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Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures

  • Genotoxicity and Carcinogenicity
  • Published:
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Abstract

Adductomics is expected to be useful in the characterization of the exposome, which is a new paradigm for studying the sum of environmental causes of diseases. DNA adductomics is emerging as a powerful method for detecting DNA adducts, but reliable assays for its widespread, routine use are currently lacking. We propose a novel integrated strategy for the establishment of a DNA adductomic approach, using liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS), operating in constant neutral loss scan mode, screening for both known and unknown DNA adducts in a single injection. The LC-QqQ-MS/MS was optimized using a representative sample of 23 modified 2′-deoxyribonucleosides reflecting a range of biologically relevant DNA lesions. Six internal standards (ISTDs) were evaluated for their ability to normalize, and hence correct, possible variation in peak intensities arising from matrix effects, and the quantities of DNA injected. The results revealed that, with appropriate ISTDs adjustment, any bias can be dramatically reduced from 370 to 8.4%. Identification of the informative DNA adducts was achieved by triggering fragmentation spectra of target ions. The LC-QqQ-MS/MS method was successfully applied to in vitro and in vivo studies to screen for DNA adducts formed following representative environmental exposures: methyl methanesulfonate (MMS) and five N-nitrosamines. Interestingly, five new DNA adducts, induced by MMS, were discovered using our adductomic approach—an added strength. The proposed integrated strategy provides a path forward for DNA adductomics to become a standard method to discover differences in DNA adduct fingerprints between populations exposed to genotoxins, and facilitate the field of exposomics.

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Abbreviations

5-CadC:

5-Carboxy-2′-deoxycytidine

5-EdC:

5-Ethynyl-2′-deoxycytidine

5-HmdC:

5-Hydroxymethyl-2′-deoxycytidine

5-HmdU:

5-Hydroxymethyl-2′-deoxyuridine

5-MedC:

5-Methyl-2′-deoxycytidine

5-PPGdU:

5-Propargyloxy-2′-deoxyuridine

5-PPNdU:

5-Propynyl-2′-deoxyuridine

8-oxodG:

8-Oxo-7, 8-dihydro-2′-deoxyguanosine

CAD:

Collisionally activated dissociation

CNL:

Constant neutral loss

CT-DNA:

Calf thymus DNA

dA:

2′-Deoxyadenosine

dC:

2′-Deoxycytidine

dG:

2′-Deoxyguanosine

dR:

2′-Deoxyribose

dT:

2′-Deoxythymidine

dU:

2′-Deoxyuridine

d4-N6-2HEdA:

d4-N6-(2-hydroxyethyl)-2′-deoxyadenosine

EPI:

Enhance product ion

ESI:

Electrospray ionization

IDA:

Information dependent acquisition

ISTDs:

Internal standards

LC-QqQ-MS/MS:

Liquid chromatography-triple quadrupole tandem mass spectrometry

LOD:

Limit of detection

ME:

Matrix effect

MMS:

Methyl methanesulfonate

MRM:

Multiple reaction monitoring

N1-MedA:

N1-methyl-2′-deoxyadenosine

N2-EtdG:

N2-ethyl-2′-deoxyguanosine

N3-MedA:

N3-methyl-2′-deoxyadenosine

N3-MedC:

N3-methyl-2′-deoxycytidine

N6-Bz-8-oxodA:

N6-benzoyl-8-hydroxy-2′-deoxyadenosine

1,N6-εdA:

1,N6-etheno-2′-deoxyadenosine

N6-MedA:

N6-methyl-2′-deoxyadenosine

N7-EAdG:

N7-ethoxyacetaldehyde-2′-deoxyguanosine

N7-EtdG:

N7-ethyl-2′-deoxyguanosine

N7-HEdG:

N7-(2-hydroxyethyl)-2′-deoxyguanosine

N7-MedG:

N7-methyl-2′-deoxyguanosine

N7-PrdG:

N7-propyl-2′-deoxyguanosine

NDEA:

N-nitrosodiethylamine

NDMA:

N-nitrosodimethylamine

NDPA:

N-nitrosodi-n-propylamine

NMEA:

N-nitrosomethylethylamine

NMOR:

N-nitrosomorpholine

O6-BndG:

O6-benzyl-2′-deoxyguanosine

O6-EtdG:

O6-ethyl-2′-deoxyguanosine

O6-HEdG:

O6-(2-hydroxyethyl)-2′-deoxyguanosine

O6-MedG:

O6-methyl-2′-deoxyguanosine

PA:

Peak area

PCA:

Principal component analysis

RT:

Retention time

TIC:

Total ion chromatogram.

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Acknowledgements

We greatly appreciate the assistance of Mr. Bai-Song Huang and Ms. Pei-Shan Li with experimental procedures.

Funding

This work was funded by the Ministry of Science and Technology, Taiwan (Grant nos. MOST 106-2314-B-040-015-MY3; NSC 102-2632-B-040-001-MY3).

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Author notes

  1. Chiung-Wen Hu and Mu-Rong Chao contributed equally to this work.

Authors and Affiliations

  1. Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, 402, Taiwan

    Yuan-Jhe Chang & Mu-Rong Chao

  2. Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA

    Marcus S. Cooke, Chiung-Wen Hu & Mu-Rong Chao

  3. Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA

    Marcus S. Cooke

  4. Department of Public Health, Chung Shan Medical University, Taichung, 402, Taiwan

    Chiung-Wen Hu

  5. Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung, 402, Taiwan

    Mu-Rong Chao

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  1. Yuan-Jhe Chang
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  2. Marcus S. Cooke
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Correspondence to Chiung-Wen Hu or Mu-Rong Chao.

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Chang, YJ., Cooke, M.S., Hu, CW. et al. Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures. Arch Toxicol 92, 2665–2680 (2018). https://doi.org/10.1007/s00204-018-2252-6

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