Development of fast atom bombardment mass spectral methods for the identification of carcinogen-nucleoside adducts

Genotoxic C8-Arylamino-2'-deoxyadenosines Act as Latent Alkylating Agents to Induce DNA Interstrand Cross-Links

DNA interstrand cross-links (ICLs) are extremely deleterious and structurally diverse, driving the evolution of ICL repair pathways. Discovering ICL-inducing agents is, thus, crucial for the characterization of ICL repair pathways and Fanconi anemia, a genetic disease caused by mutations in ICL repair genes. Although several studies point to oxidative stress as a cause of ICLs, oxidative stress-induced cross-linking events remain poorly characterized. Also, polycyclic aromatic amines, potent environmental carcinogens, have been implicated in producing ICLs, but their identities and sequences are unknown. To close this knowledge gap, we tested whether ICLs arise by the oxidation of 8-arylamino-2'-deoxyadenosine (ArNHdA) lesions, adducts produced by arylamino carcinogens. Herein, we report that ArNHdA acts as a latent cross-linking agent to generate ICLs under oxidative conditions. The formation of an ICL from 8-aminoadenine, but not from 8-aminoguanine, highlights the specificity of 8-aminopurine-mediated ICL production. Under the influence of the reactive oxygen species (ROS) nitrosoperoxycarbonate, ArNHdA (Ar = biphenyl, fluorenyl) lesions were selectively oxidized to generate ICLs. The cross-linking reaction may occur between the C2-ArNHdA and N2-dG, presumably via oxidation of ArNHdA into a reactive diiminoadenine intermediate followed by the nucleophilic attack of the N2-dG on the diiminoadenine. Overall, ArNHdA-mediated ICLs represent rare examples of ROS-induced ICLs and polycyclic aromatic amine-mediated ICLs. These results reveal novel cross-linking chemistry and the genotoxic effects of arylamino carcinogens and support the hypothesis that C8-modified adenines with low redox potential can cause ICLs in oxidative stress.

Extension of Diagnostic Fragmentation Filtering for Automated Discovery in DNA Adductomics

Development of high-resolution/accurate mass liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) methodology enables the characterization of covalently modified DNA induced by interaction with genotoxic agents in complex biological samples. Constant neutral loss monitoring of 2'-deoxyribose or the nucleobases using data-dependent acquisition represents a powerful approach for the unbiased detection of DNA modifications (adducts). The lack of available bioinformatics tools necessitates manual processing of acquired spectral data and hampers high throughput application of these techniques. To address this limitation, we present an automated workflow for the detection and curation of putative DNA adducts by using diagnostic fragmentation filtering of LC-MS/MS experiments within the open-source software MZmine. The workflow utilizes a new feature detection algorithm, DFBuilder, which employs diagnostic fragmentation filtering using a user-defined list of fragmentation patterns to reproducibly generate feature lists for precursor ions of interest. The DFBuilder feature detection approach readily fits into a complete small-molecule discovery workflow and drastically reduces the processing time associated with analyzing DNA adductomics results. We validate our workflow using a mixture of authentic DNA adduct standards and demonstrate the effectiveness of our approach by reproducing and expanding the results of a previously published study of colibactin-induced DNA adducts. The reported workflow serves as a technique to assess the diagnostic potential of novel fragmentation pattern combinations for the unbiased detection of chemical classes of interest.

Emerging Technologies in Mass Spectrometry-Based DNA Adductomics

The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2′-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.

The Future of DNA Adductomic Analysis

Covalent modification of DNA, resulting in the formation of DNA adducts, plays a central role in chemical carcinogenesis. Investigating these modifications is of fundamental importance in assessing the mutagenicity potential of specific exposures and understanding their mechanisms of action. Methods for assessing the covalent modification of DNA, which is one of the initiating steps for mutagenesis, include immunohistochemistry, ³²P-postlabeling, and mass spectrometry-based techniques. However, a tool to comprehensively characterize the covalent modification of DNA, screening for all DNA adducts and gaining information on their chemical structures, was lacking until the recent development of "DNA adductomics". Advances in the field of mass spectrometry have allowed for the development of this methodology. In this perspective, we discuss the current state of the field, highlight the latest developments, and consider the path forward for DNA adductomics to become a standard method to investigate covalent modification of DNA. We specifically advocate for the need to take full advantage of this new era of mass spectrometry to acquire the highest quality and most reliable data possible, as we believe this is the only way for DNA adductomics to gain its place next to the other "-omics" methodologies as a powerful bioanalytical tool.

Quantitation of DNA adducts by stable isotope dilution mass spectrometry

Exposure to endogenous and exogenous chemicals can lead to the formation of structurally modified DNA bases (DNA adducts). If not repaired, these nucleobase lesions can cause polymerase errors during DNA replication, leading to heritable mutations and potentially contributing to the development of cancer. Because of their critical role in cancer initiation, DNA adducts represent mechanism-based biomarkers of carcinogen exposure, and their quantitation is particularly useful for cancer risk assessment. DNA adducts are also valuable in mechanistic studies linking tumorigenic effects of environmental and industrial carcinogens to specific electrophilic species generated from their metabolism. While multiple experimental methodologies have been developed for DNA adduct analysis in biological samples, including immunoassay, HPLC, and ³²P-postlabeling, isotope dilution high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) generally has superior selectivity, sensitivity, accuracy, and reproducibility. As typical DNA adduct concentrations in biological samples are between 0.01-10 adducts per 10⁸ normal nucleotides, ultrasensitive HPLC-ESI-MS/MS methodologies are required for their analysis. Recent developments in analytical separations and biological mass spectrometry, especially nanoflow HPLC, nanospray ionization MS, chip-MS, and high resolution MS, have pushed the limits of analytical HPLC-ESI-MS/MS methodologies for DNA adducts, allowing researchers to accurately measure their concentrations in biological samples from patients treated with DNA alkylating drugs and in populations exposed to carcinogens from urban air, drinking water, cooked food, alcohol, and cigarette smoke.

Genotoxicity sensor response correlated with DNA nucleobase damage rates measured by LC-MS

Responses from "reagentless" DNA-based electrochemical toxicity sensors to DNA alkylating agents styrene oxide (SO), diepoxybutane (DEB), and methyl methanesulfonate (MMS) were compared to formation rates of total alkylated nucleobases in DNA measured by LC-UV-MS. Sensors utilized a catalytic metallopolymer in DNA films previously exposed to the damage agents. To achieve adequate sensitivity, LC-UV-MS analyses were done on DNA in solution reacted with the damage agents, and subsequently hydrolyzed to nucleosides with enzymes. Sensor response correlated well with nucleobase-adduct formation rates obtained by the molecule-specific analyses. Results confirm that the metallopolymer-DNA film sensors can be used to estimate relative DNA damage rates from nucleobase adduct-forming chemicals. Results from both methods correlated well with animal genotoxicity as estimated by TDL(o) values, the lowest dose producing carcinogenicity, in mice and rats. These sensors should be useful for rapid, inexpensive screening of moderately and severely genotoxic new chemicals.

Differentiation of isomeric C8-substituted alkylaniline adducts of guanine by electrospray ionization and tandem quadrupole ion trap mass spectrometry

Product ion spectra from thirteen C8-substituted alkylaniline adducts of guanine and deoxyguanosine were generated using electrospray ionization and quadrupole ion trap mass spectrometry and studied to investigate the possibility of differentiating isomeric adduct structures based upon the relative abundances of fragment ions derived from the alkylaniline-modified guanine bases (BH2(+) ions). The structural discrimination of the BH2(+) ions formed by attachment of isomeric alkylanilines to the C8 position of guanine is a challenging problem because the ions tend to yield product ion spectra that are qualitatively identical upon collisional activation. In this study, a statistical method, referred to as a similarity index, was used to compare the product ion spectra of isomeric BH2(+) ions and differentiate their structures. All the adducts investigated could be distinguished from SIs calculated using 5-6 product ions. These results suggest that a searchable database of product ion spectra may be created and used to characterize DNA adducts from aromatic amines whenever they are detected at levels amenable to mass spectral analysis.

Measurement of 8-oxo-2'-deoxyguanosine and 8-oxo-2'-deoxyadenosine in DNA and human urine by high performance liquid chromatography-electrospray tandem mass spectrometry

A method for the determination of 8-oxo-2'-deoxyguanosine and 8-oxo-2'-deoxyadenosine in DNA and urine by High Performance Liquid Chromatography (HPLC)-Tandem Mass Spectrometry is described. For the urine samples there is no sample preparation except for addition of buffer and internal standards followed by redissolvation of precipitate containing 8-oxo-2'-deoxyguanosine and a centrifugation step before the samples are injected onto the HPLC column. The detection limit for 8-oxo-2'-deoxyguanosine and 8-oxo-2'-deoxyadenosine is approximately 0.3 nM corresponding to 7.5 fmol injected. Long runs, that is, > 50 samples, can be analyzed with only minimal loss of sensitivity. The concentrations excreted into urine samples from humans are between 1 and 100 nM for 8-oxo-2'-deoxyguanosine and below 0.3 nM for 8-oxo-2'-deoxyadenosine. In calf thymus DNA levels down to about 1 oxidized guanosine and adenosine per 10(6) unmodified bases can be detected. High levels of 8-oxo-2'-deoxyguanosine were found, 30 per 10(6) 2'-deoxyguanosine, levels of 8-oxo-2'-deoxyadenosine are at or below the detection limit. These findings indicate that High Performance Liquid Chromatography-Tandem Mass Spectrometry is a highly sensitive and specific method for analysis of oxidative DNA modifications in tissue as well as for analysis of excretion of oxidized nucleotides into urine that ensures a minimum artifact formation.

New syntheses of DNA adducts from methylated anilines present in tobacco smoke

A new synthetic pathway for the formation of deoxyguanosine-monoarylamine adducts is described, involving the generation and use of arylnitrenes as electrophilic synthons. Photolysis of aryl azides, the most common method for generating arylnitrenes, was tested in the presence of 2'-deoxyguanosine. N-(2'-Deoxyguanosin-8-yl)monoarylamine (dG-C8-Ar) adducts were obtained, but the yields were typically low. Deoxygenation of nitro- and nitrosoarenes by triethyl phosphite in the presence of 2'-deoxyguanosine proved to be an effective method, by which dG-C8-Ar, (2'-deoxyguanosin-N1-yl)monoarylamine (dG-N1-Ar), and (2'-deoxyguanosin-O(6)-yl)monoarylamine (dG-O(6)-Ar) adducts were obtained in acceptable yields.

High-performance liquid chromatography/electrospray mass spectrometry for the analysis of modified bases in DNA: 7-(2-hydroxyethyl)guanine, the major ethylene oxide-DNA adduct

A method was developed for the analysis of 7-(2-hydroxyethyl)guanine (7HEG), the major DNA adduct formed after exposure to ethylene oxide (EO). The method is based on DNA neutral thermal hydrolysis, adduct micro-concentration, and final characterization and quantification by HPLC coupled to single-ion monitoring electrospray mass spectrometry (HPLC/SIR-ESMS). The method was found to be selective, sensitive, and easy to handle with no need for enzymatic digestion or previous sample derivatization. Detection limit was found to be close to 1 fmol of adduct injected (10(-10) M), thus allowing the detection of approximately three modified bases on 10(8) intact nucleotides in blood sample analysis. Quantification results are shown for 7HEG after calf thymus DNA and blood exposure to various doses of EO, in both cases obtaining clear dose-response relationships.

Identifying and testing of signatures for non-volatile biomolecules using tandem mass spectra

Identification of volatile and semi-volatile molecules using traditional electron ionization mass spectrometry has been successful. The major contributor to this success is the reproduceability of the mass spectra, which allow identification of components based on comparison of fragmentation patterns within very large databases. However, this approach is not useful for the identification of typical nonvolatile biomolecules. Tandem mass spectrometry with collision induced dissociation (CID) has the potential to provide structure-specific fragmentation from non-volatile biomolecules.The recognition of these molecules based on CID is not an easy task, since the spectra generated for a given molecule are not as reproducible as in traditional electron ionization mass spectrometry. Also, the rules governing the formation of CID produced ions are not completely understood.In this study we investigate the use of the Kohonen Self-Organized Mapping (SOM) neural network to generate and test signatures (fragmentation patterns) for a given set of non-volatile biomolecules using spectra generated by tandem mass spectrometry with CID. The signatures then may be used as a discriminator for identifying unknown non-volatile biomolecules.

Low energy tandem mass spectrometry of deoxynucleoside adducts of polycyclic aromatic hydrocarbon dihydrodiol-epoxides

The use of fast-atom bombardment ionization-tandem mass spectrometry approaches, with collision energies on the order of 30-50 eV, was developed for the analysis of low picomole quantities of polycyclic aromatic hydrocarbon dihydrodiol-epoxide deoxynucleoside adducts. This strategy combines three experimental techniques: (1) product ion scans, (2) constant neutral loss scans, and (3) precursor ion scans. Product ion scans of the protonated molecule or the BH 2 (+) ion that results from loss of the deoxyribose were dominated by fragments associated with cleavage of the sigma bond between the dihydrodiol-epoxide moiety and the nucleobase. Constant neutral loss scans were based upon the loss of deoxyribose (116 u) or the combined loss of the deoxynucleoside, water, and carbon monoxide (313 u); precursor ion scans utilized the latter fragment. The formation of trimethylsilyl derivatives increased the sensitivity of analysis, which allowed the simultaneous detection of DNA adducts in a mixture.

Differentiation of isomeric C8- and N (2)-deoxyguanosine adducts of 2-acetylaminofluorene by fast-atom bombardment and tandem mass spectrometry

Product-ion studies of source-produced ions corresponding to acetylated and nonacetylated N (2)- and C8-substituted aminofluorene adducts of deoxyguanosine were conducted to identify specific fragmentation pathways differentiating the isomers and to determine the influence of the acetyl group on the fragmentation of the arylamide modified deoxyguanosine adducts. The collision-induced dissociation spectra of the BHZ 2 (+) ion and other significant source-produced ions showed no evidence to suggest that ketene loss (deacetylation) resulted in significant alteration of the structure of the adducts. However, other significant ion formation processes, particularly loss of water from the N (2)-substituted arylamide did appear to require rearrangement, likely involving bond formation between the carcinogen moiety (acetyl group) and the N1 or N2 position of the guanine base. The combined loss of ketene and water constitute a fragmentation pattern specific for the N (2)-arylamide, 3-(deoxyguanosin-N (2)-yl)-2-acetylaminofluorene.

Methyl guanine isomer distinction by hydrogen / deuterium exchange using a fourier transform mass spectrometer

Analytical Chemistry Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Differentiation of the seven isomers of methyl guanine has been accomplished by monitoring gas-phase hydrogen/deuterium (H/D) exchange reactions of the protonated molecular ions with deuterium oxide (D2O) in a Fourier transform mass spectrometer. In each case a distinctive reaction rate for the first H/D exchange was observed, and exchanges of up to three deuterium atoms occurred with characteristic ion abundances that could be used to differentiate the isomers. O(6)-Methyl guanine, for example, showed only one slow H/D exchange with D2O, whereas l-methyl guanine exchanged two hydrogen atoms at a significantly faster rate. On comparison of the possible resonance structures of each protonated isomer with the experimental information about the number and rate of H/D exchanges observed, a reaction mechanism involving a concerted proton abstraction-deuterium cation donation was proposed.