Untapped biospecimens and novel mass spectrometry scanning techniques for DNA adductomics

A major impediment in the biomonitoring of DNA adducts is the lack of fresh-frozen biopsy samples available for biomarker research. However, archived formalin-fixed, paraffin-embedded (FFPE) tissues with a clinical diagnosis of disease are often accessible. We have established a method to fully unravel DNA crosslinks in FFPE specimens under mild conditions that preserve the structural integrity of DNA adducts. Our targeted, quantitative mass spectrometry measurements employing ion trap or high-resolution Orbitrap mass spectrometry require less than ten micrograms of DNA with limits of quantification at three adducts per 109 nucleotides. We have successfully screened FFPE tissues of rodents exposed to tobacco and dietary carcinogens and reported adduct levels comparable to those of matching fresh-frozen tissues. Our technology has been employed to identify a DNA adduct of aristolochic acid, a potent urothelial carcinogen present in Chinese herbal medicines, in human FFPE kidney blocks stored at ambient temperature for up to nine years. The method also detected DNA adducts of the bladder carcinogen 4-aminobiphenyl in human FFPE bladder, and a DNA adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, a heterocyclic aromatic amine formed in cooked meats and a potential prostate carcinogen, in FFPE prostate specimens of prostate cancer patients. Thus, the technology is versatile and can be employed to screen for DNA adducts formed with a wide range of environmental and dietary carcinogens. The ability to retrospectively analyze FFPE tissues for DNA adducts for which there is a clinical diagnosis of disease opens a previously untapped source of biospecimens for molecular epidemiology studies seeking the causal role of environmental chemicals in cancer etiology. With the recent improvements in the sensitivity and scanning rates of high-resolution MS instruments, such as quadrupole time-of-flight and Orbitrap MS detectors, it is now possible to screen for a wide array of DNA damage in the human genome using DNA adductomics approaches. We have adapted data-dependent and data-independent scanning techniques originated from proteomics and metabolomics to screen for DNA adducts of the genome. DNA adductomics is a new and developing technology for human exposure assessment. As the analytic technology matures and bioinformatics tools become available for analysis of the mass spectral data, DNA adductomics can advance our understanding of the role chemical exposures play in DNA damage and disease risk. Citation Format: Byeong Hwa Yun, Jingshu Guo, Scott Walmsley, Paari Murugan, Christopher J. Weight, Peter W. Villalta, Robert J. Turesky. Untapped biospecimens and novel mass spectrometry scanning techniques for DNA adductomics [abstract]. In: Proceedings of the AACR Special Conference on Environmental Carcinogenesis: Potential Pathway to Cancer Prevention; 2019 Jun 22-24; Charlotte, NC. Philadelphia (PA): AACR; Can Prev Res 2020;13(7 Suppl): Abstract nr A33.