Thesis (Ph. D.)--University of Missouri-Columbia, 2009. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. "May 2009" Includes bibliographical references.

Thesis (Ph.D.). / Written for the Dept. of Pharmacology & Therapeutics. Title from title page of PDF (viewed 2009/06/10). Includes bibliographical references.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2009. / Title from PDF title page (viewed on Sept. 9, 2009). Includes bibliographical references.

DNA methylation is an epigenetic mechanism that regulates the gene transcription. Folate is used in cellular synthesis of methyl groups, nucleic acids and amino acids. In complex diseases like cancer and neural tube defects (NTD), various genetic and epigenetic alterations can be found that disrupt the normal cell function. The main goals of this thesis were to analyze whether the genes responsible for the folate transport (FOLR1, PCFT, and RFC1) could be regulated by DNA methylation in placenta, blood leukocytes and colorectal cancer. We also addressed the genome-wide DNA methylation changes in colorectal cancer andcervical cancer.We found that changes in the methylated fraction of the RFC1 gene were dependent on the RFC1 80G>A polymorphism in placental specimens with NTDs and blood leukocytes from subjects with high homocysteine (Paper I). In colorectal cancer, the greatest difference in DNA methylation was observed in the RFC1 gene and was related to a lower protein expression (Paper II).In Paper III and IV we studied the DNA methylated fraction using a high-density array. Paper III was focused on genes in the DNA repair pathway and frequently mutated in colorectal cancer. We found that aberrant methylation in the DNA mismatch repair genes was not a frequent event in colorectal cancer and we identified five candidate biomarker genes in colorectal cancer, among them the GPC6 and DCLRE1C genes. In Paper IV, we found hypomethylation of genes involved in the immune system in cervical cancer specimens compared to healthy cervical scrapes and we identified twenty four candidate genes for further evaluation ofclinical value.In conclusion, the work of this thesis filled a relevant knowledge gap regarding the role of differential methylation of the folate transport genes in NTD and colorectal cancer. This thesis work also provided insights into the functional role of DNA methylation in cancer specific pathways and identified potential novel biomarker genes.

Orientador: Flavia Lombardi Lopes / Banca: Silvia Helena Venturoli Perri / Banca: José Fernando Garcia / Banca: Ricardo da Fonseca / Banca: José bento Sterman Ferraz / Resumo: O objetivo desse estudo foi identificar polimorfismos de nucleotídeo único (SNPs) potencialmente sujeitos a controle epigenético exercido por metilação do DNA via seus envolvimentos na criação, remoção ou deslocamento de sítios CpG (meSNPs) e a partir de tal identificação criar um banco de dados para meSNPs, bem como determinar a possível associação desses marcadores com ilhas CpG (CGIs) e com o perfil metilacional de tecidos submetidos ao ensaio de recuperação de ilhas CpG metiladas combinado com plataformas de sequenciamento de nova geração (MIRA-seq) em bovinos. Usando as variantes anotadas para os SNPs identificados no Run5 do projeto 1000 Bull Genomes e a sequência genômica bovina de referência UMD3.1.1, identificamos e anotamos 12.836.763 meSNPs de acordo com o padrão de variação criado por cada SNP em um sítio CpG. Também analisamos a distribuição genômica desses meSNPs, sendo a maioria deles localizados em regiões intergênicas (68,00%) e intrônicas (26,32%). Globalmente, os meSNPs representam 22,53% dos 56.969.697 SNPs descritos na base de dados e 12,35% deles estão localizados em CGIs. Comparando o número observado com o número esperado de meSNPs nas CGIs e nos tecidos submetidos ao MIRA-seq, verificamos um enriquecimento médio (P<0,01) para meSNPs de 2,47 vezes em CGIs relaxadas e 1,90 vezes em CGIs rigorosas. Nos tecidos, o enriquecimento foi de 1,52 vezes em longissimus dorsi e 2,09 vezes em intestino delgado. Dez meSNPs com metilação diferencial, sendo 1 em longi... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The aim of this study was to identify single nucleotide polymorphisms (SNPs) potentially subject to epigenetic control exerted by DNA methylation via their involvement in creating, removing or displacement CpG sites (meSNPs) and from this identification create a database for meSNPs, as well as to determine its possible association with CpG islands (CGIs) and the methylation profile of tissues submitted to the methylated-CpG island recovery assay combined with next generation sequencing platforms (MIRA-seq) in cattle. Using the variant annotations for SNPs identified in Run5 of the 1000 bull genomes project and the UMD3.1.1 bovine reference genome sequence assembly, we identified and classified 12,836,763 meSNPs according to the pattern of variation caused at the CpG site. We have also analyzed the genomic distribution of the meSNPs, with the majority being located in intergenic regions (68.00%) and then in introns (26.32%) and the remainder distributed among proximal promoters (3.93%), coding regions (1.27%), untranslated regions (UTRs) (0.29%), non-coding RNAs (0.11%) and splice regions (0.08%). Overall, meSNPs represent 22.53% of 56,969,697 SNPs described in the database of which 12.35% are located in CGIs. Comparing the observed number with the expected number of meSNPs in the CGIs and tissues submitted to the MIRAseq we found a mean enrichment (P<0.01) for meSNPs of 2.47 times in the relaxed CGIs and 1.90 times in the strict CGIs. In the tissues the enrichment was of 1.52... (Complete abstract click electronic access below) / Doutor

La méthylation de l’ADN est la marque épigénétique la plus connue. Elle consiste en l’ajout d’un groupement méthyle au niveau de la cytosine, produisant la 5-méthyl-cystosine (5mC). Cette réaction chimique est catalysée par des ADN méthyltransférases : DNMT1, DNMT3A et DNMT3B. Peu de choses sont connues concernant les changements de 5mC au cours des lignages cellulaires dans l’embryon et comment cette marque contribue à l’établissement ou au maintien de l’identité cellulaire. Nous avons cherché à mieux comprendre ces mécanismes en étudiant la 5mC dans deux lignages cellulaires : les cellules primordiales germinales (PGCs) et les cellules souches hématopoïétiques (HSCs). Nous avons généré les premiers méthylomes de ces cellules au cours de leur développement chez la souris. Chez les PGCs, nous avons mis en évidence l’existence de deux phases de reprogrammation de la 5mC. Une première phase entre E9,5 et E13,5, où le génome des PGCs se déméthyle et une phase de reméthylation entre E14,5 et E17,5, chez les gamètes mâles uniquement. Néanmoins, certaines régions, dont notamment les éléments transposables sont résistants à la vague de déméthylation. L’utilisation de souris conditionnellement, nous a permis de mettre en évidence l’implication des protéines DNMT1 et UHRF2 dans le maintien de la 5mC au niveau de ces séquences. Concernant les HSCs, nous avons mis en évidence qu’elles acquièrent un profil de 5mC qui leur est propre lors de deux phases. La première a lieu dès l’apparition des HSCs dans l’organisme tandis que l’acquisition de la signature hématopoïétique définitive se déroule à l’âge adulte dans la moelle osseuse. L’utilisation de souris conditionnelles, nous a permis de mettre en exergue l’implication de DNMT3A et DNMT3B dans la mise en place de ces profils, avec un rôle prépondérant de DNMT3B lors de la phase d’acquisition précoce et de DNMT3A lors du verrouillage de leur profil de 5mC. / The methylation of DNA is a well-known epigenetic mark. It consists in adding a methyl group to a cytosine producing the 5-methylcytosine (5mC). This is catalysed by the DNA methyltransferase (DNMT) family: DNMT1, DNMT3A and DNMT3B. Little is known about the changes in DNA methylation that follow lineage decisions in the embryo and how these contribute, establish or maintain cellular identities. We are addressing these questions using as a model the specification of mouse primordial germ cells (PGCs) and mouse hematopoietic stem cells (HSCs) in the mouse embryo. We generate the first genome-wide maps of 5mC during their development. These maps highlight two waves of DNA methylation in PGCs. The first one takes place between E9,5 and E13,5, where the genome demethylates while the second one corresponds to a remethylation phase only in male PGCs between E14,5 and E17,5. Nevertheless, some regions, notably the transposable elements, are resistant to this demethylation wave. We demonstrate the implication of DNMT1 and UHRF2 in maintaining the 5mC on these regions using transgenic mice presenting specific deletion in PGCs. In HSCs, the 5mC maps highlight two wave of DNA methylation. The first one correlates with the first appearance of the HSCs in early embryos while the second one corresponds to their migration to the bone marrow and seems to act as a definitive lock for their hematopoietic identity. Using transgenic mice presenting specific deletions in HSCs, we prove the implication of DNMT3A and DNMT3B in hematopoietic stem cells, with a major role in locking HSC identity of DNMT3B during the first wave and a DNMT3A during the second one respectively.

Schizophrenia, bipolar disorder and major depressive disorder are devastating psychiatric conditions with a complex, overlapping genetic and environmental architecture. Previously, a family has been reported where a balanced chromosomal translocation between chromosomes 1 and 11 [t(1;11)] shows significant linkage to these disorders. This translocation transects three genes: Disrupted in schizophrenia- 1 (DISC1) on chromosome 1, a non-coding RNA, Disrupted in schizophrenia-2 (DISC2) antisense to DISC1, and a non-coding transcript, DISC1 fusion partner-1 (DISC1FP1) on chromosome 11, all of which could result in pathogenic properties in the context of the translocation. This thesis focuses on the genome-wide effects of the t(1;11) translocation, primarily examining differences in gene expression and DNA methylation, using various biological samples from the t(1;11) family. To assess the genome-wide effects of the t(1;11) translocation on methylation, DNA methylation was profiled in whole-blood from 41 family members using the Infinium HumanMethylation450 BeadChip. Significant differential methylation was observed within the translocation breakpoint regions on chromosomes 1 and 11. Downstream analysis identified additional regions of differential methylation outwith these chromosomes, while pathway analysis showed terms related to psychiatric disorders and neurodevelopment were enriched amongst differentially methylated genes, in addition to more general terms pertaining to cellular function. Using induced pluripotent stem cell (iPSC) technology, neuronal samples were developed from fibroblasts in a subset of individuals profiled for genome-wide methylation in whole blood (N = 6) with an aim to replicate the significant findings around the breakpoint regions. Here, methylation was profiled using the Infinium HumanMethylation450 BeadChip’s successor: the Infinium MethylationEPIC BeadChip. The results from the blood-based study failed to replicate in the neuronal samples, which could be attributed to low statistical power or tissue-specific factors such as methylation quantitative trait loci. The differences in methylation in the most significantly differentially methylated loci were found to be driven by a single individual, rendering further interpretation of the findings from this analysis difficult without additional samples. Cross-tissue analyses of DNA methylation were performed on blood and neuronal DNA from these six individuals, revealing little correlation between cell types. DISC1 is central to a network of interacting protein partners, including the transcription factor ATF4, and PDE4; both of which are associated with the cAMP signalling pathway. Haploinsufficiency of DISC1 due to the translocation may therefore be disruptive to cAMP-mediated gene expression. In order to identify transcriptomic effects which may be related to the t(1;11) translocation, genome-wide expression profiling was performed in lymphoblastoid cell line RNA from 13 family members. No transcripts were found to be differentially expressed at the genome-wide significant level. A post-hoc power analysis suggested that more samples would be required in order to detect genome-wide significant differential expression. However, imposing a fold-change cut-off to the data identified a number of candidate genes for follow-up analysis, including SORL1: a member of the brain-expressed Sortilin gene family. Sortilin genes have been linked to multiple psychiatric disorders including schizophrenia, bipolar disorder and Alzheimer’s disease. Follow-up analyses of Sortilin family members were performed in a Disc1 mouse model of schizophrenia, containing an amino acid substitution (L100P). Here, developmental gene expression profiling was performed with an additional aim to optimise and validate work performed by others using this mouse model. However, results from these experiments were variable between two independent batches mice tested. Additional investigation of Sortilin family genes was performed using GWAS data from human samples, using machine learning techniques to identify epistatic interactions linked to depression and brain function, revealing no statistically significant interactions. The results presented in this thesis suggest a potential mechanism for differential DNA methylation in the context of chromosomal translocations, and suggests mechanisms whereby increased risk of illness is conferred upon translocation carriers through dysregulation of transcription and DNA methylation.

Les mécanismes épigénétiques contribuent à générer une variabilité phénotypique héréditaire. Le plus étudié de ces mécanismes est la méthylation de l'ADN au niveau des résidus cytosine. Cette méthylation est principalement (mais pas exclusivement) située dans le contexte CpG. En dépit d'être l'un des supports épigénétiques les plus analysés, Cette méthylation n'a pas été étudiée de manière exhaustive. Au cours de mon doctorat, j'ai contribué à développer un nouveau logiciel de prédiction de la méthylation de l'ADN basée sur les taux de mutation localisés au niveau des régions CpG. L’analyse de séquences issues de bases de données pour 150 espèces ont permis d’identifier 4 profils de méthylation dans les corps des gènes. Ces profils de méthylation ne sont pas congruents avec la classification du vivant. Ces résultats suggèrent une convergence évolutive sous contraintes environnementales ou fonctionnelles et une universalité du code de méthylation de l'ADN. Nos différents résultats permettent de générer des liens conceptuels entre méthylation de l'ADN, fonction des gènes et environnement pour une large gamme de clades phylogénétiques. Pour valider l’importance de l’épigénétique dans la plasticité phénotypique, je me suis focalisé dans une seconde partie de ma thèse au succès parasitaire de Schistosoma au sein de son hôte intermédiaire, le mollusque Biomphalaria glabrata. En effet, l'interaction entre ce parasite trématode agent de la bilharziose et ce mollusque est caractérisée par un polymorphisme de compatibilité. Du côté du parasite, le principal marqueur moléculaire de la compatibilité est le profil d'expression de mucines polymorphes appelées SmPoMuc. Nous montrons que l’utilisation d’agent épimutagènes provoque des modifications de la structure de la chromatine notamment au niveau des promoteurs SmPoMuc. Ces modifications sont à l’origine de la variabilité phénotypique puisque le succès parasitaire s’en trouve augmenter. Nous établissons ici que les changements épigénétiques peuvent être un élément important de la plasticité phénotypique adaptative chez S. mansoni, aussi importante que la composante génétique. / Epigenetic mechanisms contribute to generate heritable phenotypic variability. The most studied of these mechanisms is DNA methylation on cytosine residues. Methylation is predominantly (but not exclusively) located in CpG dinucleotides context. Surprisingly, DNA methylation has not been exhaustively studied in many species. During my PhD, I developed a new Galaxy-integrated software to predict DNA methylation based on mutation rates of methylated and unmethylated CpG regions. DNA methylation analysis from several data bases for 150 species have identified 4 typical profiles for methylation distribution all the long gene bodies. These methylation profiles are not congruent with kingdom classification. These results suggest evolutionary convergence under environmental or functional constraints and universality of the DNA methylation code. Our results contribute to pave the way for generating conceptual links between DNA methylation, genes function and environment for a large range of phylogenetic clades.To evaluate the significance of epigenetic program on the phenotypic plasticity, I focused also on the parasitic success of Schistosoma face to its intermediate host, the Biomphalaria glabrata snail. Indeed, the interaction between this trematode parasite causing of the second human disease after malaria and the mollusk is based on a compatibility polymorphism. On the side of the parasite, the main molecular marker of this compatibility is supported by expression profile of polymorphic mucins called SmPoMucs. We demonstrate that epimutator compounds induce chromatin structural modification on mucin promoters. These modifications are directly involved on the phenotypic plasticity since the infectivity rate is enhanced. In this work, we conclude that epigenetic modifications are key elements on adaptive and developmental plasticity for S. mansoni, as essential as the genetic component.

Breast cancer is a clinically and molecularly heterogeneous disease displaying distinct therapeutic responses. Although recent studies have explored the genomic and transcriptomic landscapes of breast cancer, the epigenetic architecture has received less attention. To address this, an optimised Reduced Representation Bisulfite Sequencing protocol was performed on 1482 primary breast tumours (and 237 matched adjacent normal tissues). This constitutes the largest breast cancer methylome yet, and this thesis describes the bioinformatics and statistical analysis of this study. Noticeable epigenetic drift (both gain and loss of homogeneous DNA methylation patterns) was observed in breast tumours when compared to normal tissues, with markedly higher differences in late replicating genomic regions. The extent of epigenetic drift was also found to be highly heterogeneous between the breast tumours and was sharply correlated with the tumour’s mitotic index, indicating that epigenetic drift is largely a consequence of the accumulation of passive cell division related errors. A novel algorithm called DMARC (Directed Methylation Altered Regions in Cancer) was developed that utilised the tumour-specific drift rates to discriminate between methylation alterations attained as a consequence of stochastic cell division errors (background) and those reflecting a more instructive biological process (directed). Directed methylation alterations were significantly enriched for gene expression changes in breast cancer, compared to background alterations. Characterising these methylation aberrations with gene expression led to the identification of breast cancer subtype-specific epigenetic genes with consequences on transcription and prognosis. Cancer genes may be deregulated by multiple mechanisms. By integrating with existing copy number and gene expression profiles for these tumours, DNA methylation alterations were revealed as the predominant mechanism correlated with differentially expressed genes in breast cancer. The crucial role of DNA methylation as a mechanism to target the silencing of specific genes within copy number amplifications is also explored which led to the identification of a putative tumour suppressor gene, THSZ2. Finally, the first genome-wide assessment of epigenomic evolution in breast cancer is conducted. Both, the level of intratumoural heterogeneity, and the extent of epiallelic burden were found to be prognostic, and revealed an extraordinary distinction in the role of epiclonal dynamics in different breast cancer subtypes. Collectively, the results presented in this thesis have shed light on the somatic DNA methylation basis of inter-patient as well as intra-tumour heterogeneity in breast cancer. This complements our genetic knowledge of the disease, and will help move us towards tailoring treatments to the patient's molecular profile.

abstract: Neurotoxicology has historically focused on substances that directly damage nervous tissue. Behavioral assays that test sensory, cognitive, or motor function are used to identify neurotoxins. But, the outcomes of behavioral assays may also be influenced by the physiological status of non-neural organs. Therefore, toxin induced damage to non- neural organs may contribute to behavioral modifications. Heavy metals and metalloids are persistent environmental pollutants and induce neurological deficits in multiple organisms. However, in the honey bee, an important insect pollinator, little is known about the sublethal effects of heavy metal and metalloid toxicity though they are exposed to these toxins chronically in some environments. In this thesis I investigate the sublethal effects of copper, cadmium, lead, and selenium on honey bee behavior and identify potential mechanisms mediating the behavioral modifications. I explore the honey bees’ ability to detect these toxins, their sensory perception of sucrose following toxin exposure, and the effects of toxin ingestion on performance during learning and memory tasks. The effects depend on the specific metal. Honey bees detect and reject copper containing solutions, but readily consume those contaminated with cadmium and lead. And, exposure to lead may alter the sensory perception of sucrose. I also demonstrate that acute selenium exposure impairs learning and long-term memory formation or recall. Localizing selenium accumulation following chronic exposure reveals that damage to non-neural organs and peripheral sensory structures is more likely than direct neurotoxicity. Probable mechanisms include gut microbiome alterations, gut lining damage, immune system activation, impaired protein function, or aberrant DNA methylation. In the case of DNA methylation, I demonstrate that inhibiting DNA methylation dynamics can impair long-term memory formation, while the nurse-to- forager transition is not altered. These experiments could serve as the bases for and reference groups of studies testing the effects of metal or metalloid toxicity on DNA methylation. Each potential mechanism provides an avenue for investigating how neural function is influenced by the physiological status of non-neural organs. And from an ecological perspective, my results highlight the need for environmental policy to consider sublethal effects in determining safe environmental toxin loads for honey bees and other insect pollinators. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2016