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

A l'interface de la génétique et de l'environnement, l'épigénétique contribue à la diversité phénotypique. Déterminer l'impact de la variation épigénétique sur les caractères quantitatifs (QT) est un nouveau défi. La croissance staturale fournit l’opportunité d’étudier la variabilité de plusieurs traits phénotypiques liés entre eux : des QT cliniques (la taille, l’accélération de la vitesse de croissance en réponse à l'hormone de croissance, GH) et des QT biologiques tels que la concentration d’IGF1 et la réponse de cette concentration à la GH. L’ « Insulin-like Growth Factor 1 » (IGF1) contrôle la croissance postnatale chez les mammifères, y compris l'homme. Nous l’avons choisi comme locus candidat pour nos études épigénétiques. Nous avons quantifié la méthylation des deux promoteurs P1 et P2 de ce gène, qui régulent son expression. Notre objectif était d’évaluer la contribution de la méthylation d’ADN de ces promoteurs i) à la taille des enfants en croissance, ii) à l’IGF1 circulant, iii) et à la réponse de ces paramètres à un traitement par la GH. Taille et IGF1 circulant. La relation entre la méthylation des promoteurs d’IGF1 et la taille a été étudiée au sein de deux cohortes du service d'endocrinologie pédiatrique, totalisant 216 enfants prépubères de différentes statures. Nous avons montré que la méthylation d'un groupe de six CGs situés dans la partie proximale du promoteur P2 du gène IGF1 présentait une corrélation inverse avec la croissance et l'IGF1 circulant. Les enfants les plus grands sont ainsi moins méthylés sur ces CGs que les enfants de petite taille. La contribution de la méthylation à la variance de la taille a été évaluée à environ 13%, et à 10% pour la variance de l'IGF1 sérique. Pour montrer que l’association observée reflète une causalité biologique, nous avons étudié le lien entre la méthylation des promoteurs P1 et P2 et l'activité transcriptionnelle du gène IGF1 in vivo et in vitro. Nous avons montré que les quantités de transcrits de classe II, issus du promoteur P2, sont inversement corrélés à la méthylation du promoteur P2 dans les cellules sanguines mononucléées. In vitro, nous avons cloné le promoteur P2 déméthylé ou méthylé dans un plasmide rapporteur (luciferase) transfecté dans la lignée HEK293 : le promoteur déméthylé s’est révélé nettement plus actif (+57%). Finalement, nous suggérons que l’hyperméthylation de certains CGs du P1 et du P2 d’IGF1 pourrait être un des nombreux mécanismes moléculaires responsables d’une moindre expression du gène et d’un phénotype de petite taille. La réponse au traitement par la GH. Une fraction des enfants de petite taille est traitée par l'hormone de croissance (GH) pour accélérer sa croissance, mais l’efficacité du traitement est très variable entre les individus. Les causes de cette variabilité sont partiellement comprises : la génétique joue un rôle, mais il reste une place possible pour la variabilité épigénétique. Dans ce but, nous avons étudié l'effet direct de la variabilité épigénétique sur la transcription du gène IGF1 et l’IGF1 circulant, dans un test aigu d’administration de GH, puis sur la réponse thérapeutique à un traitement d’un an par la GH. Après une injection de GH, nous avons constaté une augmentation variable du nombre de transcrits d’IGF1 chez les enfants étudiés. L'augmentation des transcrits de la classe II était inversement corrélée à la méthylation des CGs du P2. La variabilité de méthylation au CG-137 contribuait pour 20% à 67% de l’expression d’IGF1 en réponse à la GH. Chez 136 enfants de petite taille, nous avons montré que la méthylation de l'ADN du promoteur P2 était associée à la réponse au traitement par la GH au cours de la première année. Cette association est observée pour l'augmentation de la vitesse de croissance et pour les taux d’IGF1. (...) / At the interface of genetics and environment, epigenetics contributes to phenotypic diversity. Quantifying the impact of epigenetic variation on quantitative traits (QT), an emerging challenge in humans. Growth provides a handset of quantitative traits to epigenetic studies. We studied the variability of several inter-related QTs: clinical QTs (height, height reponse to growth hormone and biological QT (serum IGF1 and serum IGF1 response to GH). Since insulin-like growth factor 1 (IGF1) controls postnatal growth in mammals including human, we tested whether the CG methylation of the two promoters (P1 and P2) of the IGF1 gene could be a epigenetic contributor to the individual variation i) in circulating IGF1 and stature in growing children. ii) on response of these parameters to treatment with (GH). Child height and circulating IGF1. To explore the relation between IGF1 promoter methylation and height, we studied two cohorts of pedriatric endocrinology department, totalling 216 prepubertal children with various statures. The methylation of a cluster of six CGs located within the proximal part of the IGF1 P2 promoter showed a strong negative association with serum IGF1 and growth. These correlations were observed in two cohorts of growing children. Tall children show lower levels of methylation in several CGs in P2 and P1 promoters of IGF1 gene than short children with idiopathic short stature. CG methylation contributed 13% to the variance of height and 10% to the variance of serum IGF1. To test if the found association reflected biological causality, we tested if methylation at the P2 promoter affects the transcriptional activity of the IGF1 gene. The transcriptional activity of the P2 promoter was inversely correlated with the CG methylation in mononuclear blood cells. We established that high levels of CG methylation at the two promoters of IGF1 contributed to the many molecular mechanisms responsible for “idiopathic” short stature. Response to treatment with (GH). Short children using growth hormone (GH) to accelerate their growth respond to this treatment with a variable efficacy. The causes of this individual variability are partially understood and could involve epigenetics. In this aim, we investigated the contribution of DNA methylation to the response to GH at two levels: direct effect of GH on transcription of IGF1 gene, on circulating IGF1 and on the growth response to GH. Following a GH injection, we found a variable increase in IGF1 transcripts across the studied children. The increase in P2-driven transcripts showed a strong inverse correlation with 4/8 of P2 CGs. Among the CGs of P1 promoter, only CG-611 showed an inverse correlation with P1-driven transcripts. Variability of DNA methylation in these CGs contributes with 27% to 67% of increase in transcripts. In 136 children with idiopatic short stature, we showed that DNA methylation of the P2 promoter is associated with growth response to GH during the first year of GH administration, for both increment in growth rate and circulating IGF1. CG-137 methylation of P2 promoter contributes 25% to variance of growth response to GH. The link between DNA methylation and the response to a treatment in humans illustrating the role of epigenetic marks as potent contributors to conclusion « pharmacoepigenetics». Our work can find application in growth physiology and therapeutics, as well as for studies in aging, longevity or cancer where IGF1 has a prominent role.

A programação epigenética do genoma por metilação do DNA, modificação das histonas e remodelamento da cromatina é crucial para o desenvolvimento e o crescimento normal dos mamíferos e alterações nesses mecanismos contribuem diretamente para a transformação maligna. Em função do papel relevante da metilação do DNA na carcinogênese, da importância e da necessidade de identificação de marcadores moleculares em tumores de cabeça e pescoço e dos resultados já obtidos pelo grupo, o presente trabalho teve por objetivo geral investigar o perfil de metilação de ilhas CpG em carcinomas primários de cabeça e pescoço (CECP), bem como identificar e iniciar estudos funcionais de biomarcadores candidatos para diagnóstico e prognóstico desses tumores. Alguns genes previamente descritos com padrões anormais de metilação em neoplasias humanas (CDH1, CDH13, DAPK, CDKN2A, RASSF1A, SOCS3 e TIMP3), além de outros dois genes (MX1 e SLC15A3) identificados em nosso estudo anterior, foram analisados em amostras normais e margens cirúrgicas de CECP por meio da técnica de pirosequencimento de DNA após tratamento com bissulfito de sódio. As análises estatísticas não mostraram diferenças significativas para a maioria dos genes analisados, com exceção do gene SLC15A3, que apresentou diferença significativa (p<0,05) entre tumores e amostras de sangue de doadores saudáveis. Diferentemente, os resultados obtidos com a metodologia de PCR-MSP em nosso trabalho anterior mostraram que o gene MX1 está metilado em CECP. Os estudos funcionais do MX1, por RNA de interferência, ensaios de migração e citometria de fluxo mostraram que seu produto contribui para migração e proliferação celular, e talvez para resistência à apoptose. Os resultados sugeriram que o nível de expressão do MX1 pode ser um preditor do potencial metastático em carcinoma epidermóide / The genome epigenetic programming by DNA methylation, histone modification and chromatin remodeling is crucial for normal growth and development in mammals and changes in these mechanisms contributes directly to malignant transformation. Regarding the role of DNA methylation in carcinogenesis, the importance and necessity for the identification of molecular markers in head and neck tumors, and the results already obtained by the group, this study was aimed at investigating the methylation profile of CpG islands in primary head and neck squamous cell carcinomas (HNSCC), and to identify and initiate functional studies of candidate biomarkers for diagnosis and prognosis of these tumors. Therefore, some genes previously described with abnormal methylation pattern in humans tumors (CDH1, CDH13, DAPK, CDKN2A, RASSF1A, and TIMP3 SOCS3), and two other genes (MX1 and SLC15A3) identified in our previous study were analyzed in normal samples, surgical margins, and in HNSCC by pyrosequencing after sodium bisulfite treatment. The statistical analysis showed no significant differences for most of analyzed genes, except for the SLC15A3, which showed significant difference (p <0.05) between tumors and blood samples from healthy donors. However, our earlier results showed a higher frequency of MX1 hypermethylation in primary HNSCC using the PCR-MSP methodology. To gain a better understanding of the role MX1 in cancer biology we investigated whether a downregulation of MX1 by interference RNA contribute to apoptosis resistance and cell migration during cancer development. Wound healing and flow cytometry assays were performed to determine changes in cell motility, death and cell cycle in SCC cells. The results indicated that low levels of MX1 could regulate the cell cycle, increase proliferation, and enhance tumor cell migration in HNSCC cell lines, but it might not contribute to apoptosis resistance. It also suggests that the level of MX1 expression may be a predictor of metastatic potential in HNSCC

Numerous studies have investigated how bulk lipid metabolism is influenced in obesity and in particular how the composition of triglycerides found in the cytosol change with increased adipocyte expansion. However, in part reflecting the analytical challenge the composition of cell membranes, and in particular glycerophospholipids, an important membrane component, have been seldom investigated. Cell membrane components contribute to a variety of cellular processes including maintaining organelle functionality, providing an optimized environment for numerous proteins and providing important pools for metabolites, such as choline for one-carbon metabolism and S-adenosylmethionine for DNA methylation. Here, I have conducted a comprehensive lipidomic and transcriptomic study of white adipose tissue in mice that become obese either through genetic modification (ob/ob genotype), diet (high-fat diet) or a combination of the two across the life course. Specifically, I demonstrated that the changes in triglyceride metabolism that dominate the overall lipid composition of white adipose tissue were distinct from the compositional changes of glycerophospholipids. These latter lipids became more unsaturated to maintain the fluidity and normal function of the membrane in the initiation of obesity but then turned saturated after long-term administration of HFD and aging. This suggests that while triglycerides within the adipose tissue may be a relatively inert store of lipids, the compositional changes occur in cell membranes with more far-reaching functional consequences in both obesity and aging. The two-phase change of phospholipids can be correlated well with transcriptional and one-carbon metabolic changes within the adipocytes. The transcriptomic study demonstrated that the lipid metabolic pathways regulated by the peroxisome, AMPK, insulin and PPARγ signaling were activated in the initiation of obesity but inhibited in the adipose tissue of old ob/ob mice along with up-regulated inflammation pathways. The brown and white adipose tissue of PPARα-knock-out mice were also studied by lipidomic tools to get a deeper understanding of the effect of the peroxisome and PPAR system on adipose tissue and lipid metabolism during obesity. Most of the lipids were increased and became more saturated and shorter in adipose tissues of PPARα null mice, which is in good accordance with the results of the former animal study. In conclusion, my work using different rodent models and multi-omics techniques demonstrated a protective metabolic mechanism activated in the initiation but impaired at the end of the processes of obesity and aging, which could be an explanation of the similarity of obesity and aging in terms of high incidence of the metabolic syndrome and related diseases.

Les rapides progrès technologiques en matière de techniques de biologie à grande échelle, comprenant notamment les microarrays, conduisent en 2006 au développement d’une nouvelle génération de puces à très haute résolution, capables de cibler à la fois tous les gènes du transcriptome humain, mais également tous les exons de ces gènes pris individuellement. L’avènement de cette puce, communément appelée puce exon, permit d’obtenir une mesure précise des changements transcriptomiques affectant les cellules cancéreuses, en offrant la possibilité de prendre en compte l’expression relative de différents exons d’un même gène.L’épissage alternatif et la transcription alternative sont les deux principaux mécanismes biologiques à l’origine de l’existence de plusieurs transcrits pour un même gène. Ces processus biologiques ont été mis en évidence depuis longtemps mais leur régulation dans les cellules normales ainsi que leurs dérégulations dans les cancers sont encore mal caractérisées de par la complexité des mécanismes impliqués. Par leur design, les puces exons permettent de mettre en évidence la présence de variations d’expression entre plusieurs transcrits potentiels d’un même gène, ouvrant ainsi la voie à une meilleure compréhension de ces processus biologiques.A partir d’un important jeu de données d’échantillons de cancers de la vessie dont le profil transcriptomique fut obtenu par puces exons, nous nous sommes intéressés à l’étude des changements d’épissage alternatif et à l’utilisation de promoteurs alternatifs dans les tumeurs de vessie. L’utilisation d’outils statistiques et mathématiques dédiés à l’analyse de ces puces nous a permis dans un premier temps d’identifier de nombreux gènes dont l’expression relative des différents transcrits est spécifiquement dérégulée dans les tumeurs de vessie. Ces transcrits constituent une nouvelle source pour l’identification de cibles thérapeutiques spécifiques des tumeurs. Nous avons pu montrer qu’avec une approche ciblée sur les changements d’expression relative de transcrits alternatifs d’un même gène, il était possible de constituer un panel de potentiels marqueurs tumoraux permettant le développement de nouveaux tests urinaires utiles à la détection des cancers de vessie et à la surveillance des patients.Par une analyse non supervisée des profils d’exons potentiellement dérégulés, nous avons pu observer une stratification des tumeurs similaire à celle observée par l’étude des profils géniques issus de puces classiques, confirmant alors l’existence d’un sous groupe de tumeurs de vessie présentant des caractéristiques transcriptomiques propres. Nous avons pu associer à ce sous-groupe de mauvais pronostic, une signature d’inclusion différentielle de certains exons. Cette signature impliquant 19 gènes permet d’identifier précisément ces tumeurs de manière très spécifique et constitue par conséquent un outil puissant utilisable en clinique.L’étude ciblée d’une voie de signalisation fréquemment dérégulée dans les cancers nous a permis de mettre en évidence une dérégulation globale de l’expression relative des transcrits alternatifs de gènes impliqués dans la prolifération cellulaire, et d’en identifier de probables régulateurs. Enfin, L’analyse des données de puces exons à la lumière des données de méthylation de l’ADN nous a permis d’identifier un mécanisme épigénétique régulant l’utilisation de promoteurs alternatifs dans un sous-groupe de tumeurs de vessie.L’ensemble des résultats obtenus par l’analyse de ces puces exons a par conséquent permis de caractériser à l’échelle du transcrit les dérégulations spécifiques des tumeurs de vessie, et d’en identifier certains mécanismes. Ces dérégulations permettent non seulement d’identifier spécifiquement plusieurs sous-groupe de tumeurs dont un de mauvais pronostic, mais offrent également de nouvelles possibilités quant-à la recherche de marqueurs urinaires pour la surveillance des patients. / The development of microarray technology in the late 1990’s served as an essential tool to comprehend the scope of transcriptomic deregulations occurring in cancer cells. Signals generated from the first generation of transcriptomic microarrays gave simultaneous measures of expression from a large number of genes, therefore enabling to identify candidate genes involved in cancer progression and putative therapeutic targets. In 2006, through a fast de- velopment of high-throughput technologies, the available large scale analysis tools became enriched with a new generation of high resolution microarrays measuring expression signals both at the gene-level and at the exon-level of each gene. The advent of this high-resolution microarray, commonly called exon array, provided the opportunity to get a more accurate meas- ure of transcriptomic changes affecting cancer cells by enabling to consider relative expression changes of the exons from a same gene.Alternative splicing and alternative transcription are the two main biological mechanisms accounting for the production of several transcripts from a same gene. Although these bio- logical processes have been known for a long time, their regulation in normal cells and their deregulation in cancer still remain challenging to well-characterize, mainly due to the complex- ity of the involved mechanisms. Through their design, exon arrays enable to identify variable expression patterns within several potential transcripts of a same gene, therefore bringing new insight into these biological processes.Based on a large dataset of bladder cancer samples that were profiled on exon arrays, we focused on the study of alternative splicing changes and alternative promoter usage in bladder tumours. Analysis of these exon arrays through the use of adapted statistical and mathemat- ical tools initially resulted in the identification of numerous genes showing differential relative expression patterns of their transcripts between cancer and normal samples. These transcripts represent a new opportunity to define tumour-specific therapeutic targets. We demonstrated that using an approach targeted on relative expression changes of transcripts from a same gene, it was possible to build up a panel of potential tumour-specific markers enabling the development of new urinary test to detect bladder cancer and monitor its evolution.Through an unsupervised analysis of putatively deregulated exon profiles, we observed that the partitioning of bladder tumours was similar to the classification resulting from the study of classical gene microarray expression profiles, consequently confirming the existence of a bladder subgroup with peculiar transcriptomic properties. For this subgroup of bad prognosis, we established a signature based on the differential alternative inclusion of several exons. This signature relates to 19 genes and enables to accurately identify tumours from this subgroup, therefore providing a powerful tool to be used in clinical practice.By studying a specific pathway often deregulated in cancer, we highlighted an overall dereg- ulation of the relative expression of alternative transcripts from genes involved in cell prolifer- ation, and identified potential actors involved in the underlying regulatory process. Eventually, the analysis of exon arrays in the light of DNA methylation array data enabled us to identify an epigenetic mechanism regulating the use of alternative promoters in a subgroup of bladder tumours.Together, the results obtained from exon array analysis consequently provided a character- ization at the transcript level of bladder tumour specific deregulations and brought insight into the underlying mechanisms. The highlighted deregulations not only allow to accurately identify two subgroups of tumours, of which one has a bad prognosis, but also offer new possibilities regarding the definition of urinary markers for patient monitoring.

A cobalamina (vitamina B12) e o ácido fólico são nutrientes essenciais para síntese de DNA, metionina e S-adenosilmetionina (SAM). A SAM é uma potente doadora de grupo metil necessário nas reações de metilação do DNA. Deficiências dessas vitaminas podem comprometer as concentrações da SAM e, indiretamente, a metilação do DNA. O objetivo deste estudo foi avaliar o efeito das concentrações de vitaminas (no sangue e na dieta), metabólitos (no soro) e do polimorfismo MTHFR C677T na taxa de metilação global do DNA. Participaram do estudo 103 gestantes, das quais foram colhidas amostras de sangue nas idades gestacionais de 16, 28 e 36 semanas. Foram realizadas as determinações dos valores de folato eritrocitário, e das concentrações séricas de folato, cobalamina, vitamina B6, homocisteína (tHcy), metionina, ácido metilmalônico (MMA), SAM e S-adenosilhomocisteína (SAH), além genotipagem para o polimorfismo MTHFR C677T por PCR-RFLP. A taxa de metilação global do DNA foi avaliada indiretamente por reação de extensão usando [3H]dCTP. Para avaliação nutricional foi aplicado um inquérito recordatório de 24 horas no dia de cada coleta. Devido ao uso de suplementação com ácido fólico e/ou polivitamínicos, as participantes foram classificadas em quatro grupos: grupo 1 (50 gestantes que não usaram suplementação); grupo 2 (14 mulheres que fizeram uso de suplementos nas três idades gestacionais); grupo 3 (21 participantes que usaram suplementação até a 16ª semana de gravidez) e grupo 4 (10 gestantes que utilizaram suplementação nas idades gestacionais de 16 e 28 semanas apenas). A taxa de metilação global do DNA foi menor na 28ª semana de gravidez quando comparada àquelas encontradas nas 16 e 36ª semanas em todos os grupos estudados. No grupo 1, as seguintes variáveis: concentrações de folato eritrocitário, vitamina B6 sérica, MMA, SAM, creatinina, vitamina B6 da dieta, proteínas de carnes (dieta), idade gestacional de 36 semanas e o genótipo CT + TT do polimorfismo MTHFR C677T foram associadas com a taxa de metilação do DNA, bem como as interações entre os genótipos CT + TT e folato eritrocitário ou sérico ou SAM; entre folato sérico e vitamina B6; entre creatinina e MMA ou vitamina B6 da dieta, e entre SAM e proteínas de carnes da dieta. As interações entre: 1 - menores concentrações de folato sérico e baixa ingestão de ácido fólico; 2 - maiores concentrações de MMA e baixa ingestão de vitamina B6; 3 - idade gestacional de 36 semanas e genótipo CT + TT do polimorfismo C677T no gene MTHFR foram associadas ao maior risco de apresentar menores taxas de metilação global do DNA no grupo 1. / Cobalamin (B12 vitamin) and folic acid are essential nutrients to DNA, methionine and S-adenosylmethinone (SAM) synthesis. SAM, the main methyl group donator, is necessary to DNA methylation reactions. Cobalamin and folic acid deficiencies might implicate SAM concentrations and, moreover, DNA methylation. The objective of this study was to evaluate the effects of serum vitamin and metabolites, vitamin intake and MTHFR C677T genetic polymorphism on global DNA methylation. Blood samples from 103 pregnant women were collected at gestational age of 16, 28 and 36 weeks. Red blood cell folate levels (RBC fol), and serum concentrations of folate (Fol), cobalamin, B6 vitamin, homocysteine (tHcy), methionine, methylmalonic acid (MMA), SAM and S-adenosylhomocysteine (SAH) were evaluated. The MTHFR C677T polymorphism was detected by PCR-RFLP. A radiolabeled [3H]dCTP extension assay was used to assess the level of global DNA methylation. Nutrient intake was assessed by 24 hour dietary recall applied at 16, 28 and 36 weeks of pregnancy. According to folic acid and/or multivitamins supplementation, women were classified in four groups: group 1 (50 women with no supplementation); group 2 (14 subjects who took supplements at three gestational ages); group 3 (21 women which took supplements until 16 weeks of pregnancy) and group 4 (10 subjects that took supplements at gestational ages of 16 and 28 weeks, but not at 36 weeks). Global DNA methylation level was lower at 28 weeks compared with 16 or 36 weeks.of pregnancy in women from four studied groups. In the group 1, not only values of RBC fol; serum concentrations of B6 vitamin, MMA, SAM and creatinine; vitamin B6 and meat protein intake; gestational age of 36 weeks and MTHFR 677T allele (CT+TT genotypes) were related to global DNA methylation in these women, but also interactions between MTHFR 677T allele and RBC fol or serum Fol or SAM; among serum Fol and B6 vitamin; between creatinine and MMA or vitamin B6 intake; and among SAM and meat protein intake. The following interactions between: 1 - lower serum Fol concentration and lower folate intake; 2 - higher serum MMA concentration and lower B6 vitamin intake; and 3 - gestational age of 36 weeks and MTHFR 677T allele were associated with higher risk of global DNA hypomethylation in pregnant women from group 1.

Human pluripotent stem cells (hPSCs) exist in multiple states of pluripotency, broadly categorised as naïve and primed states. These provide an important model to investigate the earliest stages of human embryonic development. Naïve cells can be obtained through primed-to-naïve reprogramming; however, there are no reliable methods to prospectively isolate unmodified naïve cells during this process. Moreover, the current isolation strategies are incompatible for enrichment of naïve hPSCs early during reprogramming. Consequently, we know very little about the temporal dynamics of transcriptional changes and remodelling of the epigenetic landscape that occurs during the reprogramming process. To address this knowledge gap, I sought to develop an isolation strategy capable of identifying nascent naïve hPSCs early during reprogramming. Comprehensive profiling of cell-surface markers by flow cytometry in naïve and primed hPSCs revealed pluripotent state-specific antibodies. By compiling the identified state-specific markers into a multiplexed antibody panel, I was able to distinguish naïve and primed hPSCs. Moreover, the antibody panel was able to track the dynamics of primed-to-naïve reprogramming, as the state-specific surface markers collectively reflect the change in pluripotent states. Through using the newly identified surface markers, I found that naïve cells are formed at a much earlier time point than previously realised, and could be subsequently isolated from a heterogeneous cell population early during reprogramming. This allowed me to perform the first molecular characterisation of nascent naïve hPSCs, which revealed distinct transcriptional changes associated with early and late stage naïve cell formation. Analysis of the DNA methylation landscape showed that nascent naïve cells are globally hypomethylated, whilst imprint methylation is largely preserved. Moreover, the loss of DNA methylation precedes X-chromosome reactivation, which occurs primarily during the late-stage of primed-to-naïve reprogramming, and is therefore a hallmark of mature naïve cells. Using the antibody panel at discrete time points throughout reprogramming has allowed an unprecedented insight into the early molecular events leading to naïve cell formation, and permits the direct comparison between different naïve reprogramming methods. Taken together, the identified state-specific surface markers provide a robust and straightforward method to unambiguously define human PSC states, and reveal for the first time the order of transcriptional and epigenetic changes associated with primed to naïve reprogramming.

A doença de Alzheimer (DA) é a causa mais comum de demência na população, sendo responsável por cerca de 50 a 60% dos casos. Embora o diagnóstico clínico da doença na maioria das vezes seja acurado, a confirmação da DA só é feita post mortem através principalmente da caracterização dos dois tipos principais de lesões neurais: depósitos extracelulares de placas de &beta; amiloide e emaranhados de proteína tau hiperfosforilada. Até o momento, o envolvimento de apenas quatro genes foi confirmado na etiologia da DA, três deles (APP, PSEN1 e PSEN2) associados à forma familial de herança mendeliana, que corresponde a um tipo raro e grave. No entanto, apesar de inúmeros trabalhos de associação genômica, (Genome wide association studies- GWAS) sugerirem uma possível participação de vários outros genes na suscetibilidade à manifestação da forma multifatorial da DA, o gene APOE, ainda é o único consistente e reproduzivelmente associado à doença. As descobertas derivadas dos GWAS investigando o papel de SNPs coletivamente explicam somente uma pequena porcentagem da variação herdada que contribui para o risco de desenvolver a DA. Atualmente, há novas abordagens para investigar a base genética do restante da variabilidade fenotípica herdada e que pode influenciar a suscetibilidade ao desenvolvimento de doenças complexas. O papel da variação do número de cópias de segmentos de DNA (Copy Number Variation - CNV) na genética de doenças complexas foi demonstrado por diversos estudos nos últimos anos e evidencia que desequilíbrios genômicos também podem contribuir significantemente para a resistência ou susceptibilidade a várias patologias. Outro aspecto que vem assumindo crescente importância é a análise de modificações epigenéticas que podem constituir um mecanismo molecular básico e contribuir diretamente para a patogênese da DA. Logo, este trabalho teve como objetivo principal investigar dois aspectos relacionados à DA: (1) a identificação de CNVs que podem estar contribuindo para o desenvolvimento da forma multifatorial da DA, usando a técnica de array-CGH, e (2) a análise de alterações do padrão global de metilação do DNA no córtex frontal de indivíduos com a forma multifatorial da DA, usando um microarranjo que interroga o status de metilação de 450.000 sítios CpGs. Em nossa investigação sobre desequilíbrios genômicos na DA, identificamos 6 CNVs raras com conteúdo gênico relevante para o fenótipo investigado. Dois indivíduos distintos do grupo DA apresentam microduplicações em genes que codificam diferentes subunidades do mesmo tipo de canal de Ca2+ dependente de voltagem, o tipo L. Além disso, dos outros genes selecionados como especialmente interessantes, 4 estão envolvidos em diferentes processos inflamatórios e 1 é responsável por codificar a enzima nicotinamida fosforibosiltransferase, participante importante da via de biossíntese da molécula nicotinamida adenina dinucleotídeo (NAD). A implicação de um possível envolvimento de mediadores da sinalização celular do Ca2+ e da via de biossíntese da NAD na etiologia da DA também foi reforçada pelos nossos resultados sobre o padrão de metilação do DNA na DA. Dois genes importantes para a homeostasia intracelular do Ca2+ e via de biossíntese da NAD apresentaram sítios CpGs diferenciamente metilados nos sujeitos com DA / Alzheimer\'s disease (AD) is the most common form of dementia in the population, corresponding to 50-60% of all cases. Although clinical diagnosis seems to be accurate, the definitive diagnosis of the disease can only be made by a post mortem neuropathological exam that certifies the presence of the two hallmarks of AD: the accumulation of extracellular senile plaques containing &beta;-amyloid (A&beta;) and the intracellular neurofibrillary tangles containing hyperphosphorylated tau protein. Four genes are known to be involved in the etiology of AD, three of them (APP, PSEN1 and PSEN2) are associated to the familial form of the disease, which show autosomal dominant inheritance and correspond to the more severe and rare type of AD. Despite many genome wide association studies (GWAS), APOE still remains the only unequivocal genetic risk factor associated to the multifactorial form of AD. The discoveries from GWAS using SNPs collectively explain only a small percentage of heritable variation that may contribute in AD risk. Currently, new approaches have been used to investigate the genetic basis of the phenotypical variability inheritance that can influence the susceptibility of complex diseases. The important role of DNA copy number variation (CNV) has been demonstrated by several studies over the last years and shows that genomic imbalances may also significantly contribute to resistance or susceptibility to various complex diseases. Additionally, there is now increasing interest in exploring how epigenetic modifications, in particular DNA methylation, could influence complex diseases etiology. Thus, the major aim of this work were to investigate two aspects related to the multifactorial form of AD: (1) identification of rare CNVs, using array-CGH, that could contribute to the development of the disease, and (2) analysis of the DNA methylation pattern in frontal cortex of individuals with AD. In our study, we identified 6 rare CNVs with relevant gene content to the investigated phenotype. Two distinct subjects with AD from our casuistic presented microduplications in genes that encode different subunits of the same type of Ca2+ voltage channel, the L-type. Furthermore, among the other selected genes, four are involved in different inflammatory process and one encodes the nicotinamide phosphoribosyltransferase enzyme, important mediator of nicotinamide adenine dinucleotide (NAD) biosynthesis. The implication of a possible involvement of Ca2+ intracellular signaling mediators and NAD biosynthesis pathway in the etiology of AD was also reinforced by our analysis of DNA methylation pattern. Interestingly, two important genes, one to intracellular Ca2+ homeostasis and the other to NAD biosynthesis pathway presented CpGs sites differently methylated in the AD subjects

A cobalamina (vitamina B12) e o ácido fólico são nutrientes essenciais para síntese de DNA, metionina e S-adenosilmetionina (SAM). A SAM é uma potente doadora de grupo metil necessário nas reações de metilação do DNA. Deficiências dessas vitaminas podem comprometer as concentrações da SAM e, indiretamente, a metilação do DNA. O objetivo deste estudo foi avaliar o efeito das concentrações de vitaminas (no sangue e na dieta), metabólitos (no soro) e do polimorfismo MTHFR C677T na taxa de metilação global do DNA. Participaram do estudo 103 gestantes, das quais foram colhidas amostras de sangue nas idades gestacionais de 16, 28 e 36 semanas. Foram realizadas as determinações dos valores de folato eritrocitário, e das concentrações séricas de folato, cobalamina, vitamina B6, homocisteína (tHcy), metionina, ácido metilmalônico (MMA), SAM e S-adenosilhomocisteína (SAH), além genotipagem para o polimorfismo MTHFR C677T por PCR-RFLP. A taxa de metilação global do DNA foi avaliada indiretamente por reação de extensão usando [3H]dCTP. Para avaliação nutricional foi aplicado um inquérito recordatório de 24 horas no dia de cada coleta. Devido ao uso de suplementação com ácido fólico e/ou polivitamínicos, as participantes foram classificadas em quatro grupos: grupo 1 (50 gestantes que não usaram suplementação); grupo 2 (14 mulheres que fizeram uso de suplementos nas três idades gestacionais); grupo 3 (21 participantes que usaram suplementação até a 16ª semana de gravidez) e grupo 4 (10 gestantes que utilizaram suplementação nas idades gestacionais de 16 e 28 semanas apenas). A taxa de metilação global do DNA foi menor na 28ª semana de gravidez quando comparada àquelas encontradas nas 16 e 36ª semanas em todos os grupos estudados. No grupo 1, as seguintes variáveis: concentrações de folato eritrocitário, vitamina B6 sérica, MMA, SAM, creatinina, vitamina B6 da dieta, proteínas de carnes (dieta), idade gestacional de 36 semanas e o genótipo CT + TT do polimorfismo MTHFR C677T foram associadas com a taxa de metilação do DNA, bem como as interações entre os genótipos CT + TT e folato eritrocitário ou sérico ou SAM; entre folato sérico e vitamina B6; entre creatinina e MMA ou vitamina B6 da dieta, e entre SAM e proteínas de carnes da dieta. As interações entre: 1 - menores concentrações de folato sérico e baixa ingestão de ácido fólico; 2 - maiores concentrações de MMA e baixa ingestão de vitamina B6; 3 - idade gestacional de 36 semanas e genótipo CT + TT do polimorfismo C677T no gene MTHFR foram associadas ao maior risco de apresentar menores taxas de metilação global do DNA no grupo 1. / Cobalamin (B12 vitamin) and folic acid are essential nutrients to DNA, methionine and S-adenosylmethinone (SAM) synthesis. SAM, the main methyl group donator, is necessary to DNA methylation reactions. Cobalamin and folic acid deficiencies might implicate SAM concentrations and, moreover, DNA methylation. The objective of this study was to evaluate the effects of serum vitamin and metabolites, vitamin intake and MTHFR C677T genetic polymorphism on global DNA methylation. Blood samples from 103 pregnant women were collected at gestational age of 16, 28 and 36 weeks. Red blood cell folate levels (RBC fol), and serum concentrations of folate (Fol), cobalamin, B6 vitamin, homocysteine (tHcy), methionine, methylmalonic acid (MMA), SAM and S-adenosylhomocysteine (SAH) were evaluated. The MTHFR C677T polymorphism was detected by PCR-RFLP. A radiolabeled [3H]dCTP extension assay was used to assess the level of global DNA methylation. Nutrient intake was assessed by 24 hour dietary recall applied at 16, 28 and 36 weeks of pregnancy. According to folic acid and/or multivitamins supplementation, women were classified in four groups: group 1 (50 women with no supplementation); group 2 (14 subjects who took supplements at three gestational ages); group 3 (21 women which took supplements until 16 weeks of pregnancy) and group 4 (10 subjects that took supplements at gestational ages of 16 and 28 weeks, but not at 36 weeks). Global DNA methylation level was lower at 28 weeks compared with 16 or 36 weeks.of pregnancy in women from four studied groups. In the group 1, not only values of RBC fol; serum concentrations of B6 vitamin, MMA, SAM and creatinine; vitamin B6 and meat protein intake; gestational age of 36 weeks and MTHFR 677T allele (CT+TT genotypes) were related to global DNA methylation in these women, but also interactions between MTHFR 677T allele and RBC fol or serum Fol or SAM; among serum Fol and B6 vitamin; between creatinine and MMA or vitamin B6 intake; and among SAM and meat protein intake. The following interactions between: 1 - lower serum Fol concentration and lower folate intake; 2 - higher serum MMA concentration and lower B6 vitamin intake; and 3 - gestational age of 36 weeks and MTHFR 677T allele were associated with higher risk of global DNA hypomethylation in pregnant women from group 1.

La sclérose en plaques (SEP) est une maladie auto-immmune notamment marquée par une défaillance de la mise en place des mécanismes de réparation tissulaire, ne permettant pas de rétablir l'homéostasie. L'utilisation de la résolution de l'inflammation, médiée par les. macrophages phagocytant des cellules apoptotiques. a récemment été évoquée afin de proposer une nouvelle famille de médicaments basée 1 sur cette résolution de l'inflammation. Dans ce cadre, nous proposons de résoudre l'inflammation dans un modèle murin de SEP, à l'aide du surnageant de co-culture de macrophages ayant phagocyté des cellules apoptotiques. induisant la production de facteurs pro-résolutifs (SuperMApo). Nous démontrons ici que l'injection de SuperMApo dans un modéle de SEP permet de contrôler la maladie via une reprogrammation des macrophages et des pDC, mais pas des cDC. dans la rate. Ces cellules démontrent en effet une capacité accrue à générer des T régulateurs (Treg) et moins de Th1, et leur présence est nécessaire pour l'effet du SuperMApo. Cette reprogrammation se fait à deux niveaux moléculaires. Premièrement. un contrôle épigénétique de l'expression des gènes induit notamment une modification de la méthylation globale de I' ADN et des promoteurs de miRNA impliqués dans la régulation des réponses immunes. Deuxièmement, une diminution de l'activation des acteurs de la voie de transcription pro-inflammatoire NFκB (nuclear factor kappa 8) a lieu. résultant d'une baisse de l'activation de ces cellules. Ces travaux démontrent donc que cibler la résolution de l'inflammation est une stratégie intéressante afin de contrôler la SEP. / Multiple sclerosis (MS) is an autoimmune disease notably delined bv a default of mechanisms of tissue reparation which are insufficient to establish homeostasis. The active resolution of innammation mediated by macrophage effcrocytosis of apoptotic cells has emerged to propose a new branch of pharmacology named "resolution pharmacology". ln this study. we propose to resolve innammation in a murine model of MS. using the supermatanl issued from the culture between apoptotic cells and macrophages. inducing efferocytosis and the production of pro-resolutive factors (SuperMApo). Here. we demonstrate that injection of SupcrMApo in a model of MS allow the control of the disease correlated with a reduction of the inflammatory inliltrate in the central nervous system. The control of the disease is associated with a reprograrnming of macrophages and pDC, but not cDC, in the spleen, demonstrated by a higher capacity to generate Treg and a lower ability to generate Th 1, and their presence is necessary to the anti-innammatory effect of SupcrMApo. Reprogramming of macrophages and pDC occurs at two main levels. First. an epigenetic control of gene expression induces a modulation of global DNA methylation and a modulation of DNA methylation at the promoter of miRNA implicated in the regulation of immune responses. Secondly, a decreased activation of NFκB activation pathway is observed resulting to a decreased activation of these cells. Thus, this work demonstrates that targeting the resolution of inflammation is an interesting strategy to treat MS.