Identification and characterization of 2'-deoxyadenosine adducts formed by isoprene monoepoxides in vitro

Mammalian N1-adenosine PARylation is a reversible DNA modification

Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here, we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and anti-PAR reagents to show that mammalian DNA is physiologically PARylated and to different levels in primary tissues. Inhibition of PAR glycohydrolase (PARG) increases DNA PARylation, supporting that the modification is reversible. DNA PARylation requires PARP1 and in vitro PARP1 PARylates single-stranded DNA, while PARG reverts the modification. DNA PARylation occurs at the N1-position of adenosine residues to form N1-Poly(ADP-ribosyl)-deoxyadenosine. Through partial hydrolysis of mammalian gDNA we identify PAR-DNA via the diagnostic deamination product N1-ribosyl-deoxyinosine to occur in vivo. The discovery of N1-adenosine PARylation as a DNA modification establishes the conceptual and methodological framework to elucidate its biological relevance and extends the role of PARP enzymes.

Influence of the methyl group in isoprene epoxides on reactivity compared to butadiene epoxides: Biological significance

Reactions of the epoxides of 1,3-butadiene and isoprene (2-methyl-1,3-butadiene) with oxygen, nitrogen and sulfur nucleophiles have been compared to enable a better molecular understanding of the relative human toxicities of these epoxides. Hydrolysis of rac.-ethenyloxirane in (¹⁸O)water gave 77% (2-¹⁸O)but-3-ene-1,2-diol and 23% (1-¹⁸O)but-3-ene-1,2-diol. The R:S ratio for but-3-ene-1,2-diol from hydrolysis of (S)-ethenyloxirane was 75:25. Hence, hydrolysis of ethenyloxirane occurs by competing S_N2 attack at C-2 and C-3 in 3:1 ratio, with no S_N1 component. Hydrolysis of rac.-2-ethenyl-2-methyloxirane gave 2-hydroxy-2-methylbut-3-en-1-ol (73%) and 27% of a 2:1 mixture of the E- and Z-isomers of 4-hydroxy-2-methylbut-2-en-1-ol. In (¹⁸O)water (2-¹⁸O)2-hydroxy-2-methylbut-3-en-1-ol was obtained. Formation of these products occurs via S_N1 ionisation to resonance-stabilised allylic cations which are captured by water. Reaction of rac.-ethenyloxirane with l-valine methyl ester gave diastereoisomeric adducts from S_N2 attack of the valine amino at both C-2 (substituted position) and C-3 of the oxirane. The corresponding reaction of rac.-2-methyl-2-ethenyloxirane gave diastereoisomeric adducts, (R, S)- and (S, S)-N-(2-hydroxy-2-methyl-3-buten-1-yl)-l-valine methyl ester, from S_N2 attack of the valine amino solely at C-3. Reactions of rac.-2-ethenyl-2-methyloxirane with cysteine derivatives occurred at C-2 in neutral polar media (S_N1 reaction) or at C-3 in basic media (S_N2), whereas for ethenyloxirane products arose from attack at both C-2 and C-3. Reaction of meso-butadiene diepoxide (meso-2,2'-bioxirane) with l-valine methyl ester gave mainly 2:1 adducts, dimethyl 2,2'-(((2R,3S)-2,3-dihydroxybutane-1,4-diyl)bis(azanediyl))-(2S,2'S)-bis(3-methyl-butanoates), whereas 2-methyl-2,2'-bioxirane gave a mixture of 1:1 [methyl 2-(3,4-dihydroxy-3-methylpyrrolidin-1-yl)-3-methylbutanoates] and 2:1 adducts. Meso-2,2'-bioxirane reacted with N-acetylcysteine methyl ester in methanol to afford meso-thiolane-3,4-diol, by elimination of N-acetyldehydroalanine methyl ester from a precursor cyclic adduct. Similarly, 2-methyl-2,2'-bioxirane gave solely 3-methylthiolane-3,4-diols. Thus, the methyl group of isoprene has a subtle effect on the reactivity of its epoxides relative to those of butadiene and therefore, in the context of their toxicology, could abrogate crosslinking of nitrogen functions in biomolecules related to mutagenicity and carcinogenicity.

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.

The endogenous exposome

The concept of the Exposome is a compilation of diseases and one's lifetime exposure to chemicals, whether the exposure comes from environmental, dietary, or occupational exposures; or endogenous chemicals that are formed from normal metabolism, inflammation, oxidative stress, lipid peroxidation, infections, and other natural metabolic processes such as alteration of the gut microbiome. In this review, we have focused on the endogenous exposome, the DNA damage that arises from the production of endogenous electrophilic molecules in our cells. It provides quantitative data on endogenous DNA damage and its relationship to mutagenesis, with emphasis on when exogenous chemical exposures that produce identical DNA adducts to those arising from normal metabolism cause significant increases in total identical DNA adducts. We have utilized stable isotope labeled chemical exposures of animals and cells, so that accurate relationships between endogenous and exogenous exposures can be determined. Advances in mass spectrometry have vastly increased both the sensitivity and accuracy of such studies. Furthermore, we have clear evidence of which sources of exposure drive low dose biology that results in mutations and disease. These data provide much needed information to impact quantitative risk assessments, in the hope of moving towards the use of science, rather than default assumptions.

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.

Concentration- and time-dependent genotoxicity profiles of isoprene monoepoxides and diepoxide, and the cross-linking potential of isoprene diepoxide in cells

Isoprene, a possible carcinogen, is a petrochemical and a natural product being primarily produced by plants. It is biotransformed to 2-ethenyl-2-methyloxirane (IP-1,2-O) and 2-(1-methylethenyl)oxirane (IP-3,4-O), both of which can be further metabolized to 2-methyl-2,2'-bioxirane (MBO). MBO is mutagenic, but IP-1,2-O and IP-3,4-O are not. While IP-1,2-O has been reported being genotoxic, the genotoxicity of IP-3,4-O and MBO, and the cross-linking potential of MBO have not been examined. In the present study, we used the comet assay to investigate the concentration- and time-dependent genotoxicity profiles of the three metabolites and the cross-linking potential of MBO in human hepatocyte L02 cells. For the incubation time of 1 h, all metabolites showed positive concentration-dependent profiles with a potency rank order of IP-3,4-O > MBO > IP-1,2-O. In human hepatocellular carcinoma (HepG2) and human leukemia (HL60) cells, IP-3,4-O was still more potent in inducing DNA breaks than MBO at high concentrations (>200 μM), although at low concentrations (≤200 μM) IP-3,4-O exhibited slightly lower or similar potency to MBO. Interestingly, their time-dependent genotoxicity profiles (0.5-4 h) in L02 cells were different from each other: IP-1,2-O and MBO (200 μM) exhibited negative and positive profiles, respectively, with IP-3,4-O lying in between, namely, IP-3,4-O-caused DNA breaks did not change over the exposure time. Further experiments demonstrated that hydrolysis of IP-1,2-O contributed to the negative profile and MBO induced cross-links at high concentrations and long incubation times. Collectively, the results suggested that IP-3,4-O might play a significant role in the toxicity of isoprene.