title: Development of a novel approach, the epigenome-based outlier approach, to identify tumor-suppressor genes silenced by aberrant DNA methylation.
abstract: Identification of tumor-suppressor genes (TSGs) silenced by aberrant methylation of promoter CpG islands (CGIs) is important, but hampered by a large number of genes methylated as passengers of carcinogenesis. To overcome this issue, we here took advantage of the fact that the vast majority of genes methylated in cancers lack, in normal cells, RNA polymerase II (Pol II) and have trimethylation of histone H3 lysine 27 (H3K27me3) in their promoter CGIs. First, we demonstrated that three of six known TSGs in breast cancer and two of three in colon cancer had Pol II and lacked H3K27me3 in normal cells, being outliers to the general rule. BRCA1, HOXA5, MLH1, and RASSF1A had high Pol II, but were expressed only at low levels in normal cells, and were unlikely to be identified as outliers by their expression statuses in normal cells. Then, using epigenome statuses (Pol II binding and H3K27me3) in normal cells, we made a genome-wide search for outliers in breast cancers, and identified 14 outlier promoter CGIs. Among these, DZIP1, FBN2, HOXA5, and HOXC9 were confirmed to be methylated in primary breast cancer samples. Knockdown of DZIP1 in breast cancer cell lines led to increases of their growth, suggesting it to be a novel TSG. The outliers based on their epigenome statuses contained unique TSGs, including DZIP1, compared with those identified by the expression microarray data. These results showed that the epigenome-based outlier approach is capable of identifying a different set of TSGs, compared to the expression-based outlier approach.
authors.affiliation: Division of Epigenomics, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan.
authors.forename: Mizuho
authors.initials: M
authors.lastname: Kikuyama
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Takeshima
authors.forename: Takayuki
authors.initials: T
authors.lastname: Kinoshita
authors.forename: Eriko
authors.initials: E
authors.lastname: Okochi-Takada
authors.forename: Mika
authors.initials: M
authors.lastname: Wakabayashi
authors.forename: Sadako
authors.initials: S
authors.lastname: Akashi-Tanaka
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Ogawa
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Seto
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Ushijima
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D018899:CpG Islands; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D011401:Promoter Regions, Genetic; D025521:Tumor Suppressor Proteins / Q000235:genetics*
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C492524:DZIP1 protein, human; D025521:Tumor Suppressor Proteins