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.