IAC Abstract for the 2023 EMGS Meeting
The International Adductomics Consortium
Marcus S Cooke, Silvia Balbo, Yukari Totsuka, Sonia Dagnino, and William Funk
Marcus S Cooke, Silvia Balbo, Yukari Totsuka, Sonia Dagnino, and William Funk
DNA and protein adductomics aim to detect the totality of DNA and protein adducts, respectively, in a variety of cellular and extracellular contexts. While the technology to perform these analyses is increasingly well established, there remain methodological challenges, not least establishing optimal sample work-up, and guidelines for best practice.
Drawing on the experience of other consortia, such as the European Standards Committee on Oxidative DNA Damage, the European Standards Committee on Urinary DNA Lesion Analysis, and the European Comet Assay Validation Group, we are establishing an International Adductomics Consortium (IAC) to bring together researchers and other academic, industry, and government stakeholders with an interest in nucleic acid (DNA, RNA) and protein adductomics to promote collaboration and establish guidelines and best practices. The consortium will focus on becoming a reference for anyone interested in adductomics and ultimately it will promote robust analytical approaches to advance the field. This effort will be promoted through the creation of a website to be used as a common platform to share information and resources, the organization of events at scientific meetings focusing on the presentation and discussion of adductomic research and finally, the facilitation of small inter-laboratory initiatives to promote standardization procedures.
Adductomics is an emerging, and highly dynamic field. We aim that, via the activities and membership of IAC, the field will establish guidelines for best practice early, and implement them prospectively, rather than retrospectively, providing confidence in adductoic data and discoveries.
Drawing on the experience of other consortia, such as the European Standards Committee on Oxidative DNA Damage, the European Standards Committee on Urinary DNA Lesion Analysis, and the European Comet Assay Validation Group, we are establishing an International Adductomics Consortium (IAC) to bring together researchers and other academic, industry, and government stakeholders with an interest in nucleic acid (DNA, RNA) and protein adductomics to promote collaboration and establish guidelines and best practices. The consortium will focus on becoming a reference for anyone interested in adductomics and ultimately it will promote robust analytical approaches to advance the field. This effort will be promoted through the creation of a website to be used as a common platform to share information and resources, the organization of events at scientific meetings focusing on the presentation and discussion of adductomic research and finally, the facilitation of small inter-laboratory initiatives to promote standardization procedures.
Adductomics is an emerging, and highly dynamic field. We aim that, via the activities and membership of IAC, the field will establish guidelines for best practice early, and implement them prospectively, rather than retrospectively, providing confidence in adductoic data and discoveries.
Featured News
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Manuscript describing featureHunter software accepted for publication in Environmental Science & Technology.
FeatureHunter is a software that automates the detection of nucleic acid modifications facilitating exploration of the exposome. FeatureHunter successfully identifies and classifies novel types of nucleic acid modifications induced by endogenous/exogenous agents, supporting adductomics.
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Database for DNA Adductomics
The database, containing 582 entries, is a powerful tool for the annotation of DNA adducts measured in (HR)MS. The inclusion of metadata indicating the source of DNA adducts, the study design and technique used, allows for prioritization of the DNA adducts of interests and/or to enhance the annotation confidence.
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DNA Adduct Portal
The Portal contains high-resolution MS2 and MS3 mass spectra of the adduct standards via Orbitrap MS and Q-TOF MS at various collision energies to characterize adduct structures. After curation and annotation, the spectra are submitted to Massbank of North America and mzCloud for the public to visualize and download in common formats. The successful establishment of a validated DNA adduct mass spectral database in a searchable, reference library is critical for the comprehensive analysis of DNA adductome profiles from cellular DNA, urine, and other biological matrices.
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Publications from IAC members
2025
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Boysen, G.,* Alexandrov, LB.,* Rahbari, R., Nookaew, I., Ussery, D., Chao, M-R., Hu, C-W. and Cooke, MS.* (2025) Investigating the origins of the mutational signatures in cancer. Nucleic Acids Research, 53, gkae1303.
* Corresponding authors, and each author contributed equally Keidel, A.,* Virzi, J., Deloso, L., Möller, C., Chaput, D., Evans-Nguyen, T., Chang, Y-J., Chao, M-R., Hu, C-W. and Cooke MS.* (2025) Development of an optimized two-step SPE method for urinary nucleic acid adductomics. Biomolecules, 15, 594- * Corresponding authors. La Barbera, G., Shuler, M. S., Beck, S. H., Ibsen, P. H., Lindberg, L. J., Karstensen, J. G., & Dragsted, L. O. (2025). Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry. Talanta, 282, 126985. |
2024
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Hu, C-W., Chang, Y-J., Chang, W-H., Cooke, MS., Chen, Y-R. and Chao, M-R. (2024) A Novel Adductomics Workflow Incorporating “FeatureHunter” Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. Environmental Science & Technology. 58, 75-89.
Walmsley, SJ., Guo, J., Tarifa, A., DeCaprio, AP., Cooke, MS., Turesky, RJ. and Villalta, PW. (2024) A mass spectral library for DNA adductomics. Chemical Research in Toxicology. 37, 302–310. Chung, MK., House, JS., Akhtari, FS., Makris, KC., Langston, MA., Islam, KT., Holmes, P., Chadeau-Hyam, M., Smirnov, AI., Du, X., Thessen, AE., Cui, Y., Zhang, K., Manrai, AK., Motsinger-Reif, M., Patel, CJ. Members of the Exposomics Consortium* (2024) Decoding the exposome: Data science methodologies and implications in Exposome-Wide association studies (ExWASs). Exposome. 4, osae001. Möller, C., Virzi, J., Chang, Y-J., Keidel, A., Chao, M-R., Hu, C-W. and Cooke, MS. (2024) DNA modifications: biomarkers for the exposome? Environmental Toxicology and Pharmacology. 108, 104449- |
2023
Hu, C-W., Chang, Y-J., Chang, W-H., Cooke, MS., Chen, Y-R. and Chao, M-R. (2023) A Novel Adductomics Workflow Incorporating “FeatureHunter” Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. Environmental Science & Technology. (In press.)
Cooke, MS., Chang, Y-J., Chen, Y-R, Hu, C-W. and Chao, M-R. (2023) Nucleic acid adductomics – the next generation of adductomics assays towards assessing environmental health risks. Science of the Total Environment. 856, 159192-
More publications coming soon.
Cooke, MS., Chang, Y-J., Chen, Y-R, Hu, C-W. and Chao, M-R. (2023) Nucleic acid adductomics – the next generation of adductomics assays towards assessing environmental health risks. Science of the Total Environment. 856, 159192-
More publications coming soon.
2022
More publications coming soon.
2021
Chang, Y-J., Cooke, MS., Chen, Y-R., Yang, S-F., Lia, P-S., Hu, C-W., and Chao, M-R. (2021) Is high resolution a strict requirement for mass spectrometry-based cellular DNA adductomics? Chemosphere, 274, 129991-
Funk, W., Montgomery, N., Bae, Y., Chen. J., Chow, T., Martinez, M., Lurmann, F., Eckel, S., McConnell, R., Xiang, A. (2021) HSA-Cys34 Adducts in Newborn Dried Blood Spots: Associations with Air Pollution Exposure During Pregnancy. Frontiers in Public Health, 9, 1-9.
Funk, W., Montgomery, N., Bae, Y., Chen. J., Chow, T., Martinez, M., Lurmann, F., Eckel, S., McConnell, R., Xiang, A. (2021) HSA-Cys34 Adducts in Newborn Dried Blood Spots: Associations with Air Pollution Exposure During Pregnancy. Frontiers in Public Health, 9, 1-9.
2020
Guo, J., Turesky, RJ., Tarifa, A., DeCaprio, AP., Cooke, MS., Walmsley, SJ. and Villalta, PW. (2020) Development of a DNA Adductome Mass Spectral Database. Chemical Research in Toxicology, 33, 4, 852-854.
Dagnino S., Bodinier B., Grigoryan H., Rappaport S.M., Karimi M., Guida F., Polidoro S., Edmands W.B., Naccarati A, Fiorito G., Sacerdote C., Krogh V., Vermeulen R., Vineis P., Chadeau-Hyam M (2020) Agnostic Cys34-albumin adductomics and DNA methylation: implication of N-acetylcysteine in lung carcinogenesis years before diagnosis. International Journal of Cancer, 146, 3294-3303.
Preston G., Dagnino S., Ponzi E., Sozeri O., van Veldhoven K., Baratta B., Liu S., Grigoryan H., Lu S., Rappaport S., Chunge K.F., Cullinan P., Sinharayg R., Kelly F., Chadeau-Hyam M., Vineis P., Phillips D (2020). Relationships between airborne pollutants, serum albumin adducts and short-term health outcomes in an experimental crossover study. Chemosphere, 239, 124667.
Vineis P., Robinson O., Chadeau-Hyam M, Dehghan A., Mudway I., Dagnino S (2020). What’s new in the Exposome? Environment International, 143, 105887.
Totsuka Y, Maesako Y, Ono H, Nagai M, Kato M, Gi M, Wanibuchi H, Fukushima S, Shiizaki S, Nakagama H. (2020) Comprehensive analysis of DNA adducts (DNA adductome analysis) in the liver of rats treated with 1,4-dioxane. Proc Jpn Acad Ser B Phys Biol Sci. 96, 180-187.
Dagnino S., Bodinier B., Grigoryan H., Rappaport S.M., Karimi M., Guida F., Polidoro S., Edmands W.B., Naccarati A, Fiorito G., Sacerdote C., Krogh V., Vermeulen R., Vineis P., Chadeau-Hyam M (2020) Agnostic Cys34-albumin adductomics and DNA methylation: implication of N-acetylcysteine in lung carcinogenesis years before diagnosis. International Journal of Cancer, 146, 3294-3303.
Preston G., Dagnino S., Ponzi E., Sozeri O., van Veldhoven K., Baratta B., Liu S., Grigoryan H., Lu S., Rappaport S., Chunge K.F., Cullinan P., Sinharayg R., Kelly F., Chadeau-Hyam M., Vineis P., Phillips D (2020). Relationships between airborne pollutants, serum albumin adducts and short-term health outcomes in an experimental crossover study. Chemosphere, 239, 124667.
Vineis P., Robinson O., Chadeau-Hyam M, Dehghan A., Mudway I., Dagnino S (2020). What’s new in the Exposome? Environment International, 143, 105887.
Totsuka Y, Maesako Y, Ono H, Nagai M, Kato M, Gi M, Wanibuchi H, Fukushima S, Shiizaki S, Nakagama H. (2020) Comprehensive analysis of DNA adducts (DNA adductome analysis) in the liver of rats treated with 1,4-dioxane. Proc Jpn Acad Ser B Phys Biol Sci. 96, 180-187.
2019
Totsuka Y, Lin Y, He Y, Ishino K, Sato H, Kato M, Nagai M, Elzawahry A, Totoki Y, Nakamura H, Hosoda F, Shibata T, Matsuda T, Matsushima Y, Song G, Meng F, Li D, Liu J, Qiao Y, Wei W, Inoue M, Kikuchi S, Nakagama H, Shan B. (2019) DNA adductome analysis identifies N-nitrosopiperidine involved in the etiology of esophageal cancer in Cixian, China. Chem Res Toxicol. 32, 1515-1527.
Cooke, MS., Hu, C-W. and Chao, M-R. (2019) Editorial: Mass Spectrometry for Adductomic Analysis. Frontiers Chemistry. doi: 10.3389/fchem.2019.00794
Hu, C-W., Chang, Y-J., Cooke, MS. and Chao, M-R. (2019) DNA crosslinkomics: a tool for the comprehensive assessment of inter-strand crosslinks using high resolution mass spectrometry. Analytical Chemistry. 91, 15193-15203.
Grigoryan H., Shiffman C., Gunter M.J, Dagnino S., Naccarati A., Polidoro S., Dudoit S., Vineis P. Rappaport S.M (2019). Cys34 Adductomics Provides Evidence Linking Colorectal Cancer with Redox Biology and the Gut Microbiota. Cancer Research, 79, (23), 6024-6031.
Cooke, MS., Hu, C-W. and Chao, M-R. (2019) Editorial: Mass Spectrometry for Adductomic Analysis. Frontiers Chemistry. doi: 10.3389/fchem.2019.00794
Hu, C-W., Chang, Y-J., Cooke, MS. and Chao, M-R. (2019) DNA crosslinkomics: a tool for the comprehensive assessment of inter-strand crosslinks using high resolution mass spectrometry. Analytical Chemistry. 91, 15193-15203.
Grigoryan H., Shiffman C., Gunter M.J, Dagnino S., Naccarati A., Polidoro S., Dudoit S., Vineis P. Rappaport S.M (2019). Cys34 Adductomics Provides Evidence Linking Colorectal Cancer with Redox Biology and the Gut Microbiota. Cancer Research, 79, (23), 6024-6031.
2018
Cooke, MS., Chao, M-R., Chang, Y-J. and Hu, C-W*. (2018) Urinary DNA Adductomics – A Novel Approach for Exposomics. Environment International. 121, 1033-1038.
Chang, Y-J., Cooke, MS., Hu, C-W. and Chao, M-R. (2018) Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures. Archives of Toxicology. 92, 2665-2680.
Liu S., Grigoryan H., Edmands WMB, Dagnino S., Sinharay R., Cullinan P., Collins P., Chung K.F., Barratt B., Kelly F.J., Vineis P., Rappaport S.M (2018). Cys34 adductomes differ between patients with chronic lung or heart disease and healthy controls in central London. Environmental Science and Technology 52, (4) 2307-2313.
Chang, Y-J., Cooke, MS., Hu, C-W. and Chao, M-R. (2018) Novel approach to integrated DNA adductomics for the assessment of in vitro and in vivo environmental exposures. Archives of Toxicology. 92, 2665-2680.
Liu S., Grigoryan H., Edmands WMB, Dagnino S., Sinharay R., Cullinan P., Collins P., Chung K.F., Barratt B., Kelly F.J., Vineis P., Rappaport S.M (2018). Cys34 adductomes differ between patients with chronic lung or heart disease and healthy controls in central London. Environmental Science and Technology 52, (4) 2307-2313.
Earlier publications
Grigoryan, H., Edmands, W., Lu, SS., Yano, Y., Regazzoni, L., Iavarone, AT., Williams, ER., Rappaport, SM. (2016) Adductomics Pipeline for Untargeted Analysis of Modifications to Cys34 of Human Serum Albumin. Anal Chem. 88, 10504-10512.
Rappaport, S., He, L., Grigoryan, H., Funk, W., Williams, E. (2012) Adductomics: Characterizing Exposures to Reactive Electrophiles. Toxicology Letters, 13, 83-90.
Rappaport, S., He, L., Grigoryan, H., Funk, W., Williams, E. (2012) Adductomics: Characterizing Exposures to Reactive Electrophiles. Toxicology Letters, 13, 83-90.
