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De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells.

It has been a controversial issue as to how many DNA cytosine methyltransferase mammalian cells have and whether de novo methylation and maintenance methylation activities are encoded by a single gene or two different genes. To address these questions, we have generated a null mutation of the only known mammalian DNA methyltransferase gene through homologous recombination in mouse embryonic stem cells and found that the development of the homozygous embryos is arrested prior to the 8-somite stage. Surprisingly, the null mutant embryonic stem cells are viable and contain low but stable levels of methyl cytosine and methyltransferase activity, suggesting the existence of a second DNA methyltransferase in mammalian cells. Further studies indicate that de novo methylation activity is not impaired by the mutation as integrated provirus DNA in MoMuLV-infected homozygous embryonic stem cells become methylated at a similar rate as in wild-type cells. Differentiation of mutant cells results in further reduction of methyl cytosine levels, consistent with the de novo methylation activity being down regulated in differentiated cells. These results provide the first evidence that an independently encoded DNA methyltransferase is present in mammalian cells which is capable of de novo methylating cellular and viral DNA in vivo.

Animals↗

Cloned cytosine deaminase gene expression of Bifidobacterium longum and application to enzyme/pro-drug therapy of hypoxic solid tumors.

Bifidobacterium longum is a nonpathogenic anaerobic bacterium among normal bacterial flora. Recently, it was reported that B. longum accumulated in hypoxic solid tumors. The gene of interest was expressed in transfected B. longum by the shuttle vector pBLES100 in solid tumors. In this report, we constructed pBLES100-S-eCD, which included the cytosine deaminase gene. We confirmed by western blotting that transfected B. longum produced cytosine deaminase. In addition, transfected B. longum produced cytosine deaminase that converted 5-fluorocytosine into 5-fluorouracil. B. longum could be useful for enzyme/pro-drug therapy of hypoxic solid tumors.

Antimetabolites, Antineoplastic↗

Effects of cytosine methylation on pyrimidine dimer formation in DNA.

The relative induction of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone photoproducts ([6-4]PD) was quantified in the duplex homopolymers polydeoxyadenosine:polydeoxythymidine, polydeoxyguanosine:polydeoxycytidine and polydeoxyguanosine:polydeoxy-5-methylcytidine irradiated with UVC or UVB radiation. Cytosine methylation significantly increased the yield of cytosine (6-4)PD after irradiation with UVC light and of cytosine CPD and (6-4)PD after irradiation with UVB light. The data suggest that CPD and (6-4)PD are preferentially induced at 5-methylcytosine bases in DNA of cells exposed to sunlight and comprise a major component of the mutation spectrum leading to the initiation of sunlight-induced skin cancer.

Cytosine↗

Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction.

Cytosine methylation at CpG dinucleotides is an important control mechanism in development, differentiation, and neoplasia. Bisulfite genomic sequencing and its modifications have been developed to examine methylation at these CpG dinucleotides. To use these methods, one has to (i) manually convert the sequence to that produced by bisulfite conversion and PCR amplification, taking into account that cytosine residues at CpG dinucleotides may or may not be converted depending on their methylation status, (ii) identify relevant restriction sites that may be used for methylation analysis, and (iii) conduct similar steps with the other DNA strand since the two strands of DNA are no longer complementary after bisulfite conversion. To automate these steps, we have developed a macro that can be used with Microsoft Word. This macro (i) converts genomic sequence to modified sequence that would result after bisulfite treatment facilitating primer design for bisulfite genomic sequencing and methylation-sensitive PCR assay and (ii) identifies restriction sites that are preserved in bisulfite-converted and PCR-amplified product only if cytosine residues at relevant CpG dinucleotides are methylated (and thereby not converted to uracil) in the genomic DNA.

Base Sequence↗

Single-stranded DNA breaks adjacent to cytosines occur during Ig gene class switch recombination.

Class switch recombination (CSR) at the DNA level underlies ability of B lymphocytes to switch from expressing IgM to expressing IgG, IgA, or IgE. The mechanism of CSR is largely unknown, but it is clear that CSR is stimulated by T cell signals and is mediated in part by activation-induced deaminase (AID), an enzyme that is also required for somatic hypermutation of Ig genes. In one current model, AID is proposed to initiate CSR by deaminating cytosines in the unpaired nontemplate strand of DNA displaced from its complementary strand by the "sterile" RNA transcript across the switch region. We have used LM-PCR to analyze single-strand breaks in CH12F3-2, a murine cell line that switches in vitro to IgA expression. In contrast to the above model, we have detected CSR-associated ssDNA breaks in the template strand of the H chain alpha switch region, the strand thought to be complexed with RNA. Most breaks are adjacent to cytosines, consistent with mediation by AID, and occur within the novel consensus sequence C*AG, which occurs much more frequently on the template strand than on the putatively displaced nontemplate strand. These results suggest that AID may target the DNA strand bound to RNA, perhaps resembling APOBEC-3G, a cytosine deaminase related to AID that inhibits HIV replication by mutating viral DNA. Furthermore, the absence of detectable breaks in the nontemplate strand within the DNA segment under study suggests that the two DNA strands are handled differently in the generation or processing of strand breaks.

Animals↗

Cytotoxic effects of 5-fluorocytosine on melanoma cells transduced with cytosine deaminase gene.

To investigate the cytotoxic effects of 5-fluorocytosine on melanoma cells genetically modified with cytosine deaminase gene, the gene was transduced into the tumor cells with the retroviral method. The cytotoxicity effects of 5-fluorocytosine on the tumor cells were measured with the MTT assay and clonogenic assay. It was found that the prodrug 5-fluorocytosine had significant cytotoxic effects on melanoma cells transduced with cytosine deaminase in vitro. The IC50 value of 5-fluorocytosine on transgenic and nontransgenic melanoma cells was 572 microg/mL(-1) and 3870 microg/mL(-1), respectively. Our experiment demonstrated the potential value of the cytosine deaminase gene/5-fluorocytosine system in the treatment of melanoma.

3T3 Cells↗

Cytosine methylation represses glutathione S-transferase P1 (GSTP1) gene expression in human prostate cancer cells.

Methylation of the glutathione S-transferase P1 (GSTP1) gene has been described as a highly specific and sensitive biomarker for prostate cancer. However, at present, it is not known whether methylation represses GSTP1 gene expression in human prostate cancer. We found the GSTP1 gene promoter to be completely methylated in the LNCaP prostate cancer cell line, where this gene is transcriptionally inactive. In contrast, Du145 and PC3 prostate cancer cells express the GSTP1 gene and exhibit methylated and unmethylated GSTP1 alleles. In a transient transfection assay using LNCaP cells, methylation of the GSTP1 promoter-driven luciferase reporter vector (GSTP1-pGL3) resulted in a >20-fold inhibition of transcription, and this repression was not relieved by the presence of a histone deacetylase inhibitor, trichostatin A (TSA). Treatment of LNCaP cells with a DNA methyltransferase inhibitor, 5-Aza-2'-deoxycytidine, resulted in demethylation and activation of the GSTP1 gene. In contrast, TSA treatment failed to demethylate or activate the GSTP1 gene. Fully methylated but not unmethylated GSTP1 promoter fragment was shown to bind to a complex similar to methyl cytosine-binding protein complex 1 that contains methyl-CpG-binding domain 2 protein (MBD2) in electrophoretic mobility shift assays using LNCaP cell nuclear extracts. These data demonstrate that cytosine methylation can repress GSTP1 gene expression in LNCaP prostate cancer cells and that this effect is possibly mediated by a methyl cytosine-binding protein complex 1-like complex. Furthermore, these data also support the notion of the dominance of methylation over TSA-sensitive histone deacetylation in silencing genes with a high CpG density in the promoter region.

Azacitidine↗

Transduction of thymidine phosphorylase cDNA facilitates efficacy of cytosine deaminase/5-FC gene therapy for malignant brain tumor.

The in vivo gene delivery of E. coli cytosine deaminase (cd) cDNA and systemic 5-fluorocytosine (5-FC) administration have been studied extensively because of their clinical relevance to cancer gene therapy. This approach has the potent advantage of a stronger bystander effect compared to the previous thymidine kinase suicide gene system of the herpes simplex virus. However, 5-fluorouracil (5-FU), an active metabolite in cd with 5-FC therapy, is not always effective for every type of tumor since the enzymes responsible for further drug metabolism vary significantly in each tissue. In this study, we aimed to increase the sensitivity of 5-FU by transduction of thymidine phosphorylase (dThdPase) cDNA into brain tumor cells. After retroviral transfer of the cDNA, we obtained 9L murine gliosarcoma cells showing stable expression of the target enzyme (9L-dThdPase). The growth of the cells was identical to wild type (9L-WT) or control-vector transfected (9L-Neo) cells in vitro. Sensitivity to 5-FU was increased in 9L-dThdPase cells. After the adenoviral delivery of cytosine deaminase gene into these cells, 9L-dThdPase cells also demonstrated an increased sensitivity to 5-FC. Moreover, we showed that transduction of dThdPase cDNA prolongs the survival of animals bearing intracerebral tumors after experimental in vivo cytosine deaminase gene therapy. These results suggest that transduction of thymidine phosphorylase may be a beneficial approach to increasing the efficacy of cd/5-FC suicide gene therapy in certain types of tumor.

Adenoviridae↗

Treatment of human tumor cells by combine gene therapy harnessing plasmids expressing human tumor necrosis factor alpha and bacterial cytosine deaminase suicide gene.

We have assessed the effect of combine cancer gene therapy with exogenous human tumor necrosis factor alpha (hTNFalpha) and Escherichia coli cytosine deaminase (CD) suicide gene on two human breast adenocarcinoma cell lines MDA-MB-361 and SK-BR-3. Transfection of a plasmid containing hTNFalpha under the control of a hybrid promoter resulted in expression of hTNFalpha gene in vitro. Transduction of retroviral plasmid containing bacterial cytosine deaminase led to the expression of cytosine deaminase in adenocarcinoma cell lines as well. The significant increase in apoptotic cells and decrease of cell proliferation in both tumor cell lines was observed using combination treatment with hTNFalpha expression plus CD/5-FC suicide system. Corresponding data were generated by MTT cell proliferation assay and by flow cytometric analysis. The presence of both genes after transduction of retroviral vector containing CD and transfection of hTNFalpha plasmid was confirmed by PCR and RT-PCR. The additive cell killing effect due to the presence of bacterial CD and hTNFalpha gene after activation of non-toxic prodrug was observed. Whether the bicistronic vector containing both therapeutic genes improve the therapy need to be assessed in the future.

Adenocarcinoma↗

[Isolation and properties of DNA-cytosine methyltransferase from Escherichia coli C].

The method of isolation and partial purification of DNA-cytosine-methyltransferase (DC-methylase) from E. coli C is described. The enzyme underwent approximately 100-fold purification. The obtained preparation of DC-methylase can be additionally considerably purified by sedimentation in sucrose gradient. Native molecular weight of DC-methylase from E. coli C. is 70,000. The activity of enzyme does not depend on the Mg2+ ions. DC-methylase E. coli C provides DNA of lambda phage in vitro with full resistance against restriction endonuclease EcoRII. In DNA methylated by DC-methylase the modified cytosine, mainly in C-MC and C-MC-T sequences, corresponds to the pyrimidine sequences of specific site EcoRII. DNA of lambda.B phage contains approximately 80 sites for modification by DC-methylase E. coli C. The results obtained point to the same specificity in vitro of DNA-cytosine-methylase E. coli C and DNA-methylase EcoRII.

Binding Sites↗

Evidence of 2-aminopurine-cytosine base mispairs involving two hydrogen bonds.

It is shown that the mutagen base analogue 2-aminopurine is hydrogen-bonded at its 1-ring position when annealed with cytosine in DNA. The presence of stably hydrogen-bonded regions proximal to the 2-aminopurine-cytosine base mispair is a prerequisite for the occurrence of two hydrogen bonds coupling the bases at their 1-3- and 2-2-positions. We consider the possibility that, in the resulting heteroduplex base mispair, 2-aminopurine or cytosine may be present as a disfavored imino tautomer.

2-Aminopurine↗

Possible heterogeneity of Streptococcus milleri determined by DNA mol % (guanine plus cytosine) measurement and physiological characterization.

DNA base pair ratios (mol % guanine + cytosine) were calculated, for eighteen strains of Streptococcus milleri, from measurements of DNA melting temperature (Tm). Strains of vaginal origin which were also 'atypical' physiologically had a value of 40.3. The two culture collection of 'minute' beta-haemolytic strains of Lancefield groups G and F had values of 36.8 and 38.8 mol%, respectively. Three other reference strains had a DNA guanine plus cytosine content ranging from 40.4 to 43.0 mol%, including Streptococcus sp MG which had a value of 42.0 mol%. Strain 7H of oral origin had a value of 40.9 mol%. The remaining physiologically typical strains, of medical origin, had guanine plus cytosine contents ranging from 36.6 to 42.1 mol%. It therefore seems possible that genetic heterogeneity may exist among representatives of Streptococcus milleri.

Cytosine↗

Cytosine deaminase. The roles of divalent metal ions in catalysis.

Cytosine deaminase (CDase, EC 3.5.4.1) isolated from Escherichia coli contains a catalytically essential divalent metal ion. Fe2+ was efficiently removed from the enzyme with o-phenanthroline to yield an apoenzyme with less than 5% of the catalytic activity of native enzyme. The time courses for inactivation and for removal of Fe2+ from the enzyme by o-phenanthroline were similar. Apoenzyme reconstituted with Fe2+, Mn2+, Co2+, or Zn2+ (M2+CDase) had kcat values of 185, 88, 50, and 32 s-1, respectively. The Km values of these M2+CDases for cytosine were similar (0.22-0.39 mM). Cytosine potently inhibited reconstitution of the apoenzyme with Fe2+. Fe2+CDase was rapidly inactivated by 1 mM H2O2 (t1/2 < 1 s), whereas Mn2+CDase, Co2+CDase, and Zn2+CDase were not inactivated by H2O2. CDase was also inhibited by excess divalent cations. Cu2+ and Zn2+ reversibly inhibited Fe2+CDase activity with inhibition constants of 1.8 and 5.8 microM, respectively. Cu2+ dissociated slowly from the secondary binding on CDase with a rate constant of 2 x 10(-3) s-1.

Catalysis↗

Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase.

Uracil-DNA glycosylase (UDG) protects the genome by removing mutagenic uracil residues resulting from deamination of cytosine. Uracil binds in a rigid pocket at the base of the DNA-binding groove of human UDG and the specificity for uracil over the structurally related DNA bases thymine and cytosine is conferred by shape complementarity, as well as by main chain and Asn204 side chain hydrogen bonds. Here we show that replacement of Asn204 by Asp or Tyr147 by Ala, Cys or Ser results in enzymes that have cytosine-DNA glycosylase (CDG) activity or thymine-DNA glycosylase (TDG) activity, respectively. CDG and the TDG all retain some UDG activity. CDG and TDG have kcat values in the same range as typical multisubstrate-DNA glycosylases, that is at least three orders of magnitude lower than that of the highly selective and efficient wild-type UDG. Expression of CDG or TDG in Escherichia coli causes 4- to 100-fold increases in the yield of rifampicin-resistant mutants. Thus, single amino acid substitutions in UDG result in less selective DNA glycosylases that release normal pyrimidines and confer a mutator phenotype upon the cell. Three of the four new pyrimidine-DNA glycosylases resulted from single nucleotide substitutions, events that may also happen in vivo.

Binding Sites↗

Cytosine deaminase adenoviral vector and 5-fluorocytosine selectively reduce breast cancer cells 1 million-fold when they contaminate hematopoietic cells: a potential purging method for autologous transplantation.

Ad.CMV-CD is a replication incompetent adenoviral vector carrying a cytomegalovirus (CMV)-driven transcription unit of the cytosine deaminase (CD) gene. The CD transcription unit in this vector catalyzes the deamination of the nontoxic pro-drug, 5-fluorocytosine (5-FC), thus converting it to the cytotoxic drug 5-fluorouracil (5-FU). This adenoviral vector prodrug activation system has been proposed for use in selectively sensitizing breast cancer cells, which may contaminate collections of autologous stem cells products from breast cancer patients, to the toxic effects of 5-FC, without damaging the reconstitutive capability of the normal hematopoietic cells. This system could conceivably kill even the nondividing breast cancer cells, because the levels of 5-FU generated by this system are 10 to 30 times that associated with systemic administration of 5-FU. The incorporation of 5-FU into mRNA at these high levels is sufficient to disrupt mRNA processing and protein synthesis so that even nondividing cells die of protein starvation. To test if the CD adenoviral vector sensitizes breast cancer cells to 5-FC, we exposed primary explants of normal human mammary epithelial cells (HMECs) and the established breast cancer cell (BCC) lines MCF-7 and MDA-MB-453 to the Ad.CMV-CD for 90 minutes. This produced a 100-fold sensitization of these epithelial cells to the effects of 48 hours of exposure to 5-FC. We next tested the selectivity of this system for BCC. When peripheral blood mononuclear cells (PBMCs), collected from cancer patients during the recovery phase from conventional dose chemotherapy-induced myelosuppression, were exposed to the Ad.CMV-CD for 90 minutes in serum-free conditions, little or no detectable conversion of 5-FC into 5-FU was seen even after 48 hours of exposure to high doses of 5-FC. In contrast, 70% of 5-FC was converted into the cytotoxic agent 5-FU when MCF-7 breast cancer cells (BCCs) were exposed to the same Ad.CMV-CD vector followed by 5-FC for 48 hours. All of the BCC lines tested were shown to be sensitive to infection by adenoviral vectors when exposed to a recombinant adenoviral vector containing the reporter gene betagalactosidase (Ad.CMV-betagal). In contrast, less than 1% of the CD34-selected cells and their more immature subsets, such as the CD34+CD38- or CD34(+)CD33- subpopulations, were positive for infection by the Ad.CMV-betagal vector, as judged by fluorescence-activated cell sorting (FACS) analysis, when exposed to the adenoviral vector under conditions that did not commit the early hematopoietic precursor cells to maturation. When artificial mixtures of hematopoietic cells and BCCs were exposed for 90 minutes to the Ad.CMV-CD vector and to 5-FC for 10 days or more, a greater than 1 million fold reduction in the number of BCCs, as measured by colony-limiting dilution assays, was observed. To test if the conditions were damaging for the hematopoietic reconstituting cells, marrow cells collected from 5-FU-treated male donor mice were incubated with the cytosine deaminase adenoviral vector and then exposed to 5-FC either for 4 days in vitro before transplantation or for 14 days immediately after transplantation in vivo. There was no significant decrease in the reconstituting capability of the male marrow cells, as measured by their persistence in female irradiated recipients for up to 6 months after transplantation. These observations suggest that adenovirus-mediated gene transfer of the Escherichia coli cytosine deaminase gene followed by exposure to the nontoxic pro-drug 5-FC may be a potential strategy to selectively reduce the level of contaminating BCCs in collections of hematopoietic cells used for autografts in breast cancer patients.

Adenoviridae↗

In vitro effect on human leukemic K562 cells of co-administration of liposome-associated retinoids and cytosine arabinoside (Ara-C).

The administration of retinoids has been demonstrated to be of potential utility in the therapy of a wide spectrum of neoplastic pathologies due to the ability to induce differentiation in a large variety of primary tumor cells as well as in vitro cultured cell lines. Moreover, a number of compounds, including hemin, cytosine arabinoside, and 5-azacytidine are able to induce erythroid differentiation of the erythroleukemic cell line K562. In this paper we determined whether a combined treatment of K562 cells with suboptimal concentrations of cytosine arabinoside and retinoids containing liposomes lead to a full expression of differentiated functions. Liposomes were prepared by reverse phase evaporation technique followed by extrusion through polycarbonate filters. Cell growth kinetics studies and intracellular detection of hemoglobin by benzidine staining were performed. The results obtained showed that the combined treatment with liposomes containing retinoids and sub-optimal concentration of ara-C is an effective strategy to induce K562 cell differentiation, minimizing at the same time toxic effects. Control experiments aimed to determine possible selection of subpopulations of K562 cells suggest that the observed results are not related to toxicity and/or potential selection of induced cells. In conclusion, liposomally delivered retinoids could be proposed for differentiation therapy as an effective strategy in the treatment and management of malignancy. In addition, the finding that liposomally delivered retinoids increase the capacity of cytosine arabinoside to induce erythroid differentiation, could be of interest in studies aimed at the development of treatment able to reactivate fetal globin genes in beta-thalassemia patients.

Cell Differentiation↗

The effect of cytosine arabinoside on platelet aggregation.

Platelet aggregation induced by ADP, collagen, epinephrine, and thrombin was studied in patients with acute leukemia in complete remission, before and after a continuous 5-day intravenous infusion of cytosine arabinoside at a dose of 100 mg/m2 per day. Aggregation was also measured in normal subjects with cytosine arabinoside added in vitro. Cytosine arabinoside had no significant effect on platelet aggregation after either in vitro or in vivo administration.

Acute Disease↗

Paraparesis following intrathecal cytosine arabinoside: a case report with neuropathologic findings.

A 65-year-old white male with acute myelogenous leukemia received whole brain irradiation (2550 rads) and intrathecal cytosine arabinoside for CNS prophylaxis. Bone marrow remission had been previously achieved with systemic chemotherapy (vincristine, Adriamycin, prednisone, and cytosine arabinoside). Two weeks following the last intrathecal cytosine arabinoside treatment, the patient developed a spastic paraparesis requiring the use of a walker. A gas myelogram was normal and CSF examination revealed a protein of 50 mg/100 ml but was otherwise unremarkable. Five months later, the patient had improved in that he could stand on his own. A relapse of his leukemia subsequently occurred and the patient died the following month. Striking degenerative changes were found in the spinal cord at postmortem examination. These included microvacuolization, axonal swellings, and loss of myelin with scattered macrophages laden with fat.

Aged↗