Abstract A11: Role of chromatin remodeler mutations in urothelial cell carcinoma of the bladder
Authors: Duymich Christopher E. , Charlet Jessica , Liang Gangning , Jones Peter A. 
Published: August 2014

Abstract
Traditionally cancer is viewed as a disease driven by the accumulation of genetic alterations; nowadays this view has been expanded to include epigenetic alterations. Recent developments such as exome-sequencing have enabled researchers to analyze the entire exome of cancer cell lines and tissue samples to determine possible genetic mutations causing tumor onset/progression, leading to improved disease prognosis and treatment therapies. These studies have uncovered that genes encoding components of the epigenetic machinery are frequently mutated in urothelial cell carcinoma (UCC) of the bladder and many other tumor types. The effects of these mutations on the epigenetic landscape, e.g. DNA methylation, histone modification, and nucleosome positioning are as yet unknown. Given that the disruption of normal epigenetic patterns contributes to carcinogenesis, it is critical to study the effect of genetic alterations on the epigenome, since the latter are reversible by pharmacological intervention.
In this study, we sequenced the exomes of 15 bladder cancer cell lines and compared them to 17 additional cell lines analyzed by the Cancer Cell Line Encyclopedia (CCLE). We have identified that epigenetic regulators in UCC of the bladder are commonly mutated, confirming other reports pertaining to UCC. The most frequently mutated genes include chromatin regulators such as KDM6A, ARID1A, HDAC4, and CREBBP. In addition to the discovery of genetic modifications in UCC cell lines, we studied the potential impact of these mutations on DNA methylation and nucleosome positioning by performing the Infinium Human Methylation 450K Array and the novel AcceSssIble assay, which is also based on the 450K array; comparing M.SssI CpG methyltransferase treated chromatin samples against controls, leading to the identification of nucleosome occupied CpG sites.
To identify possible correlations between chromatin regulator mutations and DNA methylation patterns, we compared UCC cell lines bearing a specific chromatin regulator mutation to cell lines without the mutation and searched for significantly differentially methylated CpG sites. We found that UCC cell lines with mutations in ARID1A and HDAC4 show significant DNA methylation changes compared to cell lines not carrying the mutation. Our results show a possible direct impact of genetic mutations leading to epigenetic changes that may contribute to the tumor phenotype and might lead to novel therapeutic targets in UCC.
Further studies will determine the effects of these specific chromatin regulator mutations on their target gene expression, DNA methylation and nucleosome occupancy. Loss and gain of function studies of these chromatin regulators will further our understanding of their roles in UCC tumor progression. The target genes of these studies will be further interrogated with commonly used epigenetic drugs such as 5-Azacitidine and HDAC inhibitors.
Citation Format: Christopher E. Duymich, Jessica Charlet, Gangning Liang, Peter A. Jones. Role of chromatin remodeler mutations in urothelial cell carcinoma of the bladder. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A11.