Here, drawing from this experience, we share insights on how integrating this approach can enhance current effect-based assessment.
DNA adductomics: advancing environmental monitoring
OMICS-based ecosurveillance. Current discussions center on integrating OMICS-based technologies (genomics, transcriptomics, proteomics, lipidomics, metabolomics, and adductomics) into ecosurveillance monitoring frameworks. This integration aims to capture the comprehensive biological responses of ecosystems under perturbation \cite{Beale2022,Bahamonde2016}. These technologies and the data they can provide have greatly enhanced our grasp of how environmental chemicals impact ecosystems and human health. However, despite progress, most environmental OMICS are currently in the data collection phase, with crucial gaps in linking toxicity data with OMICS endpoints \cite{Machuca-Sepúlveda2023a}. Future efforts are expected to address real environmental challenges, focusing on issues like chemical mixture toxicity, biomarker identification, and the development of innovative OMICS approaches towards more effective chemical toxicity testing, risk monitoring, and sustainable natural resource utilization \cite{Beale2022}.
DNA adductome - an exposome component. Adductomics, an emerging research field, provides structural insights into chemical exposures and serves as a platform for discovering biomarkers to identify both the occurrence of exposure and associated effects. DNA adductomics, one of the newest OMICS techniques, is particularly well suited for assessing exposure and effects of environmental contaminants \cite{Lockridge2023} and elucidating genotoxic and epigenetic changes due to chemical stressors.
DNA adducts are well-established biomarkers in (eco)toxicology. They are chemical modifications occurring when certain chemicals bind covalently to DNA molecules. Unrepaired DNA adducts can disrupt DNA structure and function, potentially leading to mutations and adverse biological effects \cite{Phillips_2009}. These adducts are associated with health issues, reproductive toxicity, genotoxicity, and epigenetic alterations in humans and wildlife. For the last 50 years, DNA adducts have been used as biomarkers of exposure in human health diagnostics and environmental toxicology, where the focus has mainly been on the adducts derived from polycyclic aromatic hydrocarbons (PAHs) in fish and mussels as exposure biomarkers \cite{Pampanin2017,Dolcetti2002}. In environmental toxicology, PAHs have been most commonly linked to DNA adduct formation \cite{Skarphédinsdóttir2007,Amat_2004,Meier2020}, both in the laboratory and in field observations after oil spills. However, other contaminants have also been found to induce DNA modifications \cite{Guilherme_2012,letters}. Also, in amphipods, abundant epigenetic DNA modifications have been associated with contaminated environments \cite{Martella2023} and females that carry embryos with various developmental disorders \cite{Gorokhova2020}. Thus, ample evidence supports the informative value of detecting and quantifying DNA adducts in biological samples for assessing contaminant exposure and genomic effects.
Traditional analytical methods for DNA adducts. The detection of DNA adducts has commonly been conducted using immunochemical \cite{Müller1982} and 32P-postlabelling \cite{Poirier2000} assays. Although useful, these assays do not provide chemical or structural information about the adducts to trace back to specific exposures. Moreover, these techniques have significant limitations: the immunochemical method is not sensitive enough to detect DNA adducts at trace levels and requires an antibody to each chemical. Albeit highly sensitive, 32P-postlabelling involves radioactive phosphorus usage, implying safety concerns and regulatory challenges \cite{Hwa2020}. The method is also labour-intensive and further complicated by highly variable labelling efficiency \cite{Totsuka_1996}. Nowadays, researchers need to adhere to strict safety protocols for handling radioactive materials and waste disposal, which has led to a gradual disappearance of laboratories willing to conduct these measurements. Moreover, key limitations include the scarcity of information on the detected DNA adduct structure and occasional co-migration of adducts on the thin layer chromatography plate \cite{Phillips_2007}. These challenges collectively impede the chemical structural characterization and identification of the adducts.
A novel approach to measure old biomarker. Nowadays, one of the most powerful techniques for detecting and quantifying DNA adducts is liquid chromatography-mass spectrometry (LC-MS). Using high-resolution mass spectrometry (HRMS), sensitive and selective analytical methods for detecting and identifying DNA adducts in the genome have been developed \cite{Hemeryck_2016} and successfully applied in human health research \cite{Hwa2020,Totsuka2021} and ecotoxicological \cite{Gorokhova2020,Martella2023} diagnostics of adverse effects due to chemical exposure. Instead of analyzing a few adducts from a specific chemical exposure ( (i.e., bottom-up approach), HRMS gives the possibility to screen for DNA adducts from multiple classes of exposure, an “adductomics” approach. Thus, this is a new OMICS approach, with both target and non-targeted analytical methods available to comprehensively investigate the adductome via screening for all known and unknown adducts in the genome (i.e., top-down approach). Various modification types, e.g., bulky PAH-adducts, methylation and oxidation, can be analyzed in a single sample by HRMS, including the determination of their chemical structures, which is useful for exposure diagnostics \cite{Balbo2014,Villalta2017}. Thus, the current capacity for DNA adduct characterization is superior to the classical assays, advocating this OMICS approach to detect and monitor the biological effects of contaminants \cite{Martella2023}.
Methodology
Using various cell types and matrices, several DNA adductomics methods based on LS-HRMS have been developed for applications in human toxicology \cite{Balbo2014a,Guo2018,Hemeryck2017}. These developments are poised to be applicable to any biological sample and allow proposing a workflow for low- and high-mass DNA adduct analysis in wildlife as a part of ecotoxicological surveillance \cite{Martella2023}.
Test organisms. Any plant or animal tissue is suitable for the analysis, including the whole body (for small-sized planktonic and benthic animals as well as embryos), blood, liver and muscle tissues. If fertilized eggs or embryos are present in small specimens, they should be dissected out and either analyzed separately or not included in the female DNA samples to avoid the natural ontogenetic variability in the epigenetic DNA modifications related to embryogenesis \cite{Gorokhova2020}. In fish, liver and muscle tissues are commonly used as test tissues, and more work is needed to identify target tissues and organs for specific adducts if we are to improve the diagnostic properties of the method.