Characterization of human DNA polymerase κ promoter in response to benzo[a]pyrene diol epoxide

Chemical Insights into Oxidative and Nitrative Modifications of DNA

This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.

Regulation of the error-prone DNA polymerase Polκ by oncogenic signaling and its contribution to drug resistance

The DNA polymerase Polκ plays a key role in translesion synthesis, an error-prone replication mechanism. Polκ is overexpressed in various tumor types. Here, we found that melanoma and lung and breast cancer cells experiencing stress from oncogene inhibition up-regulated the expression of Polκ and shifted its localization from the cytoplasm to the nucleus. This effect was phenocopied by inhibition of the kinase mTOR, by induction of ER stress, or by glucose deprivation. In unstressed cells, Polκ is continually transported out of the nucleus by exportin-1. Inhibiting exportin-1 or overexpressing Polκ increased the abundance of nuclear-localized Polκ, particularly in response to the BRAF^V600E-targeted inhibitor vemurafenib, which decreased the cytotoxicity of the drug in BRAF^V600E melanoma cells. These observations were analogous to how Escherichia coli encountering cell stress and nutrient deprivation can up-regulate and activate DinB/pol IV, the bacterial ortholog of Polκ, to induce mutagenesis that enables stress tolerance or escape. However, we found that the increased expression of Polκ was not excessively mutagenic, indicating that noncatalytic or other functions of Polκ could mediate its role in stress responses in mammalian cells. Repressing the expression or nuclear localization of Polκ might prevent drug resistance in some cancer cells.

Mammalian DNA Polymerase Kappa Activity and Specificity

DNA polymerase (pol) kappa is a Y-family translesion DNA polymerase conserved throughout all domains of life. Pol kappa is special6 ized for the ability to copy DNA containing minor groove DNA adducts, especially N²-dG adducts, as well as to extend primer termini containing DNA damage or mismatched base pairs. Pol kappa generally cannot copy DNA containing major groove modifications or UV-induced photoproducts. Pol kappa can also copy structured or non-B-form DNA, such as microsatellite DNA, common fragile sites, and DNA containing G quadruplexes. Thus, pol kappa has roles both in maintaining and compromising genomic integrity. The expression of pol kappa is altered in several different cancer types, which can lead to genome instability. In addition, many cancer-associated single-nucleotide polymorphisms have been reported in the POLK gene, some of which are associated with poor survival and altered chemotherapy response. Because of this, identifying inhibitors of pol kappa is an active area of research. This review will address these activities of pol kappa, with a focus on lesion bypass and cellular mutagenesis.

Single-molecule studies contrast ordered DNA replication with stochastic translesion synthesis

High fidelity replicative DNA polymerases are unable to synthesize past DNA adducts that result from diverse chemicals, reactive oxygen species or UV light. To bypass these replication blocks, cells utilize specialized translesion DNA polymerases that are intrinsically error prone and associated with mutagenesis, drug resistance, and cancer. How untimely access of translesion polymerases to DNA is prevented is poorly understood. Here we use co-localization single-molecule spectroscopy (CoSMoS) to follow the exchange of the E. coli replicative DNA polymerase Pol IIIcore with the translesion polymerases Pol II and Pol IV. We find that in contrast to the toolbelt model, the replicative and translesion polymerases do not form a stable complex on one clamp but alternate their binding. Furthermore, while the loading of clamp and Pol IIIcore is highly organized, the exchange with the translesion polymerases is stochastic and is not determined by lesion-recognition but instead a concentration-dependent competition between the polymerases.

Mechanisms of DNA damage, repair, and mutagenesis

Living organisms are continuously exposed to a myriad of DNA damaging agents that can impact health and modulate disease-states. However, robust DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival. Deviations in this fine-tuning are known to destabilize cellular metabolic homeostasis, as exemplified in diverse cancers where disruption or deregulation of DNA repair pathways results in genome instability. Because routinely used biological, physical and chemical agents impact human health, testing their genotoxicity and regulating their use have become important. In this introductory review, we will delineate mechanisms of DNA damage and the counteracting repair/tolerance pathways to provide insights into the molecular basis of genotoxicity in cells that lays the foundation for subsequent articles in this issue. Environ. Mol. Mutagen. 58:235-263, 2017. © 2017 Wiley Periodicals, Inc.

Maintenance of Genome Integrity: How Mammalian Cells Orchestrate Genome Duplication by Coordinating Replicative and Specialized DNA Polymerases

Precise duplication of the human genome is challenging due to both its size and sequence complexity. DNA polymerase errors made during replication, repair or recombination are central to creating mutations that drive cancer and aging. Here, we address the regulation of human DNA polymerases, specifically how human cells orchestrate DNA polymerases in the face of stress to complete replication and maintain genome stability. DNA polymerases of the B-family are uniquely adept at accurate genome replication, but there are numerous situations in which one or more additional DNA polymerases are required to complete genome replication. Polymerases of the Y-family have been extensively studied in the bypass of DNA lesions; however, recent research has revealed that these polymerases play important roles in normal human physiology. Replication stress is widely cited as contributing to genome instability, and is caused by conditions leading to slowed or stalled DNA replication. Common Fragile Sites epitomize “difficult to replicate” genome regions that are particularly vulnerable to replication stress, and are associated with DNA breakage and structural variation. In this review, we summarize the roles of both the replicative and Y-family polymerases in human cells, and focus on how these activities are regulated during normal and perturbed genome replication.

Adaptive upregulation of DNA repair genes following benzo(a)pyrene diol epoxide protects against cell death at the expense of mutations

A coordinated and faithful DNA damage response is of central importance for maintaining genomic integrity and survival. Here, we show that exposure of human cells to benzo(a)pyrene 9,10-diol-7,8-epoxide (BPDE), the active metabolite of benzo(a)pyrene (B(a)P), which represents a most important carcinogen formed during food preparation at high temperature, smoking and by incomplete combustion processes, causes a prompt and sustained upregulation of the DNA repair genes DDB2, XPC, XPF, XPG and POLH. Induction of these repair factors on RNA and protein level enhanced the removal of BPDE adducts from DNA and protected cells against subsequent BPDE exposure. However, through the induction of POLH the mutation frequency in the surviving cells was enhanced. Activation of these adaptive DNA repair genes was also observed upon B(a)P treatment of MCF7 cells and in buccal cells of human volunteers after cigarette smoking. Our data provide a rational basis for an adaptive response to polycyclic aromatic hydrocarbons, which occurs however at the expense of mutations that may drive cancer formation.

Role of DNA polymerase κ in the maintenance of genomic stability

To ensure high cell viability and genomic stability, cells have evolved two major mechanisms to deal with the constant challenge of DNA replication fork arrest during S phase of the cell cycle: (1) induction of the ataxia telangiectasia and Rad3-related (ATR) replication checkpoint mechanism, and (2) activation of a pathway that bypasses DNA damage and DNA with abnormal structure and is mediated by translesion synthesis (TLS) Y-family DNA polymerases. This review focuses on how DNA polymerase kappa (Pol κ), one of the most highly conserved TLS DNA polymerases, is involved in each of these pathways and thereby coordinates them to choreograph the response to a stalled replication fork. We also describe how loss of Pol κ regulation, which occurs frequently in human cancers, affects genomic stability and contributes to cancer development.

In vivo exposure to benzo(a)pyrene induces significant DNA damage in mouse oocytes and cumulus cells

STUDY QUESTION

Does in vivo exposure to benzo(a)pyrene (BaP) induce DNA damage in oocytes and cumulus cells (CCs) in mice?

SUMMARY ANSWER

Significant increases in DNA strand breaks in oocytes and CCs and in BaP-induced DNA adducts in CCs were detected in exposed mice compared with controls.

WHAT IS KNOWN ALREADY

BaP has well-known mutagenic and carcinogenic effects on somatic cells, and is also registered as potential reproductive toxicant by several environmental protection agencies. It has been shown to cause a significant increase in DNA adducts in ovarian tissues; however, to our knowledge, the genotoxic effects of BaP on oocytes and CCs have not been studied to date.

STUDY DESIGN, SIZE, DURATION

Female CD1 mice were exposed to BaP via the oral administration of a single dose of 13 mg/kg body weight (bw); matched controls were exposed to the vehicle only (soya oil). A total of 15 groups of 6 mice (exposed or controls) were sacrificed 2, 4, 6, 15 or 22 days after BaP exposure, and after collection of oviducts, the oocyte-CC complexes (COC) were released.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The alkaline comet assay was used to quantify the DNA breaks in oocytes and CCs; DNA damage was expressed as the Olive Tail Moment (OTM). Immunofluorescent staining was used to quantify BaP-induced DNA adducts in CCs. Fluorescence was expressed as the average grey value (AGVA; arbitrary units). The differences between the exposed and control groups were assessed using analysis of variance (ANOVA) and the non-parametric Mann-Whitney test.

MAIN RESULTS AND THE ROLE OF CHANCE

Higher levels of DNA damage were observed in the oocytes and CCs of BaP-exposed mice than in those of vehicle controls. Significant increases in OTM (mean ± SE) were detected in (i) oocytes from females exposed for 4 (10.5 ± 0.9 versus 3.1 ± 0.4, P < 0.0001) or 6 days before collection (15.6 ± 2.0 versus 3.6 ± 0.9, P < 0.0001) and (ii) CCs from females exposed 2 (6.4 ± 0.6 versus 2.1 ± 0.2, P < 0.0001), 4 (7.8 ± 0.4 versus 2.4 ± 0.1, P < 0.0001) or 6 days before collection (7.3 ± 0.3 versus 3.2 ± 0.5, P < 0.0001) compared with controls. A significant increase in benzo(a)pyrene-7,8-9,10 diol epoxide (BPDE)-DNA adducts and higher AGVA (mean ± SE) scores were observed in CCs from females exposed 2 (6.1 ± 0.3 versus 3.6 ± 0.5, P < 0.0001), 4 (7.5 ± 0.1 versus 3.4 ± 0.1, P < 0.0001) or 6 days before collection (11.6 ± 0.4 versus 3.7 ± 0.1, P < 0.0001) compared with control mice.

LIMITATIONS, REASONS FOR CAUTION

Mice were given one treatment via the oral route because this dose and mode of administration have been shown to induce detectable BPDE-DNA adduct levels in mouse organs and sperm cells. Additional data are needed to assess DNA damage in oocytes and CCs after chronic exposure to BaP in vivo.

WIDER IMPLICATIONS OF THE FINDINGS

To our knowledge, this is the first study examining the in vivo genotoxicity of BaP in oocytes and CCs. We observed significant DNA damage in the oocytes and CCs of mice after acute BaP exposure. BPDE-DNA adducts result directly from BaP metabolism while DNA breaks could result mainly from BPDE-DNA adduct excision and repair and/or through direct genotoxicity from increased reactive oxygen species. These results add new and important insights regarding the recently suggested toxicity of chronic BaP exposure in the ovary.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by a grant (93-CPQ 2012-05) from the DIRRECTE, Provence Alpes Côte d'Azur, France. None of the authors have any conflict of interest to declare.

Transcriptional regulation of human DNA repair genes following genotoxic stress: trigger mechanisms, inducible responses and genotoxic adaptation

DNA repair is the first barrier in the defense against genotoxic stress. In recent years, mechanisms that recognize DNA damage and activate DNA repair functions through transcriptional upregulation and post-translational modification were the focus of intensive research. Most DNA repair pathways are complex, involving many proteins working in discrete consecutive steps. Therefore, their balanced expression is important for avoiding erroneous repair that might result from excessive base removal and DNA cleavage. Amelioration of DNA repair requires both a fine-tuned system of lesion recognition and transcription factors that regulate repair genes in a balanced way. Transcriptional upregulation of DNA repair genes by genotoxic stress is counteracted by DNA damage that blocks transcription. Therefore, induction of DNA repair resulting in an adaptive response is only visible through a narrow window of dose. Here, we review transcriptional regulation of DNA repair genes in normal and cancer cells and describe mechanisms of promoter activation following genotoxic exposures through environmental carcinogens and anticancer drugs. The data available to date indicate that 25 DNA repair genes are subject to regulation following genotoxic stress in rodent and human cells, but for only a few of them, the data are solid as to the mechanism, homeostatic regulation and involvement in an adaptive response to genotoxic stress.

The effect of aryl hydrocarbon receptor ligands on the expression of polymerase (DNA directed) kappa (Polκ), polymerase RNA II (DNA directed) polypeptide A (PolR2a), CYP1B1 and CYP1A1 genes in rat liver

The aryl hydrocarbon receptor (AhR) mediates a variety of biological responses to ubiquitous environmental pollutants. AhR is ligand activated transcription factor with high affinities for aromatic planar compounds such as β-naphthoflavone (BNF), 3-methylcholanthrene (3-MC), benzo[a]pyrene (BaP) or dioxin (TCDD). After binding appropriate ligand, AhR trigger induction of expression of some phase I and phase II drug metabolizing genes together with numerous other genes. One of such gene appear to be polymerase (DNA directed) kappa (Polκ). Polκ gene encodes newly identified low fidelity DNA polymerase. The enzyme bypasses benzo[a]pyrene-N2-dG lesions in a mostly error free manner by incorporating predominantly dC opposite the bulky lesions. It was demonstrated that AhR activation increases expression of the mouse Polκ gene and probably human POLK gene. In this study we examined the effect of i.p. administration of different AhR ligands on the expression of Polκ, RNA polymerase II polypeptide A (PolR2a) and cytochrome P450 1B1 (CYP1B1), the genes controlled by AhR in Sprague-Dawley rat liver. Quantitative real-time RT-PCR analysis revealed significant induction in the mRNA expression levels of Polκ and PolR2a following BNF treatment. Time courses of mRNA expression after treatment with BNF were similar in both genes, with maximal increases at 8h after treatment. The maximal induction of CYP1B1 and CYP1A1 expression was observed after 24 and 8h after BNF injection, respectively. TCDD treatment caused the significant increase in the mRNA level of CYP1B1 at 72h after administration of the ligand but no effect on Polκ and PolR2a mRNA expression was observed. These results confirm connection between AhR and Polκ, and strongly suggest that AhR up-regulates the mRNA transcription of PolR2a as well. However physiological importance of AhR dependent regulation of PolR2a expression must be further elucidated.