Thesis (M.S.)--University of Alabama at Birmingham, 2010. / Title from PDF title page (viewed on June 25, 2010). Includes bibliographical references (p. 31-37).

Deoxycytidylate (dCMP) hydroxymethylase (CH) catalyzes the formation of 5-hydroxymethyl-dCMP (Hm5CMP) from dCMP and methylene tetrahydrofolate (CH2THF), analogous to the reaction between dUMP and CH2THF catalyzed by thymidylate synthase (TS), an enzyme of known structure. The amino acid sequence identity between invariant TS residues and CH is at least 50%. Most of the residues which contact the dUMP and CH2THF in TS are conserved in CH. It is hypothesized that CH is homologous to TS in both structure and mechanism. The project described in this thesis tests this hypothesis. In-vitro studies on catalysis by CH variants. The roles of three residues in catalysis by CH have been tested using site-directed mutagenesis. Conversion of Cys148 to Asp, Gly or Ser decreases CH activity at least 105 fold, consistent with a nucleophilic role for Cys148 (analogous to the catalytic Cys in TS). In crystalline TS, hydrogen bonds connect O4 and N3 of bound dUMP to the side chain of an Asn; the corresponding CH residue is Asp179. Conversion of Asp179 in CH to Asn reduces kcat/KM for dCMP by 104 fold and increases kcat/KM for dUMP 60 fold, changing the nucleotide specificity of the enzyme. Other studies have shown that the specificity of TS was changed from dUMP to dCMP by conversion of the appropriate Asn to Asp. Based on the crystal structure of TS, a Glu residue (also conserved in CH) is proposed to catalyze formation of the N5 iminium ion methylene donor by protonation of N10 of CH2THF. In CH and TS, overall turnover and tritium exchange are tightly coupled. Replacement of Glu60 in CH or Glu58 in TS uncouples these catalytic steps. Conversion the Glu60/58 to Gln or Asp results in a 5-50 fold decrease in the ability to catalyze tritium exchange, consistent with an inability to catalyze formation of the N5 iminium ion, but also results in a 104-105 decrease in product formation. This suggests that Glu60/58is also involved in a step in catalysis after nucleotide and folate binding and proton removal from carbon 5 of the nucleotide. Isotope effect studies. The observed value of the α-secondary tritium inverse equilibrium isotope effect (EIE = 0.8) on formation of the complex between FdUMP, CH2THF and both wild-type CH and CH(D179N) indicates that carbon 6 of FdUMP is sp3 hybridized (tetrahedral) in the ternary complex. This is consistent with the hypothesis that that carbon 6 is bonded to Cys148 in the complex. Removal of Cys148in CH prevents complex formation with FdUMP. Lack of an observed α-secondary tritium kinetic isotope effect (KIE) for position 6 of dCMP for both enzymes suggests that the intrinsic KIE is masked by other rate-limiting steps or that rehybridization follows the first irreversible step. An observed KIE on carbon 6 of dUMP by CH(D179N) suggests the rate-limiting steps for the two nucleotide substrates is different. In-vivo studies catalysis by CH variants. In order to prevent recombination between CH deficient T4 phage and plasmid borne copies of CH variants, the gene coding for CH, gene 42, was deleted from the T4 chromosome. The T4Δ42 phage requires wild-type CH expressed from a plasmid to kill their host cell. CH variants C148G, D179N, E60Q, and E60D, all which exhibit at least 2000 fold lower activity in vitro, do not complement the T4Δ42 phage in vivo. Interchanging the functional domains of CH and TS. It is proposed that shortening the C-terminal loop seen in the structure of TS changes the solvent structure of the CH active-site such that it becomes more hydrated. Differences in the solvent structure of the active-site may account for differences in the catalytic specificity between CH and TS, respectively, hydration versus reduction. In order to test the hypothesis that these catalytic differences between TS and CH lie within the C-terminal portion of the enzyme, the N-terminus of the CH(D179N) variant was fused to the C-terminus of the wild-type TS to create a chimeric CH/TS enzyme. The chimeric enzyme was predicted to have specificity for dUMP and a active-site solvent structure similar to that for wild-type TS. However, the resulting protein cannot be overproduced to significant levels and does not have any detectable TS activity in vivo.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Les papillomavirus humains (HPV) sont des petits virus non enveloppés à ADN double brin, qui infectent les épithéliums cutanés et muqueux. Très largement répandus dans la population humaine, les infections sont la plupart du temps asymptomatiques, tandis qu'une minorité provoquent des verrues cutanées, des condylomes acuminés et des carcinomes. Les cancers induits par HPV représentent 640 000 cas en 2012 dans le monde et sont localisés au niveau anogénital et au niveau des voies aérodigestives supérieures.La transformation des cellules est induite en particulier par la surexpression de deux oncoprotéines virales : E6 et E7, qui sont nécessaires à l'initiation, la promotion et la progression du phénotype cancéreux. Leur extinction provoque d'ailleurs la mort des cellules cancéreuses. E6 et E7 favorisent par exemple la dégradation de p53 et pRb, induisant ainsi une prolifération non contrôlée et accrue des cellules infectées. Mais les deux oncoprotéines virales interagissent aussi avec plus de 150 partenaires protéiques et dérégulent l'homéostasie cellulaire. Fait intéressant, E6 et E7 modulent l'expression de nombreuses protéines impliquées dans l'établissement des marques épigénétiques, impliquées dans la régulation de l'expression des gènes. D'ailleurs, la surexpression des oncoprotéines virales peut être liée à la méthylation de l'ADN d'une partie du génome viral.Puisque E6 et E7 détournent la machinerie épigénétique de la cellule, l'objectif du travail de thèse a été d'étudier les mécanismes moléculaires régulant l'expression des oncoprotéines lors du traitement des cellules de cancers du col par un agent déméthylant de l'ADN, le 5-aza-2'-déoxycytidine (5azadC).Dans des cellules issues de cancers du col de l'utérus, nous avons observé qu'un traitement déméthylant induisait une répression de la protéine E6 et une déstabilisation de ses transcrits, suggérant l'implication d'un miARN. Parmi les miARN ciblant les transcrits viraux, le miR-375 était le plus susceptible d'être impliqué dans la déstabilisation des transcrits car (i) la méthylation de son promoteur augmente avec la gravité des lésions du col de l'utérus, (ii) il cible les transcrits viraux au niveau de cinq régions différentes, et (iii) son expression est augmentée lors du traitement de cellules dérivées du cancer du col de l'utérus avec le 5azadC. Il s'est avéré que le miR-375 était effectivement impliqué dans la répression partielle des transcrits viraux lors du traitement. Les résultats de cette étude suggèrent par ailleurs qu'un autre mécanisme moléculaire pourrait être impliqué dans cette répression. C'est pourquoi, dans un deuxième temps, nous avons étudié l'implication possible d'un facteur de transcription, TBX2, dans la répression des transcrits viraux. Bien que le taux transcriptionnel de TBX2 soit augmenté lors du traitement des cellules avec des fortes concentrations de 5azadC, nos résultats suggèrent que la protéine n'est pas exprimée dans les cellules, même après traitement, et que TBX2 ne régule pas l'activité du promoteur viral intégré au génome cellulaire.Le traitement des cellules par l'agent déméthylant entraîne aussi une perte de viabilité en particulier des cellules Ca Ski. En effet, le 5azadC induit un blocage du cycle en G2/M dans ces cellules, une augmentation du pourcentage de cellules en Sub-G1 et un clivage de la PARP. Si le 5azadC est déjà utilisé en clinique pour le traitement d'autres cancers, nos données apportent un éclairage nouveau sur les mécanismes moléculaires du 5azadC dans les cancers induits par HPV, qui pourraient ainsi être traités par cette molécule. / Human papillomaviruses (HPV) are small, non-enveloped double-stranded DNA viruses and infect cutaneous and mucosal epithelia. Highly widespread in the human population, infections are mostly asymptomatic, while a minority causes cutaneous and genital warts, and carcinomas. HPV-induced cancers represent 640 000 cases in 2012 worldwide and are localized at the anogenital and head and neck sites.Cell transformation is induced by the overexpression of two viral oncoproteins E6 and E7, which are necessary for the initiation, promotion and progression of the cancerous phenotype. Indeed, their extinction causes cancer cell death. E6 and E7, for example, promote the degradation of p53 and pRb, thus inducing uncontrolled and increased proliferation of infected cells. But the two viral oncoproteins also interact with more than 150 protein partners and deregulate cell homeostasis. Interestingly, E6 and E7 modulate the expression of many proteins involved in the establishment of epigenetic marks, regulating gene expression. Furthermore, the overexpression of viral oncoproteins may be related to viral genome DNA methylation.Since E6 and E7 hijack epigenetic mechanisms, the aim of the thesis was to study the molecular mechanisms regulating the oncoprotein expression during the treatment of cervical cancer cells by a DNA demethylating agent, the 5-aza-2'-deoxycytidine (5azadC).In cervical cancer cells, we observed that a demethylating treatment induced E6 protein repression and destabilization of its transcripts, suggesting the involvement of a miRNA. Among miRNAs targeting viral transcripts, miR-375 was most likely to be involved this destabilization because (i) its promoter methylation increases with the severity of cervical lesions, (ii) it targets viral transcripts at five different regions, and (iii) its expression is increased in cervical cancer cells treated with 5azadC. In our experiences, miR-375 was indeed involved in the partial repression of viral transcripts during treatment. The results of this study further suggest that another molecular mechanism might be implicated in this repression. This is why, in a second step, we studied the possible involvement of a transcription factor, TBX2, in the viral transcript repression. Although the transcriptional rate of TBX2 is increased in cells treated with high concentrations of 5azadC, our results suggest that the protein is not expressed in cells, even after treatment, and that TBX2 does not regulate the viral promoter activity integrated into the cellular genome.Cell treatment with demethylating agent also leads to loss of viability, in particular in Ca Ski cells. Indeed, 5azadC induces a G2/M cycle arrest in these cells, an increase of Sub-G1 cells percentage and a PARP cleavage. While 5azadC is already used in clinical practice for the treatment of other cancers, our data shed new light on the molecular mechanisms of 5azadC in cancers induced by HPV, which could be treated by this molecule or analogues.

Background: The genes coding for human (h) chorionic somatomammotropin (CS), hCS-A and hCS-B, and placental growth hormone (GH-V), hGH-V are located at a single locus on chromosome 17q22-24. Local regulatory (5´ P and 3´ enhancer) sequences and a remote locus control region (LCR) containing a placenta-specific hypersensitive site (HS) IV, have been implicated in the efficient expression of the placental hCS/GH-V genes, in part through gene transfer studies in placental and non-placental tumor cell lines. However, low levels of endogenous expression are reported in placental tumor cells compared to normal term placenta. Thus it was hypothesized that the hCS/GH-V chromatin structure in human choriocarcinoma cells is less accessible to regulatory regions essential for efficient expression due to DNA and/or histone modifications, specifically methylation and acetylation, respectively. Approach: To assess individual hCS-A, hCS-B and hGH-V gene expression in placental and non-placental tumor cells, and assess the effect of increasing “chromatin accessibility” on hCS/GH-V RNA levels by inhibiting DNA methylation and histone deacetylation using 5-aza-2´-deoxycytidine (azadC) and trichostatin A (TSA). Principal Findings: Low levels of hCS-A, hCS-B and hGH-V RNA were detected in placental and non-placental tumor cells compared to term placenta. A significant >5-fold increase in promoter activity was seen in placental but not non-placental cells transfected with hybrid hCS promoter luciferase genes containing 3´-enhancer sequences. Placental JEG-3 cells pretreated with azadC and TSA resulted in a significant >10-fold increase in hCS-A, hCS-B and hGH-V RNA levels compared to TSA treatment alone, however, a modest ~3-fold effect was seen in non-placental MCF-7 cells. By contrast to the effect of pretreatment with azadC, post-treatment with azadC mutes the stimulatory effects of TSA on hCS/GH-V transcripts. The specificity of the response suggests that azadC treatment, and presumably hypomethylation of DNA, results in an increase in response to TSA and histone hyperacetylation at the hGH/CS locus. An assessment of histone H3/H4 hyperacetylation in JEG-3 cells treated with azadC and TSA versus TSA alone revealed significant increases consistent with a more open chromatin structure including the hCS 3´-enhancer sequences and LCR. Conclusions: These observations suggest that accessibility of remote and local regulatory regions required for efficient placental hGH/CS expression can be restricted by DNA methylation and histone acetylation status. This includes restricting access of the hCS 3´-enhancer sequences to available placental enhancer transcription factors. / May 2016

Les analogues nucléosidiques ont prouvé leur efficacité thérapeutique et sont désormais couramment utilisés en chimiothérapies antivirale et anticancéreuse. Depuis, il a récemment été démontré que les analogues de configuration non naturelle L pouvaient présenter des activités biologiques remarquables au même titre que ceux de configuration naturelle D. La recherche de nouveaux analogues nucléosidiques de configuration L apparaît ainsi prometteuse. Dans notre travail, nous nous sommes plus particulièrement intéressés aux dérivés de la L-2'-désoxyuridine substitués en position 5 de la nucléobase. La synthèse de ces composés a été réalisée à partir de la L-5-iodo-2'-désoxyuridine, un intermédiaire clé que nous avons préalablement obtenu à partir du L-ribose. Nous avons ensuite fonctionnalisé ce composé en position 5 via l'utilisation de réactions organopalladées. Les composés obtenus ont été évalués sur divers virus à ADN et à ARN, ainsi que sur des lignées cellulaires tumorales exprimant une enzyme modifiée de la désoxycytidine kinase, enzyme impliquée dans la métabolisation de nombreux nucléosides. Nous avons ensuite réalisé la synthèse des dérivés fluorés en position 2'-arabino. Dans ce cas, les analogues nucléosidiques ont été obtenus dans les deux configurations D et L afin de comparer leurs effets biologiques et de confirmer l'intérêt biologique de la configuration L. / Nucleosidic analogues have proven their therapeutic efficiency and are commonly used in antiviral and cancer chemotherapies. Recently, it has been shown that nucleosidic analogues with a L non-natural configuration could present notable biological activities as well as their D counterparts. Therefore, discovery of new nucleosidic analogues with L configuration appears promising. In our study, we were interested in L-2'-deoxyuridine derivatives including modification on the position 5 of the nucleobase. The synthesis of these compounds was performed from the L-5-iodo-2'-deoxyuridine, a key intermediate which was synthesized from L-ribose. Then, we functionalized the 5 position of this intermediate using palladium-catalyzed cross-couplings. The desired compounds were tested on various DNA and RNA viruses, and on tumor cell lines expressing a modified deoxycytidine kinase, an enzyme responsible for the metabolism of a number of nucleosides. Finally, we synthesized nucleoside derivatives containing a fluorine atom on the 2'-arabino position. In this case, both compounds with D and L configuration were obtained, in order to compare their biological effects and to confirm the biological interest of L configuration.

Promoter hypermethylation mediated gene silencing is a frequent epigenetic finding in many cancers that affects genes known to have important roles in several aspects of cell biology. Hematological malignancies have been reported to harbor multiple genes aberrantly silenced by promoter hypermethylation and as a result, cytosine analogs known to inhibit the DNA methylation machinery are currently being evaluated in clinical trials. As such, the general goal of this thesis was to identify genes silenced by promoter hypermethylation in human acute myeloid leukemia (AML) and to study the mechanism of promoter hypermethylation mediated gene silencing. Interestingly, the cyclin dependent kinase inhibitor p15 was found to be methylated at a high frequency in AML patients and cell lines in association with a lack of detectable p15 mRNA. Treatment with the cytosine analog 5-Aza-2-deoxycytidine (5-Aza-dC) in vitro resulted in promoter demethylation and p15 mRNA re-expression, which was associated with a release of a transcriptionally repressive complex at the p15 promoter. Importantly, 5-Aza-dC treatment also reversed specific histone amino-terminal modifications at the p15 promoter which are normally associated with transcriptionally inactive chromatin regions, implicating chromatin remodeling in promoter hypermethylation mediated gene silencing. The recently discovered DNA methylation inhibitor, zebularine considered more stable than 5-Aza-dC was also able to reconstitute p15 mRNA in vitro in association with promoter demethylation, regional enrichment of histone acetylation, and growth inhibition. To identify novel genes silenced by promoter hypermethylation in AML, cDNA microarray analysis was employed following in vitro pharmacological inhibition of DNA methylation and histone deacetylation. Of note, four genes from the metallothionein family of cysteine rich small molecules were consistently upregulated following drug treatment and further evaluation identified the gene MT1H to be hypermethylated at a high frequency in AML patients and cell lines. Taken together, the data suggests that aberrant promoter hypermethylation mediated gene silencing occurs in multiple genes from different gene families during the molecular pathogenesis of human AML. Furthermore, the mechanism of promoter methylation mediated transcriptional silencing acts in concert with specific histone modifications which, importantly, can be reversed by treatment with pharmacological inhibitors of DNA methylation.

Promoter hypermethylation mediated gene silencing is a frequent epigenetic finding in many cancers that affects genes known to have important roles in several aspects of cell biology. Hematological malignancies have been reported to harbor multiple genes aberrantly silenced by promoter hypermethylation and as a result, cytosine analogs known to inhibit the DNA methylation machinery are currently being evaluated in clinical trials. As such, the general goal of this thesis was to identify genes silenced by promoter hypermethylation in human acute myeloid leukemia (AML) and to study the mechanism of promoter hypermethylation mediated gene silencing. Interestingly, the cyclin dependent kinase inhibitor p15 was found to be methylated at a high frequency in AML patients and cell lines in association with a lack of detectable p15 mRNA. Treatment with the cytosine analog 5-Aza-2-deoxycytidine (5-Aza-dC) in vitro resulted in promoter demethylation and p15 mRNA re-expression, which was associated with a release of a transcriptionally repressive complex at the p15 promoter. Importantly, 5-Aza-dC treatment also reversed specific histone amino-terminal modifications at the p15 promoter which are normally associated with transcriptionally inactive chromatin regions, implicating chromatin remodeling in promoter hypermethylation mediated gene silencing. The recently discovered DNA methylation inhibitor, zebularine considered more stable than 5-Aza-dC was also able to reconstitute p15 mRNA in vitro in association with promoter demethylation, regional enrichment of histone acetylation, and growth inhibition. To identify novel genes silenced by promoter hypermethylation in AML, cDNA microarray analysis was employed following in vitro pharmacological inhibition of DNA methylation and histone deacetylation. Of note, four genes from the metallothionein family of cysteine rich small molecules were consistently upregulated following drug treatment and further evaluation identified the gene MT1H to be hypermethylated at a high frequency in AML patients and cell lines. Taken together, the data suggests that aberrant promoter hypermethylation mediated gene silencing occurs in multiple genes from different gene families during the molecular pathogenesis of human AML. Furthermore, the mechanism of promoter methylation mediated transcriptional silencing acts in concert with specific histone modifications which, importantly, can be reversed by treatment with pharmacological inhibitors of DNA methylation.

Thesis (M.S.)--University of Florida, 2005. / Typescript. Title from title page of source document. Document formatted into pages; contains 50 pages. Includes Vita. Includes bibliographical references.

Epigenetic mechanisms play an important role during the morphogenesis of the hair follicle and the hair cycle. Work on hair regeneration is of importance as no products are available which can provide complete reversal of hair loss. Tet2 promotes DNA demethylation by the hydroxylation of 5mC to 5hmC which in turn causes gene transcription activation. Dermal papilla (DP) cells located within the hair follicle are responsible for the regulation of development and the growth of hair follicles. Fgf20 signalling controls commitment of the mesenchymal precursor cells to the DP progenitor lineage. An immature DP cells is then formed during maturation by Shh signalling which then stimulates these to differentiate into a DP cell by BMP and Wnt signalling. Methylated DNA can be bound by the proteins recruiting transcription corepressors. DNA methyltransferases (DNMT’s) can be degraded by decitabine which reverses gene silencing. Conditional knockout of Tet2 in mouse DP cells results in a delay in anagen initiation, suggesting Tet2 is involved in the telogen-anagen transition. Additionally, by using dermal fibroblasts and RA-DPAC (Dermal Papilla activating medium supplemented with retinoic acid), it was found that decitabine can increase plasticity in dermal fibroblasts and RA-DPAC can be used to accelerate a lineage change to DP cells which is supported by the significant increase in the DP specific gene expression. Examples include AlPl, LEF1, BMP4/6/7, FGF10, BMPR1A and PDGFA. Additionally, by way of siRNA and conditional Tet2 knockout data in dermal fibroblasts, it was found Tet2 regulates signature DP genes such as Bmpr1a, ALPL, Tcf4 and SOX2.