Analytical methods in DNA and protein adduct analysis

The Key Characteristics of Carcinogens: Relationship to the Hallmarks of Cancer, Relevant Biomarkers, and Assays to Measure Them

The key characteristics (KC) of human carcinogens provide a uniform approach to evaluating mechanistic evidence in cancer hazard identification. Refinements to the approach were requested by organizations and individuals applying the KCs. We assembled an expert committee with knowledge of carcinogenesis and experience in applying the KCs in cancer hazard identification. We leveraged this expertise and examined the literature to more clearly describe each KC, identify current and emerging assays and in vivo biomarkers that can be used to measure them, and make recommendations for future assay development. We found that the KCs are clearly distinct from the Hallmarks of Cancer, that interrelationships among the KCs can be leveraged to strengthen the KC approach (and an understanding of environmental carcinogenesis), and that the KC approach is applicable to the systematic evaluation of a broad range of potential cancer hazards in vivo and in vitro We identified gaps in coverage of the KCs by current assays. Future efforts should expand the breadth, specificity, and sensitivity of validated assays and biomarkers that can measure the 10 KCs. Refinement of the KC approach will enhance and accelerate carcinogen identification, a first step in cancer prevention.See all articles in this CEBP Focus section, "Environmental Carcinogenesis: Pathways to Prevention."

Screening for protein adducts of naphthalene and chrysene in plasma of exposed Atlantic cod (Gadus morhua)

Polycyclic aromatic hydrocarbons (PAHs) are well known contaminants, ubiquitously present in the habitat and spawning areas for Atlantic cod (Gadus morhua). The Atlantic cod is a key species and a globally important food source, thus continuous monitoring of PAHs is considered highly valuable to ensure ecosystem sustainability and human food safety. PAH adducts to plasma proteins are applied as sensitive biomarkers of PAH exposure in humans and other species, thus the presence of PAH protein adducts in Atlantic cod plasma was investigated to identify PAH protein adduct biomarker candidates of exposure to PAHs. Blood plasma samples were collected from Atlantic cod (n = 66) one week after exposure by intramuscular injection of single PAHs (i.e. naphthalene and chrysene), and their corresponding dihydrodiol metabolites (i.e. (-)-(1R,2R)-1,2-dihydronaphthalene-1,2-diol and (-)-(1R,2R)-1,2-dihydrochrysene-1,2-diol). The samples were analyzed by shotgun tandem mass spectrometry (MS) and the resulting MS data were analyzed in Byonic™ to screen for proteins susceptible to adduct formation with naphthalene and chrysene. Furthermore, a wildcard modification search was performed to obtain additional information regarding potential modifications other than the targeted metabolites. The amino acid adductation sites and the metabolites involved in PAH adductation are reported. Forty-four proteins were found to bind PAHs. Alpha-2-macroglobulin-like proteins, apolipoproteins B-100-like proteins and an alpha-2-HS-glycoprotein were detected with the highest number of bound PAHs. This first insight into PAH protein adducts of Atlantic cod plasma generates valuable knowledge for the development of highly sensitive biomarkers of PAH exposure.

Strategies for the evaluation of DNA damage and repair mechanisms in cancer

DNA lesions and the repair mechanisms that maintain the integrity of genomic DNA are important in preventing carcinogenesis and its progression. Notably, mutations in DNA repair mechanisms are associated with cancer predisposition syndromes. Additionally, these mechanisms maintain the genomic integrity of cancer cells. The majority of therapies established to treat cancer are genotoxic agents that induce DNA damage, promoting cancer cells to undergo apoptotic death. Effective methods currently exist to evaluate the diverse effects of genotoxic agents and the underlying molecular mechanisms that repair DNA lesions. The current study provides an overview of a number of methods that are available for the detection, analysis and quantification of underlying DNA repair mechanisms.

DNA adducts in marine fish as biological marker of genotoxicity in environmental monitoring: The way forward

DNA adducts in fish represent a very important genotoxicity endpoint in environmental monitoring, being a pre-mutagenic lesion that plays an essential role in the initiation of carcinogenesis. The analysis of DNA adducts is a challenging task due to the low concentration of the analyte. Methods are available to determine the presence of DNA adducts, although further knowledge is required to fully understand the nature of the adducts and responsible xenobiotics (i.e. position of adduct in DNA, most active xenobiotic and metabolite forms, structural information). At present, ³²P-postlabeling is the most used method that has the required sensitivity for DNA adduct analyses in both human health and environmental monitoring. Development of new mass spectrometry based methods for identifying DNA adducts in complex matrixes is now considered as a necessary mission in toxicology in order to gain the necessary information regarding adduct formation and facilitate tracking sources of contamination. Mass spectrometry therefore represents the future of DNA adduct detection, bringing along a series of challenges that the scientific community is facing at present.

Identification of protein adduction using mass spectrometry: Protein adducts as biomarkers and predictors of toxicity mechanisms

The determination of protein-xenobiotic adducts using mass spectrometry is an emerging area which allows detailed understanding of the underlying mechanisms involved in toxicity. These approaches can also be used to reveal potential biomarkers of exposure or toxic response. The following review covers studies of protein adducts resulting from exposure to a wide variety of xenobiotics including organophosphates, polycyclic aromatic hydrocarbons, acetaminophen, alkylating agents and other related compounds.

Benzeno: reflexos sobre a saúde pública, presença ambiental e indicadores biológicos utilizados para a determinação da exposição

O uso indiscriminado de um número cada vez maior de substâncias químicas vem aumentando e a contaminação ambiental associada tem trazido sérias consequências para o sistema público de saúde devido à elevação de danos para a saúde humana. Uma das substâncias que desperta grande interesse devido à contaminação contemporânea é o benzeno, composto aromático classificado pela International Agency for Research on Cancer como reconhecidamente carcinogênico para humanos. O objetivo do presente estudo foi elaborar e discutir um panorama sobre a contaminação por benzeno, seu metabolismo, consequências para a saúde e sua determinação ambiental e biológica a partir de informações existentes na literatura científica. O levantamento de dados possibilitou o acesso a mais de 200 artigos científicos tanto de âmbito nacional quanto internacional, demonstrando a atualidade do tema e a necessidade de minimização da exposição humana a essa substância. A maioria preocupa-se em explorar o metabolismo e investigar indicadores de exposição, muitos já amplamente estudados e com sérias limitações. Contudo, um crescente número de pesquisadores estão empenhados em elucidar fatores relacionados à suscetibilidade e à interferência da exposição no material genético e proteico. Indicadores de exposição inovadores têm sido propostos com o objetivo de complementar as lacunas de informações anteriormente obtidas, contribuindo para o delineamento da estrutura da biologia de sistemas orgânicos frente à exposição ao benzeno.

Gold nanoprobes for detecting DNA adducts

A colorimetric probe for the detection of a mutagenic DNA adduct within a sequence was created. The probe involves incorporation of a synthetic nucleoside that selectively pairs opposite a target DNA adduct into oligonucleotides conjugated to gold nanoparticles (AuNPs).

Mass spectrometry analysis of nucleosides and nucleotides

Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants

DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.

Chloropicrin-induced toxic responses in human lung epithelial cells

Chloropicrin is a slowly evaporating toxic irritant that is known to cause damage in the respiratory system. Here we used a lung epithelial cell line (A549) to study the molecular responses underlying chloropicrin toxicity. Glutathione (GSH), synthetic peptide and 2'-deoxyguanosine were used as in vitro trapping agents to identify early markers of chloropicrin toxicity. Microscopy of the cells revealed massive vacuolization by chloropicrin exposure (80-100μM). The number of apoptotic cells increased with the chloropicrin concentration as assessed by flow cytometry. Immunoblotting analysis revealed increases in the amount of four proteins (p53, p21, p27 and phospho-Erk1/2) that are involved in DNA-damage, cell cycle regulation and apoptosis. Chloropicrin evoked a dose-dependent increase in levels of reactive oxygen species within one hour of exposure. The treatment triggered also the formation of disulphide bonds between the model thiol-containing peptides as analysed by LC/MS. Chloropicrin did not form stable adducts with the model peptides or 2'-deoxyguanosine. N-acetyl-cysteine (1mM NAC) fully prevented the vacuoles and chloropicrin-induced cytotoxicity. The results suggest that an oxidative insult, particularly modification of free sulfhydryl groups in proteins is involved in the acute toxicity evoked by chloropicrin in airway epithelial cells. The protective effect of NAC as a potential antidote in chloropicrin intoxication will require further investigation.

Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition

The challenges posed by the analysis of mono-nucleotide mixtures by direct infusion electrospray ionization were examined in the context of recent advances of mass spectrometry (MS) technologies. In particular, we evaluated the merits of high-resolution mass analysis, multistep gas-phase dissociation, and ion mobility determinations for the characterization of species with very similar or identical elemental composition. The high resolving power afforded by a linear trap quadrupole-orbitrap allowed the complete differentiation of overlapping isotopic distributions produced by nucleotides that differed by a single mass unit. Resolving (12)C signals from nearly overlapped (13)C contributions provided the exact masses necessary to calculate matching elemental compositions for unambiguous formulae assignment. However, it was the ability to perform sequential steps of gas-phase dissociation (i.e. MS(n)-type analysis) that proved more valuable for discriminating between truly isobaric nucleotides, such as the AMP/dGMP and UMP/ΨMP couples, which were differentiated in the mixture from their unique fragmentation patterns. The identification of diagnostic fragments enabled the deconvolution of dissociation spectra containing the products of coexisting isobars that could not be individually isolated in the mass-selection step. Approaches based on ion mobility spectrometry-MS provided another dimension upon which isobaric nucleotides could be differentiated according to their distinctive mobility behaviors. Subtle structural variations, such as the different positions of an oxygen atom in AMP/dGMP or the glycosidic bond in UMP/ΨMP, produced detectable differences in the respective ion mobility profiles, which enabled the differentiation of the isobaric couples in the mixture. Parallel activation of all ions emerging from the ion mobility element provided an additional dimension for differentiating these analytes on the basis of both mobility and fragmentation properties.

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.

A fluorescence-based analysis of aristolochic acid-derived DNA adducts

Aristolochic acids (AAs), major components of plant extracts from Aristolochia species, form (after metabolic activation) pro-mutagenic DNA adducts in renal tissue. The DNA adducts can be used as biomarkers for studies of AA toxicity. Identification of these adducts is a complicated and time-consuming procedure. We present here a fast, nonisotopic, fluorescence-based assay for the detection of AA-DNA adducts in multiple samples. This approach allows analysis of AA adducts in synthetic DNA with known nucleotide composition and analysis of DNA adducts formed from chemically diverse AAs in vitro. The method can be applied to compare AA-DNA adduct formation in cells and tissues.

Polycyclic aromatic hydrocarbons within airborne particulate matter (PM(2.5)) produced DNA bulky stable adducts in a human lung cell coculture model

To extend current knowledge on the underlying mechanisms of air pollution particulate matter (PM(2.5))-induced human lung toxicity, the metabolic activation of polycyclic aromatic hydrocarbons (PAH) within PM(2.5) and PAH-DNA bulky stable adduct patterns in human alveolar macrophage (AM) and/or human lung epithelial L132 cells in mono- and cocultures were studied. In the coculture system, only human AM were exposed to air pollution PM(2.5), unlike L132 cells. Particles, inorganic fraction and positive controls [i.e. TiO(2), thermally desorbed PM (dPM) and benzo[a]pyrene, B[a]P, respectively] were included in the experimental design. Cytochrome P450 (CYP) 1A1 gene expression, CYP1A1 catalytic activity and PAH-DNA bulky stable adducts were studied after 24, 48 and/or 72 h. Relatively low doses of PAH within PM(2.5) induced CYP1A1 gene expression and CYP1A1 catalytic activity in human AM and, thereafter, PAH-DNA bulky stable adduct formation. Adduct spots in PM(2.5) -exposed human AM were higher than those in dPM-exposed ones, thereby showing the incomplete removal of PAH by thermal desorption. PAH within air pollution PM(2.5) induced CYP1A1 gene expression but not CYP1A1 catalytic activity in L132 cells. However, despite the absence of PAH-DNA bulky stable adduct in L132 cells from human AM/L132 cell cocultures exposed to dPM(2.5) or PM(2.5), reliable quantifiable PAH-DNA bulky stable adducts were observed in L132 cells from human AM/L132 cell coculture exposed to B[a]P. Taken together, these results support the exertion of genotoxicity of highly reactive B[a]P-derived metabolites produced within human AM not only in primary target human AM, but also in secondary target L132 cells.

Screening nucleotide binding to amino acid-coated supports by surface plasmon resonance and nuclear magnetic resonance

Here, we describe a rapid and efficient screening method using surface plasmon resonance (SPR) and saturation transfer difference-nuclear magnetic resonance (STD-NMR) spectroscopy to yield information regarding the residues involved in nucleotide binding to amino acid-coated supports. The aim of this work was to explore the use of these spectroscopic techniques to study amino acid-nucleotide interactions in order to improve the binding specificity of the amino acid ligands used to purify plasmid DNA. For SPR, we present a strategy that immobilizes arginine and lysine on a surface as model supports, and we analyze binding responses when synthetic homo-deoxyoligonucleotides are injected over the amino acid surface. The binding responses are detectable and reproducible despite the small size of the immobilized amino acids. Using STD-NMR, we performed epitope mapping of homo-deoxyoligonucleotides bound to L-arginine-bisoxyran-Sepharose and L-lysine-Sepharose supports. Polynucleotide binding preferences differed; for example, polyC interacted preferentially through its backbone with the two supports, whereas polyT bound the supports through its thymine moiety. STD-NMR combined with SPR measurements was successfully used to screen amino acid-nucleotide interactions and determine the binding affinities of the complexes.

DNA damage induced by endogenous aldehydes: current state of knowledge

DNA damage plays a major role in various pathophysiological conditions including carcinogenesis, aging, inflammation, diabetes and neurodegenerative diseases. Oxidative stress and cell processes such as lipid peroxidation and glycation induce the formation of highly reactive endogenous aldehydes that react directly with DNA, form aldehyde-derived DNA adducts and lead to DNA damage. In occasion of persistent conditions that influence the formation and accumulation of aldehyde-derived DNA adducts the resulting unrepaired DNA damage causes deregulation of cell homeostasis and thus significantly contributes to disease phenotype. Some of the most highly reactive aldehydes produced endogenously are 4-hydroxy-2-nonenal, malondialdehyde, acrolein, crotonaldehyde and methylglyoxal. The mutagenic and carcinogenic effects associated with the elevated levels of these reactive aldehydes, especially, under conditions of stress, are attributed to their capability of causing directly modification of DNA bases or yielding promutagenic exocyclic adducts. In this review, we discuss the current knowledge on DNA damage induced by endogenously produced reactive aldehydes in relation to the pathophysiology of human diseases.