Biomarkers of nucleic acid oxidation – A summary state-of-the-art

Abstract

Oxidatively generated damage to DNA has been implicated in the pathogenesis of a wide variety of diseases. Increasingly, interest is also focusing upon the effects of damage to the other nucleic acids, RNA and the (2′-deoxy-)ribonucleotide pools, and evidence is growing that these too may have an important role in disease. LC-MS/MS has the ability to provide absolute quantification of specific biomarkers, such as 8-oxo-7,8-dihydro-2′-deoxyGuo (8-oxodG), in both nuclear and mitochondrial DNA, and 8-oxoGuo in RNA. However, significant quantities of tissue are needed, limiting its use in human biomonitoring studies. In contrast, the comet assay requires much less material, and as little as 5 μL of blood may be used, offering a minimally invasive means of assessing oxidative stress in vivo , but this is restricted to nuclear DNA damage only. Urine is an ideal matrix in which to non-invasively study nucleic acid-derived biomarkers of oxidative stress, and considerable progress has been made towards robustly validating these measurements, not least through the efforts of the European Standards Committee on Urinary (DNA) Lesion Analysis. For urine, LC-MS/MS is considered the gold standard approach, and although there have been improvements to the ELISA methodology, this is largely limited to 8-oxodG. Emerging DNA adductomics approaches, which either comprehensively assess the totality of adducts in DNA, or map DNA damage across the nuclear and mitochondrial genomes, offer the potential to considerably advance our understanding of the mechanistic role of oxidatively damaged nucleic acids in disease.

Genome-wide mapping of genomic DNA damage: methods and implications

“…This will require integration of multiple approaches, many of which will need to be 'omics in nature, as co-analysis of mutational and gene expression profiles have shown [157]. Yet, additional levels of co-analysis will be required and DNA adductomics, both mapping (including the 3D spatial mapping) and cellular DNA adductomics (the totality of lesions), will both make a valuable contribution to this, particularly if the two approaches can be combined into an approach which maps the totality of lesions, across both the nuclear and mitochondrial genomes [15]. Author contributions All authors contributed to the original draft, based upon initial discussions between SA (Amente), GS, BM and MSC.…”

“…While the degree of chromatin condensation is a relatively well-known factor influencing the sensitivity to damage, local changes to DNA structure caused by protein binding is certainly worth further investigation; (B) to provide a standard tool, as part of human exposomic studies, to better characterise simple and complex exposures based upon the topography of damage. This, in particular, will require mapping DNA adductomics to be demonstrated to be applicable to human studies [e.g., suitable amounts of DNA can be obtained, relevance of surrogate tissues vs. target tissues (discussed in [ 15 ]) is address] and the assays are properly validated, in terms of establishing norms for the assays, such as assay variability and controls, intra- and inter-individual variability, age and sex differences, as has been performed for other biomarkers [ 156 ]; (C) the identification of potential environmental threats to public health; (D) the further elucidation of the “black box”, i.e., the nature, sequence and outcome of pathogenic, cellular events that occur between the formation of DNA damage and the onset of early- and late-stage disease. The goal is to elucidate the type and sequence of events that occur between damage formation and the onset of disease.…”

“…However, the challenges to the measurement of mitochondrial DNA damage include the requirement for additional steps to isolate mitochondria and the low levels of DNA obtained and hence damage, in isolated mitochondrial DNA, which is challenging to assess using the conventional methods described below. Methods for assessing mitochondrial DNA damage and repair have been considered elsewhere [ 15 ], which highlighted two recent descriptions of mapping DNA damage across the mitochondrial genome [ 41 , 42 ] that are discussed further below.…”

“…1 )], the mechanisms and sequence of events, linking DNA damage to disease in vivo is often unclear. Although we understand a great deal about the events between formation of DNA damage and the onset of disease, there remains something of a “black box”, which obscures our full understanding of the precise processes and hence limits our ability to intervene [ 15 ]. Herein, we aim to review an emerging field within the study of DNA damage, i.e.…”

Special issue on ‘Biomarkers of Oxidative Stress, Aging and Nutrition in Human Studies’

“…Altomare et al discuss the most novel analytical approaches for lipid peroxidation biomarkers and their application for profiling reactive carbonyl species and their enzymatic and non-enzymatic metabolites as an index of lipid peroxidation and oxidative stress including methodological limits and perspectives [ 2 ]. The state-of-the-art in biomarkers of nucleic acid oxidation is presented by Chao et al [ 3 ]. In their review, Rabbani and Thornalley describe the clinical diagnostic application of glycation adducts as biomarkers, most commonly used in diabetes, diabetic complications, arthritis, autism and aging [ 4 ].…”