Papers presented at the New England Biolabs Workshop on Biological DNA Modification. Gloucester, MA (U.S.A.), 20-23 May 1988.
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Animals↗
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Results for “DNA Modification Methylases”
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CDKN2 gene silencing in lung cancer by DNA hypermethylation and kinetics of p16INK4 protein induction by 5-aza 2'deoxycytidine.
Absent expression of the cyclin dependent kinase-inhibitor, p16INK4, is observed in a wide range of primary human cancers. Although homozygous deletions and point mutations have been reported in a subset of these tumors, the molecular basis for absent p16INK4 in other samples is unknown. We have examined 33 tumor cell lines and have shown that hypermethylation of a G:C-rich region within exon 1 of the CDKN2 gene was present in 100% of samples with wildtype RB expression and no detectable CDKN2 mutations. Treatment for at least 4 hours with the demethylating agent 5-aza 2'deoxycytidine, but not 5-azacytidine or 6-azacytidine, induces the prolonged expression of p16INK4 protein in each of these samples following a discrete 24-48 hour lag period. Consistent with the hypothesis that hypermethylation of the CDKN2 gene is a tumor-specific mechanism for gene inactivation, we observed hypomethylation at the exon 1 site exclusively in tumor lines that expressed p16INK4 or that had sustained inactivating point mutations within the CDKN2 open reading frame. These findings demonstrate a link between DNA methylation and the p16INK4:RB tumor suppressor pathway.
Azacitidine↗
DNA methyltransferases of Neisseria gonorrhoeae.
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Base Sequence↗
Coordinate regulation of Igf-2 and H19 in cultured cells.
The insulin-like growth factor 2 (Igf-2) and H19 genes are physically linked on mouse distal chromosome 7 and are reciprocally imprinted. We investigated the molecular basis of the parental imprints in somatic cell cultures derived from normal embryos or from their littermates with maternal uniparental disomy for distal chromosome 7 (MatDi7). In normal cells, the two genes appeared to respond to similar regulatory factor(s), since both genes were coordinately up-regulated upon growth arrest and cell clones which had lost expression of one gene had lost expression of the other. However, in a clone of MatDi7 cells (MatDi7 1-1a), which spontaneously began to express the maternally derived copy of Igf-2, Igf-2 and H19 were not coordinately regulated. MatDi7 1-1a cells showed de novo methylation of sites upstream of Igf-2 and also within the H19 promoter, epigenetic modifications normally seen only on the paternal chromosome. The data provide new experimental evidence for previously hypothesized mechanisms suggesting that Igf-2 and H19 are coordinately regulated.
Animals↗
Effect of thyroxine on DNA methyltransferase activity in cerebellum of rat.
DNA methyltransferase activity increased significantly in cerebellum from day 4 to day 8 and decreased in 30 day old rats. It was maintained at lower levels in the adult rats. Thyroxine administration markedly stimulated DNA methyl- transferase activity in the newly born pups. However, it did not cause any effect on this enzyme activity in 8 day old rat cerebellum. These results show that thyroxine has a role in the regulation of DNA methyltransferase activity in cerebellum of rat during early stages of development.
Aging↗
Induction by 5-aza-2'-deoxycytidine, an inhibitor of DNA methylation, of Le(y) antigen, apoptosis and differentiation in human lung cancer cells.
We recently developed a monoclonal antibody directed to carbohydrate antigen Le(y), BM-1/JIMRO, and found that expression of Le(y) antigen defined by BM-1/JIMRO was associated with the process of apoptosis, but not with cell proliferation or necrosis. In the present experiments, we examined with BM-1/JIMRO the effects of various differentiation inducers on the growth and expression of Le(y) antigen in human lung cancer A549 cells. We found that a specific inhibitor of methylation of DNA, 5-aza-2' deoxycytidine (ADC), could markedly induce expression of Le(y) antigen in association with induction of apoptosis and differentiation in the A549 cells. These results suggest that hypomethylation of DNA is involved in the molecular mechanisms of induction of Le(y) antigen, apoptosis and differentiation in the cells.
Alkaline Phosphatase↗
Retention of unmethylated CpG island alleles in human diploid fibroblast x fibrosarcoma hybrids expressing high levels of DNA methyltransferase.
The mechanisms underlying ectopic methylation of CpG islands in neoplastic cells are poorly understood. One determinant may be the increased expression of DNA methyltransferase (DNA MTase) observed frequently in neoplastic cells. To evaluate the role of DNA MTase overexpression in aberrant CpG island methylation, we assessed methylation of fibroblast-derived CpG islands in human diploid fibroblast x fibrosarcoma hybrid cell lines. Each of six independently derived, immortalized hybrid cell lines exhibited a high level of DNA MTase expression, comparable to that of the fibrosarcoma parental line. The methylation status of five CpG island loci, each of which was methylated extensively in the fibrosarcoma parental cells but not in the fibroblasts, was then determined in the hybrid cell lines. The patterns of methylation were consistent and highly locus dependent among the hybrid lines. Unmethylated alleles were retained stably at three loci. The parental origin of alleles could be determined at two other loci in the hybrid cells. Whereas no methylation of parental fibroblast-derived alleles of the HIC-1 locus was noted in hybrid cell lines, a marked increase in methylation of fibroblast-derived alleles of the estrogen receptor was observed in all hybrid cell lines. Therefore, despite high-level DNA MTase expression, widespread loss of unmethylated CpG islands was not observed in the hybrid cell lines. The nonrandom pattern of increased CpG island methylation in the hybrid cell lines suggests that locus-specific features and/or clonal selection, and not just DNA MTase expression, affect the evolution of ectopic methylation in neoplastic cells. Somatic cell hybrids may provide useful models for studying aberrant epigenetic events in neoplastic cells.
Alleles↗
Genetic analysis of genomic methylation patterns in plants and mammals.
While it is now accepted that methylation of cytosine residues plays a role in various epigenetic phenomena in mammals and flowering plants, the involvement of methylation patterns in the regulation of normal development has remained a controversial and essentially untested issue in the 20 years since such a role was first proposed. Antisense suppression of a DNA methyltransferase in Arabidopsis and characterization of methylation-defective mutants of Arabidopsis have shown that perturbations of methylation patterns disrupt the development of plants, and targeted mutation of the murine gene that encodes the one known from of DNA methyltransferase has shown that methylation is required for cellular differentiation, genomic imprinting, and X chromosome inactivation in mammals. Ectopic expression of homeotic genes and homeotic transformations of floral organs in methylation-defective plants suggest that (in plants and perhaps mammals) heritable methylation patterns reinforce and may have supplanted heritable gene control mediated by chromosomal proteins of the Polycomb and trithorax groups. It is also possible that the developmental abnormalities are the result of ectopic gene expression caused by activation of transcription from nearby parasitic sequence elements that are normally repressed by methylation. Application of modern methods of genetic analysis promises to give definite answers to long-standing questions as to the roles and significance of genomic methylation patterns in normal development and genome defense.
Animals↗
Reversal of loss of imprinting in tumor cells by 5-aza-2'-deoxycytidine.
To determine whether loss of imprinting in cancer might be reversed by altering DNA methylation, we treated tumor cells with 5-aza-2'-deoxycytidine, a specific inhibitor of cytosine DNA methyltransferase. Treated cells showed several significant and reproducible changes. (a) Equal expression of maternal and paternal alleles of insulin-like growth factor 2 switched to predominant expression of a single parental allele. (b) H19 expression was reactivated. (c) Biallelic H19 expression switched to monoallelic expression. (d) Biallelic methylation of H19 switched to preferential allelic methylation. These results imply that abnormally imprinted cells are susceptible to epigenetic modification and that the effect of 5-aza-2'-deoxycytidine on tumor cells with loss of imprinting is not random but specific to one allele.
Azacitidine↗
Pharmacological approach for optimization of the dose schedule of 5-Aza-2'-deoxycytidine (Decitabine) for the therapy of leukemia.
5-Aza-2'-deoxycytidine (5-Aza-CdR; Decitabine) is an active antineoplastic agent in patients with leukemia. Since 5-Aza-CdR is an S phase specific agent and has a short plasma half-life, its antileukemic activity is dose schedule-dependent. Leukemia patients who are candidates for 5-Aza-CdR therapy following relapse after therapy with cytosine arabinoside are at greater risk for the problem of drug resistance since these cytosine nucleoside analogues are metabolized by the same enzymes. Due to its unique mechanism of action of demethylating DNA, 5-Aza-CdR has the potential to activate tumor (growth) suppressor and differentiation genes that have been accidentally silenced by DNA methylation in leukemic cells. All these factors should be taken into account in the design of the optimal dose schedule of this analogue. The optimal dose schedule of 5-Aza-CdR should be based on the kinetic parameters of deoxycytidine kinase, its pharmacokinetics, its effects on DNA methylation and the cell cycle parameters of the leukemic cells and the normal hematopoietic stem cells. Since granulocytopenia is the major toxic effect produced by 5-Aza-CdR, the use of hematopoietic growth factors to shorten the duration of leukopenia should be investigated. Another approach which we are investigating is to use the methods of gene therapy to insert the cytidine deaminase gene into normal hematopoietic progenitor cells so as to make them drug resistant to 5-Aza-CdR. The use of other agents that can induce the differentiation of leukemic cells in combination with 5-Aza-CdR may have the potential to increase the clinical effectiveness of this analogue for the therapy of leukemia.
Animals↗
Pharmacokinetics and tissue distribution of a DNA-methyltransferase antisense (MT-AS) oligonucleotide and its catabolites in tumor-bearing nude mice.
The pharmacokinetics of a 20-mer phosphorothioate antisense oligodeoxynucleotide was investigated in nude mice bearing a s.c. human lung carcinoma. The oligodeoxynucleotide, referred to as DNA-methyltransferase antisense (MT-AS) was designed to bind to the mRNA that coded for DNA-methyltransferase, an enzyme that controls the extent of methylation of 5'-cytosine. MT-AS was administered at four different doses (10, 30, 100 and 300 mg/kg) as an i.v. bolus in a composite study design. A maximum of four blood samples were collected from any single animal, followed by sacrifice to obtain tissues. The plasma and tissue samples were collected from 5 min to 48 h after dosing and were processed by anion-exchange HPLC (high performance liquid chromatography) and by capillary gel electrophoresis. On the basis of total (i.e., 15-mer to 20-mer species) MT-AS plasma concentrations as determined by HPLC, total clearance ranged from 7.9 ml/min/kg at the 30-mg/kg dose level to 15.2 ml/min/kg at 10 mg/kg; however, there were no definitive dose-dependent changes in clearance. The volume of distribution at steady state increased from a low value of 379 ml/kg at 30 mg/kg to a high of 1983.0 ml/kg at 300 mg/kg, a result that suggests saturable protein binding. In vitro plasma protein binding data supported this possibility, because the percentage of MT-AS bound decreased at high MT-AS concentrations. MT-AS distributed into most tissues, with a general rank order of kidney > liver > tumor > lung > muscle > brain. Analysis of plasma samples by capillary gel electrophoresis from 2 h to 8 h revealed that about 50% of the total oligodeoxynucleotides were due to the parent 20-mer MT-AS; the remainder consisted of 15-mer to 19-mer catabolites. Of particular interest was the relatively high tumor uptake of MT-AS. These results will support future studies designed to characterize the pharmacological action of MT-AS and its efficacy in preclinical models.
Animals↗
Inhibition of DNA methylation by 5-aza-2'-deoxycytidine suppresses the growth of human tumor cell lines.
Alterations in DNA methylation patterns accompany the establishment of immortal cell lines. De novo methylation of CpG islands within the control regions of growth-regulatory genes may inactivate their transcription, giving cells selective growth advantages in culture. We exposed seven human tumor cell lines and two human fibroblast cell strains to the demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-CdR), to determine whether the silencing of growth-regulatory genes by de novo methylation in immortalized cell lines could be reversed, possibly restoring growth control. After recovery from the immediate cytotoxic effects of 5-Aza-CdR, this agent suppressed cellular growth in all seven tumor lines but not in either fibroblast strain. Because alterations in the p16 (CDKN2/MTS1) cell cycle regulatory gene are associated with numerous cancers, we analyzed expression of this gene before and after 5-Aza-CdR treatment. The gene was reactivated by 5-Aza-CdR treatment in three of four tumor cell lines not expressing p16, whereas the fourth tumor line contained a p16 homozygous deletion. p16 was shown to be hypermethylated only in the cell lines and its up-regulation by 5-Aza-CdR was associated with demethylation of the p16 promoter. The remaining tumor lines expressed p16 at constant levels before and after 5-Aza-CdR treatment and showed minimal p16 promoter methylation, suggesting that other growth-regulatory genes may have been silenced by de novo methylation in these cells. p16 expression, cell growth inhibition, and G1 cell cycle arrest by 5-Aza-CdR in the T24 bladder tumor cell line were also heritable after prolonged passage in culture. Furthermore, a dormant p16 gene was reactivated in T24 cells growing in nu/nu rats, and 5-Aza-CdR treatment of T24 cells before inoculation into nu/nu mice decreased the rate of tumor growth. These results suggest that 5-Aza-CdR may slow the growth of tumor cells by reactivating growth-regulatory genes silenced by de novo methylation.
Animals↗
[Bis-chloromethyl ether and carcinogenesis of alkylating agents].
Bis-Chloro-Methyl-Ether is an alkylating agent and a recognised carcinogen. It can form spontaneously from the reaction of chloridric acid with formaldehyde. In the past it was extensively used as a chemical intermediate in organic synthesis, particularly as a crosslinking agent in the manufacture of ion-exchange resins. Recently, since its carcinogenicity has been proved in animal studies and confirmed in epidemiological studies of occupationally exposed cohorts, its use has been consistently reduced. A characteristic association has been observed between BCME exposure and a peculiar lung cancer histotype (oat cell carcinoma). In spite of these data, little information is available on the molecular alterations related to BCME exposure and possibly to its carcinogenic activity. Some suggestions can reasonably be obtained considering how the class of alkylating agents acts. They form adducts, binding different positions of DNA bases. The reaction that seems more relevant for mutagenesis and carcinogenesis is the alkylation at the atom O6 of guanine in DNA, which is followed by mis-coding and GC-->AT transition mutation. This kind of alteration determines the activation of a group of enzyme like DNA repair, mismatch repair, excision repair and a specific one, methyl guanine methyl transferase (MGMT). This last repair protein transfers alkyl groups from the O6 position of guanine to an internal cysteine residue, inactivating itself. Thus, the possibility for the cell to eliminate alkylated DNA bases depends strictly upon the cellular content of MGMT. In this view reduced or absent levels of the enzyme are associated with an increased number of adducts and hence increased risk of DNA mutations and cancer. At the moment no molecular studies in vivo have been performed to verify this hypothesis. The peculiar association BCME-oat cell carcinoma, the most chemosensitive tumor, need further investigation.
Air Pollutants, Occupational↗
Establishment of a hybrid SalI-HgiDII type II restriction-modification system.
In the SalI system, endonuclease activity can be only achieved in the presence of a functional modification gene. Thus, the DNA methyltransferase is involved in the control of restriction. By fusion of the restriction gene of the SalI system to the modification gene of the isospecific HgiDII system a hybrid type II restriction-modification system was created. Although in the hybrid situation the level of endonuclease activity was significantly lower than in the natural system, the HgiDII modification enzyme clearly supports SalI restriction. The mechanism by which the two isospecific methyltransferases control restriction is currently under study.
DNA Modification Methylases↗
The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands.
A DNA fragment of about 3.4 kilobase pairs that expressed the HgaI modification activity was cloned from the chromosomal DNA of Haemophilus gallinarum, and its nucleotide sequence was determined. Two open reading frames (ORF) which could code for structurally similar proteins were identified in the upstream and middle regions and a truncated ORF in the downstream region in the same orientation. When the respective ORFs were separately cloned, the clones carrying the upstream and middle ORFs both expressed the modification activity, indicating that the two genes are involved in modification of the HgaI restriction-modification system. In order to determine the sites of modification precisely, the respective genes were recloned into an expression vector, from which gene products were purified. A short DNA fragment carrying the HgaI recognition site was treated with each of these enzymes, and, after separation of the two strands by duplex formation with M13 viral DNAs carrying the respective strands, the presence or absence of modification was judged from susceptibility to HgaI endonuclease. The results of analysis showed that different strands were modified in an asymmetric way by each gene product. Analysis of the species and positions of modified bases by the Maxam-Gilbert method further demonstrated that the gene products from the upstream and middle ORFs participated in methylation of the internal cytosine residues of the strands carrying 3'-CTGCG-5' and 5'-GACGC-3', respectively. We concluded that the HgaI modification system consisted of two cytosine methylase genes responsible for modification of different strands in the target DNA.
Amino Acid Sequence↗
[A method for detecting new strains producing DNA modification and restriction enzymes--isoschizomers and isomethylomers of known restrictases and methylases].
The paper describes a technique for the detection of new strains producing enzymes which mediate DNA modification and restriction, and isoschizomers and isomethylomers of the known restriction endonucleases and methylases. Three Bacillus subtilis strains whose DNA carries a BamH1 modification have been found. Two of these strains exert the restrictase activity with an R BamH1 specificity.
Bacillus subtilis↗
EcoRI cleavage and methylation of DNAs containing modified pyrimidines in the recogintion sequence.
The effects of substituents at position 5 in the pyrimidine ring of a variety of phage DNAs upon EcoRI endonuclease and methylase activities have been examined. The replacement of cytidine in DNA with glucosylated hydroxymethylcytidine confers resistance to cleavage by the EcoRI endonuclease. Substitution of thymidine in DNA by hydroxy-methyluridine(a change in the methyl at position 5 of thymidine for a hydroxymethyl) lowers the maximal velocity of endonucleolytic cleavage 20-fold, but has no detectable effect upon the Km. Substitution of thymidine in DNA by uridine (a change in the methyl at position 5 of thymidine for a hydrogen atom) has no effect upon either the maximal velocity or the Km. The effect of these modifications upon EcoRI methylase activity was markedly different. DNA containing glucosylated hydroxymethylcytidine is methylated as well as normal DNA. DNA containing uridine or hydroxy-methyluridine, in place of thymidine, is much more poorly methylated than normal DNA. These different sensitivities of the EcoRI endonuclease and methylase to modifications in the pyrimidine rings of DNA suggest there are significant differences in the manner by which these enzymes recognize and bind to the canonical EcoRI sequence.
Bacteriophages↗
Methylated oligonucleotides derived from bacteriophage fd RF-DNA modified in vitro by E. coli B modification methylase.
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Autoradiography↗