Potential artifacts in the measurement of DNA deamination

Reflections of an Aging Free Radical Part 2: Meeting Inspirational People

Significance: During my long career in the field of redox biology, I met many inspiring people, especially Lester Packer. Recent Advances: This special issue of Antioxidants & Redox Signaling is dedicated to Lester Packer. Critical Issues: In this short review, I explore how Lester and other pioneers helped to develop the redox biology field and how I interacted with them. Future Directions: In our research to advance the field of redox biology, we stand on the shoulders of giants, including Lester Packer.

Mitochondrial DNA Damage Does Not Determine C. elegans Lifespan

The mitochondrial free radical theory of aging (mFRTA) proposes that accumulation of oxidative damage to macromolecules in mitochondria is a causative mechanism for aging. Accumulation of mitochondrial DNA (mtDNA) damage may be of particular interest in this context. While there is evidence for age-dependent accumulation of mtDNA damage, there have been only a limited number of investigations into mtDNA damage as a determinant of longevity. This lack of quantitative data regarding mtDNA damage is predominantly due to a lack of reliable assays to measure mtDNA damage. Here, we report adaptation of a quantitative real-time polymerase chain reaction (qRT-PCR) assay for the detection of sequence-specific mtDNA damage in C. elegans and apply this method to investigate the role of mtDNA damage in the aging of nematodes. We compare damage levels in old and young animals and also between wild-type animals and long-lived mutant strains or strains with modifications in ROS detoxification or production rates. We confirm an age-dependent increase in mtDNA damage levels in C. elegans but found that there is no simple relationship between mtDNA damage and lifespan. MtDNA damage levels were high in some mutants with long lifespan (and vice versa). We next investigated mtDNA damage, lifespan and healthspan effects in nematode subjected to exogenously elevated damage (UV- or γ-radiation induced). We, again, observed a complex relationship between damage and lifespan in such animals. Despite causing a significant elevation in mtDNA damage, γ-radiation did not shorten the lifespan of nematodes at any of the doses tested. When mtDNA damage levels were elevated significantly using UV-radiation, nematodes did suffer from shorter lifespan at the higher end of exposure tested. However, surprisingly, we also found hormetic lifespan and healthspan benefits in nematodes treated with intermediate doses of UV-radiation, despite the fact that mtDNA damage in these animals was also significantly elevated. Our results suggest that within a wide physiological range, the level of mtDNA damage does not control lifespan in C. elegans.

Radiation metabolomics. 5. Identification of urinary biomarkers of ionizing radiation exposure in nonhuman primates by mass spectrometry-based metabolomics

Mass spectrometry-based metabolomics has previously demonstrated utility for identifying biomarkers of ionizing radiation exposure in cellular, mouse and rat in vivo radiation models. To provide a valuable link from small laboratory rodents to humans, γ-radiation-induced urinary biomarkers were investigated using a nonhuman primate total-body-irradiation model. Mass spectrometry-based metabolomics approaches were applied to determine whether biomarkers could be identified, as well as the previously discovered rodent biomarkers of γ radiation. Ultra-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry analysis was carried out on a time course of clean-catch urine samples collected from nonhuman primates (n = 6 per cohort) exposed to sham, 1.0, 3.5, 6.5 or 8.5 Gy doses of (60)Co γ ray (∼0.55 Gy/min) ionizing radiation. By multivariate data analysis, 13 biomarkers of radiation were discovered: N-acetyltaurine, isethionic acid, taurine, xanthine, hypoxanthine, uric acid, creatine, creatinine, tyrosol sulfate, 3-hydroxytyrosol sulfate, tyramine sulfate, N-acetylserotonin sulfate, and adipic acid. N-Acetyltaurine, isethionic acid, and taurine had previously been identified in rats, and taurine and xanthine in mice after ionizing radiation exposure. Mass spectrometry-based metabolomics has thus successfully revealed and verified urinary biomarkers of ionizing radiation exposure in the nonhuman primate for the first time, which indicates possible mechanisms for ionizing radiation injury.

Measurement of deoxyinosine adduct: Can it be a reliable tool to assess oxidative or nitrosative DNA damage?

Adenosine deaminases (ADA) are key enzymes that deaminate adenosine (A) or deoxyadenosine (dA) and produce inosine or deoxyinosine (dI), respectively. While ADA only deaminates free dA, reactive nitrogen species (RNS) or reactive oxygen species (ROS) deaminate adenine base on the DNA and leave dI, which is a pre-mutagenic lesion. Therefore, dI adduct in the genomic DNA has been considered a biomarker of DNA damage caused by RNS or by ROS. In the presented study, genomic DNA was isolated from frozen calf thymus in low or room temperature, with or without an addition of antioxidant. The number of dI in the DNA was measured using liquid chromatography-tandem mass spectrometry. While low temperature (LT) work-up with an addition of antioxidant in reagents helped to prevent artifactual formation of oxidative DNA lesions in the calf thymus DNA (CTD), it also significantly inhibited activities of proteinase, which in turn resulted in significant ADA contamination in the final DNA samples. ADA remained in LT-CTD completely deaminated most dA when the DNA was subjected to enzymatic hydrolysis to single nucleosides. The ADA contamination in the DNA was significantly reduced when DNA was isolated from pre-isolated nuclear fraction rather than from entire tissue homogenates. However, enzymes used for DNA hydrolysis were confirmed to contain significant amounts of ADA. Therefore, these enzymes would increase deamination of dA during DNA hydrolysis. Artifactual dI production by contaminated ADA was dramatically reduced by an addition of EHNA (erythro-9-(2-hydroxy-3-nonyl)adenine), which is a potent inhibitor of ADA. However, time- and temperature-dependent dI production from dA in phosphate buffer solution was observed. More importantly, TEMPO, an antioxidant commonly used to prevent DNA oxidation, was found to deaminate dA independent to ADA. Overall, these findings indicate that assay methods measuring dI or other dA DNA adducts in genomic DNA should be carefully validated to minimize artificial errors caused by dA deamination. Recommendations to overcome those technical challenges were discussed in this presentation.

Mammalian DNA δ15N exhibits 40‰ intramolecular variation and is unresponsive to dietary protein level

We report the first high-precision characterization of molecular and intramolecular δ(15)N of nucleosides derived from mammalian DNA. The influence of dietary protein level on brain amino acids and deoxyribonucleosides was determined to investigate whether high protein turnover would alter amino acid (15)N or (13)C values. Pregnant guinea pig dams were fed control diets, or high or low levels of dietary protein throughout gestation, and all pups were fed control diets. The cerebellar DNA of offspring was extracted at 2 and 120 days of life, nucleosides isolated and δ(15)N and δ(13)C values characterized. Mean diet δ(15)N was 0.45 ± 0.33‰, compared with cerebellar whole tissue and DNA δ(15) N= +4.1 ± 0.7‰ and -4.5 ± 0.4‰, respectively. Cerebellar deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), and deoxyguanosine (dG) δ(15)N were +1.4 ± 0.4, -2.1 ± 0.9, -7.2 ± 0.3, and -10.4 ± 0.5‰, respectively. There were no changes in amino acid or deoxyribonucleoside δ(15) N values due to dietary protein level. Using known metabolic relationships, we developed equations to calculate the intramolecular δ(15)N values originating from aspartate (asp) in purines (pur) or pyrimidines (pyr), glutamine (glu), and glycine (gly) to be δ(15)N(ASP-PUR), δ(15)N(ASP-PYR), δ(15) N(GLN), and δ(15) N(GLY) +11.9 ± 2.3‰, +7.0 ± 2.0‰, -9.1 ± 2.4‰, and -31.8 ± 8.9‰, respectively. A subset of twelve amino acids from food and brain had mean δ(15) N values of 4.3 ± 3.2‰ and 13.8 ± 3.1‰, respectively, and δ(15)N values for gly and asp were 12.6 ± 2.2‰ and 15.2 ± 0.8‰, respectively. A separate isotope tracer study detected no significant turnover of cerebellar DNA in the first six months of life. The large negative δ(15)N difference between gly and cerebellar purine N at the gly (7) position implies either that there is a major isotope effect during DNA synthesis, or that in utero gly has a different isotope ratio during rapid growth and metabolism from that in adult life. Our data show that cerebellar nucleoside intramolecular δ(15)N values vary over more than 40‰ and are not influenced by dietary protein level or age.

Reactive species and DNA damage in chronic inflammation: reconciling chemical mechanisms and biological fates

Chronic inflammation has long been recognized as a risk factor for many human cancers. One mechanistic link between inflammation and cancer involves the generation of nitric oxide, superoxide and other reactive oxygen and nitrogen species by macrophages and neutrophils that infiltrate sites of inflammation. Although pathologically high levels of these reactive species cause damage to biological molecules, including DNA, nitric oxide at lower levels plays important physiological roles in cell signaling and apoptosis. This raises the question of inflammation-induced imbalances in physiological and pathological pathways mediated by chemical mediators of inflammation. At pathological levels, the damage sustained by nucleic acids represents the full spectrum of chemistries and likely plays an important role in carcinogenesis. This suggests that DNA damage products could serve as biomarkers of inflammation and oxidative stress in clinically accessible compartments such as blood and urine. However, recent studies of the biotransformation of DNA damage products before excretion point to a weakness in our understanding of the biological fates of the DNA lesions and thus to a limitation in the use of DNA lesions as biomarkers. This review will address these and other issues surrounding inflammation-mediated DNA damage on the road to cancer.

Challenges in developing DNA and RNA biomarkers of inflammation

Inflammation is now a proven cause of human diseases such as cancer and cardiovascular disease. One potential link between inflammation and disease involves secretion of reactive chemical species by immune cells, with chronic damage to host epithelial cells leading to disease. This suggests pathophysiologically that DNA and RNA damage products are candidate biomarkers of inflammation, both for mechanistic understanding of the process and for risk assessment. Of the current approaches to quantifying DNA damage products, mass spectrometry-based methods provide the most rigorous quantification needed for biomarker development, while antibody-based approaches provide the most practical way to implement biomarkers in a clinical setting. Nonetheless, all approaches are biased by adventitious formation of DNA and RNA damage products during sample processing. Recent studies of tissue-derived DNA biomarkers in mouse models of inflammation reveal significant changes only in DNA adducts derived from lipid peroxidation. These and other observations raise the question of the most appropriate sampling compartment for DNA biomarker studies and highlight the emerging role of lipid damage in inflammation.

Enzymatic methylation of DNA in cultured human cells studied by stable isotope incorporation and mass spectrometry

Enzymatic methylation of cytosine residues in DNA, in conjunction with covalent histone modifications, establishes an epigenetic code essential for the proper control of gene expression in higher organisms. Once established during cellular differentiation, the epigenetic code must be faithfully transmitted to progeny cells. However, epigenetic perturbations can be found in most if not all cancer cells, and the mechanisms leading to these changes are not well understood. In this paper, we describe a series of experiments aimed at understanding the dynamic process of DNA methylation that follows DNA replication. Cells in culture can be propagated in the presence of (15)N-enriched uridine, which labels the pyrimidine precursor pool as well as newly replicated DNA. Simultaneous culture in the presence of (2)H-enriched methionine results in labeling of newly methylated cytosine residues. An ensemble of 5-methylcytosine residues differing in the degree of isotopic enrichment is generated, which can be examined by mass spectrometry. Using this method, we demonstrate that the kinetics of both DNA replication and methylation of newly replicated DNA are indistinguishable. The majority of methylation following DNA replication is shown to occur on the newly synthesized DNA. The method reported here does, however, suggest an unexpected methylation of parental DNA during DNA replication, which might indicate a previously undescribed chromatin remodeling process. The method presented here will be useful in monitoring the dynamic process of DNA methylation and will allow a more detailed understanding of the mechanisms of clinically used methylation inhibitors and environmental toxicants.

The wanderings of a free radical

In my career I have moved from chemistry to biochemistry to plant science to clinical chemistry and back again (in a partial way) to plants. This review presents a brief history of my research achievements (ascorbate-glutathione cycle, role of iron in oxidative damage and human disease, biomarkers of free radical damage, and studies on atherosclerosis and neurodegeneration) and how they relate to my research activities today. The field of free radicals/other reactive species/antioxidants underpins all of modern Biology. These agents helped to drive human evolution and the basic principles of the field are repeatedly found to be relevant in other research areas. It was an exciting field when I started some 40 years ago, and it still is today, but some major challenges must be faced.

Surveying the damage: the challenges of developing nucleic acid biomarkers of inflammation

Epidemiological evidence points to a cause and effect relationship between chronic inflammation and human maladies such as cancer, atherosclerosis and autoimmune disease. A critical link between inflammation and disease may lie in the secretion of highly reactive oxygen and nitrogen species by macrophages and neutrophils, including hypohalous acids, nitrous anhydride, and nitrosoperoxycarbonate. Exposure of host epithelial cells to the resulting oxidation, nitration, nitrosation and halogenation chemistries leads to damage of all types of cellular molecules. Since nucleic acids sustain damage representative of the full spectrum of different chemistries and the damage likely plays a causative role in disease etiology, DNA and RNA damage products can serve as surrogates for the short-lived chemical mediators of inflammation, and as markers that provide both mechanistic understanding of the disease process and a means to quantify risk of disease. However, the very small quantities of the damaged molecules pose a challenge to the simultaneous quantification of the spectrum of lesions in the manner of proteomics or metabolomics. The goal of this Highlight is to provide an update on the chemistry of inflammation and the development of biomarkers of inflammation in the age of -omics technologies.

Lipid peroxidation dominates the chemistry of DNA adduct formation in a mouse model of inflammation

In an effort to define the prevalent DNA damage chemistry-associated chronic inflammation, we have quantified 12 DNA damage products in tissues from the SJL mouse model of nitric oxide (NO) overproduction. Using liquid chromatography-mass spectrometry/MS and immunoblot techniques, we analyzed spleen, liver and kidney from RcsX-stimulated and control mice for the level of the following adducts: the DNA oxidation products 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), guanidinohydantoin (Gh), oxazolone (Ox); 5-guanidino-4-nitroimidazole (NitroIm); spiroiminodihydantoin (Sp) and M(1)dG; the nitrosative deamination products 2'-deoxyxanthosine, 2'-deoxyoxanosine (dO), 2'-deoxyinosine and 2'-deoxyuridine and the lipid peroxidation-derived adducts 1,N(6)-etheno-deoxyadenosine and 1,N(2)-etheno-deoxyguanosine. The levels of dO, Gh, Ox, NitroIm and Sp were all below a detection limit of approximately 1 lesion per 10(7) bases. Whereas there were only modest increases in the spleens of RcsX-treated compared with control mice for the nucleobase deamination products (10-30%) and the DNA oxidation products 8-oxodG (10%) and M(1)dG (50%), there were large (3- to 4-fold) increases in the levels of 1,N(6)-etheno-deoxyadenosine and 1,N(2)-etheno-deoxyguanosine. Similar results were obtained with the liver and with an organ not considered to be a target for inflammation in the SJL mouse, the kidney. This latter observation suggests that oxidative and nitrosative stresses associated with inflammation can affect tissues at a distance from the activated macrophages responsible for NO overproduction during chronic inflammation. These results reveal the complexity of NO chemistry in vivo and support an important role for lipids in the pathophysiology of inflammation.

NO* chemistry: a diversity of targets in the cell

NO(*) alone is a poorly reactive species; however, it is able to undergo secondary reactions to form highly oxidizing and nitrating species, NO(2)(*), N(2)O(3), and ONOO(-). These secondary reactive nitrogen species (RNS) are capable of modifying a diversity of biomolecular structures in the cell. The chemical properties of individual RNS will be discussed, along with their ability to react with amino acids, metal cofactors, lipids, cholesterol, and DNA bases and sugars. Many of the identified RNS-induced modifications have been observed both in vitro and in vivo. Several of these chemical modifications have been attributed with a functional role in the cell, such as the modulation of enzyme activity. Other areas in the field will be discussed, including the ability of RNS to react with metabolites, RNA, and substrates in the mitochondrion, and the cellular removal/repair of RNS-modified structures.

Quantitative gas chromatography mass spectrometric analysis of 2′-deoxyinosine in tissue DNA

Several studies examining DNA deamination have published levels of 2'-deoxyinosine that illustrated a large variation between studies. Most of them are the result of artifactual DNA deamination that occurs during the process of sample preparation, particularly acid hydrolysis. This protocol for measurement of 2'-deoxyinosine describes the use of nuclease P1 and alkaline phosphatase to achieve release of nucleosides from DNA, followed by HPLC prepurification with subsequent gas chromatography-mass spectrometry analysis of the nucleosides. It has been used in the measurement of the levels of 2'-deoxyinosine in DNA of commercial sources and DNA from cells and animal tissues, and gives values ranging from 3 to 7 2'-deoxyinosine per 10(6) 2-deoxyadenosine. This protocol should take approximately 7 days to complete.