DNA Adductomics

Abstract

Systems toxicology is a broad based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term “exposome” has been employed to refer to the totality of all exposures and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the 32P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. While triple quadrupole and ion trap mass spectrometry, in particular when using multistage scanning (LC-MSn), have shown promise in the field of DNA adductomics, it is anticipated that high resolution and accurate mass LC-MSn instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other –omics tools will contribute greatly to the field of systems toxicology.

Mass Spectrometric Mapping of the DNA Adductome as a Means to Study Genotoxin Exposure, Metabolism, and Effect

“…32 MSbased DNA adductomics therefore is particularly suited for research on the exposure of the human body to both known and unknown endo-and exogenous hazardous chemicals and any subsequently formed DNA adducts. 27 Nevertheless, the search for answers does not end with DNA adduct mapping or biomarker establishment, as the described top-down approach does not evidently link genotoxin exposure to a certain environmental factor as a causal risk factor on the one hand, or disease outcome on the other. 4 Any information obtained from top-down omics studies will only prove its value if combined with bottom-up targeted analyses in both long-term studies and purposeful short-term intervention studies.…”

“…Insufficient knowledge of DNA adduct fragmentation patterns and limited availability of DNA adduct standards currently act as a bottleneck for the full characterization and correct identification of untargeted and unknown DNA adducts with MS. 27 In this context, the need for accurate mass measurements is indisputable, whereas the establishment of a database to assemble all information on chemical structure and characteristics of DNA adducts, fragmentation patterns, stability, 33 At the time, the number of published DNA adductomics methods that make use of hybrid HRMS/MS technology are very limited (n = 2). 32,66 However, due to the still ongoing establishment of these hybrid MS systems in the field, the number of DNA adductomics applications could increase significantly in the near future.…”

“…However, one disadvantage of tandem MS/MS is the loss of sensitivity with CNL or the need for SRM transition optimization for each different DNA adduct in order to achieve sufficient detection sensitivity with pseudo-CNL. 27,31 Secondly, since triple quadrupoles only allow low resolution data acquisition, and DNA adduct databases providing MS/MS spectra are not available, DNA adduct identity confirmation is dependent on the availability of analyte standards or the use of additional analytical techniques.…”

“…12,27 The envisioned removal of unmodified DNA building blocks and interfering contaminants (e.g. highly polar compounds that interfere with ionization) is required to minimize signal and ionization suppression.…”

“…14,28 Frequently utilized on-or off-line techniques for DNA adduct enrichment include immunoaffinity column purification, HPLC column switching and solid phase extraction. 14,27,28 However, care must be taken with selection of the appropriate stationary phases and elution buffers to avoid degradation/loss of the adducts. In addition, immunoaffinity column purification can only be implemented prior to targeted analysis due to the specificity of the antibodies in use.…”