated in the mammary gland of 7 weeks old offspring. There was no diffrence (p>0,05) in DNA global methylation pattern and DNMTs expression. There was an increase in acetilated H4K16 expression in groups SUP and DEF (p< 0,05). Lastly, when compared to DEF offspring, the SUP offspring presented a marginal increase in the methylation of two CpG dinucleotides in the Er&#945; promoter region. In conclusion, the consumption of different selenium concentration in maternal diet plays a role in the progeny\'s breast cancer susceptibility through the modulation of receptors and oncogenes expression, in addition to modifications in epigenetic patterns. These results indicate the presence of a \"programming window\" in the beggining of development susceptible to selenium effects, resulting in decreased breast cancer risk when supplemented and the opposite when deficient.

A leucemia linfóide aguda (LLA) é a neoplasia hematológica mais comum na infância e representa uma doença heterogênea em relação à biologia e ao prognóstico e seu tratamento consiste principalmente em quimioterapia. Apesar dos avanços no tratamento, cerca de 20% dos pacientes apresentam recaída da doença e/ou óbito indicando a necessidade de terapias diferenciadas para esse grupo. Recentemente, drogas epigenéticas como inibidores de DNA metiltransferases (iDNMTs) tem mostrado efeitos anti-neoplásicos promissores para o tratamento de diversos tipos de neoplasias incluindo a LLA. Nos tumores, a hipermetilação gênica é encontrada em vários genes, incluindo genes de reparo do DNA, reguladores do ciclo celular e apoptose. Sendo assim, drogas desmetilantes estão sendo apontadas como promissores agentes para o tratamento do câncer. A Zebularina (ZB) é um iDNMT análogo de citidina que inibe a metilação do DNA. Esta droga tem mostrado resultados animadores para o tratamento de diversas neoplasias, incluindo glioblastoma, leucemia mielóide aguda, câncer de mama, próstata e outros. O objetivo deste trabalho foi avaliar os efeitos do tratamento com a ZB, associada ou não à quimioterápicos, em linhagens celulares pediátricas de LLA, por meio de ensaios funcionais como proliferação celular, capacidade clonogênica, apoptose e ciclo celular. Além disso, foi analisada a capacidade desmetilante da droga e a expressão dos genes DNMT1, DNMT3a e DNMT3b após o tratamento com a ZB. A ZB inibiu a proliferação celular de maneira dose e tempo-dependente e agiu sinergicamente quando combinada com o MTX em ambas as linhagens. Ela também diminuiu a capacidade clonogênica e aumentou a taxa de apoptose nas duas linhagens estudadas. Além disso, o tratamento com ZB causou uma parada na fase S do ciclo celular na linhagem ReH. A ZB foi capaz de desmetilar parcialmente o gene AhR e reduzir a expressão dos genes DNMT1, DNMT3a e DNMT3b. Todos os dados encontrados no presente trabalho sugerem que as drogas desmetilantes podem ser interessantes agentes para o tratamento da LLA pediátrica. / Acute lymphoblastic leukemia (ALL) is the most common hematologic malignancy in childhood and represents a heterogeneous disease regarding its biology and prognosis. Its treatment consists mainly of chemotherapy. Despite advances in treatment, about 20% of patients experience disease recurrence and/or death indicating the need for differentiated therapies for this group. Recently, epigenetic drugs such as DNA methyltransferases inhibitors (iDNMTs) has shown antineoplastic and promising results for several types of tumors including ALL. Gene hypermethylation is found in several genes in tumors cells, including genes responsible for DNA repair, cell cycle and apoptosis regulators. Therefore, demethylating agents may be promising agents for cancer treatment. Zebularine (ZB) an iDNMT is a cytidine analogue that inhibits DNA methylation. This drug has shown promising results for the treatment of many cancers, including glioblastoma, acute myeloid leukemia, breast and prostate cancer and others. The aim of this study was to evaluate the effects of ZB treatment, associated or not with chemotherapeutic agents, in childhood ALL cell lines through functional tests such as cell proliferation, clonogenic capacity, apoptosis and cell cycle. In addition, we examined the demethylating ability of ZB and the expression of DNMT1, DNMT3a and DNMT3b genes after treatment with this agent. ZB inhibited cell proliferation in a dose- and time-dependent manner and showed synergistic effects when combined with MTX in both cell lines. ZB treatment also reduced clonogenic capacity and increased the number of apoptotic cells in both cell lines studied. Furthermore, treatment with ZB caused an S phase cell cycle arrest in ReH cell line. ZB was able to partially demethylate AhR gene and reduce the expression of genes DNMT1, DNMT3a and DNMT3b. These results suggest that demethylating drugs may be interesting agents for the treatment of childhood ALL.

Orientador: Fabíola Traina / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-24T22:39:22Z (GMT). No. of bitstreams: 1 Scopim-Ribeiro_Renata_M.pdf: 3643524 bytes, checksum: fec865c6ccea452efda050e40c6f1aa1 (MD5) Previous issue date: 2014 / Resumo: As neoplasias mieloides compreendem um grupo heterogêneo de doenças hematológicas que se originam de um precursor mieloide comum, em diferentes fases de diferenciação. As alterações celulares que levam ao desenvolvimento de neoplasias podem ocorrer através de mecanismos epigenéticos ou de alterações genéticas. DNMT3A codifica metiltransferases que adicionam grupamentos metil a resíduos de citosina do DNA e TET2 promove a hidroxilação da citosina metilada, o que os caracteriza como elementos importantes no controle epigenético. DNMT3A e TET2 encontram-se frequentemente mutados em neoplasias mieloides, mas o impacto prognóstico destas mutações ainda é controverso. A consequência funcional da mutação de DNMT3A em neoplasias mieloides ainda não foi definida, mas o silenciamento da proteína em células progenitoras murinas favorece a autorrenovação e compromete a diferenciação celular. A mutação de TET2 tem como consequência a perda de função do gene e participa da transformação neoplásica das células mieloides, favorecendo a proliferação da série mielomonocítica. Entretanto, a expressão de TET2 e DNMT3A nestas doenças ainda é pouco elucidada. Assim, os objetivos deste estudo foram (1) investigar a expressão de TET2 e DNMT3A em células hematopoéticas de indivíduos normais e pacientes com síndrome mielodisplásica (SMD) e leucemia mieloide aguda (LMA), (2) correlacionar a expressão de TET2 e DNMT3A com o fenótipo clínico e sobrevida de pacientes com SMD; (3) investigar a expressão de TET2 e DNMT3A durante a diferenciação celular hematopoética e (4) avaliar o efeito do silenciamento de DNMT3A no fenótipo de linhagens celulares leucêmicas. No presente estudo, verificamos redução na expressão de TET2 em células provenientes de pacientes com SMD e LMA quando comparada à expressão em controles normais (p<.001), e redução em SMD alto risco quando comparada à SMD baixo risco (p=.02). Os resultados em amostras sequenciais de cinco pacientes com SMD indicaram redução da expressão de TET2 no momento da progressão da doença. A análise univariada evidenciou que fatores clínicos tiveram impacto tanto na sobrevida livre de evento como sobrevida global, incluindo a classificação de risco pela OMS 2008 (alto vs. baixo, p<.0001), IPSS (int-2/alto vs. baixo/int-1, p<.0001), hemoglobina (<10 vs. ? 10, p<.05), contagem de leucócitos (< 3 vs. ? 3 x109/L, p<.05), contagem absoluta de neutrófilos (< 1.5 vs. ? 1.5, p<.05) e porcentagem de blastos na medula óssea (? 5 vs. <5 ou ? 10 vs. <10, p<.0004). Além disso, a baixa expressão de TET2 teve impacto negativo na sobrevida livre de evento (HR: 6.51 [2.42-17.49], p=.0002) e na sobrevida global (HR: 7.25 [2.77-18.99], p<.0001). A análise multivariada indicou que a baixa expressão de TET2 (p <.0001), IPSS alto/intermediate-2 (p <.0001), e hemoglobina <10 g/dL (P<.03) são fatores prognósticos para menor sobrevida livre de evento e sobrevida global. Durante a diferenciação eritroide de células CD34+ de indivíduos normais e pacientes com SMD, observamos um aumento significativo da expressão de TET2 (p=. 03). Na avaliação da diferenciação celular de linhagens leucêmicas, observamos aumento significativo na expressão de TET2 durante as diferenciações granulocítica (p=.04) e megacariocítica (p=.03); e um aumento não significativo durante a diferenciação eritrocítica. A expressão de DNMT3A foi semelhante entre pacientes com LMA, SMD e controles normais, e não teve impacto significativo na sobrevida dos pacientes com SMD. A expressão de DNMT3A não foi modulada durante a diferenciação eritroide de células CD34+ de indivíduos normais e pacientes com SMD. Nos modelos de diferenciação celular de linhagens leucêmicas, observamos aumento significativo da expressão de DNMT3A durante a diferenciação granulocítica, mas não durante a diferenciação eritrocítica e megacariocítica. A redução na expressão de DNMT3A não resultou em alteração significativa na apoptose, na proliferação e no ciclo celular em linhagens leucêmicas HL60 e U937. A expressão gênica e proteica de PTEN não foi modulada em células leucêmicas submetidas à inibição de DNMT3A. Os achados aqui descritos sugerem que, similarmente à presença de mutação no TET2, a baixa expressão de TET2 pode participar do processo de transformação celular em SMD de alto risco e LMA; estudos clínicos deveriam considerar a investigação da expressão gênica de TET2 em conjunto com a pesquisa de mutação TET2 na definição de prognóstico. Os resultados de expressão e função de DNMT3A sugerem que a mutação, e não a expressão, deva ser o principal mecanismo pelo qual o DNMT3A participa da transformação neoplásica e que a função de DNMT3A pode depender da linhagem celular estudada / Abstract: Myeloid neoplasms comprise a heterogeneous group of hematologic malignancies that originate from a common myeloid precursor at different stages of differentiation. Cellular changes that lead to development of malignancies may occur through epigenetic mechanisms or genetic alterations. DNMT3A encodes methyltransferases that add methyl groups to cytosine residues in DNA, TET2 promotes hydroxylation of methylated cytosine, and both proteins are important elements in epigenetic control. TET2 and DNMT3A are recurrently mutated in myeloid malignancies, but the prognostic consequence of TET2 and DNMT3A mutation is still controversial. The functional consequences of DNMT3A mutation has not been defined, but the protein silencing in murine progenitor cells promotes self-renewal and reduces cell differentiation. TET2 mutation results in loss of function and participates in the neoplastic transformation of myeloid cells, favoring the proliferation of granulomonocytic cells. However, the expression of TET2 and DNMT3A in these diseases has been rarely addressed. Then, the aims of this study were (1) to evaluate TET2 and DNMT3A gene expression in hematopoietic cells from healthy individuals and from patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML); (2) to correlate TET2 and DNMT3A expression with clinical phenotype and outcomes of MDS patients; (3) to investigate TET2 and DNMT3A expression during hematopoietic cell differentiation; and (4) to evaluate the effect of DNMT3A silencing in the phenotype of leukemia cell lines. In this study, the expression of TET2 was decreased in cells from patients with MDS and AML compared to healthy donors (p<.001) and reduced high-risk MDS compared to low risk MDS (p=.02). The results in sequential samples from five patients with MDS indicate reduced expression of TET2 at the time of disease progression. By univariate analysis, clinical factors that significantly affected both event free survival (EFS) and overall survival (OS) included risk stratification by WHO 2008 (high vs. low, p<.0001), IPSS (int-2/high vs. low/int-1, p <.0001), hemoglobin (<10 vs. ? 10, p<.05), white blood cell counts (< 3 vs. ? 3 x109/L, p<.05), absolute neutrophil counts (< 1.5 vs. ? 1.5, p<.05) and bone marrow blast percentage (? 5 vs. <5 or ? 10 vs. <10, p<.0004). Furthermore, low TET2 expression negatively impacted both EFS (HR: 6.51 [2.42-17.49], p=.0002) and OS (HR: 7.25 [2.77-18.99], p<.0001). Multivariate analyses indicated that low TET2 expression (p <.0001), along with IPSS high/intermediate-2 risk group (p <.0001), and hemoglobin <10 g/dL (p<.03) were independently prognostic for worse EFS and OS. During erythroid differentiation of CD34+ cells from normal individuals and patients with low-risk MDS, we observed an increased expression of TET2 (p=.03). During cell differentiation of leukemic cell lines, we observed a significantly increase in the expression of TET2 during granulocytic and megakaryocytic differentiation (p=.04 and p=.03, respectively); there was also an increased expression during erythrocytic differentiation, but this was not statistically significant. The expression of DNMT3A was similar between patients with AML, MDS and healthy donors, and it did not impact survival outcomes in MDS patients. DNMT3A expression was not modulated during erythroid differentiation of CD34+ cells from normal individuals and patients with MDS. In leukemic cell lines models of differentiation, we observed a significantly increase in the DNMT3A expression during granulocytic differentiation, but not in erythrocytic and megakaryocytic differentiation. The DNMT3A silencing did not result in significant changes in apoptosis, proliferation and cell cycle in leukemic cell lines HL60 and U937. PTEN gene and protein expression was not modulated in leukemic cell lines submitted to inhibition of DNMT3A. The findings reported here suggest that, similarly to the presence of TET2 mutations, the low expression of TET2 can participate in the process of cell transformation in high risk MDS and AML. Clinical studies should consider the investigation of TET2 expression together with the studies of TET2 mutation to defining prognosis. Our results of expression and function suggest that DNMT3A mutation, instead of the expression, should be the main mechanism by which DNMT3A participates in neoplastic transformation and that DNMT3A function may vary according to the cell line studied / Mestrado / Clinica Medica / Mestra em Ciências

Orientador: Maria Luiza Silveira Mello / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-20T21:08:55Z (GMT). No. of bitstreams: 1 Felisbino_MarinaBarreto_M.pdf: 5744960 bytes, checksum: 792f3ed20bbe7d53c917089733be679f (MD5) Previous issue date: 2012 / Resumo: O ácido valproico (VPA) é um potente anti-convulsante conhecido como inibidor de deacetilases de histonas (HDACi) de classe I em diversos tipos celulares. Buscando conhecer se a estrutura cromatínica se alteraria quando da ação de HDACi, investigamos a supraorganização cromatínica de células tumorais HeLa e de células NIH 3T3, estas últimas caracterizadas por apresentarem áreas de heterocromatina conspícuas, sob tratamento com VPA. Essas informações foram associadas a da atividade enzimática de HDACs assim como do nível de acetilação das histonas H3 nesses modelos celulares tratados por VPA. As frequências de anomalias cromossômicas, morte celular e índices mitóticos também foram investigados. As células tratadas com VPA nas concentrações 0,05, 0,5 e 1,0 mM por 1-24 h foram submetidas à reação de Feulgen e analisadas através de microespectrofotometria de varredura automática e microscopia óptica. Western blots, análises enzimáticas e ensaio TUNEL também foram utilizados neste estudo. Células tratadas com tricostatina A (TSA), uma HDACi de atividade mais ampla do que o VPA, foram utilizadas como controles positivos. Em todas as condições de tratamento com VPA e TSA foi demonstrada descompactação cromatínica acompanhada de diminuição na atividade de HDACs e aumento na acetilação de histona H3. Essa alteração textural cromatínica também atingiu áreas heterocromáticas de células NIH 3T3. Nenhuma alteração nas frequências de anomalias cromossômicas, índices mitóticos e morte celular foi observada nesses modelos celulares nas condições relatadas, embora tenha ocorrido um aumento de fragmentação de DNA em células HeLa tratadas com VPA por 24 h e por TSA a partir de 4 h. Diminuição na proliferação celular nas células HeLa ocorreu apenas sob tratamento com VPA 5,0 mM por 48 h. Os resultados indicam que o VPA e a TSA promovem remodelação cromatínica em células tumorais HeLa e em células fibroblásticas NIH 3T3, que pode ser atribuída à sua ação de HDACi. Não se pôde descartar, porém, que o VPA atue sobre outras proteínas nucleares, cuja expressão poderia se apresentar diminuída sob sua ação / Abstract: Valproic acid (VPA) is a potent anticonvulsant that inhibits class I histone deacetylases (HDACi) in several cell types. Seeking to know whether the chromatin structure would change when the action of HDACi, we investigated whether VPA would affect chromatin supraorganization of tumoral HeLa cells and NIH 3T3 cells, this latter characterized by presenting areas of conspicuos heterochromatin. This information was associated with enzymatic activity of HDACs as well as the level of H3 histone acetylation in these cell models treated with VPA. The frequency of chromosome abnormalities and cell death and mitotic indices were also investigated. VPA-treated cells at concentration 0.05, 0.5 and 1.0 mM for 1-24 h were subjected to the Feulgen reaction and analysed by automatic scanning microspectrophotometry and optical microscopy. Western blots, enzymatic analysis and TUNEL assay were also performed in this study. Trichostatin A (TSA)-treated cells, an HDACi whose activity is broader than VPA, were used as positive control. Chromatin decondensation was demonstrated under all TSA and VPA treatments and was associated with decrease in HDAC activity and with increase in the level of H3 histone acetylation. This chromatin textural change also affected heterochromatic areas of NIH 3T3 cells. No changes in chromosome abnormalities, mitotic indices or morphologically identified cell death were found in both cellular models with the VPA treatment conditions mentioned above, although there was an increase of DNA fragmentation after a 24 h-VPA treatment and a 4 h-TSA treatment in HeLa cells. Decrease in cell proliferation in HeLa cells ocurred only under a 5.0 mM 48 h-VPA treatment. The results indicate that VPA and TSA promote chromatin remodeling in tumoral HeLa cells and fibroblastic NIH 3T3 cells, which may be attrituted to their HDACi action. It may not be discarded, however, that VPA acts on other nuclear proteins whose expression could be reducted under its action / Mestrado / Biologia Celular / Mestre em Biologia Celular e Estrutural

Técnicas de reprodução assistida (TRAs) são utilizadas tanto na medicina humana quanto na medicina veterinária com o objetivo principal de corrigir infertilidades adquiridas ou herdadas. A transferência nuclear de célula somática (TNCS) ocupa um lugar de destaque na veterinária pela possibilidade de geração de indivíduos geneticamente idênticos, permitindo a produção de rebanhos homogêneos de alto mérito genético e servindo como modelo de estudo para técnicas de reprogramação. Porém, a utilização de TRAs, e em especial da TNCS, é considerada responsável pelo aumento na geração de conceptos portadores de alterações durante e após o desenvolvimento embrionário e fetal. A provável causa principal é a alteração na regulação da reprogramação epigenética devido à manipulação de gametas e embriões no período inicial do desenvolvimento, levando a alterações na regulação epigenética de genes imprinted. O presente estudo teve como objetivo principal avaliar marcas epigenéticas e expressão de genes imprinted no desenvolvimento de conceptos bovinos produzidos por TNCS ou inseminação artificial (IA). Para tal, foram coletadas amostras de tecido muscular e membranas corioalantoideana e amniótica de animais na fase pré natal (fetal) e tecidos muscular, nervoso e hepático na fase pós natal (animais nascidos saudáveis adultos ou não) de animais derivados de IA ou TNCS. Foi analisada a expressão dos genes imprinted H19, IGF2, IGF2R e Airn quando possível, assim como a metilação do DNA no locus H19/IGF2 na fase pós natal. Foi observado que na fase pré natal não foi detectada expressão do IGF2, enquanto que a expressão de H19 é aumentada em relação ao IGF2R, porém, sem diferenças entre os grupos nos tecidos estudados. Na fase pós natal, o padrão de expressão dos genes IGF2, H19 e IGF2R indica diminuição da expressão gênica relativa no fígado de animais TNCS e no aumento da expressão gênica do H19 na musculatura de animais adultos (saudáveis) bovinos produzidos por TNCS, apesar de o padrão de metilação dos genes imprinted IGF2/H19 não ser diferente entre organismos considerados saudáveis e não saudáveis. Os resultados deste projeto contribuem para o entendimento dos mecanismos epigenéticos relacionados ao desenvolvimento embrionário e fetal, em especial aqueles relacionados à dinâmica das alterações epigenéticas envolvidas no imprinting genômico / Assisted reproductive technologies (ARTs) are usually used in both human and veterinary medicine aiming the correction of heritable or acquired infertilities. The somatic cell nuclear transfer technique (SCNT) is of particular importance in veterinary as it enables the generation of genetically identical organisms, allowing the production of homogeneous genetically improved herds, and also serving as a model for reprogramming studies. However, the use of TRAs, SCNT in special, may be responsible for the increase of developmental-related abnormalities in the conceptuses. Such phenotypes are probably caused by a disruption during the epigenetic reprogramming due to the manipulation of gametes and embryos during the early development period, and therefore leading to disturbances in the epigenetic regulation of imprinted genes. The present study aimed to evaluate epigenetic marks and expression of imprinted genes in different developmental periods of cattle generated by SCNT or artificial insemination (AI). For that, corionic/alantoic and amniotic membranes from fetuses and muscular, nervous and hepatic tissues from born animals, healthy (adult) or not, produced by SCNT or AI were collected. The expression of the imprinted genes H19, IGF2, IGF2R and Airn was analyzed as well as the DNA methylation at locus H19/IGF2 in post-natal period. It was observed that IGF2 was not detected during pre-natal period, whereas H19 expression is increased when compared to IGF2R in the groups studied herein. At post-natal period the IGF2, H19 and IGF2R expression patterns infers the decrease of relative gene expression in the liver and the increase of H19 expression in the muscle of SCNT adult animals. The methylation pattern of IGF2/H19 locus, however, did not differ between healthy or not animals. The results described herein may contribute to the understanding of the epigenetic mechanisms related to embryonic and fetal development, and in special, to those related to the epigenetic dynamics during genomic imprinting

Phenotypic plasticity is the ability of a given genotype to exhibit different phenotypes in response to environmental variables, which can impact population level processes. Plasticity of ecologically-relevant traits is important to an organism’s environmental response; however, the underlying mechanisms of plasticity are largely unknown. Ecological epigenetics may offer mechanisms (e.g. DNA methylation) underlying phenotypic plasticity. Epigenetics can be defined as the underlying molecular mechanisms that allow one genotype to exhibit different phenotypes. Differential DNA methylation is one epigenetic mechanism that has been correlated with a number of ecologically-relevant traits; including, differential herbivory in Viola cazorlensis, spinescence in Ilex aquifolium, flower morphology in Linaria vulgaris, and fitness in Arabidopsis thaliana. The epigenetic correlations with traits found in these studies are interesting, but they are also partially confounded by a potential correlation between genetic and epigenetic variation. Teasing apart the correlation between genetic and epigenetic variation is one of the challenges within ecological epigenetics. This correlation has resulted in epigenetic variation being partitioned into three types by researchers: obligate, facilitated, and pure. Changes in obligate epigenetic variation are directly correlated with genetic variation. Changes in pure epigenetic variation are completely independent from genetic variation. Changes in facilitated epigenetic variation are partially dependent on genetic variation, but the outcome of the phenotype is context-dependent based on environmental conditions. Since our predictions about the outcome of phenotypic variation are driven largely by population genetics theories, which make no room for variation that operates in non-Mendelian ways, epigenetics research needs to utilize unique ways to tease apart the interaction between genetic and epigenetic variation where facilitated or pure epigenetic variation exists outside of the realm of population genetics theory. To address these issues, I performed a literature review and two research-based studies. In Chapter 1 I performed a literature review on the topic of population epigenetics addressing the correlation with genetic variation and recommending an extension to the Modern Synthesis to accommodate the non-Mendelian nature of DNA methylation. While population genetics has approximately 85-years of data to support it, epigenetics is beginning to show some of the limitations associated with predictions made using populations genetics models. One of these limitations is that population genetics as defined by the Modern Synthesis does not allow for violations of Mendelian genetics (i.e. random assortment and segregation of alleles). This limitation does not allow for phenotypic variation that is directly due to environmental conditions; however, recent ecological epigenetics data shows that this can, indeed, occur. Within this review I propose epigenetic questions that we should focus on at the population level, and I make recommendations for how to approach these questions in future studies. In the second and third research-based chapters, I investigated whether an independent component of epigenetic variation was correlated with habitat, while controlling for a correlation with genetic variation, for Spartina alterniflora and Borrichia frutescens, respectively. Previous work has shown that there is no consistent genetic response to environment in these species. I, therefore, hypothesized that there would be a significant epigenetic correlation with habitat instead. To test this hypothesis, I collected leaf samples from five different sites for each species on Sapelo Island, GA. Within each site I established three 10m transects (n=20 for each microhabitat) in low, middle, and high marsh microhabitats, respectively. Plants of both species exhibit different phenotypes for height (tall, intermediate, short, respectively) based on their location within the marsh. I screened AFLP and methylation-sensitive AFLP (MS-AFLP) markers for genetic and epigenetic variation, respectively. I used a variety of statistical tests to attempt to tease apart a potential correlation between genetic and epigenetic variation and found that when genetic population structure is controlled for, significant epigenetic population structure persists across all populations for S. alterniflora and within 3 of 5 populations for B. frutescens. These results suggest that regulation of certain genomic elements via DNA methylation may play an important role in dealing with environmental variables. To fully determine the significance of these findings, future studies should examine the interaction between environmentally-mediated epigenetic variation and gene expression to determine its importance to phenotypic plasticity and habitat differentiation. The body of work I produced supports that epigenetics may play a role in environmental response in populations within relatively small spatial scales. I used a combination of statistical tests to control for potential correlations with genetic variation which allowed me to see patterns that may normally be hidden. These findings expand upon traditional views of evolution by suggesting that environment can play a role in phenotypic variation, and other research supports that the variation due to epigenetic mechanisms can be inherited in future generations. Much of the current epigenetic research is based upon studies involving model species in highly controlled studies. While this research is been incredibly informative about some of the mechanisms underlying epigenetics, to fully understand the role of epigenetics to environmental response and evolution we must pair these data with field studies of non-model organisms. Only then will we begin to see the full role of epigenetics in organisms.

Les études d'association pangénomiques (GWAS) ont permis l'identification de plusieurs dizaines de gènes et de polymorphismes nucléotidiques (SNPs) contribuant au risque de diabète de type 2.Plus généralement, les GWAS ont permis d'identifier des milliers de SNPs contribuant à des maladies complexes chez l'Homme.Cependant, la caractérisation fonctionnelle et les mécanismes biologiques impliquant ces SNPs et ces gènes restent en grande partie à explorer.En effet, les conséquences de ces polymorphismes sont complexes et peu connues. Une conséquence directe est l'altération de la protéine codée par un gène, voire une extinction complète de la transcription du gène (p.ex. via l’introduction d’un codon stop dans la séquence).Par ailleurs, ces polymorphismes peuvent avoir un rôle de régulation dans l'expression des gènes, par exemple, en perturbant la liaison de facteurs de transcription et d'enzymes impliqués dans la méthylation de l'ADN.Malgré des associations fortes des SNPS identifiés, ils ne peuvent expliquer la totalité de l'héritabilité du diabète de type 2, suggérant par le fait même des mécanismes d'interactions entre les différentes couches que représentent la génomique, la transcriptomique et l'épigénomique.Le changement de paradigme en statistique génétique et la disponibilité de données transcriptomiques et épigénomiques sont responsables de l'évolution du domaine, passant des analyses d'associations à des analyses transversales de type multi-omique, et permettant de fournir des éléments de réponse sur l’aspect fonctionnel des SNPs ou des gènes impliqués, et dans certains cas, permettant d'évaluer le lien causal de ces variants sur la pathologie.Les développements et applications méthodologiques proposés dans cette thèse sont variés, allant d’une approche similaire aux GWAS, mettant à profit les données longitudinales disponibles dans certaines cohortes (p.ex. D.E.S.I.R.), au moyen d'un modèle joint; de la caractérisation fonctionnelle de gènes candidats, identifiés par GWAS, dans la sécrétion d'insuline par une étude transcriptomique multi tissu et dans un modèle cellulaire; de l'identification d'un nouveau gène candidat (PDGFA) impliqué dans la dérégulation de la voie de l'insuline dans le diabète de type 2 via des mécanismes épigénétiques et transcriptomiques; et enfin de la caractérisation de l'effet sur le transcriptome de deux substituts du bisphénol A dans un modèle d’adipocyte primaire.L'augmentation des connaissances des processus biologiques dans lesquels sont impliqués les SNPs et gènes identifiés par GWAS pourrait permettre l'élaboration de stratégies diagnostiques plus efficaces, ainsi que l'identification de cibles thérapeutiques pour le traitement du diabète de type 2 et des complications associées (p.ex. insulinorésistance, NAFLD, cancer, etc.). Plus généralement, ces études multi-omiques ouvrent la voie à l'approche émergente que représente la médecine de précision, permettant le traitement et la prévention des pathologies tout en prenant en compte ce qui fait la spécificité d'un individu, à savoir son génome et son environnement, tous deux interagissant sur son transcriptome et son épigénome. / Genome-wide association studies (GWAS) have resulted in the identification of several dozen of genes and single nucleotide polymorphisms (SNPs) contributing to type 2 diabetes.More generally, GWAS have identified thousands of SNPs contributing to complex diseases in humans.However, the functional characterization and biological mechanisms involving these SNPs and genes remain largely to be explored. Indeed, the consequences of these polymorphisms are complex and little known.One direct consequence of the SNPs is the alteration of the protein encoded by a gene, or even a complete transcriptional gene silencing (e.g. codon stop in the sequence). Furthermore, these polymorphisms may have a regulatory role in gene expression, for example, by interfering with the binding of transcription factors and enzymes involved in DNA methylation.Despite the strong associations of identified SNPs, they cannot explain the full heritability of type 2 diabetes, suggesting interactions mechanisms between the different layers of -omics, such as genomics, transcriptomics and Epigenomics.The shift of paradigm in statistical genetics and the availability of transcriptomic and epigenomic data are responsible for the evolution of the discipline, moving from association studies to multi-omics, and providing insights on the functional aspect of the SNPs or genes involved, and in some cases allowing to evaluate the causal link of these variants on the pathology.The methodological developments and their applications proposed in this thesis are various, ranging from a similar approach to GWAS, leveraging the longitudinal data available in some cohorts (e.g. D.E.S.I.R.), using an joint model approach; the functional characterisation of candidate genes in insulin secretion by a multi tissue transcriptomic study and transcriptomic study in a cell model; the identification of a new candidate gene (PDGFA) involved in the deregulation of the insulin\\\'s pathway in type 2 diabetes through epigenetic and transcriptomic mechanisms; and finally, the characterisation of the effect on the transcriptome of two substitutes of bisphenol A in a primary adipocyte model.The increase of knowledge in biological processes involving SNPs and genes identified by GWAS could enable the development of more effective diagnostic strategies, and the identification of therapeutic targets for the treatment of type 2 diabetes and associated complications (e.g., insulin resistance, NAFLD, cancer, etc.).More generally, these multi-omics studies pave the way for the emerging approach of precision medicine, allowing the treatment and prevention of pathologies while taking into account what makes the specificity of an individual, namely his genome and his environment, both interacting on his transcriptome and his epigenome.

La méthylation et déméthylation de l'ADN jouent un rôle majeur dans la stabilité des génomes, l'empreinte génomique, la paramutation et le développement. En revanche, le rôle de cette régulation épigénétique a été peu étudiée dans les interactions hôtes-pathogènes. Dans ce projet de thèse, nous avons tout d'abord montré que la méthylation de l'ADN régule négativement la résistance d'Arabidopsis thaliana à une souche de Pseudomonas syringae pathogène. Nous avons également identifié un grand nombre de gènes de l'immunité ciblés directement par la méthylation de l'ADN dirigée par petits ARN dans leurs régions promotrices. Nous proposons que cette régulation génique permettrait de maintenir une faible expression basale de ces gènes et d'éviter ainsi des effets délétères qui seraient causés par une expression constitutive de la réponse immunitaire. De plus, nous montrons que la déméthylase active REPRESSOR OF SILENCING 1 (ROS1) facilite l'activation transcriptionnelle de gènes de l'immunité en laissant potentiellement des éléments de régulation en cis accessibles à des facteurs de transcription. Nous avons également démontré que ce facteur contribue à la résistance à P. syringae chez Arabidopsis, caractérisant ainsi la première déméthylase eucaryote dans la résistance antibactérienne. Sur la base de ces résultats, nous proposons que la méthylation de l'ADN maintient une faible expression basale de gènes de l'immunité en absence de pathogène, tandis que la déméthylation active assure une induction rapide de ces gènes au cours de la réponse immunitaire en favorisant potentiellement le recrutement de facteurs de transcription sur la chromatine. / DNA methylation and demethylation are regulatory processes involved in genome stability, genomic imprinting, paramutation and development. Until recently, very little was known about the role of these epigenetic processes in plant disease resistance and in the transcriptional control of immune-responsive genes. Here we provide evidence that DNA methylation negatively regulates antibacterial resistance against a virulent Pseudomonas syringae strain in Arabidopsis. Accordingly, we have identified a subset of defense genes that are targeted and repressed by RNA-directed DNA methylation (RdDM), presumably to prevent trade-off effects that would be caused by their constitutive expression and/or sustained induction. In addition, we found that the active DNA demethylase facilitates the transcriptional activation of some of these defense genes by pruning DNA methylation at their promoter regions and leaving cis-elements accessible for transcription factor binding. In addition, we show that the active demethylase REPRESSOR OF SILENCING 1 (ROS1) positively regulates late immune responses including Pathogen Associated Molecular Pattern (PAMP)-triggered callose deposition and salicylic acid (SA)-dependent defense response. We also demonstrate that ROS1 restricts Pto DC3000 propagation in Arabidopsis leaf secondary veins, providing the first example for a role of an active DNA demethylase in antibacterial resistance. Based on these findings we propose that DNA methylation maintains a low basal expression of some immune-responsive genes in normal growth condition, while active DNA demethylation ensures a rapid and pervasive induction of these genes upon bacterial pathogen detection.

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