京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19270号 / 医博第4034号 / 新制||医||1011(附属図書館) / 32272 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙橋 良輔, 教授 渡邉 大, 教授 富樫 かおり / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

<p>Mammalian development is orchestrated by global transcriptional changes, which drive cellular differentiation, giving rise to diverse cell types. The mechanisms that mediate the temporal control of early differentiation can be studied using embryonic stem cell (ESCs) and embryonal carcinoma cells (ECCs) as model systems. In these stem cells, differentiation signals induce transcriptional repression of genes that maintain pluripotency (PpG) and activation of genes required for lineage specification. Expression of PpGs is controlled by these genes’ proximal and distal regulatory elements, promoters and enhancers, respectively. Previously published work from our laboratory showed that during differentiation of ESCs, the repression of PpGs is accompanied by enhancer silencing mediated by the Lsd1/Mi2-NuRD-Dnmt3a complex. The enzymes in this complex catalyze histone H3K27Ac deacetylation and H3K4me1/2 demethylation followed by a gain of DNA methylation mediated by the DNA methyltransferase, Dnmt3a. The absence of these chromatin changes at PpG enhancers during ESC differentiation leads to their incomplete repression. In cancer, abnormal expression of PpG is commonly observed. Our studies show that in differentiating F9 embryonal carcinoma cells (F9 ECCs), PpG maintain substantial expression concomitant with an absence of Lsd1-mediated H3K4me1 demethylation at their respective enhancers. The continued presence of H3K4me1 blocks the downstream activity of Dnmt3a, leading to the absence of DNA methylation at these sites. The absence of Lsd1 activity at PpG enhancers establishes a “primed” chromatin state distinguished by the absence of DNA methylation and the presence of H3K4me1. We further established that the activity of Lsd1 in these cells was inhibited by Oct3/4, which was partially repressed post-differentiation. Our data reveal that sustained expression of the pioneer pluripotency factor Oct3/4 disrupts the enhancer silencing mechanism. This generates an aberrant “primed” enhancer state, which is susceptible to activation and supports tumorigenicity. </p> <p>As differentiation proceeds and multiple layers of cells are produced in the early embryo, the inner cells are depleted of O₂, which triggers endothelial cell differentiation. These cells form vascular structures that allow transport of O₂ and nutrients to cells. Using ESC differentiation to endothelial cells as a model system, studies covered in this thesis work elucidated a mechanism by which the transcription factor Vascular endothelial zinc finger 1 (Vezf1) regulates endothelial differentiation and formation of vascular structures. Our data show that Vezf1-deficient ESCs fail to upregulate the expression of pro-angiogenic genes in response to endothelial differentiation induction. This defect was shown to be the result of the elevated expression of the stemness factor Cbp/p300-interacting transactivator 2 (Cited2) at the onset of differentiation. The improper expression of Cited2 sequesters histone acetyltransferase p300 from depositing active histone modifications at the regulatory elements of angiogenesis-specific genes that, in turn, impedes their activation. </p> <p>Besides the discovery of epigenetic mechanisms that regulate gene expression during differentiation, our studies also include development of a sensitive method to identify activities of a specific DNA methyltransferase at genomic regions. In mammals, DNA methylation occurs at the C5 position of cytosine bases. The addition of this chemical modification is catalyzed by a family of enzymes called DNA methyltransferases (Dnmts). Current methodologies, which determine the distribution of Dnmts or DNA methylation levels in genomes, show the combined activity of multiple Dnmts at their target sites. To determine the activity of a particular Dnmt in response to an external stimulus, we developed a method, Transition State Covalent Crosslinking DNA Immunoprecipitation (TSCC-DIP), which traps catalytically active Dnmts at their transition state with the DNA substrate. Our goal is to produce a strategy that would enable the determination of the direct genomic targets of specific Dnmts, creating a valuable tool for studying the dynamic changes in DNA methylation in any biological process.</p>

O transtorno do espectro do autismo (TEA) é um transtorno do neurodesenvolvimento com apresentação clínica heterogênea. A nova classificação dimensional do DSM-5 permitiu a inclusão de toda a variabilidade fenotípica sob o mesmo guarda-chuva, criando a oportunidade de entender melhor os subgrupos de TEA de acordo com seus mecanismos fisiopatológicos heterogêneos. O objetivo deste estudo foi buscar componentes de vulnerabilidade a partir de fatores de risco (escolaridade materna, classe social, estresse e exposição tóxico ambiental durante a gestação, complicações na gravidez e história psiquiátrica familiar) e caracterizar subgrupos de TEA a partir destes componentes. Para evitar qualquer possível agrupamento baseado em parâmetros fenotípicos estabelecidos, como QI e gravidade, analisamos especificamente um grupo de pacientes homogêneos com TEA grave. A análise de componentes principais (PCA) foi realizada em dados de 68 crianças com TEA entre 3 e 7 anos de idade, e encontramos dois componentes principais: PC1, componente de vulnerabilidade genética e metabólica e PC2 componente de vulnerabilidade psicosocial. Com os escores do PCA, realizamos uma análise de clusters . Os resultados mostraram um cluster representando uma dimensão com maior vulnerabilidade genética, e outro com maior exposição a ambiente desfavorável e estressante durante a gestação. A análise de metiloma foi realizada para validar e explorar melhor a diferença entre os subgrupos. Encontramos 11.879 probes (p < 0.05) diferencialmente metiladas (DMPs). Os sítios CpG das DMPs estavam enriquecidos para regiões de metilação variáveis (VMRs). Sondas hipermetiladas apresentaram taxas mais altas nas características rVarBase associadas a SNPs funcionais, indicando maior risco de doença explicado por variações comuns (SNPs). A análise do módulo funcional dos promotores de genes encontrou diferenças relacionadas à resposta imune, processos metabólicos e estresse. A análise do relógio de metilação do DNA mostrou uma tendência de aumento do DNAm Age para ambos o clusters, mas sem diferença estatística. Por fim, a análise do exoma de 33 pacientes representantes dos dois clusters mostrou como esperado que ambos os subgrupos têm variantes raras deletérias, mas sem diferenças entre eles no número de variantes em genes intolerantes à variância de acordo com o escore RVIS. Nossos resultados mostram que estes grupos apresentam diferenças quanto aos componentes de vulnerabilidade uma relacionada com antecedentes genéticos hereditários comuns e, outra mais relacionada à resposta ambiental ao estresse. Este estudo corrobora que variações comuns e raras são importantes, mas influências ambientais devem ser consideradas para melhor encontrar subgrupos de TEA / Autism spectrum disorder (ASD) is a neurodevelopmental disorder with highly heterogeneous clinical presentation. The new dimensional DSM-5 classification allowed the inclusion of all phenotypic variability under the same umbrella, creating the opportunity to better understand ASD subgroups according to its heterogeneous pathophysiology mechanisms. The aim of this study was to search components of vulnerability from risk factors during gestation (mother schooling, social class, stress and environmental toxic exposition during gestation, pregnancy complications and familial psychiatric history) e characterize ASD subgroups from those components. To avoid any possible grouping based on phenotypic established parameters such as IQ and severity, we analysed a group of homogeneous patients with severe ASD specifically. Principal component analysis (PCA) was performed on data from 68 children with ASD between 3 and 7 years of age, and we found two principal components: PC1, component of genetic and metabolic vulnerability e PC2 component of unfavorable social environment vulnerability. With the PCA scores we performed clustering analysis. The results showed one cluster representing a dimension with stronger genetic vulnerability, and the other with more exposure to unfavorable and stressful environment during gestation. Methylome analysis has been performed to better explore subgroup difference. We found 11.879 (p < 0.05) differentially methylated probes (DMPs). CpG sites from those DMPs were found to be enriched in variable methylated regions (VMRs). The clusters have hypermethylated probes presented higher rates in different rVarBase regulatory regions associated to functional SNPs, indicating they may have different affected regulatory regions and more liability to disease explained by common variations (SNPs). Functional module analysis on gene promoters found differences related to immune response , metabolic processes and stress. DNA methylation clock analysis showed a tendency of higher DNAm Age for both Clusters, but here was no statistical DMAm Age acceleration difference. Lastly exome analysis of 33 patients representing both clusters showed as expected that both subgroups have deleterious rare variants, but without differences between them in the number of variants in genes intolerants to variance according to RVIS score. Our results show that this groups presents differences of vulnerability components, one related to common hereditary genetic antecedents, and another more related to the environmental response to stress. This study corroborates that common and rare variants are important, but environmental influences should be considered to better find subgroups of ASD

<div>Vertebrate neurogenesis is a multistep process that coordinates complex signaling pathways and chromatin-based regulatory machinery to generate highly specialized cells (Hsieh and Zhao 2016; Urban and Guillemot 2014; Alunni and Bally-Cuif 2016; Yao and Jin 2014; Schmidt, Strahle, and Scholpp 2013). Epigenetic factors play a fundamental role in underwriting neurogenesis in part by contributing to control of gene expression in differentiating neurons. A mechanistic understanding of the epigenetic machinery underlying neurogenesis in vertebrates is necessary both to fully understand biogenesis of neural tissue in this subphylum as well as to develop effective therapeutic strategies to treat diseased or damaged neural tissue. </div><div>An example of an epigenetic factor that is important for both neuronal differentiation and disease states is CHD5, a vertebrate-specific member of the CHD family of ATP-dependent chromatin remodeling proteins. Chromodomain / Helicase / DNA-binding (CHD) proteins play a variety of roles in vertebrate development, and misregulation or loss of CHD proteins has been linked to numerous diseases (Mayes et al. 2014; Marfella and Imbalzano 2007; Bartholomew 2014). CHD5 is expressed primarily in neural tissue, where it is thought to contribute to neurogenesis, and has been strongly linked to tumor suppression (Thompson et al. 2003; Vestin and Mills 2013). Loss of CHD5 plays a significant role in development of neuroblastoma, a devastating tumor that is a leading cause of cancer-related death in children (Jiang, Stanke, and Lahti 2011; Maris and Matthay 1999). Consistent with the disease phenotype associated with loss of CHD5, reduced expression of CHD5 impairs differentiation of neuronal cells (Egan et al. 2013b). However, ablation of CHD5 in mice surprisingly resulted in no detectable defects in brain development (Li et al. 2014; Zhuang et al. 2014). A subsequent report revealed that mice conditionally ablated for CHD5 in neural tissue exhibit symptoms consistent with an autism spectrum disorder (Pisansky et al. 2017). Much remains to be learned about the role of CHD5 in these processes to clarify these observations.</div><div>Further, Chd5 is unique among the family of Chd remodelers in that it provides a biochemical basis for crosstalk between the critical epigenetic marks H3K27me3 and DNA methylation. Chd5 and the closely related remodelers Chd3 and Chd4 are all components of the Mi-2/NuRD histone deacetylase complex that plays a critical role in mediating transcriptional repression in response to DNA methylation in mammals (Allen, Wade, and Kutateladze 2013). Only CHD5 is preferentially expressed in neural tissue, however, and only Chd5 remodelers have biochemical evidence of direct interaction with H3K27me3, which plays a critical role in enabling proper expression of transcriptional programs during neurogenesis (Egan et al. 2013b). Chd5 is thus unique among CHD remodelers in that it is biochemically linked to both DNA methylation and H3K27me3 in addition to being preferentially expressed in neural tissue.</div><div>With regards to mechanism, much remains to be learned regarding how Chd5 remodelers contribute to gene expression and tumor suppression. However, the data to date do not show extensive transcript phenotypes and it is not clear how the biochemical action of CHD5 contributes to the neurological phenotypes ascribed to altered expression of CHD5. Therefore, it is critical to determine a suitable context to study the role of CHD5 in these processes. Identification of CHD5-dependent genes in neurons is likely to generate insight into how loss of CHD5 contributes to tumorigenesis, in particular with regards to development of neuroblastoma. Regulatory pathways that drive neurogenesis have been found to be extensively conserved between humans and zebrafish. Therefore, we have turned to the power of the zebrafish model system to characterize how loss of Chd5 alters brain development during embryogenesis.</div><div>Importantly zebrafish development, and neurogenesis in particular, occurs largely over the first 5-days of development. Zebrafish are born outside of the mother, which can produce large clutches of several hundred embryos per week, providing us with an accessible context to study the role of chd5, the zebrafish homolog of human CHD5. The central nervous system of the zebrafish develops rapidly, and shares many of the organization features of the mammalian brain (Kalueff, Stewart, and Gerlai 2014). In particular, neuroblastoma arises from a population of cells known as sympathetic ganglion cells that are derived from the neural crest (Pei et al. 2013). These cells are conserved in vertebrates, and several models to study how these cells transform into neuroblastoma exist in zebrafish (Zhu et al. 2017; Morrison et al. 2016; Zhu and Thomas Look 2016). However, our understanding of the mechanisms controlling ganglion cell differentiation is incomplete and requires further investigation to understand how epigenetic and transcriptional mechanisms contribute to development of these cells and how failure of these processes leads to cancer. The neural crest undergoes a series of differentiation steps to form mature sympathetic neurons that are guided by bone morphogenic protein signaling, and transcription changes (Ernsberger and Rohrer 2018). These cells express key enzymes for synthesizing dopamine and norephinephrine to control the sympathetic system throughout the central nervous system (Ernsberger and Rohrer 2018).</div><div>To address these questions about Chd5, we have used CRISPR/Cas9 to generate chd5-/- zebrafish that are protein nulls as determined by western blot. These chd5-/- fish are phenotypically indistinguishable from wild-type fish under standard growth conditions as was previously observed for mice lacking CHD5 (Zhuang et al. 2014; Li et al. 2014). By using zebrafish, we are able to perform transcriptome analyses to identify Chd5 target genes at stages much earlier than has previously been performed in mice because we can harvest large amounts of the tissue of interest from the readily accessible embryos. We have therefore undertaken RNA-seq analysis of isolated brains from wild-type and chd5-/- fish to identify chd5-dependent genes in predominantly differentiating (2-day old) and substantially differentiated (5-day old) neural tissue. These data provide a substantively different perspective from previous studies that examine the role of CHD5 in gene expression of differentiated SY-SH5Y cells (Egan et al. 2013a) or in the forebrain of 8-week-old mice (Pisansky et al. 2017). (Jiang, Stanke, and Lahti 2011). One role we identified from this data, is the promotion of development of sympathetic ganglion cells (detailed below), illuminating for the first time a role for chd5 in promoting differentiation of cells directly involved in neuroblatoma.</div><div>We observe not only extensive changes in gene expression, but also identify a novel role for Chd5 in enabling proper splicing during this critical window of neurogenesis in the zebrafish brain. We are further exploring the role of CHD5 in these processes by creating comparable cell culture-based models of loss of CHD5 to determine the conservation of molecular phenotypes observed in zebrafish. Furthermore, this model enables us to leverage the extensive biochemical tools available in cell culture to examine alterations to the chromatin that are difficult to interpret from studies of complex tissues such as the brain. </div><div>Herein I will describe the research progress we have made to understand the role of Chd5 in gene expression and splicing in zebrafish, as well as ongoing work to engineer mouse embryonic stem cells as an additional model to study the transcriptional consequences of loss of CHD5. Critically, the addition of the cell culture model will greatly enable biochemical characterization of the changes that are leading in particular to the changes in gene expression and splicing and will provide us with a context to test for a direct role of CHD5 in these processes. In addition, this thesis will detail the results from ongoing projects using the zebrafish model system, including: development of models in zebrafish to study the tumor suppressive role of Chd5, phenotypes observed using a targeted chemical-genetic screen, and advancement in developing new tools in zebrafish to engineer specific genomic modifications that will greatly expand the power of this vertebrate model.</div><div><br></div>

A idade normal para início da puberdade em meninas varia bastante, de 8 a 13 anos, e os genes envolvidos nesse controle são parcialmente conhecidos. Fatores ambientais, como alimentação e exposição a disruptores endócrinos, contribuem para essa variabilidade, de modo que genes modulados epigeneticamente podem justificar parte da complexidade desse processo. O termo epigenética se refere às modificações na expressão gênica que não são causadas por alterações na sequência do DNA. A metilação do DNA é o mecanismo epigenético mais bem estudado. Na última década surgiram evidências demonstrando a relação entre metilação do DNA e desenvolvimento puberal. Em fêmeas de roedores, a hipermetilação do DNA levou à puberdade precoce. Em humanos, a puberdade precoce central (PPC) familial causada por mutações nos genes MKRN3 e DLK1 é considerada um defeito do imprinting, fenômeno epigenético no qual apenas um dos alelos parentais é expresso, estando o outro metilado e inativo. Além disso, um conceito atual propõe que o início da puberdade requer a repressão epigenética de fatores inibidores do eixo gonadotrófico. Recentemente, genes zinc finger (ZNF) foram relacionados ao processo puberal, e muitos deles codificam repressores transcricionais. Neste trabalho, estudamos a metilação do DNA do sangue periférico de 10 pacientes do sexo feminino com PPC familial (casos índices) e 33 meninas com desenvolvimento puberal normal (15 pré-púberes e 18 púberes), usando a plataforma Human Methylation 450 BeadChip. Duas pacientes tinham PPC de causa genética (uma com mutação no MKRN3 e outra com deleção no DLK1) e oito tinham PPC idiopática, sem mutações identificadas pelo sequenciamento exômico global. Cento e vinte regiões diferencialmente metiladas foram identificadas entre as meninas saudáveis pré-púberes e púberes, estando 74% delas no cromossomo X. Apenas uma região mostrou-se hipometilada no grupo púbere e, de maneira importante, contém a região promotora do ZFP57, fator necessário para manutenção do imprinting. Uma vez que a hipermetilação nas regiões promotoras dos genes é relacionada à inibição transcricional, o achado de hipermetilação global do DNA na puberdade sugere que haja inibição de fatores inibidores do eixo gonadotrófico, o que resultaria no início do processo puberal. O receptor estrogênico destacou-se como um fator transcricional que se liga a sete genes diferencialmente metilados entre os controles pré-púberes e púberes. As pacientes com PPC apresentaram mais sítios CpG hipermetilados tanto na comparação com as meninas pré-púberes (81%) quanto púberes (89%). Há doze genes ZNF contendo sítios CpG hipermetilados na PPC. Não foram encontradas anormalidades de metilação nos genes MKRN3 e DLK1 nem em suas regiões regulatórias. Em conclusão, este estudo evidenciou hipermetilação global do DNA em meninas com puberdade normal e precoce, sugerindo que esse padrão é uma marca epigenética da puberdade. Pela primeira vez, mudanças no metiloma de pacientes com PPC foram descritas. Modificações na metilação de vários genes ZNF parecem compor a complexa rede de mecanismos que leva ao início da puberdade humana / Normal puberty initiation varies greatly among girls, from 8 to 13 years, and the genetic basis for its control is partially known. Environmental factors, such as nutrition and exposure to endocrine disruptors, contribute to this variance, and epigenetically modulated genes may justify some of the complexity observed in this process. Epigenetics refers to alterations in gene expression that are not caused by changes in DNA sequence itself. DNA methylation is the best studied epigenetic mechanism. In the last decade, evidence has emerged showing the relationship between DNA methylation and pubertal development. In female mice, DNA hypermethylation led to precocious puberty. In humans, familial central precocious puberty (CPP) caused by mutations in the MKRN3 and DLK1 genes is considered a disorder of imprinting, an epigenetic phenomenon in which only one parental allele is expressed, and the other allele is methylated and inactive. In addition, animal studies indicated that pubertal timing requires epigenetic repression of inhibitory factors of the gonadotrophic axis. Recently, zinc finger genes (ZNF) were related to pubertal development, many of which encode transcriptional repressors. In the present study, we analyzed the DNA methylation of peripheral blood samples from 10 female patients with familial CPP (index cases) and 33 girls with normal pubertal development (15 pre-pubertal and 18 pubertal), using the Human Methylation 450 BeadChip assay. Genetic CPP was diagnosed in two patients (one with a MKRN3 mutation and the other with a DLK1 deletion). The remaining eight cases with idiopathic CPP were previously evaluated by whole exome sequencing and no causative mutations were identified so far. We evidenced 120 differentially methylated regions between pre-pubertal and pubertal healthy girls, and 74% of them were located at the X chromosome. Only one genomic region was hypomethylated in the pubertal group. Of note, it contains the promoter region of ZFP57, an important factor for imprinting maintenance. As DNA hypermethylation in gene promoters is related to gene silencing, the finding of global DNA hypermethylation in puberty suggests inhibition of inhibitory factors of the hypothalamic-pituitary-gonadal axis that results in puberty onset. Importantly, the estrogen receptor was identified as a transcriptional factor that binds to seven differentially methylated genes associated with pubertal process. Patients with CPP exhibited more hypermethylated CpG sites compared to both pre-pubertal (81%) and pubertal (89%) controls. Twelve ZNF genes were recognized as having hypermethylated CpG sites in CPP. The methylation analyses of MKRN3 and DLK1 genes showed no abnormalities. In conclusion, this study revealed a widespread DNA hypermethylation in girls with normal and precocious puberty, suggesting that this pattern can be an epigenetic signature of puberty. For the first time, changes in the methylome of patients with CPP were described. We highlight that alterations in methylation levels of several ZNF genes may impact the onset of human puberty

Craniofacial development is a tightly regulated event that requires expression of many genes at a precise space-temporal specificity. Interference in the regulation of such genes and their pathways is known to lead to abnormal phenotypes affecting the face and cranium. In this manner, regulation of these pathways is further complicated by interaction between genetic and environmental factors such that disturbance to either may result in craniofacial malformation, as orofacial clefts. Despite several at-risk loci have been identified, they do not completely explain the high heritability observed for the orofacial clefts and many questions remain open. For example, concerning the orofacial clefts transcriptome, the gene pathways which may be dysregulated and the affected cellular processes are still poorly understood. Further, if there is gene expression dysregulation in orofacial clefts, the causes leading to that need to be elucidated, such as the investigation of epigenetic factors. Also, since the multifactorial contribution makes environment relevant to this malformation, epigenetic and epigenomic differences in orofacial clefts should clarified. At last, rare syndromic forms of orofacial clefts with still unknown molecular cause and mechanisms should be elucidated in order to better understand craniofacial development and their impact in non-syndromic forms. Therefore, the main objective of this study was to investigate the molecular mechanisms involved in the aetiology of orofacial clefts, which was focused in gene expression and epigenetic analysis in non-syndromic cleft lip and/or palate (NSCL/P) as well as genetic, gene expression, animal modelling and epigenetics in Richieri-Costa-Pereira Syndrome (RCPS), a rare autosomal recessive syndromic form of orofacial cleft. We found significant transcriptome differences in NSCL/P in comparison to controls, revealing the BRCA1-dependent DNA damage repair pathway as compromised in NSCL/P cells leading to DNA damage accumulation. Next, we studied the potential of DNA methylation in those cells and found a slight but significant increase of BRCA1 promoter DNA methylation in NSCL/P cells and a distinct DNA methylation distribution, point to a possible epigenetic contribution in this phenomenon. We also evaluated the contribution of DNA methylation in 8q24.21 region, one of the most replicated regions in NSCL/P Genome-wide association studies and found no significant differences in our sample. Attempting to investigate DNA methylation in NSCL/P in an epigenomic level, we analysed methylomes and found 578 methylation variable positions in NSCL/P, highly enriched in regulatory regions and in relevant gene pathways for craniofacial development as Epithelial-Mesenchymal Transition pathway. We also studied effect of DNA methylation in familial NSCL/P displaying incomplete penentrance and found a significant increase of CDH1 promoter hypermethylation in penetrant cases in comparison to non-penetrants. Finally, by the use of different sequencing strategies and identity-by-descent analysis we mapped the mutation region of RCPS to EIF4A3 5\'UTR/promoter and found a complex structure of expanded repeats in RCPS patients leading to EIF4A3 downregulation. We were also able to validate the phenotypes using an animal modelling strategy in zebrafish. Because those repeats are CG rich, we investigated whether they were submitted to DNA hypermethylation in RCPS patients as a cause for EIF4A3 hypomorphism, however we found no evidence of methylation increase in RCPS. In conclusion, we were able to associate dysregulated pathways to NSCL/P susceptibility and DNA methylation differences to both non-familial and familial NSCLP. Besides, we were able to identify the genetic cause of RCPS, which now can be molecularly diagnosed. Altogether, our results add to the understanding of craniofacial development and the aetiology of orofacial clefts / O desenvolvimento craniofacial é um evento finamente regulado que requer a expressão de muitos genes em uma precisão espaço-temporal específica. A interferência na regulação de tais genes e suas respectivas vias é sabidamente causadora de fenótipos que afetam a face e o crânio. Neste sentido, a regulação destas vias é decorrente da interação entre fatores genéticos e ambientais, de tal forma que a perturbação de quaisquer destes fatores pode resultar em malformações craniofaciais, como as fissuras orofaciais. Apesar dos muitos loci de risco já identificados, estes não explicam completamente a alta herdabilidade observadas nas fissuras orofaciais e muitas questões permanecem em aberto. Por exemplo, em relação ao transcriptoma em fissuras orofaciais, as vias genéticas que podem estar desreguladas, assim como processos celulares afetados em decorrência, são ainda pouco compreendidos. Além disso, se há desregulação na expressão de genes em fissuras orofaciais, as causas que levam a essas diferenças necessitam ser elucidadas, como, por exemplo, por meio da investigação de fatores epigenéticos. Também, uma vez que o componente multifatorial torna a influência do ambiente relevante para esta malformação, diferenças epigenéticas e epigenômicas nas fissuras orofaciais devem ser melhor compreendidas. Por fim, formas raras e sindrômicas de fissuras orofaciais sem elucidação de causa moleculares devem ser estudadas para que melhor se compreenda o desenvolvimento craniofacial e o impacto destes mecanismos moleculares em formas não-sindrômicas. Portanto, nosso objetivo principal neste estudo foi investigar os mecanismos moleculares envolvidos na etiologia das fissuras orofaciais, com o foco na análise de expressão gênica e epigenètica em fissuras de lábio-palatinas não-sindrômicas (FL/P NS) e também o estudo genético, de expressão gênica, modelagem animal e epigenética na Síndrome de Richieri-Costa-Pereira (RCPS), uma forma sindrômica e autossômica recessiva de fissura orofacial. Nós encontramos diferenças significantes no transcriptoma de FL/P NS em comparação com controles, que revelaram o comprometimento da via do BRCA1 no reparo ao dano de DNA e o acúmulo de dano de DNA em células FL/P NS. Em seguida, nós estudamos o potencial da metilação de DNA nestas células e encontramos um pequeno, porém significante, aumento de metilação de DNA no promotor do BRCA1 e uma distribuição diferente de metilação, apontando para uma possível contribuição epigenética na desregulação do gene. Nós também avaliamos a contribuição da metilação de DNA na região 8q24.21, uma das mais associadas às FL/P NS por meio de Genome-wide association studies, porém não encontramos diferenças significantes na nossa amostra. Com o intuito de investigar a metilação de DNA em FL/P NS em uma escala epigenômica, nós analisamos o perfil de metilomas e encontramos 578 sítios diferencialmente metilados nas FL/P NS, altamente enriquecidos em regiões regulatórias e em vias relevantes para o desenvolvimento craniofacial como a via de Transição Epitélio-Mesenquimal. Nós também estudamos o efeito da metilação de DNA em casos famílias de FL/P NS com penetrância incompleta e encontramos um aumento significativo de metilação do promotor do CDH1 nos casos penetrantes em comparação aos não-penetrantes. Por último, por meio de diferentes estratégias de sequenciamento e análise de segregação de haplótipos nós mapeamos a mutação de RCPS na região 5\'UTR/promotor do EIF4A3 e encontramos uma estrutura complexa de expansão de repetições nos pacientes RCPS, ocasionando a diminuição da expressão do EIF4A3. Nós também reproduzimos fenótipos comparáveis aos da RCPS por meio de modelo animal em zebrafish. Uma vez que tais repetições são ricas em CG, nós investigamos se estas poderiam ser submetidas à metilação de DNA em pacientes RCPS como uma causa para a redução dos transcritos do EIF4A3, porém não encontramos evidências de aumento de metilação em RCPS. Em conclusão, nós conseguimos associar vias gênicas desreguladas à susceptibilidade para as FL/P NS e diferenças de metilação de DNA tanto em casos familiais como não-familiais de FL/P NS. Além disso, identificamos a causa genética de RCPS, sendo que a síndrome pode ser agora diagnosticada molecularmente. Em conjunto, nossos resultados adicionam ao conhecimento do desenvolvimento craniofacial e na etiologia das fissuras orofaciais

<p>Žučne kiseline deluju kao signalni molekuli u organizmu i uključene su u regulaciju brojnih metaboličkih, inflamatornih i imunomodulatornih procesa. Ova endogena jedinjenja ostvaruju svoje efekte najvećim delom putem nuklearnih receptora. Farnezoid X receptor (FXR) je glavni regulator homeostaze žučnih kiselina, a pokazano je da je značajno uključen i u procese inflamacije i kancerogeneze, prevashodno u jetri i intestinalnom traktu. Aktivacija FXR receptora predstavlja značajnu farmakolo&scaron;ku strategiju za terapiju holestatskih bolesti jetre, inflamatorne bolesti creva i karcinoma kolona. Definisana je uloga žučnih kiselina u signalnim putevima koji reguli&scaron;u ćelijski ciklus i doprinose razvoju ili regresiji maligniteta, ali je malo poznat uticaj ovih jedinjenja na epigenetske mehanizme regulacije ključnih ćelijskih procesa. Imajući u vidu da su efekti žučnih kiselina determinisani njihovom polarno&scaron;ću, cilj istraživanja je bio da se ispita uticaj sintetski dobijenog keto derivata holne kiseline, 12-monoketoholne kiseline (MKH), u komparaciji sa prirodnim žučnim kiselinama, hidrofobnom henodeoksiholnom kiselinom (HDH) i hidrofilnom ursodeoksiholnom kiselinom (UDH), na ćelijske procese apoptoze, oksidativnog stresa i inflamacije, koji su od značaja za hemoprevenciju i terapiju karcinoma kolona, u in vitro i in vivo sistemima. Cilj istraživanja je takođe obuhvatao i ispitivanje uloge odabranih žučnih kiselina u epigenetskoj regulaciji ovih procesa u ćelijama karcinoma kolona. Na in vivo modelu intrahepatične holestaze kod eksperimentalnih životinja, pokazano je da UDH i MKH ispoljavaju antiapoptotski, antioksidativni i antiinflamatorni efekat u jetri i intestinumu. Utvrđeno je da UDH i MKH sprečavaju mitohondrijalni put aktivacije apoptoze u jetri, dok UDH ispoljava antiapoptotski efekat i u intestinumu eksperimentalnih životinja sa holestazom. Ove dve žučne kiseline su u značajnoj meri modulirale ekspresiju gena uključenih u antioksidativnu za&scaron;titu, kao i aktivnost antioksidativnih enzima, u jetri i intestinumu eksperimentalnih životinja sa holestazom, ka nivoima ekspresije i aktivnosti kod zdravih, netretiranih životinja. Dok su UDH i MKH u dozi od 4 mg/kg ispoljile antiinflamatorno dejstvo u jetri i intestinumu smanjenjem ekspresije gena za proinflamatorni transkripcioni faktor NF-&kappa;B, primena HDH i MKH u dozi od 20 mg/kg je imala suprotan efekat. Na modelu HT-29 ćelijske linije adenokarcinoma kolona, utvrđeno je da polusintetska žučna kiselina MKH ispoljava značajno manju citotoksičnost u odnosu na HDH i ne&scaron;to veću citotoksičnost u odnosu na UDH. Epigenetski lek vorinostat je ispoljio sinergističko citotoksično dejstvo sa sve tri ispitivane žučne kiseline. Vorinostat je ostvario proapoptotski i antiproliferativni efekat u HT-29 ćelijama, koji je bio najizraženiji u kombinaciji sa MKH, s obzirom da je do&scaron;lo do značajnog povećanja odnosa ekspresije BAX i BCL2 gena i smanjenja ekspresije gena za marker proliferacije ciklin D1. Vorinostat je, takođe, značajno smanjio antioksidativni kapacitet HT-29 ćelija smanjenjem ekspresije NRF2 gena i sledstvenim smanjenjem ekspresije gena za antioksidativne enzime. HDH je dodatno smanjila, a MKH pobolj&scaron;ala antioksidativni kapacitet HT-29 ćelija modulacijom ekspresije NRF2 gena. U in vitro i in vivo sistemu u okviru ove doktorske disertacije je pokazano da, pored HDH kao poznatog endogenog agoniste FXR receptora, MKH takođe povećava ekspresiju gena za FXR i njegovog ciljnog gena za transkripcioni korepresor SHP, &scaron;to ukazuje da ova polusintetska žučna kiselina može da aktivira FXR. Osim toga, utvrđeno je da žučne kiseline ispoljavaju različite efekte prema ekspresiji gena za histon deacetilaze HDAC1 i HDAC2 u jetri i intestinumu eksperimentalnih životinja, kao i u HT-29 ćelijama karcinoma kolona, a jedino je UDH značajno smanjila ekspresiju gena za oba ispitivana enzima uključena u epigenetsku regulaciju ćelijskih procesa, i u isptivanim tkivima i HT-29 ćelijama. Rezultati na&scaron;eg rada ukazuju da bi se UDH i MKH mogle koristiti u hemoprevenciji karcinoma kolona u niskim dozama, s obzirom na utvrđene efekte u modulaciji ekspresije gena uključenih u procese apoptoze, oksidativnog stresa i inflamacije. Takođe, s obzirom na ostvaren sinergistički efekat žučnih kiselina sa epigenetskim antitumorskim agensom vorinostatom, otvara se mogućnost kombinovane farmakolo&scaron;ke strategije u terapiji solidnih tumora, koji u najvećem procentu pokazuju rezistenciju prema samom vorinostatu.</p> / <p>Bile acids act as signaling molecules in the organism and they are involved in the regulation of numerous metabolic, inflammatory and immunomodulatory processes. These endogenous compounds exert their effects mostly by binding and activation of nuclear receptors. Farnesoid X receptor (FXR) is the main regulator of bile acid homeostasis, and has been shown to be significantly involved in processes of inflammation and carcinogenesis, primarily in the liver and intestinal tract. Activation of FXR receptor represents a significant pharmacological strategy for the treatment of cholestatic liver disease, inflammatory bowel disease, and colon carcinoma. The role of bile acids in signaling pathways regulating the cell cycle and contributing to the development or regression of malignancies is well determined, but the effects of these compounds on epigenetic mechanisms of key cellular processes regulation is yet to be elucidated. Given that the effects of bile acids are mostly determined by their polarity, the aim of our study was to investigate in vitro and in vivo effects of semi-synthetic keto derivative of cholic acid, 12-monoketocholic acid (MKC), in comparison to natural bile acids, hydrophobic chenodeoxycholic acid (CDC) and hydrophilic ursodeoxycholic acid (UDC), on processes of apoptosis, oxidative stress and inflammation, which are significant for both&nbsp; chemoprevention and therapy of colon cancer. Besides, the aim of our study was to examine the role of selected bile acids in the epigenetic regulation of these processes in colon cancer cells. In in vivo model of intrahepatic cholestasis in experimental animals, it has been demonstrated that UDC and MKC exhibit antiapoptotic, antioxidant, and antiinflammatory effects in the liver and intestine. It was shown that UDC and MKC prevent the mitochondrial pathway of apoptosis activation in the liver, while UDC exhibits an antiapoptotic effect in the intestine of experimental animals with cholestasis as well. These two bile acids significantly modulated the expression of genes involved in antioxidant protection, as well as the activity of antioxidant enzymes, in the liver and intestine of experimental animals with cholestasis, towards levels of expression and activity in healthy, untreated animals. While UDC and MKC at a low dose of 4 mg/kg exhibited an antiinflammatory effect in the liver and intestine by reducing the expression of the gene encoding the proinflammatory transcription factor NF-&kappa;B, the application of CDC and MKC at a high dose of 20 mg/kg exerted the opposite effect. In HT-29 human adenocarcinoma cell line, it has been demonstrated that semi-synthetic bile acid MKC exhibits significantly lower cytotoxicity than CDC and slightly higher cytotoxicity than UDC. The epigenetic drug vorinostat has exhibited a synergistic cytotoxic effect with all three investigated bile acids. Vorinostat exerted proapoptotic and antiproliferative effects in HT-29 cells, which were most pronounced in combination with MKC, as there was a significant increase in the ratio of BAX and BCL2 genes expression and a decrease of the proliferation marker cyclin D1 gene expression. Vorinostat also significantly reduced the antioxidant capacity of HT-29 cells by reducing the expression of NRF2 gene and consequently decreasing the expression of genes encoding antioxidant enzymes. CDC further reduced, while MKC improved the antioxidant capacity of HT-29 cells by modulating the expression of NRF2 gene. In both in vitro and in vivo systems, it was demonstrated that, in addition to CDC as a known endogenous FXR agonist, MKC also increased the expression of the gene encoding FXR, and FXR target gene encoding transcriptional co-repressor SHP as well, indicating that this semi-synthetic bile acid can also activate FXR. Besides, bile acids have been shown to exert distinct effects on the expression of the histone deacetylases HDAC1 and HDAC2 gene in the liver and intestine of experimental animals, and in HT-29 colon cancer cells. Only UDC significantly reduced the expression of the genes for both studied enzymes involved in the epigenetic regulation of cell processes, in both tissues and HT-29 cells. The results of our work indicate that UDC and MKC could be used in chemoprevention of colon cancer at low doses, considering determined effects in the modulation of expression of the genes involved in processes of apoptosis, oxidative stress and inflammation. Furthermore, synergistic effects of bile acids with the epigenetic antitumor agent vorinostat open up the possibility of a combined pharmacological strategy in the treatment of solid tumors, which are at the high percentage resistant to the effects of vorinostat alone.</p>

L'influence de l'hypothèse de la programmation fœtale sur la stéato-hépatite non-alcoolique (NASH) n’a pas été suffisamment étudiée. La carence en donneurs de méthyles pendant la grossesse et l'allaitement est fréquente dans la population et est un modèle expérimental de programmation fœtale. Dans ce modèle, elle entraîne une stéatose hépatique chez les ratons de 21 jours, résultant notamment d'une déficience de l'oxydation des acides gras. Nous avons évalué les effets de la programmation fœtale sur la NASH chez des rats Wistar nés de mères recevant soit un régime standard, soit un régime carencé en donneurs de méthyles (iMDD), pendant la gestation et l'allaitement. Les ratons sevrés ont ensuite reçu un régime standard (D21 à D50), puis une partie de ces rats devenus adultes ont ensuite été soumis à un régime hyper-énergétique (HF) (D50 à D185). Les animaux ont été sacrifiés à D50 et D185. Nous avons observé une augmentation de la graisse abdominale et du rapport ASAT/ALAT, mais aucune anomalie histologique hépatique chez les rats D50 iMDD. En revanche, les rats D185 iMDD/HF ont développé une NASH, avec les caractéristiques d'une insulino-résistance ainsi qu'une augmentation de l'expression de nombreux gènes et protéines impliqués dans l'inflammasome, l'activation des cellules étoilées hépatiques, la fibrose et le remodelage tissulaire, incluant l'AngII, TGFβ1 et NFκB. En conclusion, la carence en donneurs de méthyles pendant la gestation et l'allaitement produit une NASH chez des animaux soumis ultérieurement à un régime hyper-énergétique à l'âge adulte, malgré le retour préalable à une alimentation standard. Ces résultats suggèrent qu'une carence gestationnelle en donneurs de méthyles est un facteur de risque de NASH chez les individus exposés ultérieurement à un régime hyper-énergétique. / The influence of fetal programming hypothesis on non-alcoholic steato-hepatitis (NASH) has deserved insufficient interest. Methyl donor deficiency during pregnancy and lactation is frequent in population and is an experimental model of fetal programming. In this model, it produces a liver steatosis in 21 days old pups, which results from decreased fatty acid oxidation. We evaluated the effects of fetal programming on NASH in Wistar rats born from mothers fed either a control or a methyl donor deficient (iMDD) diet during pregnancy and lactation. Pups received a control diet after weaning (D21 to D50) and a part from adult rats were fed with an high-fat diet (HF) (D50 to D185). Animals were sacrificed at D50 and D185. In D50 iMDD rats, we observed an increased abdominal fat and ASAT/ALAT ratio, but no liver histological abnormality. However, D185 iMDD/HF rats have developed NASH, with hallmarks of insulin resistance and increased expression of several genes and proteins involved in inflammasome, stellate cell stimulation, fibrosis and tissu remodelling, including AngII, TGFβ1 and NFκB. In conclusion, MDD during pregnancy and lactation produces NASH in animals subjected subsequently to an high-fat diet during adulthood, despite the recovery of a control diet. These results suggest that MDD during pregnancy is a risk factor of NASH development in subjects subsequently exposed to high-fat diet.

Primates are one of the best characterized phylogenies with vast amounts of comparative data available, including genomic sequences, gene expression, and epigenetic modifications. Thus, they provide an ideal system to study sequence evolution, regulatory evolution, epigenetic evolution as well as their interplays. Comparative studies of primate genomes can also shed light on molecular basis of human-specific traits. This dissertation is mainly composed of three chapters studying human and non-human primate evolution. The first study investigated evolutionary rate difference between sex chromosome and autosomes across diverse primate species. The second study developed an unbiased approach without the need of prior information to identify genomic segments under accelerated evolution. The third study investigated interplay between genomic and epigenomic evolution of humans and chimpanzees. Research advance 1: evolutionary rates of the X chromosome are predicted to be different from those of autosomes. A theory based on neutral mutation predicts that the X chromosome evolves slower than autosomes (slow-X evolution) because the numbers of cell division differ between spermatogenesis and oogenesis. A theory based on natural selection predicts an opposite direction (fast-X evolution) because newly arising beneficial mutations on the autosomes are usually recessive or partially recessive and not exposed to natural selection. A strong slow-X evolution is also predicted to counteract the effect of fast-X evolution. In our research, we simultaneously studied slow-X evolution, fast-X evolution as well as their interaction in a phylogeny of diverse primates. We showed that slow-X evolution exists in all the examined species, although their degrees differ, possibly due to their different life history traits such as generation times. We showed that fast-X evolution is lineage-specific and provided evidences that fast-X evolution is more evident in species with relatively weak slow-X evolution. We discussed potential contribution of various degrees of slow-X evolution on the conflicting population genetic inferences about human demography. Research advance 2: human-specific traits have long been considered to reside in the genome. There has been a surge of interest to identify genomic regions with accelerated evolution rate in the human genome. However, these studies either rely on a priori knowledge or sliding windows of arbitrary sizes. My research provided an unbiased approach based on previously developed “maximal segment” algorithm to identify genomic segments with accelerated lineage-specific substitution rate. Under this framework, we identified a large number of human genomic segments with clustered human-specific substitutions (named “maximal segments” after the algorithm). Our identified human maximal segments cover a significant amount of previously identified human accelerated regions and overlap with genes enriched in developmental processes. We demonstrated that the underlying evolutionary forces driving the maximal segments included regionally increased mutation rate, biased gene conversion and positive selection. Research advance 3: DNA methylation is one of the most common epigenetic modifications and plays a significant role in gene regulation. How DNA methylation status varies on the evolutionary timescale is not well understood. In this study, we investigated the role of genetic changes in shaping DNA methylation divergence between humans and chimpanzees in their sperm and brain, separately. We find that for orthologous promoter regions, CpG dinucleotide content difference is negatively correlated with DNA methylation level difference in the sperm but not in the brain, which may be explained by the fact that CpG depleting mutations better reflect germline DNA methylation levels. For the aligned sites of orthologous promoter regions, sequence divergence is positively correlated with methylation divergence for both tissues. We showed that the evolution of DNA methylation can be affected by various genetic factors including transposable element insertions, CpG depleting mutations and CpG generating mutations.