title: Aberrantly methylated genes in human papillary thyroid cancer and their association with BRAF/RAS mutation.
abstract: Cancer arises through accumulation of epigenetic and genetic alteration. Aberrant promoter methylation is a common epigenetic mechanism of gene silencing in cancer cells. We here performed genome-wide analysis of DNA methylation of promoter regions by Infinium HumanMethylation27 BeadChip, using 14 clinical papillary thyroid cancer samples and 10 normal thyroid samples. Among the 14 papillary cancer cases, 11 showed frequent aberrant methylation, but the other three cases showed no aberrant methylation at all. Distribution of the hypermethylation among cancer samples was non-random, which implied existence of a subset of preferentially methylated papillary thyroid cancer. Among 25 frequently methylated genes, methylation status of six genes (HIST1H3J, POU4F2, SHOX2, PHKG2, TLX3, HOXA7) was validated quantitatively by pyrosequencing. Epigenetic silencing of these genes in methylated papillary thyroid cancer cell lines was confirmed by gene re-expression following treatment with 5-aza-2'-deoxycytidine and trichostatin A, and detected by real-time RT-PCR. Methylation of these six genes was validated by analysis of additional 20 papillary thyroid cancer and 10 normal samples. Among the 34 cancer samples in total, 26 cancer samples with preferential methylation were significantly associated with mutation of BRAF/RAS oncogene (P = 0.04, Fisher's exact test). Thus, we identified new genes with frequent epigenetic hypermethylation in papillary thyroid cancer, two subsets of either preferentially methylated or hardly methylated papillary thyroid cancer, with a concomitant occurrence of oncogene mutation and gene methylation. These hypermethylated genes may constitute potential biomarkers for papillary thyroid cancer.
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo Tokyo, Japan ; Department of Metabolic Care and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo Tokyo, Japan.
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Kikuchi
authors.affiliation: Department of Metabolic Care and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo Tokyo, Japan.
authors.forename: Eiichi
authors.initials: E
authors.lastname: Tsuji
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo Tokyo, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Yagi
authors.affiliation: Department of Pathology, Graduate School of Medicine, The University of Tokyo Tokyo, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Matsusaka
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo Tokyo, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Tsuji
authors.affiliation: Department of Breast and Endocrine Surgery, Kawasaki Medical University Okayama, Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Kurebayashi
authors.affiliation: Department of Metabolic Care and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo Tokyo, Japan.
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Ogawa
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo Tokyo, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo Tokyo, Japan ; Department of Molecular Oncology, Graduate School of Medicine, Chiba University Chiba, Japan ; CREST, Japan Science and Technology Agency Saitama, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kaneda
keywords: BRAF; CIMP (CpG island methylator phenotype); DNA methylation; RAS; oncogene mutation; thyroid cancer