Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic.

Stable-isotope-dilution tandem mass spectrometry is the most advanced technique used for quantitative determination of a wide spectrum of endogenously generated DNA nucleobase modifications. It is regarded as a gold standard for such analyses. Here, we consider the requirements for reliable identification and quantification of DNA adducts/modifications, whether endogenously derived or not, and discuss how their quantification can provide information on the mechanism of action and the biological relevance of individual nucleobase modifications. A clinical application of such measurements will only be possible after a full validation of the assay and once we have gained a better understanding of the exact role that these DNA modifications play in disease pathogenesis. Once these prerequisites are satisfied, DNA modification measurements may be helpful as clinical parameters for treatment monitoring, for risk group identification and for the development of prevention strategies.

[1]  M. Cooke,et al.  Endogenously generated DNA nucleobase modifications source, and significance as possible biomarkers of malignant transformation risk, and role in anticancer therapy. , 2018, Biochimica et biophysica acta. Reviews on cancer.

[2]  D. Gackowski,et al.  Urinary Measurement of Epigenetic DNA Modifications: A Non‐Invasive Assessment of the Whole‐Body Epigenetic Status in Healthy Subjects and Colorectal Cancer Patients , 2016, ChemistryOpen.

[3]  P. Ueland,et al.  Uracil in human DNA from subjects with normal and impaired folate status as determined by high-performance liquid chromatography-tandem mass spectrometry. , 2002, Analytical chemistry.

[4]  Marek Foksinski,et al.  In vivo evidence of ascorbate involvement in the generation of epigenetic DNA modifications in leukocytes from patients with colorectal carcinoma, benign adenoma and inflammatory bowel disease , 2018, Journal of Translational Medicine.

[5]  J. Irudayaraj,et al.  Quantification of 5-methylcytosine, 5-hydroxymethylcytosine and 5-carboxylcytosine from the blood of cancer patients by an enzyme-based immunoassay. , 2014, Analytica chimica acta.

[6]  Yang Wang,et al.  Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA , 2011, Science.

[7]  A. Meyer,et al.  The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs , 2014, PloS one.

[8]  D. Gackowski,et al.  Enigmatic 5-hydroxymethyluracil: Oxidatively modified base, epigenetic mark or both? , 2016, Mutation research. Reviews in mutation research.

[9]  Z. Ling,et al.  Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation , 2013, Oncogene.

[10]  D. Gackowski,et al.  Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships , 2015, PloS one.

[11]  A. H. Smits,et al.  Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives , 2013, Cell.

[12]  G. Teebor,et al.  5-Hydroxymethylcytosine DNA glycosylase activity in mammalian tissue. , 1988, Biochemical and biophysical research communications.

[13]  H. Krokan,et al.  A robust, sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported. , 2013, DNA repair.

[14]  T. Carell,et al.  Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing. , 2012, Angewandte Chemie.

[15]  A. Ishchenko,et al.  An interplay of the base excision repair and mismatch repair pathways in active DNA demethylation , 2016, Nucleic acids research.

[16]  M. Vermeulen,et al.  Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. , 2014, Nature chemical biology.

[17]  Pål Sætrom,et al.  AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature. , 2015, DNA repair.

[18]  M. Chao,et al.  Direct analysis of 5-methylcytosine and 5-methyl-2'-deoxycytidine in human urine by isotope dilution LC-MS/MS: correlations with N-methylated purines and oxidized DNA lesions. , 2012, Chemical research in toxicology.

[19]  Steffen Loft,et al.  Measurement and Meaning of Oxidatively Modified DNA Lesions in Urine , 2008, Cancer Epidemiology Biomarkers & Prevention.

[20]  Hongjun Song,et al.  Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA , 2013, Nucleic acids research.

[21]  H. Blau,et al.  DNA Demethylation Dynamics , 2011, Cell.

[22]  G. Ficz.  New insights into mechanisms that regulate DNA methylation patterning , 2015, Journal of Experimental Biology.

[23]  Bifeng Yuan,et al.  Sensitive and simultaneous determination of 5-methylcytosine and its oxidation products in genomic DNA by chemical derivatization coupled with liquid chromatography-tandem mass spectrometry analysis. , 2015, Analytical chemistry.

[24]  J. Rzeszowska-Wolny,et al.  Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2′-deoxycytidine level in cultured cancerous cell lines , 2017, PloS one.

[25]  Fan Shen,et al.  Quantification of 5-methylcytosine and 5-hydroxymethylcytosine in genomic DNA from hepatocellular carcinoma tissues by capillary hydrophilic-interaction liquid chromatography/quadrupole TOF mass spectrometry. , 2013, Clinical chemistry.

[26]  T. Carell,et al.  Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. , 2011, Chemistry.

[27]  J. Cadet,et al.  TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. , 2014, Mutation research. Genetic toxicology and environmental mutagenesis.

[28]  D. Gackowski,et al.  Accurate, Direct, and High-Throughput Analyses of a Broad Spectrum of Endogenously Generated DNA Base Modifications with Isotope-Dilution Two-Dimensional Ultraperformance Liquid Chromatography with Tandem Mass Spectrometry: Possible Clinical Implication. , 2016, Analytical chemistry.

[29]  A. Maiti,et al.  Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine , 2011, The Journal of Biological Chemistry.

[30]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[31]  M. Evans,et al.  DNA repair is responsible for the presence of oxidatively damaged DNA lesions in urine. , 2005, Mutation research.

[32]  S. Balasubramanian,et al.  5-Formylcytosine can be a stable DNA modification in mammals. , 2015, Nature chemical biology.

[33]  M. Cooke,et al.  Urinary measurement of 8-OxodG, 8-OxoGua, and 5HMUra: a noninvasive assessment of oxidative damage to DNA. , 2006, Antioxidants & redox signaling.

[34]  H. Aburatani,et al.  Loss of 5‐hydroxymethylcytosine is accompanied with malignant cellular transformation , 2012, Cancer science.

[35]  G. Schackert,et al.  5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. , 2011, Cancer research.

[36]  Svend K. Petersen-Mahrt,et al.  AID and APOBEC deaminases: balancing DNA damage in epigenetics and immunity. , 2014, Epigenomics.

[37]  Abraham J. Khorasani,et al.  Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma , 2012, Cell.

[38]  A. Marszałek,et al.  Characteristic profiles of DNA epigenetic modifications in colon cancer and its predisposing conditions—benign adenomas and inflammatory bowel disease , 2018, Clinical Epigenetics.

[39]  Hailin Wang,et al.  Detection of human urinary 5-hydroxymethylcytosine by stable isotope dilution HPLC-MS/MS analysis. , 2015, Analytical chemistry.

[40]  M. Biel,et al.  Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates , 2010, PloS one.