Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

• Published in: Epigenetics 2013-12, Vol.8 (12), p.1355-1372
• Main Authors: Sánchez-Vega, Francisco, Gotea, Valer, Petrykowska, Hanna M, Margolin, Gennady, Krivak, Thomas C, DeLoia, Julie A, Bell, Daphne W, Elnitski, Laura
• Format: Article
• Language: English
• Subjects: cancer; Carcinoma, Endometrioid - genetics; Carcinoma, Endometrioid - metabolism; CASP8; Caspase 8 - genetics; Cell Line, Tumor; chromatin; Chromatin - genetics; Chromatin - metabolism; DNA Methylation; Endometrial Neoplasms - genetics; Endometrial Neoplasms - metabolism; endometrioid endometrial cancer; endometrioid ovarian cancer; Epigenesis, Genetic; epigenetics; Female; Humans; Kruppel-Like Transcription Factors - genetics; Kruppel-Like Transcription Factors - metabolism; Neoplasms, Glandular and Epithelial - genetics; Neoplasms, Glandular and Epithelial - metabolism; Ovarian Neoplasms - genetics; Ovarian Neoplasms - metabolism; ovarian papillary serous tumors of low malignant potential; pan-cancer; Promoter Regions, Genetic; Research Paper; serous ovarian cancer; VHL; Von Hippel-Lindau Tumor Suppressor Protein - genetics; Zinc Fingers; ZNF154
• ISSN: 1559-2294; 1559-2308
• DOI: 10.4161/epi.26701

The study of aberrant DNA methylation in cancer holds the key to the discovery of novel biological markers for diagnostics and can help to delineate important mechanisms of disease. We have identified 12 loci that are differentially methylated in serous ovarian cancers and endometrioid ovarian and endometrial cancers with respect to normal control samples. The strongest signal showed hypermethylation in tumors at a CpG island within the ZNF154 promoter. We show that hypermethylation of this locus is recurrent across solid human epithelial tumor samples for 15 of 16 distinct cancer types from TCGA. Furthermore, ZNF154 hypermethylation is strikingly present across a diverse panel of ENCODE cell lines, but only in those derived from tumor cells. By extending our analysis from the Illumina 27K Infinium platform to the 450K platform, to sequencing of PCR amplicons from bisulfite treated DNA, we demonstrate that hypermethylation extends across the breadth of the ZNF154 CpG island. We have also identified recurrent hypomethylation in two genomic regions associated with CASP8 and VHL. These three genes exhibit significant negative correlation between methylation and gene expression across many cancer types, as well as patterns of DNaseI hypersensitivity and histone marks that reflect different chromatin accessibility in cancer vs. normal cell lines. Our findings emphasize hypermethylation of ZNF154 as a biological marker of relevance for tumor identification. Epigenetic modifications affecting the promoters of ZNF154, CASP8, and VHL are shared across a vast array of tumor types and may therefore be important for understanding the genomic landscape of cancer.