title: Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure.
abstract: Altered expression of tumor suppressor genes and oncogenes, which is regulated in part at the level of DNA methylation, is an important event involved in non-genotoxic carcinogenesis. This may serve as a marker for early detection of non-genotoxic carcinogens. Therefore, we evaluated the effects of non-genotoxic hepatocarcinogens, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), hexachlorobenzene (HCB), methapyrilene (MPY) and male rat kidney carcinogens, d-limonene, p-dichlorobenzene (DCB), chloroform and ochratoxin A (OTA) on global and CpG island promoter methylation in their respective target tissues in rats. No significant dose-related effects on global DNA hypomethylation were observed in tissues of rats compared to vehicle controls using LC-MS/MS in response to short-term non-genotoxic carcinogen exposure. Initial experiments investigating gene-specific methylation using methylation-specific PCR and bisulfite sequencing, revealed partial methylation of p16 in the liver of rats treated with HCB and TCDD. However, no treatment related effects on the methylation status of Cx32, e-cadherin, VHL, c-myc, Igfbp2, and p15 were observed. We therefore applied genome-wide DNA methylation analysis using methylated DNA immunoprecipitation combined with microarrays to identify alterations in gene-specific methylation. Under the conditions of our study, some genes were differentially methylated in response to MPY and TCDD, whereas d-limonene, DCB and chloroform did not induce any methylation changes. 90-day OTA treatment revealed enrichment of several categories of genes important in protein kinase activity and mTOR cell signaling process which are related to OTA nephrocarcinogenicity.
authors.affiliation: Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey. Electronic address: stopuz@istanbul.edu.tr.
authors.forename: Sibel
authors.initials: S
authors.lastname: Ozden
authors.affiliation: Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey.
authors.forename: Neslihan
authors.initials: N
authors.lastname: Turgut Kara
authors.affiliation: Department of Biostatistics and Medical Informatics, Acibadem University, Istanbul, Turkey.
authors.forename: Osman Ugur
authors.initials: OU
authors.lastname: Sezerman
authors.affiliation: Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey.
authors.forename: İlknur Melis
authors.initials: İM
authors.lastname: Durasi
authors.affiliation: Department of Toxicology, School of Public Health, Soochow University, Suzhou, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
authors.forename: Goksun
authors.initials: G
authors.lastname: Demirel
authors.affiliation: Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
authors.forename: Buket
authors.initials: B
authors.lastname: Alpertunga
authors.affiliation: School of Biosciences, The University of Birmingham, Birmingham, UK.
authors.forename: J Kevin
authors.initials: JK
authors.lastname: Chipman
authors.affiliation: Department of Toxicology, University of Würzburg, Würzburg, Germany.
authors.forename: Angela
authors.initials: A
authors.lastname: Mally
mesh_terms: D000818:Animals; D001483:Base Sequence; D002273:Carcinogens / Q000633:toxicity*; D002471:Cell Transformation, Neoplastic / Q000139:chemically induced / Q000235:genetics / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid; D018899:CpG Islands; D019175:DNA Methylation / Q000187:drug effects*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D007668:Kidney / Q000187:drug effects* / Q000378:metabolism; D007680:Kidney Neoplasms / Q000139:chemically induced* / Q000235:genetics / Q000378:metabolism; D008099:Liver / Q000187:drug effects* / Q000378:metabolism; D008113:Liver Neoplasms / Q000139:chemically induced* / Q000235:genetics / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D011916:Rats, Inbred F344; D021241:Spectrometry, Mass, Electrospray Ionization; D053719:Tandem Mass Spectrometry; D013997:Time Factors
chemical_list: D002273:Carcinogens
keywords: DNA methylation; MeDIP-microarray; Non-genotoxic carcinogen; Rat kidney; Rat liver