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

ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification

Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.

Human Mitochondrial Protein HSPD1 Binds to and Regulates the Repair of Deoxyinosine in DNA

The generation of deoxyinosine (dI) in DNA is one of the most important sources of genetic mutations, which may lead to cancer and other human diseases. A further understanding of the biological consequences of dI necessitates the identification and functional characterizations of dI-binding proteins. Herein, we employed a mass spectrometry-based proteomics approach to detect the cellular proteins that may sense the presence of dI in DNA. Our results demonstrated that human mitochondrial heat shock protein 60 (HSPD1) can interact with dI-bearing DNA. We further demonstrated the involvement of HSPD1 in the sodium nitrite-induced DNA damage response and in the modulation of dI levels in vitro and in human cells. Together, these findings revealed HSPD1 as a novel dI-binding protein that may play an important role in the mitochondrial DNA damage control in human cells.

Development of an Endonuclease V-Assisted Analytical Method for Sequencing Analysis of Deoxyinosine in DNA

Deoxyinosine (dI) is a highly mutagenic lesion that preferentially pairs with deoxycytidine during replication, which may induce A to G transition and ultimately contribute to carcinogenesis. Therefore, finding the site of dI modification in DNA is of great value for both basic research and clinical applications. Herein, we developed a novel method to sequence the dI modification site in DNA, which utilizes endonuclease V (EndoV)-dependent deamination repair to specifically label the modification site with biotin-14-dATP that allows the affinity enrichment of dI-bearing DNA for sequencing. We have achieved efficient determination of the location of the modified nucleotide in dI-bearing plasmid DNA with the assistance of EndoV-dependent deamination repair. We have also successfully applied this approach to locate the dI modification sites in the mitochondrial DNA of human cells. Our method should be generally applicable for genome-wide sequencing analysis of dI modifications in living organisms.

Assessment of Oxidative DNA Damages in Radiography Staff via Evaluation of Its Urinary Biomarker (8-hydroxy2-deoxyguanosine)

Background

Studies have shown that one of the most important complications of exposure to ionizing radiation is the emergence of cancer tumors, as a result of oxidative DNA. Since different radiography groups have high rate of exposure to ionizing radiation, examining the susceptibility rate of cancer in these groups is of prime importance. Therefore, the present study was conducted to measure the level of 8-hydroxy2-deoxyguanosine (8-OHdG) in the radiographers' urine as a biomarker of oxidative damage while comparing it with the nonradiography staff.

Methods

Samples of two groups were selected for this case-control study, wherein 35 subjects were selected from different radiography groups (including nuclear medicine, radiology, radiotherapy, and CT scan) while the other 35 subjects were staffs who had no exposure to radiation. Later, urine samples were collected at the end of the working shift to determine the 8-OHdG concentration. The samples were obtained via SPE (solid-phase extraction) method. Subsequently, the 8-OHdG concentration was measured by the GC-MS analyzer.

Results

The results confirmed that, the average concentration of 8-OHdG in the radiographers' urine (253.4 ± 31.2 ng/mg of creatinine) had a significant difference as compared to the nonradiographers' urine (141.1 ± 21.9 ng/mg of creatinine) (P = 0.004).

Conclusions

In conclusion, due to elimination of interfering factors, ionizing radiation affects the increase in 8-OHdG levels and acts as a potential biomarker for the damaged oxidative DNA.

5-Carboxylcytosine is resistant towards phosphodiesterase I digestion: implications for epigenetic modification quantification by mass spectrometry

DNA cytosine modifications are important epigenetic modifications in gene regulation and pathogenesis. DNA hydrolysis followed by HPLC-MS/MS is the gold standard in DNA modification quantification. In particular, it is the only sensitive and accurate method for low abundance modifications, such as 5-carboxylcytosine (5caC). Here, we report the discovery of the nuclease resistance property of 5caC to snake venom phosphodiesterase I (PDE1), a 3' to 5' exonuclease commonly used in several DNA hydrolysis protocols. We conducted a systematic evaluation of six commonly used hydrolysis protocols and found that all protocols that use PDE1 underestimate the level of 5caC. Finally, we identified the best method for cytosine modification quantification of biological samples, which leads to an over 10-fold higher amount of 5caC being detected compared with other methods. Our results highlight that caution should be taken when choosing a DNA hydrolysis protocol to quantify certain DNA modifications.

Induction of 8,5'-cyclo-2'-deoxyadenosine and 8,5'-cyclo-2'-deoxyguanosine in isolated DNA by Fenton-type reagents

Exposure of aqueous solutions of DNA to X- or γ-rays, which induces the hydroxyl radical as one of the major reactive oxygen species (ROS), can result in the generation of a battery of single-nucleobase and bulky DNA lesions. These include the (5'R) and (5'S) diastereomers of 8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine (cdG), which were also found to be present at appreciable levels in DNA isolated from mammalian cells and tissues. However, it remains unexplored how efficiently the cdA and cdG can be induced by Fenton-type reagents. By employing HPLC coupled with tandem mass spectrometry (LC-MS/MS/MS) with the use of the isotope-dilution technique, here we demonstrated that treatment of calf thymus DNA with Cu(II) or Fe(II), together with H2O2 and ascorbate, could lead to dose-responsive formation of both the (5'R) and (5'S) diastereomers of cdA and cdG, though the yields of cdG were 2-4 orders of magnitude lower than that of 8-oxo-7,8-dihydro-2'-deoxyguanosine. This result suggests that the Fenton reaction may constitute an important endogenous source for the formation of the cdA and cdG. Additionally, the (5'R) diastereomers of cdA and cdG were induced at markedly higher levels than the (5'S) counterparts. This latter finding, in conjunction with the previous observations of similar or greater levels of the (5'S) than (5'R) diastereomers of the two lesions in mammalian tissues, furnishes an additional line of evidence to support the more efficient repair of the (5'R) diastereomers of the purine cyclonucleosides in mammalian cells.

Quantification of oxidative DNA lesions in tissues of Long-Evans Cinnamon rats by capillary high-performance liquid chromatography-tandem mass spectrometry coupled with stable isotope-dilution method

The purpose of our study was to develop suitable methods to quantify oxidative DNA lesions in the setting of transition metal-related diseases. Transition metal-driven Fenton reactions constitute an important endogenous source of reactive oxygen species (ROS). In genetic diseases with accumulation of transition metal ions, excessive ROS production causes pathophysiological changes, including DNA damage. Wilson's disease is an autosomal recessive disorder with copper toxicosis due to deficiency of ATP7B protein needed for excreting copper into bile. The Long-Evans Cinnamon (LEC) rat bears a deletion in Atp7b gene and serves as an excellent model for hepatic Wilson's disease. We used a sensitive capillary liquid chromatography-electrospray-tandem mass spectrometry (LC-ESI-MS/MS/MS) method in conjunction with the stable isotope-dilution technique to quantify several types of oxidative DNA lesions in the liver and brain of LEC rats. These lesions included 5-formyl-2'-deoxyuridine, 5-hydroxymethyl-2'-deoxyuridine, and the 5'R and 5'S diastereomers of 8,5'-cyclo-2'-deoxyguanosine and 8,5'-cyclo-2'-deoxyadenosine. Moreover, the levels of these DNA lesions in the liver and brain increased with age and correlated with age-dependent regulation of the expression of DNA repair genes in LEC rats. These results provide significant new knowledge for better understanding the implications of oxidative DNA lesions in transition metal-induced diseases, such as Wilson's disease, as well as in aging and aging-related pathological conditions.

Metabolomics study with gas chromatography-mass spectrometry for predicting valproic acid-induced hepatotoxicity and discovery of novel biomarkers in rat urine

Three different doses of valproic acid (20, 100, and 500 mg/kg/d) are administered orally to Sprague-Dawley rats for 5 days, and the feasibility of metabolomics with gas chromatography-mass spectrometry as a predictor of the hepatotoxicity of valproic acid is evaluated. Body weight is found to decrease with the 100-mg/kg/d dose and significantly decrease with the 500-mg/kg/d dose. Mean excreted urine volume is lowest in the 500-mg/kg/d group among all groups. The plasma level of alpha-glutathione-S-transferase, a sensitive and earlier biomarker for hepatotoxicity, increases significantly with administration of 100 and 500 mg/kg/d; however, there is not a significant difference in alpha-glutathione-S-transferase plasma levels between the control and 20-mg/kg/d groups. Clusters in partial least squares discriminant analysis score plots show similar patterns, with changes in physiological conditions and plasma levels of alpha-glutathione-S-transferase; the cluster for the control and 20-mg/kg/d groups does not clearly separate, but the clusters are separate for 100- and 500-mg/kg/d groups. A biomarker of hepatotoxicity, 8-hydroxy-2'-deoxyguanosine and octanoylcarnitine, is identified from nontargeted and targeted metabolic profiling. These results validate that metabolic profiling using gas chromatography-mass spectrometry could be a useful tool for finding novel biomarkers. Thus, a nontargeted metabolic profiling method is established to evaluate the hepatotoxicity of valproic acid and demonstrates proof-of-concept that metabolomic approach with gas chromatography-mass spectrometry has great potential for predicting valproic acid-induced hepatotoxicity and discovering novel biomarkers.

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.