Analysis Of DNA Adducts Research Articles

Targeted High Resolution LC/MS3 Adductomics Method for the Characterization of Endogenous DNA Damage.

DNA can be damaged through covalent modifications of the nucleobases by endogenous processes. These modifications, commonly referred to as DNA adducts, can persist and may lead to mutations, and ultimately to the initiation of cancer. A screening methodology for the majority of known endogenous DNA adducts would be a powerful tool for investigating the etiology of cancer and for the identification of individuals at high-risk to the detrimental effects of DNA damage. This idea led to the development of a DNA adductomic approach using high resolution data-dependent scanning, an extensive MS2 fragmentation inclusion list of known endogenous adducts, and neutral loss MS3 triggering to profile all DNA modifications. In this method, the detection of endogenous DNA adducts is performed by observation of their corresponding MS3 neutral loss triggered events and their relative quantitation using the corresponding full scan extracted ion chromatograms. The method's inclusion list consists of the majority of known endogenous DNA adducts, compiled, and reported here, as well as adducts specific to tobacco exposure included to compare the performance of the method with previously developed targeted approaches. The sensitivity of the method was maximized by reduction of extraneous background signal through the purification and minimization of the amount of commercially obtained enzymes used for the DNA hydrolysis. In addition, post-hydrolysis sample purification was performed using off-line HPLC fraction collection to eliminate the highly abundant unmodified bases, and to avoid introduction of plasticizers found in solid-phase extraction cartridges. Also, several instrument parameters were evaluated to optimize the ion signal intensities and fragmentation spectra quality. The method was tested on an animal model of lung carcinogenesis where A/J mice were exposed to the tobacco specific lung carcinogen 4-methylnitrosamino-1-3-pyridyl-1-butanone (NNK) with its effects enhanced by co-exposure to the pro-inflammatory agent lipopolysaccharide (LPS). Lung DNA were screened for endogenous DNA adducts known to result from oxidative stress and LPS-induced lipid peroxidation, as well as for adducts due to NNK exposure. The relative quantitation of the detected DNA adducts was performed using parallel reaction monitoring MS2 analysis, demonstrating a general workflow for analysis of endogenous DNA adducts.

Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry.

The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.

Methods and Challenges for Computational Data Analysis for DNA Adductomics.

Frequent exposure to chemicals in the environment, diet, and endogenous electrophiles leads to chemical modification of DNA and the formation of DNA adducts. Some DNA adducts can induce mutations during cell division and, when occurring in critical regions of the genome, can lead to the onset of disease, including cancer. The targeted analysis of DNA adducts over the past 30 years has revealed that the human genome contains many types of DNA damages. However, a long-standing limitation in conducting DNA adduct measurements has been the inability to screen for the total complement of DNA adducts derived from a wide range of chemicals in a single assay. With the advancement of high-resolution mass spectrometry (MS) instrumentation and new scanning technologies, nontargeted "omics" approaches employing data-dependent acquisition and data-independent acquisition methods have been established to simultaneously screen for multiple DNA adducts, a technique known as DNA adductomics. However, notable challenges in data processing must be overcome for DNA adductomics to become a mature technology. DNA adducts occur at low abundance in humans, and current softwares do not reliably detect them when using common MS data acquisition methods. In this perspective, we discuss contemporary computational tools developed for feature finding of MS data widely utilized in the disciplines of proteomics and metabolomics and highlight their limitations for conducting nontargeted DNA-adduct biomarker discovery. Improvements to existing MS data processing software and new algorithms for adduct detection are needed to develop DNA adductomics into a powerful tool for the nontargeted identification of potential cancer-causing agents.

Analysis of methyl DNA adducts and metabolites in BEAS-2B cells induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone

The tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is classified as a Group 1 human carcinogen. It is metabolically activated by P450 enzymes to intermediate methylate and pyridyloxobutylate DNA, resulting in the formation of DNA adduct that is critical for the carcinogenicity of NNK. To directly and objectively examine the DNA adduct formation profiles without the complexity of factors in vivo, in the present study, five kinds of methyl DNA adducts were first identified in the incubation model of NNK established with human lung epithelial cells (BEAS-2B). The level of methyl DNA adducts and metabolites of NNK were quantitatively analyzed, respectively. With the increase of exposure time and dose, the level of methyl DNA adducts and metabolites increased. Furthermore, with the changes of the activity of P450 enzymes, which is the main enzyme regulating the α-hydroxylation of NNK, we found the levels of both methyl adducts and metabolites formed via α-hydroxylation in experimental groups showed the same trend compared with those in control group, while the metabolites formed via other pathways changed in the opposite trend. The result proves that the methyl adducts induced by NNK generate via α-hydroxylation pathway in BEAS-2B cells.

Adductomics: a promising tool for the verification of chemical warfare agents' exposures in biological samples.

Humans are constantly exposed to a wide range of reactive and toxic chemicals from the different sources in everyday life. Identification of the exposed chemical helps in the detection and understanding the exposure associated adverse health effects. Covalent adducts of proteins and DNA formed after xenobiotics exposure may serve as readily measurable indicators of these exposures. Measuring the exposed chemicals with focus on adducts resulting from the nucleophilic interactions with blood proteins is useful in the development of diagnostic markers. Particularly, the most abundant proteins such as albumin and hemoglobin acts as dominant scavengers for many reactive chemicals in blood and can serve as excellent diagnostic candidates to determine the type of chemical exposure. This review focuses on the potential application of an adductomics approach for the screening of bimolecular adducts of chemical warfare agents (CWAs). Recent incidents of CWAs use in Syria, Malaysia, and the UK illustrate the continuing threat of chemical warfare agents in the modern world. Detection of CWAs and their metabolites in blood or in other body fluids of victims depends on immediate access to victims. Concentrations of intact CWAs in body fluids of surviving victims may decline rapidly within a few days. Certain CWAs, particularly nerve agents and vesicants, form covalent bonds with certain amino acids to form CWA-protein adducts. Proteins that are abundant in the blood, including albumin and hemoglobin, may carry these adducts longer after the original exposure. We searched MEDLINE and ISI Web of Science databases using the key terms "adductomics" "adducts of CWAs," "CWAs adducts detection in the biological samples," "protein adducts of CWAs," alone and in combination with the keywords "detection" "intoxication" "exposure" "adverse effects" and "toxicity." We also included non-peer-reviewed sources such as text books, relevant newspaper reports, and applicable Internet resources. We screened bibliographies of identified articles for additional relevant studies including non-indexed reports. These searches produced 1931 citations of which only relevant and nonduplicate citations were considered for this review. The analysis of biomedical samples has several purposes including detecting and identifying the type of chemical agent exposed, understanding the biological mechanism, assists in giving adequate treatment, determining the cause of death and providing evidence in a court of justice for forensic investigations. Rapid advances in the mass spectrometry to acquire high-quality data with greater resolution enabled the analysis of protein and DNA adducts of xenobiotics including CWAs and place the rapidly advancing 'adductomics' next to the other "-omics" technologies. Adductomics can serve as a powerful bioanalytical tool for the verification of CWAs exposure. This review mostly describes the protein adducts for nerve agents and vesicants, outlines the procedures for measuring adducts, and suggests the evolving (or future) use of adducts in the detection and verification of CWAs.

Method for Biomonitoring DNA Adducts in Exfoliated Urinary Cells by Mass Spectrometry.

Tobacco smoking contributes to about 50% of the bladder-cancer (BC) cases in the United States. Some aromatic amines in tobacco smoke are bladder carcinogens; however, other causal agents of BC are uncertain. Exfoliated urinary cells (EUCs) are a promising noninvasive biospecimen to screen for DNA adducts of chemicals that damage the bladder genome, although the analysis of DNA adducts in EUCs is technically challenging because of the low number of EUCs and limiting quantity of cellular DNA. Moreover, EUCs and their DNA adducts must remain viable during the time of collection and storage of urine to develop robust screening methods. We employed RT4 cells, a well-differentiated transitional epithelial bladder cell line, as a cell-model system in urine to investigate cell viability and the chemical stability of DNA adducts of two prototypical bladder carcinogens: 4-aminobiphenyl (4-ABP), an aromatic amine found in tobacco smoke, and aristolochic acid I (AA-I), a nitrophenanthrene found in Aristolochia herbaceous plants used for medicinal purposes worldwide. The cell viability of RT4 cells pretreated with 4-ABP or AA-I in urine exceeded 80%, and the major DNA adducts of 4-ABP and AA-I, quantified by liquid chromatography-mass spectrometry, were stable for 24 h. Thereafter, we successfully screened EUCs of mice treated with AA-I to measure DNA adducts of AA-I, which were still detected 25 days following treatment with the carcinogen. EUCs are promising biospecimens that can be employed for the screening of DNA adducts of environmental and dietary genotoxicants that may contribute to the development of BC.

Abstract 3088: Deciphering components of mutational signatures arising from carcinogen co-exposures: A genome-scale experimental approach

Abstract Pan-cancer analyses of tumor genomes reveal mutational signatures characteristic of particular etiologic factors. The signatures are extracted mathematically from mixed patterns typically observed by tumor sequencing. However, the components of signatures originating from complex carcinogen mixtures have not been studied in detail. Lung, head and neck and liver tumors of tobacco smokers exhibit COSMIC signature 4 marked by predominant G>N mutations, involving mainly G:C>T:A transversions with transcription strand bias, consistent with the mutagenic effects of benzo[a]pyrene (B[a]P). Additionally, A>N mutations (strand-biased A:T>T:A transversions and A:T>G:C transitions) are also prominently present, yet their origins are less understood. By using exposure-coupled clonal immortalization of human and mouse primary cells and deep sequencing, we were able to dissect ‘clean' mutational signatures of tobacco smoke carcinogens B[a]P and glycidamide (GA), a key reactive metabolite of acrylamide (ACR). Whole-genome sequencing of multiple clones derived from primary B[a]P-treated human mammary epithelial cells identified a robust mutational signature marked by strand-biased G>N mutations and increased GG>TT dinucleotides, while no apparent enrichment of A:T>T:A mutations was observed. Next, in ACR and GA-treated primary mouse embryonic fibroblasts, we established by the LC-MS/MS DNA adduct analysis that ACR exerts its mutagenic effects exclusively via GA. We then extracted from 15 treated clones the exome-scale mutational signature of GA, marked by predominant A:T>T:A transversions followed by A:T>G:C transitions and G:C>T:A transversions, all showing transcription strand bias. Similarity analysis involving known primary-cancer and experimental mutational signatures indicated that the GA mutational signature was novel. A more in-depth comparison with mutation patterns from lung adenocarcinomas of heavy smokers revealed that the GA signature, including its strand bias features, matched closely with and may thus account for the A>N mutation component of the tobacco smoking-derived signature 4. Thus, mutational signatures generated in controlled experimental settings may explain particular sub-features of cancer signatures arising from co-exposures to multiple carcinogens. Furthermore, the use of innovative in vitro systems, characterized by biological barrier bypass to mimic early steps of cell transformation, can provide revealing insights into the molecular links between mutagenesis and carcinogenesis. Funding: INCa-INSERM Plan Cancer 2015; NIH/NIEHS 1R03ES025023-01A1 Citation Format: Manuraj Pandey, Maria Zhivagui, Mona I. Churchwell, Alvin W. Ng, Liacine Bouaoun, Vincent Cahais, Martha R. Stampfer, Magali Olivier, Zdenko Herceg, Ewy Mathé, Steven G. Rozen, Frederick A. Beland, Michael Korenjak, Jiri Zavadil. Deciphering components of mutational signatures arising from carcinogen co-exposures: A genome-scale experimental approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3088.

A Rapid Throughput Method To Extract DNA from Formalin-Fixed Paraffin-Embedded Tissues for Biomonitoring Carcinogenic DNA Adducts.

Formalin-fixed paraffin-embedded (FFPE) tissues are rarely used for screening DNA adducts of carcinogens because the harsh conditions required to reverse the formaldehyde-mediated DNA cross-links can destroy DNA adducts. We recently adapted a commercial silica-based column kit used in genomics to manually isolate DNA under mild conditions from FFPE tissues of rodents and humans and successfully measured DNA adducts of several carcinogens including aristolochic acid I (AA-I), 4-aminobiphenyl (4-ABP), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) (Yun et al. (2013) Anal. Chem. 85, 4251-8, and Guo et al. (2016) Anal. Chem. 88, 4780-7). The DNA retrieval methodology is robust; however, the procedure is time-consuming and labor intensive, and not amenable to rapid throughput processing. In this study, we have employed the Promega Maxwell 16 MDx system, which is commonly used in large scale genomics studies, for the rapid throughput extraction of DNA. This system streamlines the DNA isolation procedure and increases the sample processing rate by about 8-fold over the manual method (32 samples versus 4 samples processed per hour). High purity DNA is obtained in satisfactory yield for the measurements of DNA adducts by ultra performance liquid chromatography-electrospray-ionization-ion trap-multistage scan mass spectrometry. The measurements show that the levels of DNA adducts of AA-I, 4-ABP, and PhIP in FFPE rodent and human tissues are comparable to those levels measured in DNA from matching tissues isolated by the commercial silica-based column kits and in DNA from fresh frozen tissues isolated by the conventional phenol-chloroform extraction method. The isolation of DNA from tissues is one major bottleneck in the analysis of DNA adducts. This rapid throughput methodology greatly decreases the time required to process DNA and can be employed in large-scale epidemiology studies designed to assess the role of chemical exposures and DNA adducts in cancer risk.

Abstract 382: Genome-wide location analysis of DNA adducts in vivo

Abstract DNA adducts are the biochemical consequences of exposure to UV light, carcinogens or DNA-reactive drugs. They play a central role in malignant transformation and the selective killing of cancer cells by chemotherapeutic agents. The functional consequences of DNA adducts is likely to depend on their exact location in the genome with respect to histones and sites where histones and DNA are modified. However, tools that permit precise genome-wide mapping of adduct locations have poor resolution or are too specific to the type of DNA-adduct. Here we present the development of a molecular assay (Ad-Seq) capable of identifying the genomic location of damaged DNA bases in whole cells. Using naked DNA treated with cisplatin (cDDP) or ultra-violet (UV) light as the damaging agents, the strategy relies on differential exonuclease digestion to enrich genome-wide libraries for fragments containing DNA adducts, followed by high-throughput sequencing. Consistent with the expected adduct chemistry, the 5’ end of the reads were enriched in TT, TC or CT di-nucleotides in the UV treated DNA (>4x) and in AG or GG in the cDDP treated DNA (1.5x), suggesting a positive predictive value of 76% and 44% and UV (TT) and cDDP (GG) adduct detection, respectively. Applied in vivo to IMR90 cells, Ad-Seq revealed that the fraction of AG/GG loci was higher in DNA from the cDDP-treated cells at all coverage depths, reaching 1.5x enrichment for the highest depth quartile. This indicates that the method is selective and that even low covered loci show enrichment of AG/GG sequences. The enrichment in purines was limited to 3 nucleotides downstream of the read start site, confirming the high resolution of the exonuclease digestion. A total of 11 x 103 AG/GG loci were identified in replicate in cDDP-treated samples and were absent from untreated controls. With about 60 x103 expected adducts per genome, the current assay therefore captured up to 18% of cDDP adducts. The most covered adduct sites were significantly enriched in the quiescent chromatin domains (depleted of histone modifications, p=6.7x10-31), and depleted in the transcription start sites (p=4.9x10-12), as defined by the ENCODE consortium. This may be reflective of the differences in DNA accessibility or the mechanisms of repair in these distinct regions of the genome. The analysis was performed using the PipeDuct computational package, which was developed to align the sequencing reads and provide general statistics and quality control information of Ad-Seq data. Ad-Seq is therefore a novel, unbiased method to map DNA-adducts and study in vivo the genome-wide specificity of their formation and repair. Citation Format: Brian Woo, Christopher Fang, Paolo Abada, Stephen B. Howell, Olivier Harismendy. Genome-wide location analysis of DNA adducts in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 382. doi:10.1158/1538-7445.AM2017-382

Time-matched analysis of DNA adduct formation and early gene expression as predictive tool for renal carcinogenesis in methylazoxymethanol acetate treated Eker rats.

Genotoxic carcinogens pose great hazard to human health. Uncertainty of current risk assessment strategies and long latency periods between first carcinogen exposure and diagnosis of tumors have raised interest in predictive biomarkers. Initial DNA adduct formation is a necessary step for genotoxin induced carcinogenesis. However, as DNA adducts not always translate into tumorigenesis, their predictive value is limited. Here we hypothesize that the combined analysis of pro-mutagenic DNA adducts along with time-matched gene expression changes could serve as a superior prediction tool for genotoxic carcinogenesis. Eker rats, heterozygous for the tuberous sclerosis (Tsc2) tumor suppressor gene and thus highly susceptible towards genotoxic renal carcinogens, were continuously treated with the DNA alkylating carcinogen methylazoxymethanol acetate (MAMAc). Two weeks of MAMAc treatment resulted in a time-dependent increase of O6-methylguanine and N7-methylguanine adducts in the kidney cortex, which was however not reflected by significant expression changes of cyto-protective genes involved in DNA repair, cell cycle arrest or apoptosis. Instead, we found a transcriptional regulation of genes involved in the tumor-related MAPK, FoxO and TGF-beta pathways. Continuous MAMAc treatment for up to 6months resulted in a mild but significant increase of cancerous lesions. In summary, the combined analysis of DNA adducts and early gene expression changes could serve as a suitable predictive tool for genotoxicant-induced carcinogenesis.

P1.01-012 Kava Effects on the Metabolism of Tobacco-Specific Carcinogen 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanone (NNK) in Humans

Kava is extracted from the roots of piper methysticum and is consumed by South Pacific Islanders as a relaxing beverage. Epidemiologic evidence points to a protective effect of kava against tobacco-induced lung cancer. NNK is a potent tobacco-specific carcinogen indisputably linked to lung cancer formation. Kava reduced NNK-induced lung adenoma formation in the A/J mouse model. Data also suggest that enhanced NNAL detoxification may be a potential mechanism by which kava exerts a chemopreventive effect. In humans, urinary NNAL is a validated biomarker of NNK uptake. We conducted a clinical trial in smokers to assess the effect of kava on NNK metabolism. The primary objective was to compare urinary total NNAL before and after kava administration. Secondary objectives included comparing the NNAL-gluc/NNAL-free ratio, determining the safety of kava, and quantifying O6-methylguanine adducts. The hypothesis was that kava administration would result in increased levels of NNAL in the urine (and increased NNAL-gluc/NNAL-free ratio), reflecting increased elimination and/or increased detoxification of NNK. Additionally, we hypothesized that kava could reduce O6-methylguanine adducts. We conducted a single-arm, open-label clinical trial in adult healthy smokers, in which subjects took a commercial kava supplement three times daily for seven days. Twenty-four hour urine collections were collected at baseline, days 4-5, and days 6-7 of the kava intervention for NNAL quantification. Blood samples were collected at baseline, day 4, and day 7 of the kava intervention for safety monitoring and for DNA adduct analysis. Subjects also completed a detailed tobacco questionnaire, food diary, smoking diary, and cigarette evaluation scale (CES) questionnaire. To date, 17 subjects (goal = 18) have completed the study. The results and statistics are being finalized. Short-term kava administration was safe with no evidence of hepatotoxicity. Subjects experienced less of the reinforcing effects of smoking after short-term kava administration as determined by the CES scores. The total CES score decreased on average by 4.47, from 45.53 to 41.06 (p=0.053, 95% CI -0.06-9.01). Notably, the smoking “satisfaction” scores decreased by 0.607 (p=0.024, 95% CI 0.09-1.12). This is the first study investigating the effect of kava on NNK metabolism in humans and is the first step to gain a more sophisticated mechanistic understanding of kava’s role in potentially modulating tobacco-related lung cancer risk. Short-term kava administration is safe in healthy adult smokers. Kava holds potential as a possible chemopreventive agent for smokers or tobacco cessation aide.

S - and N-alkylating agents diminish the fluorescence of fluorescent dye-stained DNA

Sulfur mustard (SM), a chemical warfare agent, causes DNA alkylation, which is believed to be the main cause of its toxicity. SM DNA adducts are commonly used to verify exposure to this vesicant. However, the required analytical state-of-the-art mass-spectrometry methods are complex, use delicate instruments, are not mobile, and require laboratory infrastructure that is most likely not available in conflict zones. Attempts have thus been made to develop rapid detection methods that can be used in the field. The analysis of SM DNA adducts (HETE-G) by immunodetection is a convenient and suitable method. For a diagnostic assessment, HETE-G levels must be determined in relation to the total DNA in the sample. Total DNA can be easily visualized by the use of fluorescent DNA dyes. This study examines whether SM and related compounds affect total DNA staining, an issue that has not been investigated before. After pure DNA was extracted from human keratinocytes (HaCaT cells), DNA was exposed to different S- and N-alkylating agents. Our experiments revealed a significant, dose-dependent decrease in the fluorescence signal of fluorescent dye-stained DNA after exposure to alkylating agents. After mass spectrometry and additional fluorescence measurements ruled out covalent modifications of ethidium bromide (EthBr) by SM, we assumed that DNA crosslinks caused DNA condensation and thereby impaired access of the fluorescent dyes to the DNA. DNA digestion by restriction enzymes restored fluorescence, a fact that strengthened our hypothesis. However, monofunctional agents, which are unable to crosslink DNA, also decreased the fluorescence signal. In subsequent experiments, we demonstrated that protons produced during DNA alkylation caused a pH decrease that was found responsible for the reduction in fluorescence. The use of an appropriate buffer system eliminated the adverse effect of alkylating agents on DNA staining with fluorescent dyes. An appropriate buffer system is thus crucial for DNA quantification with fluorescent dyes in the presence of alkylating compounds.

Optimized Liquid Chromatography Nanoelectrospray-High-Resolution Tandem Mass Spectrometry Method for the Analysis of 4-Hydroxy-1-(3-pyridyl)-1-butanone-Releasing DNA Adducts in Human Oral Cells.

Metabolic activation of the carcinogenic tobacco-specific N-nitrosamines leads to the formation of 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB)-releasing DNA adducts. We recently developed a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) method for the analysis of HPB-releasing DNA adducts in human oral cells. However, given the limited amounts of DNA that can be extracted from oral cells, higher sensitivity and selectivity are required for the reliable analysis of these adducts in future studies. We have developed a new sensitive LC-nanoelectrospray ionization-high-resolution MS/MS method for the analysis of HPB-releasing DNA adducts in oral cells. A new procedure was also developed for guanine analysis by LC-MS/MS. The detection limit of the developed assay is 5 amol, and the limit of quantitation is 0.35 fmol HPB on-column, starting with 50 pg of DNA. The method was tested by analyzing oral samples from 65 smokers, including 30 head and neck squamous cell carcinoma (HNSCC) patients and 35 cancer-free controls. In all smokers, the levels of HPB-releasing DNA adducts averaged 6.22 ± 16.18 pmol/mg DNA, with significant interindividual variation being consistent with previous reports. The median HPB-releasing DNA adduct level was 6.6 times greater for those with HNSCC than for smokers without HNSCC (p = 0.002). The developed highly sensitive and selective method is a valuable tool for future measurement of HPB-releasing DNA adducts in tobacco users, which can potentially provide critical insights for the identification of individuals at risk for cancer.

Mass Spectrometric Mapping of the DNA Adductome as a Means to Study Genotoxin Exposure, Metabolism, and Effect.

Covalent binding of endo- or exogenous chemicals to DNA results in the formation of DNA adducts which are reflective of exposure of the human body to DNA-damaging molecules and their metabolic pathways. The study of DNA adduct types and levels in human tissue therefore offers an interesting tool in several fields of research, including toxicology and cancer epidemiology. Over the years, a range of techniques and methods have been developed to study the formation of endo- and exogenous DNA adducts. However, for the simultaneous detection, identification and quantification of both known and unknown DNA adducts, mass spectrometry (MS) is deemed to be the most promising technique. In this perspective, we focus on the analysis of multiple DNA adducts within a sample with the emphasis on untargeted analysis. The advantageous use of MS methodologies for DNA adductome mapping is discussed comprehensively with relevant field examples. In addition, several aspects of study design, sample pretreatment, and analysis are addressed as these factors significantly affect the reliability of DNA adductomics studies.

Liquid chromatography-mass spectrometry as a general approach for investigating covalent binding of drugs to DNA.

This paper aims at developing a general strategy to study the detection of adducts of drugs with DNA. In particular, ethacrynic acid has been chosen as a model reactive drug that could be able to bind covalently to DNA bases. Such interactions were detected by ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). Principal component analysis (PCA) was applied as an unsupervised method to try to find the potential candidate adduct from MS features. The occurrence of adducts was investigated preliminarily using deoxynucleosides of the guanine, cytosine, adenine, and thymine separately as a way to optimize both separation and detection conditions. Interpretations of MS and MS/MS spectra provided tentative structures of the compounds formed. Conclusions extracted from such simple nucleoside models were further extended to the analysis of DNA adducts. For such a purpose, DNA was incubated in the presence of ethacrynic acid under appropriate experimental conditions and its further enzymatic hydrolysis released the corresponding nucleosides. UHPLC-MS analysis of the resulting test samples under the SRM detection mode confirmed the presence of ethacrynic acid derivatives of nucleosides occurring at very low concentration levels, thus proving the overall performance of the method. Graphical Abstract General approach for investigating drug-DNA adduct formation.

Identification of cancer chemopreventive isothiocyanates as direct inhibitors of the arylamine N-acetyltransferase-dependent acetylation and bioactivation of aromatic amine carcinogens.

Aromatic amines (AAs) are chemicals of industrial, pharmacological and environmental relevance. Certain AAs, such as 4-aminobiphenyl (4-ABP), are human carcinogens that require enzymatic metabolic activation to reactive chemicals to form genotoxic DNA adducts. Arylamine N-acetyltransferases (NAT) are xenobiotic metabolizing enzymes (XME) that play a major role in this carcinogenic bioactivation process. Isothiocyanates (ITCs), including benzyl-ITC (BITC) and phenethyl-ITC (PEITC), are phytochemicals known to have chemopreventive activity against several aromatic carcinogens. In particular, ITCs have been shown to modify the bioactivation and subsequent mutagenicity of carcinogenic AA chemicals such as 4-ABP. However, the molecular and biochemical mechanisms by which these phytochemicals may modulate AA carcinogens bioactivation and AA-DNA damage remains poorly understood.This manuscript provides evidence indicating that ITCs can decrease the metabolic activation of carcinogenic AAs via the irreversible inhibition of NAT enzymes and subsequent alteration of the acetylation of AAs. We demonstrate that BITC and PEITC react with NAT1 and inhibit readily its acetyltransferase activity (ki = 200 M−1.s−1 and 66 M−1.s−1 for BITC and PEITC, respectively). Chemical labeling, docking approaches and substrate protection assays indicated that inhibition of the acetylation of AAs by NAT1 was due to the chemical modification of the enzyme active site cysteine. Moreover, analyses of AAs acetylation and DNA adducts in cells showed that BITC was able to modulate the endogenous acetylation and bioactivation of 4-ABP. In conclusion, we show that direct inhibition of NAT enzymes may be an important mechanism by which ITCs exert their chemopreventive activity towards AA chemicals.

Tracking matrix effects in the analysis of DNA adducts of polycyclic aromatic hydrocarbons

LC–MS using electrospray ionization is currently the method of choice in bio-organic analysis covering a wide range of applications in a broad spectrum of biological media. The technique is noted for its high sensitivity but one major limitation that hinders achievement of its optimal sensitivity is the signal suppression due to matrix inferences introduced by the presence of co-extracted compounds during the sample preparation procedure. The analysis of DNA adducts of common environmental carcinogens is particularly sensitive to such matrix effects as sample preparation is a multistep process which involves “contamination” of the sample due to the addition of enzymes and other reagents for digestion of the DNA in order to isolate the analyte(s). This problem is further exacerbated by the need to reach low levels of quantitation (LOQ in the ppb level) while also working with limited (2–5μg) quantities of sample. We report here on the systematic investigation of ion signal suppression contributed by each individual step involved in the sample preparation associated with the analysis of DNA adducts of polycyclic aromatic hydrocarbon (PAH) using as model analyte BaP-dG, the deoxyguanosine (dG) adduct of benzo[a]pyrene (BaP). The individual matrix contribution of each one of these sources to analyte signal was systematically addressed as were any interactive effects. The information was used to develop a validated analytical protocol for the target biomarker at levels typically encountered in vivo using as little as 2μg of DNA and applied to a dose response study using a metabolically competent cell line.

Comprehensive DNA adduct analysis reveals pulmonary inflammatory response contributes to genotoxic action of magnetite nanoparticles.

Nanosized-magnetite (MGT) is widely utilized in medicinal and industrial fields; however, its toxicological properties are not well documented. In our previous report, MGT showed genotoxicity in both in vitro and in vivo assay systems, and it was suggested that inflammatory responses exist behind the genotoxicity. To further clarify mechanisms underlying the genotoxicity, a comprehensive DNA adduct (DNA adductome) analysis was conducted using DNA samples derived from the lungs of mice exposed to MGT. In total, 30 and 42 types of DNA adducts were detected in the vehicle control and MGT-treated groups, respectively. Principal component analysis (PCA) against a subset of DNA adducts was applied and several adducts, which are deduced to be formed by inflammation or oxidative stress, as the case of etheno-deoxycytidine (εdC), revealed higher contributions to MGT exposure. By quantitative-LC-MS/MS analysis, εdC levels were significantly higher in MGT-treated mice than those of the vehicle control. Taken together with our previous data, it is suggested that inflammatory responses might be involved in the genotoxicity induced by MGT in the lungs of mice.

Acrylamide induces specific DNA adduct formation and gene mutations in a carcinogenic target site, the mouse lung.

Acrylamide (AA) is a contaminant in heated foods and is carcinogenic in multiple organs of rodents. There have been many reports regarding AA-induced DNA modification and genotoxicity. However, the data are insufficient to understand fully the relationship between the two events. A recent report demonstrated carcinogenicity in the mouse lung. The lung is advantageous for investigation of AA-induced genotoxicity because DNA adduct levels are relatively high in this organ. In the present study, reporter gene mutation assays and quantitative analyses of specific DNA adducts were performed in the lungs of mature gpt delta mice treated with AA at doses of 100, 200 and 400 p.p.m. in drinking water for 4 weeks. N7-GA-Gua was detected in all AA-treated mice in a dose-dependent manner. gpt mutant frequencies (MFs) were significantly increased in the middle- and high-dose groups. In the analysis of mutation spectra, significant increases in GC-TA transversions and single base deletion mutations were observed in the high-dose group. Spi(-) MFs were significantly increased in the high-dose group. Analysis of Spi(-) mutants revealed significant increases in the frequencies of single base deletion mutation in runs of G/C and A/T. Analyses of immature mice under the same experimental conditions showed that there were no differences of susceptibility to AA-induced genotoxicity in the two age classes. The overall data clearly show the causal relationship between AA-induced DNA adducts and the gene mutations at carcinogenic target sites.

Erratum to: NanoLC/ESI+ HRMS3 Quantitation of DNA Adducts Induced by 1,3-Butadiene

Human exposure to 1,3-butadiene (BD) present in automobile exhaust, cigarette smoke, and forest fires is of great concern because of its potent carcinogenicity. The adverse health effects of BD are mediated by its epoxide metabolites such as 3,4-epoxy-1-butene (EB), which covalently modify genomic DNA to form promutagenic nucleobase adducts. Because of their direct role in cancer, BD-DNA adducts can be used as mechanism-based biomarkers of BD exposure. In the present work, a mass spectrometry-based methodology was developed for accurate, sensitive, and precise quantification of EB-induced N-7(1-hydroxy-3-buten-2-yl) guanine (EB-GII) DNA adducts in vivo. In our approach, EB-GII adducts are selectively released from DNA backbone by neutral thermal hydrolysis, followed by ultrafiltration, offline HPLC purification, and isotope dilution nanoLC/ESI-HRMS analysis on an Orbitrap Velos mass spectrometer. Following method validation, EB-GII lesions were quantified in human fibrosarcoma (HT1080) cells treated with micromolar concentrations of EB and in liver tissues of rats exposed to sub-ppm concentrations of BD (0.5–1.5 ppm). EB-GII concentrations increased linearly from 1.15±0.23 to 10.11±0.45 adducts per 10 nucleotides in HT1080 cells treated with 0.5–10 μM EB. EB-GII concentrations in DNA of laboratory rats exposed to 0.5, 1.0, and 1.5 ppm BD were 0.17±0.05, 0.33±0.08, and 0.50±0.04 adducts per 10 nucleotides, respectively. We also used the new method to determine the in vivo half-life of EB-GII adducts in rat liver DNA (2.20±0.12 d) and to detect EB-GII in human blood DNA. To our knowledge, this is the first application of nanoLC/ESI-HRMS Orbitrap methodology to quantitative analysis of DNA adducts in vivo. The online version of the original article can be found at http://dx.doi.org/ 10.1007/s13361-014-0916-x. Correspondence to: Natalia Tretyakova; e-mail: trety001@umn.edu Published online: 4 July 2014