Thesis (MSc (Biomedical Technology))--Cape Peninsula University of Technology, 2016. / The early detection of individuals who are at risk of developing type 2 diabetes mellitus (T2DM) would decrease the morbidity and mortality associated with this disease. DNA methylation, the most widely studied epigenetic mechanism, offers unique opportunities in this regard. Aberrant DNA methylation is associated with disease pathogenesis and is observed during the asymptomatic stage of disease. DNA methylation has therefore attracted increasing attention as a potential biomarker for identifying individuals who have an increased risk of developing T2DM. The identification of high risk biomarkers for T2DM could facilitate risk stratification and lifestyle interventions, which could ultimately lead to better ways to prevent, manage and control the T2DM epidemic that is rampant worldwide. The aim of the study was to investigate global DNA methylation as a potential risk factor for T2DM by studying the association between the global DNA methylation levels and hyperglycaemic states. A cross-sectional, quantitative study design, involving 564 individuals of mixed ancestry descent, residing in Bellville South, South Africa was used. Participants were classified as normal, pre-diabetic (impaired fasting glucose (IFG) and/or impaired glucose tolerance (IGT)) or diabetic (screen detected diabetic and known diabetics) according to WHO criteria of 1998. DNA was extracted from whole blood using the salt extraction method. The percentage global DNA methylation was measured by an enzyme-linked immunosorbent assay (ELISA). The association between global DNA methylation and hyperglycaemia, as well as other biochemical markers of T2DM was tested in a robust linear regression analysis adjusted for age, gender and smoking.

Thesis (MTech (Biomedical Technology))--Cape Peninsula University of Technology, 2016. / The early detection of individuals who are at risk of developing type 2 diabetes mellitus (T2DM) would decrease the morbidity and mortality associated with this disease. DNA methylation, the most widely studied epigenetic mechanism, offers unique opportunities in this regard. Aberrant DNA methylation is associated with disease pathogenesis and is observed during the asymptomatic stage of disease. DNA methylation has therefore attracted increasing attention as a potential biomarker for identifying individuals who have an increased risk of developing T2DM. The identification of high risk biomarkers for T2DM could facilitate risk stratification and lifestyle interventions, which could ultimately lead to better ways to prevent, manage and control the T2DM epidemic that is rampant worldwide. The aim of the study was to investigate global DNA methylation as a potential risk factor for T2DM by studying the association between the global DNA methylation levels and hyperglycaemic states. A cross-sectional, quantitative study design, involving 564 individuals of mixed ancestry descent, residing in Bellville South, South Africa was used. Participants were classified as normal, pre-diabetic (impaired fasting glucose (IFG) and/or impaired glucose tolerance (IGT)) or diabetic (screen detected diabetic and known diabetics) according to WHO criteria of 1998. DNA was extracted from whole blood using the salt extraction method. The percentage global DNA methylation was measured by an enzyme-linked immunosorbent assay (ELISA). The association between global DNA methylation and hyperglycaemia, as well as other biochemical markers of T2DM was tested in a robust linear regression analysis adjusted for age, gender and smoking.

Folates are water-soluble B vitamins, which maintain DNA stability by regulating nucleotide synthesis and DNA methylation. Folates influence CRC risk and their ability to prevent or promote carcinogenesis may be dependent on several variables here investigated. No in vitro study has yet modelled the physiological folate status that human colon cells are exposed to in vivo. This study evaluates the ability of different forms and concentrations of folate to maintain DNA stability and normal cell function in folate-sufficient and stable human colonocytes and to modify DNA instability and the acquisition of abnormal characteristics in folate-deficient and genomically-unstable colonocytes. Non-malignant human NCM460 colonocytes cultured at physiologically-relevant concentrations of 5-methyl-THF or FA, representing the average deficient (2.5 ng/mL), sufficient (10 ng/mL) or highest post-supplementation (100 ng/mL) folate levels found in human plasma were used in this study as a model of colon-folate interaction. This work established that FA is taken up and/or retained to a lesser extent than 5-methylTHF and is less efficient at maintaining DNA stability and normal cellular characteristics in folate-sufficient and genomically-stable colonocytes at baseline, particularly at deficient and sufficient concentrations in the medium to longer term (14-21 days). During repletion of folate-deficient and genomically-unstable cells, sufficient concentrations of FA do not increase intracellular folate status and worsen the unstable phenotype, by perpetuating DNA instability and enabling the acquisition of a more pro-malignant protein expression. On the contrary, employing 5-methyl-THF sufficiency for repletion positively modifies the abnormal protein profile and morphological features of folate-deficient cells, mitigating potential progression to malignant transformation. When high post-supplementation concentrations are employed, both folate forms increase intracellular folate status, but drive a more promalignant and stress-induced proteome profile and, in the case of 5-methyl-THF, promote abnormal cell morphologies. In conclusion, the folate type, concentration employed, baseline folate status and timing of exposure to folate supplementation are important variables that should be taken into account by future studies evaluating the potential impact of mandatory FA fortification on CRC.

Orientador: Carmen Silvia Bertuzo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-12T17:41:14Z (GMT). No. of bitstreams: 1 Ribeiro_CintiaMarques_M.pdf: 2054933 bytes, checksum: 39195c141e4cd2e600f9454a1cfc8781 (MD5) Previous issue date: 2009 / Resumo: A síndrome de Down (SD) é uma aberração cromossômica atribuída à presença de três cópias dos genes localizados no cromossomo 21. Ocorre com uma freqüência estimada de um indivíduo em 600 nascidos vivos e de uma em 150 concepções. Os mecanismos relacionados com a não-disjunção do cromossomo 21 não foram ainda elucidados e embora a idade materna avançada seja um fator de risco, a maioria das crianças com SD nasce de mães com menos de 30 anos. Um mecanismo proposto para explicar a não-disjunção cromossômica consiste na hipometilação do centrômero levando à formação anormal do cinetócoro e ligação anormal dos microtúbulos. Tal mecanismo teria uma etiologia multifatorial e entre os fatores genéticos estariam as variantes polimórficas de enzimas envolvidas no metabolismo do folato. A via bioquímica do folato pode influenciar a estabilidade do DNA de dois modos: o primeiro está relacionado com a função que o folato desempenha na transferência de unidades de 1-carbono para a biosíntese de novo de nucleotídeos. Baixa concentração intracelular de 5, 10-metilenoTHF leva a uma diminuição da síntese de timidilato e a incorporação errônea de dUTP durante a replicação do DNA; o segundo modo envolve a produção de S-adenosilmetionina (SAM), o principal doador de grupos metil para a maioria das reações de metilação, incluindo a metilação CpG. Baixa concentração intracelular de 5,10-metilenoTHF é associado com baixa produção de SAM e conseqüentemente com a hipometilação do DNA. Diante disso, o objetivo do trabalho foi determinar se os polimorfismos MTHFD-1 1958G>A, TCII 776C>G, MTR 2756A>G, MTRR 66 A>G, RFC-1 80G>A e SHMT-1 1420C>T representam fatores de risco para gestações com SD. Para isso foi realizada a técnica de PCR utilizando 200 amostras de DNAs de mães de portadores de SD (MSD) e 340 amostras de DNAs controles seguida por digestão enzimática dos produtos obtidos e análise estatística dos resultados. Comparando a distribuição genotípica no grupo MSD e controle foi observado que o polimorfismo TCII 776C>G apresentou uma diferença estatisticamente significativa: ?2 (2) = 13,10 e p=0,0014. Nossos resultados indicam que mulheres com genótipo heterozigoto para o polimorfismo TCII 776C>G possuem um risco duas vezes maior de gerarem crianças com SD / Abstract: Down syndrome is a chromosome abnormality caused by the presence of three copies of genes located in the chromosome 21. It occurs in an estimated frequency of one out of 600 liveborns and one out of 150 conceptions. The mechanism related to the non-disjunction of the chromosome 21 has not been totally understood and even though the mother's age is a risk factor, most DS children are born to mothers aged less than 30. One mechanism proposed to explain the chromosome non-disjunction is the centromeic hypomethylation that causes abnormal formation of kinetochore and abnormal links of the microtubules. Such a mechanism is thought to have a multifactorial etiology and among the genetic factors are polymorphic variants of enzymes involved in folate metabolism. The biochemical pathway of the folate influnces the DNA stability in two ways: the first is related to the role of folate in one carbon unit transfer during "de novo" synthesis of nucleotides. Low levels of 5, 10-methylenetetrahydrofolate (5, 10-methyleneTHF) lead to a decrease in thymidylate synthesis and the misincorporation of the dUTP during replication of DNA; the second way involves the production of S-adenosyl methionine (SAM), the main donor of methyl to most methylation processes, incluing CpG methylation. Low intracellular 5,10-methyleneTHF is associated with low SAM production and consequently with DNA hypomethylation. Therefore, the purpose of the study was determining if the polymorfisms MTHFD-1 1958G>A, TCII 776C>G, MTR 2756A>G, MTRR 66A>G, RFC-1 80G>A e SHMT-1 1420C>T represent risk factors for DS pregnancies. So we used techniques of PCR followed by restriction enzyme analysis of 200 DNAs of mothers of DS children (MSD) and 340 DNAs of control mothers with statistic analyses of the results. Comparing the genotypic distribution in the groups MSD and control it has been observed that polymorphism TCII 776C>G showed a statistically remarkable difference: ?2 (2) = 13,10 e p=0,0014. Our results show that women that have heterozigote genotype for polymorphism TCII 776C>G have two times higher risk of generating DS children / Mestrado / Ciencias Biomedicas / Mestre em Ciências Médicas

Orientador: Ana Paula de Souza Pardo / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-24T15:42:26Z (GMT). No. of bitstreams: 1 Planello_AlineCristiane_D.pdf: 1888206 bytes, checksum: 00e43f6f072e313fafc04b5a4406af8b (MD5) Previous issue date: 2014 / Resumo: A inflamação crônica é conhecida por induzir alterações epigenéticas, em particular, alterações na metilação do DNA. A ilha CpG do gene SOCS1 tem sido observada hipermetilada em diferentes tipos de câncer e em doenças associadas à inflamação. No entanto, pouco se sabe sobre essas alterações epigenéticas associadas à periodontite crônica. A fim de abordar essa questão, nós investigamos a metilação do DNA no exon 2 da Ilha CpG do SOCS1 e sua relevância funcional para a periodontite crônica em 90 amostras de tecidos gengivais usando a técnica de comparação de melting sensível a metilação (MS-HRM). Nós observamos que a região analisa se encontra hipermetilada quando comparada com amostras de indivíduos saudáveis. Alterações na expressão no SOCS1 não foram encontradas. Posteriormente foram realizadas investigações da sequencia do SOCS1 que revelaram marcadores de enhancer na região. Analise de sítios hipersensíveis a Dnase I (Dnase I hipersensitivity site ¿ DHS), que são associados com região regulatória, mostraram um DHS dentro do exon2 do SOCS1, que cobre a mesma região estudada na técnica MS-HRM. Esse DHS correlacionou-se com vários promotores na vizinhança do SOCS1, sendo considerados os genes alvos. Fragmentos desmetilados e metilados cobrindo a região encontrada com diferença de metilação no SOCS1 foram clonados em um plasmídeo repórter que possui um promotor e é livre de qualquer CpG.. Os fragmentos desmetilados aumentaram a atividade da luciferase, demonstrando a atividade de enhancer da região. Já os fragmentos metilados, além de não exercerem atividade de enhancer, foram capazes de reprimir a função do promotor. Corroborando essas informações, foi observada correlação negativa entre a metilação no SOCS1 nas amostras com inflamação e a expressão de genes. Os dados apresentados indicam que a função principal da metilação do DNA em um enhancer é controlar sua função regulatória e consequentemente os níveis de transcrição dos genes alvo, o que pode ser evidenciado pela hipermetilação do exon do SOCS1 na inflamação crônica / Abstract: Chronic inflammation is known to induce epigenetic alterations, in particular alterations in DNA methylation. SOCS1 CpG island (CGI) has been demonstrated hypermethylated in many types of cancer and inflammation-associated diseases. However, little is known about the epigenetic changes associated with chronic periodontitis. In order to address this question, we investigated DNA methylation of oxon 2 of SOCS1 CGI and its functional relevance to chronic periodontitis in 90 gingival tissue samples using methylation sensitive high resolution melting (MS-HRM). We found this region to be hypermethylated when compared with healthy controls. No changes in gene expression were observed. Further investigations of SOCS1 sequence showed enhancer marker at SOCS1 region. Correlation analysis of Dnase I hypersensitivity site (DHS), which is associated with regulatory region, showed a DHS inside exon2 SOCS1 correlated with several promoter in the neighboring region, considered target genes. Fragments harboring the SOCS1 region found to be differentially methylated, were cloned into a CpG free-Luc reporter vector just upstream the promoter. Unmethylated and methylated fragments were tested. The unmethyalted fragment enhanced the promoter activity of the promoter. Strikingly, not only the exon2 of SOCS1 CGI presented enhancer activity but also it had its activity disrupted by DNA methylation. Accordingly, negative correlation between SOCS1 methylation and expression of neighboring genes was observed in chronic inflammation. The data indicate that the primary function of enhancer DNA methylation is to control its regulatory function and the transcription levels of enhancer target genes, which can be evidenced by exon 2 SOCS1 CGI hypermethylation on chronic inflammation / Doutorado / Histologia e Embriologia / Doutora em Biologia Buco-Dental

Orientador: Sérgio Roberto Peres Line / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-23T22:35:31Z (GMT). No. of bitstreams: 1 Mofatto_LucianaSouto_D.pdf: 2939657 bytes, checksum: 161ea0e68091cc76485826424b41aab0 (MD5) Previous issue date: 2013 / Resumo: Os G-quadruplexes são estruturas secundárias de DNA altamente organizadas, constituídas por sequências ricas em guaninas capazes de formar tétrades ligadas por pontes de hidrogênio. Essas sequências são capazes de modular a transcrição gênica e o splicing alternativo de éxons. Além disso, estudos também mostraram que os G-quadruplexes estão presentes na região promotora de oncogenes (como c-MYC) e nas regiões terminais dos telômeros, indicando que o G-quadruplex pode ser um possível alvo terapêutico contra o câncer. A metilação do DNA é uma modificação bioquímica que frequentemente aparece na posição C5 de citosinas da sequência do dinucleotídeo 5'- citosina guanina - 3' (CpG) em células eucarióticas. As alterações no padrão normal de metilação do DNA estão associadas a situações patológicas, como inflamação e câncer. Assim, a metilação anormal de citosinas pode ser responsável pela indução de câncer através de mutações pontuais em genes supressores de tumor presentes em células somáticas e germinativas. Este trabalho propôs estudar a estrutura e estabilidade de Gquadruplexes de DNA e sua influência na metilação do DNA. Neste intuito foram realizadas análises para verificar se a formação de G-quadruplex no DNA dupla fita poderia influenciar no padrão de metilação de citosinas, utilizando oligonucleotídeos (ricos em guaninas e com sítio para metilação) que mimetizam a fita dupla de DNA. Também foi estudado: (1) a estabilidade de G-quadruplexes contendo mais de quatro tríades de G e a possível formação de G-quadruplexes em DNA fita dupla em ensaio "in vitro"; (2) a interação entre extratos de própolis e G-quadruplexes de DNA e (3) o efeito de estabilizadores de G-quadruplex (TMPyP4 e 360A) no padrão de metilação do DNA em cultura de linhagens de células normais e tumorais / Abstract: G-quadruplexes are highly organized secondary structures of DNA, consisting of guanine rich sequences that form tetrads linked by hydrogen bonds. These sequences can modulate gene transcription and the alternative splicing of exons. Studies also showed that G-quadruplexes are present in the promoter of oncogenes (such as c-MYC) and terminal telomere regions, suggesting that the Gquadruplex can be a therapeutic target in cancer. DNA methylation is a frequent biochemical modification that appears in C5 position of cytosine in the dinucleotide sequence 5' - cytosine guanine - 3' (CpG) in eukaryotic cells. Changes in the normal patterns of DNA methylation are frequently associated with patologic situations, such as inflammation and cancer. Abnormal methylated cytosine may be responsible for induction of cancer due to mutations in tumor suppressor genes of somatic and germline cells. The aim of this study was to analyze the structure and stability of Gquadruplexes of DNA and its influence on DNA methylation. It was verified if Gquadruplex formation of double-stranded DNA could influence the pattern of cytosine methylation, using oligonucleotides (sequences with methylation site and rich in guanine) that simulated double-stranded DNA. We also evaluated: (1) the stability of G-quadruplexes containing more than four triads of guanine and the possible formation of G-quadruplexes in double-stranded DNA by "in vitro" test; (2) the interaction between propolis ethanolic extracts and DNA G-quadruplexes and (3) the effect of G-quadruplex ligands (TMPyP4 and 360A) for DNA methylation in normal and tumor cell lines / Doutorado / Histologia e Embriologia / Doutora em Biologia Buco-Dental

Background: Obesity is a disease that is caused by genetic and environmental factors. However, epigenetic mechanisms of obesity are less well known. DNA methylation provides a mechanism whereby environmental factors can influence gene transcription. The aim of our study was to investigate skeletal muscle DNA methylation of sorbin and SH3 domain containing 3 (SORBS3) with weight loss induced by Roux-en-Y gastric bypass (RYGB). Results: Previously, we had shown increased methylation (5.0 to 24.4%) and decreased gene expression (fold change -1.9) of SORBS3 with obesity (BMI > 30 kg/m(2)) compared to lean controls. In the present study, basal muscle biopsies were obtained from seven morbidly obese (BMI > 40 kg/m(2)) female subjects pre-and3months post-RYGB surgery, in combination with euglycemic-hyperinsulinemic clamps to assess insulin sensitivity. We identified 30 significantly altered promoter and untranslated region methylation sites in SORBS3 using reduced representation bisulfite sequencing (RRBS). Twenty-nine of these sites were decreased (-5.6 to -24.2%) post-RYGB compared to pre-RYGB. We confirmed the methylation in 2 (Chr. 8: 22,423,690 and Chr. 8: 22,423,702) of the 29 decreased SORBS3 sites using pyrosequencing. This decreased methylation was associated with an increase in SORBS3 gene expression (fold change + 1.7) post-surgery. In addition, we demonstrated that SORBS3 promoter methylation in vitro significantly alters reporter gene expression (P < 0. 0001). Two of the SORBS3 methylation sites (Chr. 8: 22,423,111 and Chr. 8: 22,423,205) were strongly correlated with fasting plasma glucose levels (r = 0.9, P = 0.00009 and r = 0.8, P = 0.0010). Changes in SORBS3 gene expression post-surgery were correlated with obesity measures and fasting insulin levels (r = 0.5 to 0.8; P < 0.05). Conclusions: These results demonstrate that SORBS3 methylation and gene expression are altered in obesity and restored to normal levels through weight loss induced by RYGB surgery.

No description available.

Epigenetic regulation of gene expression plays a pivotal role in the orchestration of immune responses. In particular, they have been implicated in the generation of in vitro cytokine-driven T cell polarization and therefore may determine the vigor, quality and/or longevity of such responses in vivo. Chemical allergens form two categories: skin sensitizing chemicals associated with allergic contact dermatitis, such as 2,4-dinitrochlorobenzene (DNCB) that result in type 1/type 17 responses in mice, and chemicals that cause sensitization of the respiratory tract and occupational asthma, for example trimellitic anhydride (TMA) that induces preferential type 2 responses in mice. To explore the regulation and maintenance of these divergent responses generated by polarised T cell populations in vivo, BALB/c strain mice were exposed topically DNCB and TMA. DNA from draining lymph nodes (LN) was processed for methylated DNA (5mC) immunoprecipitation (MeDIP) followed by hybridization to a whole-genome DNA promoter array. A higher number of DNCB-associated differently methylated regions (DMR) were identified and there was significant crossover between allergen treatments. Promoter-associated DMR, unique to either DNCB or TMA, were generally hypomethylated. Pathway analyses highlighted a number of immune related pathways, including chemokine and cytokine signalling. A number of these DMR were hypothesised to be candidate biomarkers of chemical allergy. To confirm this, novel analysis of hydroxymethylated (5hmC) DNA in the in vivo allergen-activated LN was compared to analysis of 5mC to identify LN specific DMR. The Gmpr DMR is suggested as a possible biomarker for contact allergen-induced immune responses and the Nwc DMR was characteristic of TMA treatment, highlighting its possible utility as a biomarker for responses induced by chemical respiratory allergens. These data not only represent novel analysis of 5hmC in response to chemical allergy in vivo, but also provide a possible basis for differentiation between classes of chemical allergens. Finally, a combined population of effector/effector memory T cells (TEff/TEM) was isolated from the CD4+ and CD8+ populations of allergen-activated draining lymph nodes (LN). Levels of 5mC and 5hmC at T cell lineage cytokine prompters was determined and analysed by comparison with concurrently sorted naïve T cells. In CD8+ TEff/TEM from DNCB-stimulated LN, increased expression of Ifng and Gzmb correlated with a reduction 5mC at their respective promoters. There were also reduced levels of 5mC at an Ifng enhancer. In contrast, TMA-simulated CD4+ TEff/TEM were characterised by high levels of Il4 expression which were associated with a decrease in promoter 5mC and an increase in 5hmC, as well as increased 5hmC at an Il4 enhancer region. These data demonstrate that exposure to chemical allergens results in characteristic DNA methylation patterns indicative of epigenetic regulation of divergent T cell populations in vivo. Furthermore, it highlights a particularly important role for DNA hydroxymethylation at the Th2 locus. In conclusion, exposure to chemical allergens results in divergent patterns of 5mC and 5hmC. These provide possible biomarkers for the different classes of chemical allergens and represent an insight into the importance of 5mC and 5hmC in the control of polarised T cell responses in vivo.

Les transposons sont des séquences d’ADN qui ont la capacité de se dupliquer de façon autonome, posant une menace pour l’intégrité et la stabilité du génome. De nombreux mécanismes existent pour contrôler l’expression des transposons, parmi lesquels la méthylation de l’ADN joue un rôle particulièrement important. Chez les mammifères, les profils de méthylation sont stables tout au long de la vie de l’individu, mis-à-part pendant deux moments clés du développement embryonnaire. Pendant ces deux périodes, la méthylation de l’ADN est globalement effacée, ce qui corrèle avec l’acquisition d’un état cellulaire pluripotent, puis rétablie. En utilisant un système cellulaire de reprogrammation de méthylation induite, ce travail s’est attaché à comprendre comment le génome parvient à maintenir le contrôle des transposons en l’absence de cette protection d’ordinaire essentielle, J’ai pu démontrer que divers mécanismes chromatiniens compensent progressivement la disparition de la méthylation de l’ADN pour le maintien de la répression des transposons. En particulier, la machinerie Polycomb prend en partie le relai et acquiert un rôle primordial, spécifiquement en l’absence de méthylation de l’ADN. Dans un second temps, la contribution du cofacteur d’ADN méthyltransférase DNMT3l lors de la méthylation de novo a été étudiée. Dans sa globalité, ces découvertes offrent des perspectives nouvelles sur la façon dont le génome se réorganise lors de moments clés du développement embryonnaire. / Transposons are DNA sequences that can duplicate autonomously in the genome, posing a threat for genome stability and integrity. To prevent their potentially harmful mobilization, eukaryotes have developed numerous mechanisms that control transposon expression, among which DNA methylation plays a particularly important role. In mammals, DNA methylation patterns are stable for life, at the exception of two key moments during embryonic development, gametogenesis and early embryogenesis. After a phase a global loss of genomic methylation accompanying the acquisition of pluripotent states, DNA methylation patterns are re- established de novo during differentiation. This work attempted to elucidate how the genome copes with the rapid loss of DNA methylation, in particular regarding the control of transposons in absence of this essential protective mark. Using an embryonic cellular model of induced methylation reprogramming, I showed that various chromatin-based mechanisms can compensate for the progressive loss of DNA methylation. In particular, my results suggest that the Polycomb machinery acquires a critical role in transposon silencing, providing a mechanistic relay specifically when DNA methylation patterns are erased. In a second phase, this work analyzed the contribution of the DNA methyltransferase cofactor DNMT3l during events of embryonic de novo methylation. Overall, these findings shed light onto the processes by which genome regulation adapts during DNA methylation reprogramming.