Abstract 4871: Genomic amplifications in ovarian carcinoma are associated with specific histone modifications

Abstract

Abstract Genomic amplification is a frequent molecular genetic alteration in many cancer types that results in upregulation and thus activation of oncogenes located in the amplified regions. However, the mechanism by which amplified genes are upregulated is poorly understood. We hypothesized that epigenetic regulation of gene expression was important for activation in addition to the increased DNA copy number for genes within amplified genomic loci. To test this hypothesis, we used ovarian cancer as an example because it is a highly lethal disease and, more importantly, ovarian cancer cells are characterized by a high level of genomic instability as reflected by widespread DNA copy number changes. We analyzed the data from chromatin immunoprecipitation array (Chip-chip) and single nucleotide polymorphism (SNP) array to determine the correlation between specific histone modifications and genome-wide DNA copy number alterations in OVCAR3 ovarian cancer cells and ovarian surface epithelial cell culture. Among 8 histone marks examined, representing both heterochromatic and euchromatic chromatin, we identified the strongest correlation between increased DNA copy number and the active histone marks, histone H4 acetylation at lysine 5 (p-value 7.8×10^-6; FDR 5.2×10^-5) and lysine 12 (p-value 7.6×10^-5; FDR 2.6×10^-4). In contrast, there was no significant correlation between DNA amplification and repressive histone marks including histone H3 methylation at lysines 9 and 27. These correlations were validated by quantitative real-time PCR of ChIP samples at confirmed amplified regions on chromosomes 11 and 19, which harbor the RSF1 and AKT2 oncogenes. Furthermore, all genes within the amplicons were overexpressed in the OVCAR3 cell line harboring the amplicons as compared to a normal ovarian surface epithelial cell line. By using ovarian cancer as a disease model, our results indicate that an amplicon-associated specific histone modification pattern facilitates gene expression and suggest that both genetic (DNA copy number gain) and epigenetic (active histone marks) events contribute to upregulation of amplified genes which may ultimately contribute to the development of human cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4871.