Intragenomic repair heterogeneity of DNA damage

DNA adducts from a tumorigenic metabolite of benzo[a]pyrene block human RNA polymerase II elongation in a sequence- and stereochemistry-dependent manner

Many carcinogens exert their cancer-causing effects by reacting with DNA either directly or following metabolic activation, resulting in covalently linked combination molecules known as carcinogen-DNA adducts. The presence of such lesions in the genome increases the error frequency of the replication machinery, causing mutations that contribute to the initiation and progression of cancer. Cellular DNA repair pathways remove carcinogen adducts from DNA, thus averting the mutagenic potential of many DNA lesions by reducing their presence in the genome. Bulky DNA adducts, like those derived from a number of activated environmental carcinogens such as polycyclic aromatic hydrocarbons (PAHs), are primarily repaired by the nucleotide excision repair (NER) pathway. Transcription-coupled NER (TC-NER) preferentially removes lesions from the transcribed strand of actively expressed genes, and RNA polymerase II stalled at the lesion quite possibly initiates the pathway. Among the bulky DNA adducts that are subject to TC-NER are those resulting from the reaction of the metabolically activated PAH benzo[a]pyrene (BP) with DNA. The P450 mixed-function oxygenases convert BP into a number of reactive intermediates, including tumorigenic (+)- and non-tumorigenic (-)-anti-benzo[a]pyrene diol epoxide (BPDE) that react with DNA via trans epoxide opening to form (+)-trans-anti-[BP]-N(2)-dG ((+)-ta[BP]G) and (-)-trans-anti-[BP]-N(2)-dG ((-)-ta[BP]G), respectively. To test the effect of these lesions on RNA synthesis, in vitro transcription assays using human nuclear extracts were performed with DNA templates containing an RNAPII promoter and a stereochemically pure (+)- or (-)-ta[BP]G adduct on the transcribed or non-transcribed strand. Transcription past (+)- or (-)-ta[BP]G adducts was investigated in the same sequence context to examine stereochemical effects. The (+)-ta[BP]G adduct was investigated in two different local sequence contexts to determine if the surrounding bases influence the adduct's ability to block transcription. These experiments revealed that (+)- and (-)-ta[BP]G adducts on the transcribed strand of the DNA template block RNAPII in a sequence and stereochemistry-dependent manner; however, adducts on the non-transcribed strand do not block elongation significantly but may increase pausing at innate pause sites. In order to elucidate biologically influential differences between the (+)- and (-)-ta[BP]G structures, the DUPLEX program was used to carry out potential energy minimization searches at model transcription junctions. The lowest-energy minimum for the (+)-ta[BP]G adduct gives a structure in which the benzo[a]pyrenyl ring system resides in the minor groove of the heteroduplex region. In contrast, the lowest-energy minimum for a (-)-ta[BP]G adduct shows an orientation in which the benzo[a]pyrenyl group adopts a carcinogen/base-stacked conformation. These conformational preferences may contribute to the differential treatment of (+)- and (-)-ta[BP]G adducts by human RNAPII. In addition, while previous experiments showed that BPDE adducts cause T7RNAP to produce a ladder of truncated transcripts, RNAPII is blocked entirely at only one or two positions by the (+)- and (-)-ta[BP]G adducts, depending on sequence context. It is likely that these differences between the behaviors of T7RNAP and human RNAPII are a result of the structural characteristics of the enzymes' active sites, a hypothesis that is explored in light of their known crystal structures.

Transcription and DNA damage: a link to a kink

Living organisms are constantly exposed to a variety of naturally occurring and man-made chemical and physical agents that pose threats to health by causing cancer and other illnesses, as well as cell death. One mechanism by which these moieties can exert their toxic effects is by inducing modifications to the genome. Such changes in DNA often result in the formation of nucleotides not normally found in the double helix, bases containing covalent chemical alterations, single- and double-strand breaks, and interstrand and intrastrand cross-links. When these lesions are present during replication, mutations often result in the newly synthesized DNA. Likewise, when such damage occurs in a gene, transcription elongation, and hence expression, can be adversely affected because of pausing or arresting of the RNA polymerase at or near the altered site; this could result in the synthesis of a defective RNA molecule. It has become increasingly clear that transcription and DNA damage are intimately linked, since the removal of certain adducts from the genome is highly dependent on their location. When such lesions are present on the transcribed strand of actively expressed genetic loci, they are better cleared from that strand when compared to the complementary DNA or other quiescent regions. This process is called transcription-coupled DNA repair, and it modulates the mutagenic spectrum of many DNA-damaging agents. Furthermore, based upon evidence from systems in which it is absent, this process has a profound effect on ameliorating the adverse consequences of exposure to many environmentally relevant genotoxins. The precise cellular pathway that mediates the preferential clearance of DNA damage from active genetic loci has not yet been established, but it appears to be effected by a repertoire of proteins that are also involved in other DNA repair pathways and transcription as well as some factors that might be unique to it. Because a cellular process as indispensable as gene expression can be thwarted by the presence of DNA damage, an understanding of the mechanism underlying transcription-coupled DNA repair is relevant to the continued discernment of how environmental genotoxins endanger human health.

Molecular dosimetry of chemical mutagens. Relationship between DNA adduct formation and genetic changes analyzed at the molecular level

This is a review of the work carried out by 16 collaborating institutes within a project which was part of the European Programme: Science and Technology for Environmental Protection (STEP). The purpose of the project was to investigate the relationship between the exposure to genotoxic chemicals and the induction of DNA damage and genetic effects as determined in in vitro and in vivo assays under laboratory conditions. Two types of investigation were performed: (i) determination of the relationship between the extent of exposure to a genotoxic chemical and the frequency of DNA adducts formed in the test organism and (ii) identification of those DNA adducts which are responsible for the biological effects of genotoxic chemicals. The research was carried out with a series of alkylating agents which all induce similar types of DNA damage but for which the proportions of the different types of adducts vary. The frequency of this type of DNA damage was also modulated by base excision repair processes. In addition, a number of genotoxic agents which cause DNA damage recognized by nucleotide excision repair were investigated. The consequences of DNA adduct formation, i.e., the induction of gene mutations, were analyzed at the DNA sequence level, generating mutational spectra. These investigations of the mutational specificities of carcinogens contributed to our understanding of the molecular mechanisms which are involved in cancer induction by genotoxins.

Role of transcription-coupled DNA repair in susceptibility to environmental carcinogenesis

Susceptibility to environmental carcinogenesis is the consequence of a complex interplay between intrinsic hereditary factors and actual exposures to potential carcinogenic agents. We must learn the nature of these interactions as well as the genetic defects that confer enhanced risk. In some genetic diseases an increased cancer risk correlates with a defect in the repair or replications of damaged DNA. Examples include xeroderma pigmentosum (XP), ataxia telangiectasia, Fanconi's anemia, and Bloom's syndrome. In Cockayne's syndrome the Specific defect in transcription-coupled repair (TCR) does not predispose the patients to the sunlight-induced skin cancer characteristic of XP. The demonstration of TCR in the XP129 partial revertant of XP-A cells indicates that ultraviolet (UV) resistance correlates with repair of cyclobutane pyrimidine dimers in active genes. Repair measured as an average over the genome can be misleading, and it is necessary to consider genomic locations of DNA damage and repair for a meaningful assessment of the biological importance of particular DNA lesions. Mutations in the p53 tumor suppressor gene are found in many human tumors. TCR accounts for the resulting mutational spectra in the p53 gene in certain tumors. Li-Fraumeni syndrome fibroblasts expressing only mutant p53 are more UV-resistant and exhibit less UV-induced apoptosis than normal human cells or heterozygotes for mutations in only one allele of p53. The p53-defective cells are deficient in global excision repair capacity but have retained TCR. The loss of p53 function may lead to greater genomic instability by reducing the efficiency of global DNA repair while cellular resistance may be assured through the operation of TCR and the elimination of apoptosis.

Mechanisms and biomarkers of genotoxicity. Molecular dosimetry of chemical mutagens

The relevance of the use of DNA adduct frequencies as a parameter for the extent of mutation induction by monofunctional alkylating agents was investigated in cultured Chinese hamster cells and in rat skin fibroblasts treated in vivo with the test chemicals. The nature of the biologically significant DNA adducts was investigated by DNA sequence analysis of mutations induced at the hypoxanthine-guanine phophoribosyltransferase (hprt) gene. The results show that under conditions where O6-alkylguanine is a persistent DNA lesion more than 50% of the mutations are GC to AT transitions indicating that the frequency of O6-alkylguanine is a good parameter for mutation induction. However, in target cells which are able to remove alkyl groups from the O6 position of guanine, alkylating agents with a low nucleophilic selectivity (e.g. N-ethyl-N-nitrosourea (ENU) and N-ethyl-N'-nitro-N-nitrosoguanidine (ENNG)) exert most of their mutagenic activity most likely via the induction of O2-ethylthymine.

Site-specific benzo[a]pyrene diol epoxide-DNA adducts inhibit transcription elongation by bacteriophage T7 RNA polymerase

Benzo[a]pyrene, an extremely potent procarcinogen and mutagen, is metabolized to a variety of products, including the ultimate carcinogen 7,8-dihydroxy-9,10-epoxy- 7,8,9,10-tetrahydrobenzo[a]pyrene. This product of biotransformation reacts with DNA, forming a series of adducts principally at the N2 position of guanine that differ in their stereochemistry and exhibit unique biological properties. In order to gain a better understanding of the effects on RNA synthesis of these adducts, we used purified bacteriophage T7 RNA polymerase to transcribe a series of templates containing one of four stereoisomerically pure BPDE-guanine lesions--(+)-trans-,(-)-trans-,(+)-cis-anti-N2-BPDE-guanine--or no damaged bases. To construct suitable double-stranded oligodeoxynucleotides for these studies, we annealed an 11-mer containing a site-specific stereoisomerically pure N2-BPDE-guanine adduct, a 37-mer, and a 10-mer to a complementary 58-base sequence of single-stranded DNA. The oligomers were ligated, purified, and reannealed. The resulting DNA template contained the promoter for T7 RNA polymerase and a BPDE adduct at position +16 following the transcription initiation site. The results of the transcription assays clearly demonstrate that each of the adducts inhibits elongation by T7 RNA polymerase, but they do so to significantly different extents, depending on the stereochemical characteristics of the BPDE-modified guanine. The order of inhibition is (+)-trans > (-)-trans > (+)-cis > (-)-cis, when the amount of full-length transcript for each is compared to that obtained for an unmodified template. Furthermore, premature termination of RNA synthesis occurs at or near the site of the BPDE lesion as evidenced by the formation of discrete, truncated transcripts. These results might be related to the fact that the pyrenyl moiety of the trans-BPDE adducts is situated in the minor groove of double-stranded DNA, but is quasi-intercalated into the double helix in the case of the cis stereoisomers.(ABSTRACT TRUNCATED AT 250 WORDS)

Prediction and monitoring of the carcinogenicity of polycyclic aromatic compounds (PACs)

Chemical carcinogenesis is a multistage process that includes initiation, promotion, and progression. Some carcinogenic PACs have been shown to activate proto-oncogenes and deactivate tumor-suppression genes in the carcinogenic process. The function of DNA repair processes appears to be changed in some cases by PACs. Many PACs are well known for their carcinogenic activity, but for this activity to be exerted, metabolic activation by microsomal enzymes must occur. The enzyme system responsible for PAC activation is the mixed-function oxidase system and, in particular, cytochrome P-450. In the case of PAHs, oxidation predominantly produces reactive diol-epoxides that can then be converted to carbonium ions as the reactive electrophiles that can then covalently bind to DNA. Regions of high activity exist in PAHs, namely, the "bay," "K," and "L" regions which are associated with pi electron distribution. The diol-epoxides can exist in either syn or anti forms, each of which has two enantiomers producing four stereoisomers in all. Energy considerations favor the formation of the anti form. Nitrogen-containing PACs can be metabolically activated in a manner similar to that for PAHs, or the nitrogen atom can be oxidized to form hydroxylamines. These reactive electrophiles can then form covalently bound DNA adducts. The monitoring of DNA adducts has been used in risk assessment for human exposure to PACs. This form of biomonitoring has advantages over the monitoring of external exposure or body levels of the chemicals in question. In the case of PACs, binding to DNA is an important step in the multistage carcinogenic process. The estimation of DNA adducts has been used in the monitoring of humans exposed to PAHs in a wide range of industrial situations. Recent research has shown a dose-response relationship between PAH adduct levels and human cancer, thus developing molecular epidemiology as a relevant science for the field of risk assessment. Techniques have been developed for the determination of DNA adducts and these include immunochemical, fluorescence spectroscopic, GC-MS, and 32P-postlabeling methods. The 32P-postlabeling assay is by far the most sensitive, with limits of detection being of the order of one adduct in 10(10) normal nucleotides. The use of HPLC for separation of adducted nucleotides in this postlabeling assay is becoming more common and gives better resolution of adducts than does the TLC technique used in the traditional assay. The detection of adducts on hemoglobin and other proteins has been used as a surrogate for DNA adduct estimation.(ABSTRACT TRUNCATED AT 400 WORDS)