Inhibition of repair of O-methyldeoxyguanosine and enhanced mutagenesis in rat-liver epithelial cells

The pro-mutagenicity of chemically-induced methylation of DNA at the O⁶ position of dexoyguanosine was studied in cultured adult rat liver epithelial cells. To modify the level of O⁶-methyldeoxyguanosine (O⁶-medGuo) resulting from exposure to an alkylating agent, partial depletion of the O⁶-alkylguanine-DNA alkyltransferase (AGT) repair system was produced by pretreatment of ARL 18 cells with a non-toxic dose of exogenous O⁶-methylguanine (O⁶-meG). Exposure of cells to 0.6 mM O⁶-meG for 4 h depleted AGT activity by about 40%. Intact and pretreated cells were exposed to a range of doses of N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), and mutagenesis at the hypoxanthine-guanine phosphoribosyl transferase (HGPRT) locus was quantified by measurement of 6-thioguanine-resistant mutants. The mutagenicity of MNNG was dose dependent and was greater in O⁶-meG pretreated cultures than in intact cultures. Immunoslot blot measurement of O⁶-medGuo employing a mouse monoclonal antibody demonstrated that MNNG produced O[su6-medGuo and that the intact liver cells were efficient in eliminating this lesion from their DNA. Since depletion of AGT would be expected to affect the rate of elimination of only O⁶-medGuo, it is concluded that this lesion is highly pro-mutagenic.     

Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli

The alkyltransferase-like (ATL) proteins contain primary sequence motifs resembling those found in DNA repair O⁶-alkylguanine-DNA alkyltransferase proteins. However, in the putative active site of ATL proteins, a tryptophan (W⁸³) residue replaces the cysteine at the known active site of alkyltransferases. The Escherichia coli atl gene was expressed as a fusion protein and purified. Neither ATL nor C⁸³ or A⁸³ mutants transferred [³H] from [³H]-methylated DNA to themselves, and the levels of O⁶-methyl guanine (O⁶-meG) in substrate DNA were not affected by ATL. However, ATL inhibited the transfer of methyl groups to human alkyltransferase (MGMT). Inhibition was reduced by prolonged incubation in the presence of MGMT, again suggesting that O⁶-meG in the substrate is not changed by ATL. Gel-shift assays show that ATL binds to short single- or double-stranded oligonucleotides containing O⁶-meG, but not to oligonucleotides containing 8-oxoguanine, ethenoadenine, 5-hydroxycytosine or O⁴-methylthymine. There was no evidence of demethylation of O⁶-meG or of glycosylase or endonuclease activity. Overexpression of ATL in E.coli increased, or did not affect, the toxicity of N-methyl-N′-nitro-N-nitrosoguanidine in an alklyltransferase-proficient and -deficient strain, respectively. These results suggest that ATL may act as a damage sensor that flags O⁶-meG and possibly other O⁶-alkylation lesions for processing by other repair pathways.     

RAD51D protects against MLH1-dependent cytotoxic responses to O6-methylguanine

S_N1-type methylating agents generate O⁶-methyl guanine (O⁶-meG), which is a potently mutagenic, toxic, and recombinogenic DNA adduct. Recognition of O⁶-meG:T mismatches by mismatch repair (MMR) causes sister chromatid exchanges, which are representative of homologous recombination (HR) events. Although the MMR-dependent mutagenicity and toxicity caused by O⁶-meG has been studied, the mechanisms of recombination induced by O⁶-meG are poorly understood. To explore the HR and MMR genetic interactions in mammals, we used the Rad51d and Mlh1 mouse models. Ablation of Mlh1 did not appreciably influence the developmental phenotypes conferred by the absence of Rad51d. Mouse embryonic fibroblasts (MEFs) deficient in Rad51d can only proliferate in p53-deficient background. Therefore, Rad51d^?/?Mlh1^?/? Trp53^?/? MEFs with a combined deficiency of HR and MMR were generated and comparisons between MLH1 and RAD51D status were made. To our knowledge, these MEFs are the first mammalian model system for combined HR and MMR defects. Rad51d-deficient MEFs were 5.3-fold sensitive to N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) compared to the Rad51d-proficient MEFs. A pronounced G2/M arrest in Rad51d-deficient cells was accompanied by an accumulation of γ-H2AX and apoptosis. Mlh1-deficient MEFs were resistant to MNNG and showed no G2/M arrest or apoptosis at the doses used. Importantly, loss of Mlh1 alleviated sensitivity of Rad51d-deficient cells to MNNG, in addition to reducing γ-H2AX, G2/M arrest and apoptosis. Collectively, the data support the hypothesis that MMR-dependent sensitization of HR-deficient cells is specific for O⁶-meG and suggest that HR resolves DNA intermediates created by MMR recognition of O⁶-meG:T. This study provides insight into recombinogenic mechanisms of carcinogenesis and chemotherapy resulting from O⁶-meG adducts.     

Development of an O(6)-alkylguanine-DNA alkyltransferase assay based on covalent transfer of the benzyl moiety from [benzene-3H]O(6)-benzylguanine to the protein

Although it is known that (i) O⁶-alkylguanine-DNA alkyltransferase (AGT) confers tumor cell resistance to guanine O⁶-targeting drugs such as cloretazine, carmustine, and temozolomide and that (ii) AGT levels in tumors are highly variable, measurement of AGT activity in tumors before treatment is not a routine clinical practice. This derives in part from the lack of a reliable clinical AGT assay; therefore, a simple AGT assay was devised based on transfer of radioactive benzyl residues from [benzene-³H]O⁶-benzylguanine ([³H]BG) to AGT. The assay involves incubation of intact cells or cell homogenates with [³H]BG and measurement of radioactivity in a 70% methanol precipitable fraction. Approximately 85% of AGT in intact cells was recovered in cell homogenates. Accuracy of the AGT assay was confirmed by examination of AGT levels by Western blot analysis with the exception of false-positive results in melanin-containing cells due to [³H]BG binding to melanin. Second-order kinetic constants for human and murine AGT were 1100 and 380 M⁻¹ s⁻¹, respectively. AGT levels in various human cell lines ranged from less than 500 molecules/cell (detection limit) to 45,000 molecules/cell. Rodent cell lines frequently lacked AGT expression, and AGT levels in rodent cells were much lower than in human cells.     

Covalent capture of a human O(6)-alkylguanine alkyltransferase-DNA complex using N(1),O(6)-ethanoxanthosine, a mechanism-based crosslinker

The DNA repair protein O⁶-alkylguanine alkyltransferase (AGT) is responsible for removing promutagenic alkyl lesions from exocyclic oxygens located in the major groove of DNA, i.e. the O⁶ and O⁴ positions of guanine and thymine. The protein carries out this repair reaction by transferring the alkyl group to an active site cysteine and in doing so directly repairs the premutagenic lesion in a reaction that inactivates the protein. In order to trap a covalent AGT–DNA complex, oligodeoxyribonucleotides containing the novel nucleoside N¹,O⁶-ethanoxanthosine (^eX) have been prepared. The ^eX nucleoside was prepared by deamination of 3′,5′-protected O⁶-hydroxyethyl-2′-deoxyguanosine followed by cyclization to produce 3′,5′-protected N¹,O⁶-ethano-2′-deoxyxanthosine, which was converted to the nucleoside phosphoramidite and used in the preparation of oligodeoxyribonucleotides. Incubation of human AGT with a DNA duplex containing ^eX resulted in the formation of a covalent protein–DNA complex. Formation of this complex was dependent on both active human AGT and ^eX and could be prevented by chemical inactivation of the AGT with O⁶-benzylguanine. The crosslinking of AGT to DNA using ^eX occurs with high yield and the resulting complex appears to be well suited for further biochemical and biophysical characterization.     

Chloroethylating and methylating dual function antineoplastic agents display superior cytotoxicity against repair proficient tumor cells

Two new agents based upon the structure of the clinically active prodrug laromustine were synthesized. These agents, 2-(2-chloroethyl)-N-methyl-1,2-bis(methylsulfonyl)-N-nitrosohydrazinecarboxamide (1) and N-(2-chloroethyl)-2-methyl-1,2-bis(methylsulfonyl)-N-nitrosohydrazinecarboxamide (2), were designed to retain the potent chloroethylating and DNA cross-linking functions of laromustine, and gain the ability to methylate DNA at the O-6 position of guanine, while lacking the carbamoylating activity of laromustine. The methylating arm was introduced with the intent of depleting the DNA repair protein O⁶-alkylguanine-DNA alkyltransferase (AGT). Compound 1 is markedly more cytotoxic than laromustine in both AGT minus EMT6 mouse mammary carcinoma cells and high AGT expressing DU145 human prostate carcinoma cells. DNA cross-linking studies indicated that its cross-linking efficiency is nearly identical to its predicted active decomposition product, 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)hydrazine (90CE), which is also produced by laromustine. AGT ablation studies in DU145 cells demonstrated that 1 can efficiently deplete AGT. Studies assaying methanol and 2-chloroethanol production as a consequence of the methylation and chloroethylation of water by 1 and 2 confirmed their ability to function as methylating and chloroethylating agents and provided insights into the superior activity of 1.     

A role for mismatch repair in production of chromosome aberrations by methylating agents in human cells

We have shown previously that certain alkylation products, or alkylation derived lesions, which induce chromosome aberrations (abs) persist for at least two cell cycles in Chinese hamster ovary cells. The increase in abs in the second cycle after treatment contrasts with the classical observation of reduction in ab yield with successive mitoses following ionizing radiation. Here we present evidence that processing of lesions by mismatch repair is a mechanism for ab induction by methylating agents.Our previous studies implicated O⁶-methylguanine (O⁶MeG) as an important lesion in induction of abs, particularly in the second cell cycle after treatment. In the absence of repair of O⁶MeG by alkylguanine DNA alkyltransferase (AGT), new abs were induced in the second cycle after treatment with e.g. methylnitronitrosoguanidine (MNNG) and methylnitrosourea (MNU). Thus, we hypothesized that abs were produced not by O⁶MeG or its repair in the first S phase, but by subsequent processing of the lesions. We suggested that after replication proceeded past the O⁶MeG lesion in the first S phase, inserting an incorrect base on the newly synthesized strand, recognition and repair by mismatch repair in the second S phase led to a chromosome ab. Here we used MT1 cells, a human lymphoblastoid cell line that has a defect in strand-specific mismatch repair. MT1 cells are alkylation tolerant and have a mutator phenotype, compared with their parent line, TK6; both MT1 and TK6 cells lack AGT so do not remove the methyl group from O⁶MeG. While the initial levels of abs at the first metaphase were similar in MT1 and TK6 cells, ab levels in MT1 cells were greatly reduced in the second and third cell cycles following treatment with MNNG, dimethylnitrosamine and MNU, in contrast with the parent TK6 cells, which had more abs in the second cell cycle than in the first. This supports the hypothesis that repair of mismatched base pairs involving O⁶MeG is one mechanism for induction of chromosome abs. In contrast to the difference in response to methylating agents between TK6 cells and mismatch repair-deficient MT1 cells, the profile of ab induction by an ethylating agent, ethylnitronitrosourea, was similar in MT1 cells to those for TK6 cells and CHO cells.     

Lesion-specific DNA-binding and repair activities of human O6-alkylguanine DNA alkyltransferase

Binding experiments with alkyl-transfer-active and -inactive mutants of human O⁶-alkylguanine DNA alkyltransferase (AGT) show that it forms an O⁶-methylguanine (6mG)-specific complex on duplex DNA that is distinct from non-specific assemblies previously studied. Specific complexes with duplex DNA have a 2:1 stoichiometry that is formed without accumulation of a 1:1 intermediate. This establishes a role for cooperative interactions in lesion binding. Similar specific complexes could not be detected with single-stranded DNA. The small difference between specific and non-specific binding affinities strongly limits the roles that specific binding can play in the lesion search process. Alkyl-transfer kinetics with a single-stranded substrate indicate that two or more AGT monomers participate in the rate-limiting step, showing for the first time a functional link between cooperative binding and the repair reaction. Alkyl-transfer kinetics with a duplex substrate suggest that two pathways contribute to the formation of the specific 6mG-complex; one at least first order in AGT, we interpret as direct lesion binding. The second, independent of [AGT], is likely to include AGT transfer from distal sites to the lesion in a relatively slow unimolecular step. We propose that transfer between distal and lesion sites is a critical step in the repair process.     

Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase

O⁶-alkylguanine-DNA alkyltransferase (AGT) is a single-cycle DNA repair enzyme that removes pro-mutagenic O⁶-alkylguanine adducts from DNA. Its functions with short single-stranded and duplex substrates have been characterized, but its ability to act on other DNA structures remains poorly understood. Here, we examine the functions of this enzyme on O⁶-methylguanine (6mG) adducts in the four-stranded structure of the human telomeric G-quadruplex. On a folded 22-nt G-quadruplex substrate, binding saturated at 2 AGT:DNA, significantly less than the ∼5 AGT:DNA found with linear single-stranded DNAs of similar length, and less than the value found with the telomere sequence under conditions that inhibit quadruplex formation (4 AGT:DNA). Despite these differences, AGT repaired 6mG adducts located within folded G-quadruplexes, at rates that were comparable to those found for a duplex DNA substrate under analogous conditions. Repair was kinetically biphasic with the amplitudes of rapid and slow phases dependent on the position of the adduct within the G-quadruplex: in general, adducts located in the top or bottom tetrads of a quadruplex stack exhibited more rapid-phase repair than did adducts located in the inner tetrad. This distinction may reflect differences in the conformational dynamics of 6mG residues in G-quadruplex DNAs.     

Synthesis and antitumor activity evaluation of a novel combi-nitrosourea prodrug: Designed to release a DNA cross-linking agent and an inhibitor of O6-alkylguanine-DNA alkyltransferase

The drug resistance of CENUs induced by O⁶-alkylguanine-DNA alkyltransferase (AGT), which repairs the O⁶-alkylated guanine and subsequently inhibits the formation of dG–dC cross-links, hinders the application of CENU chemotherapies. Therefore, the discovery of CENU analogs with AGT inhibiting activity is a promising approach leading to novel CENU chemotherapies with high therapeutic index. In this study, a new combi-nitrosourea prodrug 3-(3-(((2-amino-9H-purin-6-yl)oxy)methyl)benzyl)-1-(2-chloroethyl)-1-nitrosourea (6), designed to release a DNA cross-linking agent and an inhibitor of AGT, was synthesized and evaluated for its antitumor activity and ability to induce DNA interstrand cross-links (ICLs). The results indicated that 6 exhibited higher cytotoxicity against mer⁺ glioma cells compared with ACNU, BCNU, and their respective combinations with O⁶-benzylguanine (O⁶-BG). Quantifications of dG–dC cross-links induced by 6 were performed using HPLC–ESI-MS/MS. Higher levels of dG–dC cross-link were observed in 6-treated human glioma SF763 cells (mer⁺), whereas lower levels of dG–dC cross-link were observed in 6-treated calf thymus DNA, when compared with the groups treated with BCNU and ACNU. The results suggested that the superiority of 6 might result from the AGT inhibitory moiety, which specifically functions in cells with AGT activity. Molecular docking studies indicated that five hydrogen bonds were formed between the O⁶-BG analogs released from 6 and the five residues in the active pocket of AGT, which provided a reasonable explanation for the higher AGT-inhibitory activity of 6 than O⁶-BG.     

Cytosine Methylation Effects on the Repair of O6-Methylguanines within CG Dinucleotides

O⁶-Alkyldeoxyguanine adducts induced by tobacco-specific nitrosamines are repaired by O⁶-alkylguanine DNA alkyltransferase (AGT), which transfers the O⁶-alkyl group from the damaged base to a cysteine residue within the protein. In the present study, a mass spectrometry-based approach was used to analyze the effects of cytosine methylation on the kinetics of AGT repair of O⁶-methyldeoxyguanosine (O⁶-Me-dG) adducts placed within frequently mutated 5′-CG-3′ dinucleotides of the p53 tumor suppressor gene. O⁶-Me-dG-containing DNA duplexes were incubated with human recombinant AGT protein, followed by rapid quenching, acid hydrolysis, and isotope dilution high pressure liquid chromatography-electrospray ionization tandem mass spectrometry analysis of unrepaired O⁶-methylguanine. Second-order rate constants were calculated in the absence or presence of the C-5 methyl group at neighboring cytosine residues. We found that the kinetics of AGT-mediated repair of O⁶-Me-dG were affected by neighboring 5-methylcytosine (^MeC) in a sequence-dependent manner. AGT repair of O⁶-Me-dG adducts placed within 5′-CG-3′ dinucleotides of p53 codons 245 and 248 was hindered when ^MeC was present in both DNA strands. In contrast, cytosine methylation within p53 codon 158 slightly increased the rate of O⁶-Me-dG repair by AGT. The effects of ^MeC located immediately 5′ and in the base paired position to O⁶-Me-dG were not additive as revealed by experiments with hypomethylated sequences. Furthermore, differences in dealkylation rates did not correlate with AGT protein affinity for cytosine-methylated and unmethylated DNA duplexes or with the rates of AGT-mediated nucleotide flipping, suggesting that ^MeC influences other kinetic steps involved in repair, e.g. the rate of alkyl transfer from DNA to AGT.Metabolic activation of the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)³ produces methyl- and pyridyloxobutyldiazonium ions that can react with DNA to give O⁶-methyldeoxyguanosine (O⁶-Me-dG) and O⁶- pyridyloxobutyl deoxyguanosine (O⁶-POB-dG) lesions (1). Both adducts are strongly mutagenic because DNA polymerases preferentially misinsert thymine opposite O⁶-alkylguanines, resulting in G → A transitions (2). Studies in laboratory animals have provided evidence for a direct involvement of O⁶-Me-dG in NNK-mediated carcinogenesis (3).A specialized repair protein, O⁶-alkylguanine DNA alkyltransferase (AGT), removes the alkyl group from the O⁶ position of modified guanine bases, such as O⁶-Me-dG and O⁶-POB-dG, restoring normal guanine bases and preventing mutagenesis. AGT preferentially binds double-stranded DNA through a helix-turn-helix motif (4). In the resulting AGT-DNA complex, one recognition helix of the protein is found within the minor groove of the DNA, whereas the other one interacts with the phosphodiester backbone (4). The adducted nucleotide is flipped into a binding pocket within the protein, whereas Arg-128 takes its place in the double helix (4). A hydrogen bonding network around the active site involving His-148, Glu-172, and a water molecule promotes the deprotonation of the active site cysteine (Cys-145) (4, 5). The resulting thiolate anion acts as a nucleophile, displacing the O⁶ substituent of O⁶-alk-G and regenerating normal guanine (Fig. 1) (4, 5). The alkylated protein is inactive and is rapidly degraded by the ubiquitin proteolytic pathway (6–8).Open in a separate windowFIGURE 1.Direct repair of O⁶-alkyl-guanine adducts by AGT.AGT-mediated repair of O⁶-Me-dG lesions includes multiple kinetic steps (9). First, the AGT protein must bind adducted DNA in a reactive conformation. The alkylated nucleotide is flipped out of the DNA base stack to enter the hydrophobic pocket within AGT, and the methyl group is transferred from DNA to the protein. Finally, alkylated AGT protein dissociates from the repaired DNA. Zang et al. (9) reported that the chemical step of alkyl transfer is rate-limiting in the case of O⁶-Me-dG, but not O⁶-benzyl-dG. Furthermore, previous studies have shown that the repair of O⁶-Me-dG by mammalian AGT is influenced by the nature of the O⁶-alkyl group, the length of oligonucleotide duplex, the placement of the adduct, and the identities of neighboring nucleotides (10–14).Removing the alkyl group from O⁶-Me-dG by AGT regenerates normal guanine and protects the genome from G → A transition mutations. For example, Wolf et al. (15) examined the relationship between the inactivation of the AGT gene by promoter hypermethylation and the mutational spectrum of the p53 tumor suppressor gene in non-small cell lung cancer. These authors found that only 8% of lung tumors had G → A transition mutations in the p53 gene when the promoter region of the gene coding for AGT was not methylated, thereby allowing protein expression (15). In contrast, 33% of tumors with a methylated AGT promoter had G → A mutations within the p53 gene (15). The p53 gene is mutated in over 50% of non-small cell lung cancer tumors (16).All CpG sites within the coding sequence of the p53 gene are endogenously methylated (17). Importantly, the same sites are among the major p53 mutational “hotspots” in smoking-induced lung cancer, e.g. codons 157, 158, 245, 248, 249, and 273 (18). Of all p53 mutations, G → A transitions account for 18–24% of genetic changes observed in lung cancer, including 35% of mutations at the CG dinucleotides (15, 19). Given the established role of NNK-induced O⁶-alkylguanine lesions in tobacco carcinogenesis and mutagenesis (20), they are likely to be involved in the induction of smoking-associated G → A transitions in the p53 gene.The presence of ^MeC residues may hinder the repair of O⁶-Me-dG lesions within endogenously methylated CG dinucleotides (14). For example, Bentivenga and Bresnick (14) showed that the repair of O⁶-Me-dG by recombinant AGT in the context of codon 248 of the p53 gene was reduced by 75% when ^MeC was placed immediately 5′ to the O⁶-Me-dG lesion. However, the effects of cytosine methylation on AGT repair of O⁶-Me-dG in other sequence contexts have not been previously investigated, and it is not known which individual steps in the removal of O⁶-methyl group are affected by neighboring ^MeC.Cytosine methylation leads to small structural changes of DNA duplex, including an increase in the base pair rise, roll, and local curvature angles, narrowing of the DNA minor groove, and decreased depth of the major groove (21–23). These structural alterations may influence the affinity of the AGT protein for alkylated DNA. Furthermore, ^MeC enhances base stacking (24) and stabilizes the DNA duplex by increasing the molecular polarizability of the cytosine base (25), which can have an effect on the rate of AGT-mediated nucleotide flipping. The alkyl transfer step itself may be mediated by the presence of ^MeC through its effects on transition state geometry.The goal of the present study was to systematically examine the effects of cytosine methylation on AGT-mediated repair of O⁶-Me-dG lesions placed within 5′-CG-3′ dinucleotides representing major p53 mutational hotspots observed in lung cancer. The kinetics of alkyl transfer were analyzed using rapid-quench methods coupled with quantitative analyses of O⁶-Me-dG by isotope dilution-high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) (26). Furthermore, we examined the effects of cytosine methylation on AGT binding to O⁶-Me-dG-containing DNA and its influence on the rate of O⁶-Me-dG nucleotide flipping in the presence of AGT protein.     

6‐phenylpyrrolocytosine as a fluorescent probe to examine nucleotide flipping catalyzed by a DNA repair protein

Cellular exposure to tobacco‐specific nitrosamines causes formation of promutagenic O⁶‐[4‐oxo‐4‐(3‐pyridyl)but‐1‐yl]guanine (O⁶‐POB‐G) and O⁶‐methylguanine (O⁶‐Me‐G) adducts in DNA. These adducts can be directly repaired by O⁶‐alkylguanine‐DNA alkyltransferase (AGT). Repair begins by flipping the damaged base out of the DNA helix. AGT binding and base‐flipping have been previously studied using pyrrolocytosine as a fluorescent probe paired to the O⁶‐alkylguanine lesion, but low fluorescence yield limited the resolution of steps in the repair process. Here, we utilize the highly fluorescent 6‐phenylpyrrolo‐2′‐deoxycytidine (6‐phenylpyrrolo‐C) to investigate AGT‐DNA interactions. Synthetic oligodeoxynucleotide duplexes containing O⁶‐POB‐G and O⁶‐Me‐G adducts were placed within the CpG sites of codons 158, 245, and 248 of the p53 tumor suppressor gene and base‐paired to 6‐phenylpyrrolo‐C in the opposite strand. Neighboring cytosine was either unmethylated or methylated. Stopped‐flow fluorescence measurements were performed by mixing the DNA duplexes with C145A or R128G AGT variants. We observe a rapid, two‐step, nearly irreversible binding of AGT to DNA followed by two slower steps, one of which is base‐flipping. Placing 5‐methylcytosine immediately 5′ to the alkylated guanosine causes a reduction in rate constant of nucleotide flipping. O⁶‐POB‐G at codon 158 decreased the base flipping rate constant by 3.5‐fold compared with O⁶‐Me‐G at the same position. A similar effect was not observed at other codons.