Humans are exposed to arsenicals through many routes with the most common being drinking water. Exposure to arsenic has been associated with an increased incidence of skin, lung, liver, prostate, and bladder cancer. Although the relationship between arsenic exposure and carcinogenesis is well documented, the mechanisms by which arsenic participates in tumorigenesis are not fully elucidated. We evaluated the potential epigenetic component of arsenical action by assessing the histone acetylation and DNA methylation state of 13,000 human gene promoters in a cell line model of arsenical-mediated malignant transformation. We show changes in histone H3 acetylation and DNA methylation occur during arsenical-induced malignant transformation, each of which is linked to the expression state of the associated gene. These epigenetic changes occurred non-randomly and targeted common promoters whether the selection was performed with arsenite [As(III)] or with the As(III) metabolite monomethylarsonous acid [MMA(III)]. The epigenetic alterations of these promoters and associated malignant phenotypes were stable after the removal of the transforming arsenical. One of the affected regions was the promoter of WNT5A. This gene is transcriptionally activated during arsenical induced malignant transformation and its promoter region exhibited alterations in each of the four histone modifications examined which were linked to its transcriptional activation. Experimental reduction of WNT5A transcript levels resulted in abrogated anchorage independent growth, suggesting a participative role for the epigenetic remodeling of this promoter region in arsenical-induced malignant transformation. Taken together, these data suggest that arsenicals may participate in tumorigenesis by stably altering the DNA methylation and histone modifications associated with targeted genes, uncovering a likely set of participative genes and representing a mechanism to potentially explain the latency associated with arsenic-induced malignancy.

Epigenetics is the field of focus when determining how environmental and behavioral factors can directly impact the expression of genes that affect our behavior. Existing studies have examined links between eliciting stress behaviors in pregnant mice and the negative stress behavioral responses in offspring for several subsequent generations, which points to a disposition to adverse stress responses later in life due to early-life epigenetic modifi- cations. Similarly, research on both rats and humans has found early life trauma to be a large factor in both the hyper- and de-methylation of genes responsible for stress processing, which can be linked to depressive behav- ior later in life. The proposed study aims to address the lack of attention to positive psychology in this field of study by seeking to identify epigenetic markers such as hyper- or de-methylation in regions of the rat genome con- taining homologous genes to those in humans potentially linked to positive affect or life satisfaction. Rat offspring reared with either high or low levels of maternal care would be exposed to a novel stressful environment, and a microarray analysis would be performed to assess the differences in gene expression in the previously noted regions of the genome. Gene expression analysis may reveal that offspring who received more maternal care show increased expression of the serotonin transporter gene, down-regulation of genes for proinflammatory cytokines, and up-regulation of anti-viral re- sponse genes. These results would be consistent with the gene expression patterns previously seen in individuals with higher levels of life satisfac- tion, eudemonic pleasure, and optimism.

Small intestinal neuroendocrine tumours (SI-NETs) are rare, hormone producing and proliferate slowly. Patients usually display metastases at time of diagnosis, the tumours are difficult to cure, and the disease course is unpredictable. The gene expression pattern was investigated in paper I, with emphasis on aggressive disease and tumour progression. Expression microarrays were performed on 42 tumours. Unsupervised hierarchal clustering revealed three clusters that were correlated to clinical features, and expression changes from primary tumour to metastasis. Eight novel genes, ACTG2, GREM2, REG3A, TUSC2, RUNX1, TGFBR2, TPH1 and CDH6 may be of importance for tumour progression. In paper II, expression of ACTG2 was detected in a fraction of SI-NETs, but not in normal enterochromaffin cells. Inhibition of histone methyltransferase and transfection of miR-145 induced expression and no effect was seen after DNA methylation or selective EZH2 inhibition in vitro. miR-145 expression was reduced in metastases compared to primary tumours. Overexpression of ACTG2 inhibited cell growth, and inducing ACTG2 may have therapeutic effects. TCEB3C (Elongin A3) is located on chromosome 18 and is imprinted in some tissues. In paper III a reduced protein expression was detected. The gene was epigenetically repressed by both DNA and histone methylation in a tumour tissue specific context. The expression was also induced in primary cell cultures after DNA demethylation and pyrosequencing revealed promoter region hypermethylation. Overexpression of TCEB3C inhibited cell growth by 50%, suggesting TCEB3C to be a tumour suppressor gene. In paper IV, 69 biomarkers were analysed in blood serum using multiplex proximity ligation assay. Nineteen markers displayed different levels between patients and controls. In an extended cohort, ELISA analysis showed elevated serum levels of Mindin, DcR3 and TFF3 in patients and protein expression in tumour cells. High levels of DcR3 and TFF3 were associated with poor survival, and DcR3 may be a marker for liver metastases. Mindin, DcR3, and TFF3 are potential novel diagnostic biomarkers for SI-NETs.

<p>Glioma development and progression are driven by complex genetic alterations, including point mutations and gain or loss of genomic copy number, as well as epigenetic aberrations, including DNA methylation and histone modifications. However, the molecular mechanisms underlying the causes and effects of these alterations are poorly understood, and improved treatments are greatly needed. Here, we report a comprehensive evaluation of the recurrent genomic alterations in gliomas and further dissect the molecular effects of the most frequently-occurring genomic events. First, we performed a multifaceted genomic analysis to identify genes targeted by copy number alteration in glioblastoma, the most aggressive malignant glioma. We identify EGFR negative regulator, <italic>ERRFI1</italic>, as a glioblastoma-targeted gene within the minimal region of deletion in 1p36.23. Furthermore, we demonstrate that Aurora-A kinase substrate, <italic>TACC3</italic>, displays gain of copy number on 4p16.3 and is overexpressed in a grade-specific pattern. Next, using a gene targeting approach, we knocked-in a single copy of the most frequently observed point mutation in gliomas, <italic>IDH1<super>R132H/WT</super></italic>, into a human cancer cell line. We show that heterozygous expression of the <italic>IDH1<super>R132H</super></italic> allele is sufficient to induce the genome-wide alterations in DNA methylation characteristic of these tumors. Together, these data provide insight on genetic and epigenetic alterations which drive human gliomas.</p> / Dissertation

A fosforilação da histona 3 na serina 10 (H3S10) e a acetilação da histona 3 lisina 14 (H3K14) tem sido relacionadas com a formação da memória em paradigmas de medo condicionado. Estudos demonstram que o exercício é capaz de melhorar o desempenho em testes de memória além de modular marcadores epigenéticos. O objetivo desse estudo foi investigar o efeito de um protocolo de corrida em esteira (20min/dia durante 2 semanas) sobre os níveis de acetilação da H3K14 e de fosforilação da H3S10 em hipocampo de ratos expostos ou não expostos a um contexto de aprendizado.Ratos Wistar de 3 meses de idade foram submetidos a um protocolo de exercício crônico (grupo exercitado) ou submetidos a esteira desligada (grupo sedentário) e após parte dos animais foram expostos a um contexto de aprendizado (esquiva inibitória). Os animais foram eutanasiados por decapitação e os níveis da fosforilação da serina 10 e da acetilação da lisina 14 na histona 3 (H3 foram avaliados em hipocampos. A ANOVA de duas vias mostrou um efeito significativo dos fatores “contexto de aprendizado” e “exercício” nos níveis de acetilação da H3K14, assim como uma interação entre esses fatores. Houve uma diminuição nos níveis de acetilação 24h após o treino da esquiva inibitória (30 minutos após o teste) no hipocampo do grupo submetido ao contexto de aprendizado. Além disso, o exercício crônico aumentou os níveis de acetilação no hipocampo dos ratos expostos ao contexto de aprendizado. Os níveis de fosforilação da H3S10 não foram alterados pelo contexto de aprendizado nem pelo exercício. Nossos dados apoiam a hipótese de que a modulação da acetilação na H3K14 em hipocampo de ratos pode estar relacionada,pelo menos em parte, aos efeitos do exercício sobre memória aversiva. / The phosphorylation of histone H3 at serine 10 (H3S106) and acetylation of histone 3 at lysine 14 (H3K14) have been linked to memory processes in fear conditioning paradigms. Some studies demonstrated that exercise was able to improve the performance in memory tasks and modulate epigenetic markers. The aim of this study was to investigate the effect of treadmill exercise protocol (20min/day during 2 weeks) on H3K14 acetylation and H3S10 phosphorylation levels in hippocampi from rats exposed or not exposed to learning context. Wistar rats with 3-months-old were submitted to chronic exercise protocol (exercised group) or left on the treadmill turned off (sedentary group) and after it, some animal were exposed to learning context (inhibitory avoidance). Rats were euthanized by decapitation and the levels of serine 10 phosphorylation and lysine 14 acetylation on histone 3 (H3) were evaluated in hippocampi. Two-way ANOVA showed a significant effect of “learning context” and “exercise factors” on acetylation levels of H3K14, as well as an interaction between these factors. There was a decrease in acetylation levels twenty four hours after inhibitory avoidance training (30 minutes after test), in hippocampus from exposed to learning context groups. Besides, the chronic exercise increased acetylation levels in hippocampi from rats exposed to learning context. The H3S10 phosphorylation levels were not altered by of learning context and exercise. Our data support the hypothesis that the modulation on acetylation levels of H3K14 acetylation in hippocampus might be related, at least partially, to exercise effects on aversive memory.

A fosforilação da histona 3 na serina 10 (H3S10) e a acetilação da histona 3 lisina 14 (H3K14) tem sido relacionadas com a formação da memória em paradigmas de medo condicionado. Estudos demonstram que o exercício é capaz de melhorar o desempenho em testes de memória além de modular marcadores epigenéticos. O objetivo desse estudo foi investigar o efeito de um protocolo de corrida em esteira (20min/dia durante 2 semanas) sobre os níveis de acetilação da H3K14 e de fosforilação da H3S10 em hipocampo de ratos expostos ou não expostos a um contexto de aprendizado.Ratos Wistar de 3 meses de idade foram submetidos a um protocolo de exercício crônico (grupo exercitado) ou submetidos a esteira desligada (grupo sedentário) e após parte dos animais foram expostos a um contexto de aprendizado (esquiva inibitória). Os animais foram eutanasiados por decapitação e os níveis da fosforilação da serina 10 e da acetilação da lisina 14 na histona 3 (H3 foram avaliados em hipocampos. A ANOVA de duas vias mostrou um efeito significativo dos fatores “contexto de aprendizado” e “exercício” nos níveis de acetilação da H3K14, assim como uma interação entre esses fatores. Houve uma diminuição nos níveis de acetilação 24h após o treino da esquiva inibitória (30 minutos após o teste) no hipocampo do grupo submetido ao contexto de aprendizado. Além disso, o exercício crônico aumentou os níveis de acetilação no hipocampo dos ratos expostos ao contexto de aprendizado. Os níveis de fosforilação da H3S10 não foram alterados pelo contexto de aprendizado nem pelo exercício. Nossos dados apoiam a hipótese de que a modulação da acetilação na H3K14 em hipocampo de ratos pode estar relacionada,pelo menos em parte, aos efeitos do exercício sobre memória aversiva. / The phosphorylation of histone H3 at serine 10 (H3S106) and acetylation of histone 3 at lysine 14 (H3K14) have been linked to memory processes in fear conditioning paradigms. Some studies demonstrated that exercise was able to improve the performance in memory tasks and modulate epigenetic markers. The aim of this study was to investigate the effect of treadmill exercise protocol (20min/day during 2 weeks) on H3K14 acetylation and H3S10 phosphorylation levels in hippocampi from rats exposed or not exposed to learning context. Wistar rats with 3-months-old were submitted to chronic exercise protocol (exercised group) or left on the treadmill turned off (sedentary group) and after it, some animal were exposed to learning context (inhibitory avoidance). Rats were euthanized by decapitation and the levels of serine 10 phosphorylation and lysine 14 acetylation on histone 3 (H3) were evaluated in hippocampi. Two-way ANOVA showed a significant effect of “learning context” and “exercise factors” on acetylation levels of H3K14, as well as an interaction between these factors. There was a decrease in acetylation levels twenty four hours after inhibitory avoidance training (30 minutes after test), in hippocampus from exposed to learning context groups. Besides, the chronic exercise increased acetylation levels in hippocampi from rats exposed to learning context. The H3S10 phosphorylation levels were not altered by of learning context and exercise. Our data support the hypothesis that the modulation on acetylation levels of H3K14 acetylation in hippocampus might be related, at least partially, to exercise effects on aversive memory.

A fosforilação da histona 3 na serina 10 (H3S10) e a acetilação da histona 3 lisina 14 (H3K14) tem sido relacionadas com a formação da memória em paradigmas de medo condicionado. Estudos demonstram que o exercício é capaz de melhorar o desempenho em testes de memória além de modular marcadores epigenéticos. O objetivo desse estudo foi investigar o efeito de um protocolo de corrida em esteira (20min/dia durante 2 semanas) sobre os níveis de acetilação da H3K14 e de fosforilação da H3S10 em hipocampo de ratos expostos ou não expostos a um contexto de aprendizado.Ratos Wistar de 3 meses de idade foram submetidos a um protocolo de exercício crônico (grupo exercitado) ou submetidos a esteira desligada (grupo sedentário) e após parte dos animais foram expostos a um contexto de aprendizado (esquiva inibitória). Os animais foram eutanasiados por decapitação e os níveis da fosforilação da serina 10 e da acetilação da lisina 14 na histona 3 (H3 foram avaliados em hipocampos. A ANOVA de duas vias mostrou um efeito significativo dos fatores “contexto de aprendizado” e “exercício” nos níveis de acetilação da H3K14, assim como uma interação entre esses fatores. Houve uma diminuição nos níveis de acetilação 24h após o treino da esquiva inibitória (30 minutos após o teste) no hipocampo do grupo submetido ao contexto de aprendizado. Além disso, o exercício crônico aumentou os níveis de acetilação no hipocampo dos ratos expostos ao contexto de aprendizado. Os níveis de fosforilação da H3S10 não foram alterados pelo contexto de aprendizado nem pelo exercício. Nossos dados apoiam a hipótese de que a modulação da acetilação na H3K14 em hipocampo de ratos pode estar relacionada,pelo menos em parte, aos efeitos do exercício sobre memória aversiva. / The phosphorylation of histone H3 at serine 10 (H3S106) and acetylation of histone 3 at lysine 14 (H3K14) have been linked to memory processes in fear conditioning paradigms. Some studies demonstrated that exercise was able to improve the performance in memory tasks and modulate epigenetic markers. The aim of this study was to investigate the effect of treadmill exercise protocol (20min/day during 2 weeks) on H3K14 acetylation and H3S10 phosphorylation levels in hippocampi from rats exposed or not exposed to learning context. Wistar rats with 3-months-old were submitted to chronic exercise protocol (exercised group) or left on the treadmill turned off (sedentary group) and after it, some animal were exposed to learning context (inhibitory avoidance). Rats were euthanized by decapitation and the levels of serine 10 phosphorylation and lysine 14 acetylation on histone 3 (H3) were evaluated in hippocampi. Two-way ANOVA showed a significant effect of “learning context” and “exercise factors” on acetylation levels of H3K14, as well as an interaction between these factors. There was a decrease in acetylation levels twenty four hours after inhibitory avoidance training (30 minutes after test), in hippocampus from exposed to learning context groups. Besides, the chronic exercise increased acetylation levels in hippocampi from rats exposed to learning context. The H3S10 phosphorylation levels were not altered by of learning context and exercise. Our data support the hypothesis that the modulation on acetylation levels of H3K14 acetylation in hippocampus might be related, at least partially, to exercise effects on aversive memory.

Les Papillomavirus Humains (HPV) à haut risque carcinogène, dont HPV16, sont les agents étiologiques du cancer du col de l'utérus. Le génom d'HPV est composé d'un ADN double brin comprenant deux régions codantes : précoce« E » et tardive« L » et une région régulatrice non codante, la LCR. La protéine E2 se fixe au niveau des E2BS, situés dans la LCR et réprime l'expression d'E6 et d'E7. La perte d'expression d'E2 suite à l'intégration du génome virale induit une surexpression d'E6 et d'E7 qui favorisent la dégradation de p53 et de pRb. Des dinucléotides CpG étant présents au niveau des E2BS d'HPV16, nous avons détenniné si l'expression d'E6 était soumise à une régulation épigénétique. Nous avons développé une PCR HRM pour étudier le niveau de méthylation des E2BS dans les lésions précancéreuses et cancéreuses et nous avons noté la présence de CpG méthylés uniquement dans les cancers. Par ailleurs, nous avons montré que la méthylation des E2BS limite la fixation d'E2 et pern1et probablement la surexpression d'E6 et d'E7. Enfin, nous avons montré que le traitement des cellules HPV16 dérivées de cancer du col utérin pi le 5azadC, induit une diminution de l'expression d'E6. Ce mécanisme est indépendant d'E2 et nous avons prouvé que la ré-expression du miR-375, qu cible les transcrits E6/E7, est responsable de la répression d'E6 après traitement par SazadC. L'ensemble de nos résultats ont montré que l'expression des oncoprotéines d'HPV16 est régulée épigénétiquement par des facteurs viraux et cellulaires / High risk Human Papillomaviruses (HPV) are responsible for cervical cancer. HPV genome consists in a double-strand circular DNA harboring early "E" and late "L" genes and a Long Control Region (LCR). The E2 protcin binds to E2 Binding Sites (E2BS) present on the LCR and represses E6 and E7 transcription. The loss of E2 expression after HPV DNA integration induces an overexpression of E6 and E7 that thus favor p53 and pRb degradation. Since CpG dinucleotides are present in HPVl6 E2BS, we investigated whether E6 HPV16 expression was also submitted to epigenetic regulation. We developed a HRM PCR to study the methylation status of E2BS in precanccrous and canccrous lesions. We observed methylated CpG only in cancer samples. Otherwise, we proved that E2BS methylation prevented E2 binding and probably permitted E6 and E7 overexpression. Finally, we showed that the treatment ofHPV16 cervical cancer cell lines with a demethylating agent (SazadC) decreased the E6 expression. This regulation was independent of E2 and we proved that the up-regulation of miR-375, which targets E6/E7 transcripts, was involved in E6 repression after SazadC treatment. Taken as a whole, our data demonstrate that HPV 16 oncoprotein expression is regulated in an epigenetic manncr via viral and cellular factors.

Natural products have, historically, played an important role in drug discovery. Nevertheless, drug resistance, pathogen evolution, and global climate change threaten human health and nearly all current anti-infective treatments on the market today. It is undeniable that new drug discovery efforts are needed with increasing urgency. Bolstered by a rich history of discovering treatments in the world around us, natural products chemists continue to look to the environment with increasing understanding and emerging technologies that allow efficient, effective isolation of new chemical entities. This thesis will describe one such endeavor. Focusing on fungal natural products, herein is described the isolation and structure elucidation of new, bio-active natural products. Further, the development and implementation of a large fungal screening program will be discussed, the results of which stand to advance microbial drug discovery in the Baker lab for years to come.

Over the past five years the role of epigenetic modifiers in brain development has become increasingly evident. In this regard, Snf2l, a homolog of the chromatin remodeling protein ISWI, was shown to have enriched expression in the brain and be important for neuronal differentiation. Mice lacking functional Snf2l have hypercellularity of the cerebral cortex due to increased cell cycle re-entry. In this thesis I demonstrate the effects of Snf2l-ablation on cortical progenitor cells including increased proliferation and cell cycle deregulation, the consequence of which is a delay in neuronal migration and altered numbers of mature cortical neurons. This phenotype arises from increased expression of Foxg1, a winged-helix repressor expressed in the forebrain and anterior optic vesicle. Moreover, genetically reducing its overexpression rescues the Snf2l-ablated phenotype. Snf2l is bound directly to a promoter region of Foxg1 suggesting that it acts as a repressive regulator in vivo and is an important factor in forebrain differentiation.