Abstract 474: Changes in global chromatin landscape identify bladder cancer progression
Authors: Kim Sohyoung , Varticovski Lyuba , Grontved Lars , Baek Songjoon , Thompson Bethrice , Dean Michael , Theodoresco Daniel , Nickerson Michael L. , Hager Gordon L. 
Published: May 2015

Abstract
Bladder cancer is the 4th most common cancer in men in the US and metastatic disease has a poor prognosis. To date, only few mutations in cancer driving genes have been identified in this tumor. Altered gene expression involving an estimate of &gt;2,300 coding sequences is reported in high-grade bladder cancer. In addition to previously reported mutations in KRAS, FGFR3 and TPp53, recent data showed frequent deletions and mutations in genes involving several chromatin modifiers, such as UTX (KDM6A). These data indicate that chromatin organization may play an important role in bladder cancer development and progression. The process of in vivo passaging of a poorly tumorigenic bladder cells (T24) with subsequent injection into mice and selection for tumorigenic and metastatic phenotype specifically to the lung and liver, provides a unique opportunity for analysis of mechanisms associated with tumor development and progression.
We compared whole exome sequencing and mRNA expression with analysis of DNase I hypersensitivity combined with deep sequencing (DHS-seq) on multiple cell lines developed by in vivo selection. Bioinformatics of DHS-seq was performed using algorithms developed at LRBGE. Analysis of microarray expression was performed using Ingenuity Pathways (IPA).
Mutations in several genes, including TP53, RAS, TERT and chromatin remodeler UTX (KDM6A), were detected in parent cell line, T24. Only few additional mutations marked the progression to the metastatic phenotype. Changes in gene expression were already evident in progression from parental cells that were weakly tumorigenic (T24) to cells that were capable to form tumors in mice, but rarely formed metastasis (T24T). The highest score was assigned to genes involved in Cell-to-Cell interaction. Prominent changes included genes involved in cell adhesion and genes associated with EMT, followed by changes in genes associated with cancer. Thus, during the progression from weakly tumorigenic to fully tumorigenic but weakly metastatic cell type, bladder cancer cells acquired gene expression and chromatin landscape changes associated with tumor formation and metastasis. Gene expression profile for most genes correlated with nearby chromatin remodeling of regulatory regions. In addition, DHS analysis identified many novel areas of changes, termed “hot spots” which were located in upstream or downstream enhancer regions. Some of these changes were unique for each stage of tumor progression. Genome-wide analysis of DHS showed large-scale changes in chromatin landscape during tumorigenesis indicating massive reprogramming of regulatory networks during cancer development and progression. Thus, combination of exome sequencing with microarray gene expression and analysis of global unbiased chromatin landscape provides valuable new information on bladder cancer biology and tumor progression.
Citation Format: Sohyoung Kim, Lyuba Varticovski, Lars Grontved, Songjoon Baek, Bethrice Thompson, Michael Dean, Daniel Theodoresco, Michael L. Nickerson, Gordon L. Hager. Changes in global chromatin landscape identify bladder cancer progression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 474. doi:10.1158/1538-7445.AM2014-474