DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry

Hu, Chiung‐Wen; Chang, Yuan-Jhe; Cooke, Marcus S.; Chao, Mu‐Rong

doi:10.1021/acs.analchem.9b04068

Cited by 21 publications

(26 citation statements)

References 44 publications

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“…In the rst pair of masses, m/z 531.2062, was detected by neutral loss of dR resulting in a fragment ion of mass m/z 415.1577, which in turn triggered two MS 3 fragmentation events upon neutral loss of guanine and dR, suggesting that this adduct is a crosslink comprising two dR moieties. Indeed, masses m/z 531.2062 and 415.1577 were assigned to a previously detected crosslink formed by a deoxyguanosine, formaldehyde, and deoxyadenosine (dG-CH 2 -dA) (30).…”

Section: Resultsmentioning

confidence: 95%

Identification of New Candidate Biomarkers to Support Doxorubicin Treatments in Canine Cancer Patients

Walters¹,

Stornetta²,

Jacobs³

et al. 2021

Preprint

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Background: Human and veterinary cancer chemotherapy are undergoing a paradigm shift from a “one size fits all” approach to personalized, patient-oriented treatment strategies. Personalized chemotherapy is dependent on the identification and validation of biomarkers that can predict treatment outcome and/or risk of toxicity. Many cytotoxic chemotherapy agents, including doxorubicin, base their mechanism of action by interaction with DNA and disruption of normal cellular processes. We developed a high-resolution/accurate-mass liquid chromatography-mass spectrometry DNA screening approach for doxorubicin-induced DNA modifications (adducts) in vitro and in vivo. We used, for the first time, a new strategy involving the use of isotope-labeled DNA, which greatly facilitates adduct discovery. The overall goal of this work was to identify doxorubicin-DNA markers to be used as tools to predict drug efficacy for use in veterinary oncology. Results: We used our novel mass spectrometry approach to screen for adducts in purified DNA exposed to doxorubicin. This initial in vitro screening identified nine potential doxorubicin-DNA adduct masses, as well as an intense signal corresponding to DNA-intercalated doxorubicin. Two of the adduct masses, together with doxorubicin and its metabolite doxorubicinol, were subsequently detected in vivo in liver DNA extracted from mice exposed to doxorubicin. Finally, the presence of these adducts and analytes was explored in the DNA isolated from dogs undergoing treatment with doxorubicin. The previously identified nine DOX-DNA adducts were not detected in these preliminary three samples collected seven days post-treatment, however intercalated doxorubicin and doxorubicinol were detected. Conclusions: This work sets the stage for future evaluation of candidate DNA-related markers as biomarkers to personalize chemotherapy protocols for canine cancer patients. It demonstrates our ability to combine in one method the analysis of DNA adducts and DNA-intercalated doxorubicin and doxorubicinol, which interestingly, were persistent in samples from canine patients undergoing doxorubicin chemotherapy seven days after treatment. The presence of doxorubicin in all samples suggests a role for it as a promising biomarker for use in veterinary chemotherapy. Future studies will involve the analysis of more samples from canine cancer patients to elucidate optimal timepoints for monitoring doxorubicin-DNA adducts and the correlation of these markers with therapy outcome.

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Section: Resultsmentioning

confidence: 95%

Identification of New Candidate Biomarkers to Support Doxorubicin Treatments in Canine Cancer Patients

Walters¹,

Stornetta²,

Jacobs³

et al. 2021

Preprint

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“…However, this approach is currently largely limited to monoadducts and cannot detect dimeric adducts (e.g. CPD) or modifications which form DNA intra- or inter-strand cross-links, or DNA–protein cross-links, although a method for DNA–DNA cross-links has been reported recently [ 50 ]. The other form of DNA adductomics maps the location of a single type of damage, e.g., CPD, or 8-oxoGua, across the genome (i.e.…”

Section: Methods For Measuring Dna Damagementioning

confidence: 99%

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

Amente

Scala

Majello

et al. 2021

Cell. Mol. Life Sci.

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Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.

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“…Previously, we reported a cellular DNA adductomics approach 45 , then a HRMS approach 46 , and broadened the range of targets to include DDCL (i.e., crosslinkomics) 47 . Recently, RNA adductomics was reported, which uses neutral loss targeting of the [M+H] + > [M+H-132] + transitions, in which 132 Da corresponds to the neutral loss of the 2-ribose (R) 48 .…”

Section: Introductionmentioning

confidence: 99%

“…Test solutions were prepared by dissolving various commercially available standards in deionized water, including modified 2’-dN, modified rN, modified nB. For the DDCL, RRCL, DPCL and RPCL, these were synthesized by incubating native 2’-deoxynucleosides (i.e., dGuo, dAdo, dCyd and dThd), ribonucleosides (i.e., Guo, Ado, Cyd and Urd), and/or cysteine, with formaldehyde 47 . The fragmentation patterns were obtained using a LC-Q-LIT-OT-MS equipped with a heated electrospray ionization source, operated in positive ESI-CID mode.…”

Section: Introductionmentioning

confidence: 99%

Nucleic Acid Adductomics – the Next Generation of Adductomics for Assessing Environmental Health Risk

Cooke

Chang

Chen

et al. 2022

Preprint

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The exposome describes the totality of internal and external environmental exposures, across the life course. Components of the exposome have been linked to an increased risk of various, major diseases. To identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed to link exposure, cellular consequences, and health/disease. The most biologically informative biomarkers of the exposome should, to varying extents, reflect the dose of the exposure on the body or target organ(s), a subsequent effect on the biological system and, ideally, possess a role in disease. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and while cellular DNA adductomics aims to evaluate the totality to DNA modifications in the genome, an approach which encompasses modifications of all nucleic acids, would be far more comprehensive, and therefore informative. To address this, we propose a cellular and urinary NA adductomics approach for the assessment of both DNA and RNA modifications, including modified (2-deoxy)ribonucleosides (2dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). Supporting the feasibility of this approach, we presented preliminary, proof-of-principle results, which revealed the presence of over 1,000 modified NA moieties, and at least six types of NA modifications, in a representative, pooled urine from healthy subjects, including modified 2-dN, modified rN, modified nB, DRCL, RRCL and RPCL, many of which were novel/unexpected. We suggest that NA adductomics will provide a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.

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DNA Crosslinkomics: A Tool for the Comprehensive Assessment of Interstrand Crosslinks Using High Resolution Mass Spectrometry

Cited by 21 publications

References 44 publications

Identification of New Candidate Biomarkers to Support Doxorubicin Treatments in Canine Cancer Patients

Identification of New Candidate Biomarkers to Support Doxorubicin Treatments in Canine Cancer Patients

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

Nucleic Acid Adductomics – the Next Generation of Adductomics for Assessing Environmental Health Risk

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