Abstract 4783: Novel molecular markers of bladder cancer progression identified by global chromatin profiling
Authors: Lyuba Varticovski, Sohyoung Kim, Michael L. Nickerson, Bethtrice Thompson, Qizong Lao, Lars Grøntved, Songjoon Baek, Myong-Hee Sung, Dan Theodorescu, Michael Dean, Gordon L. Hager
Journal: Cancer Research (2015)

Abstract Bladder cancer (BCa) is the 5th most prevalent cancer in the US, and the metastatic disease has very poor prognosis with 150,000 deaths per year worldwide. The use of molecular markers to predict disease progression has been largely unsuccessful, with only few therapeutically approachable mutations. Over 2,300 alterations in the coding sequences have been described in high-grade bladder cancer, encompassing frequent alterations in genes involving chromatin modifiers. Thus, chromatin organization may play a critical role in this tumor type. The development of tumor progression models from transitional carcinoma samples that are poorly tumorigenic and non-metastatic to highly metastatic to the lung or liver by serial in vivo passaging allows analysis of the mechanisms associated with tumor progression. We examined whole exome sequencing to identify mutations, gene expression, and DNase I hypersensitivity followed by deep sequencing to identify sites of chromatin modification during tumor progression. Bioinformatic analysis of was performed using algorithms developed at LRBGE. Comparative analysis combining multiple data sets was performed using Ingenuity Pathways. Mutations in several previously identified genes associated with bladder cancer: TP53, RAS and TERT, and mutations/deletions in several chromatin modifiers KDM6A and MLL2/3 were found in parental cells. Only few additional mutations, none identifiable as cancer driver mutations marked the progression to metastatic phenotype. Changes in gene expression were already evident in progression to tumorigenic state, with high score in cells in cell-to-cell interaction pathway marked by a decrease in cell adhesion, increase in genes associated with EMT and genes associated with cancer. Changes in global chromatin landscape occurred at many known genes correlated with pathways detected by expression analysis, but many were in novel sites distant to promoters, suggestive of novel distant enhancer and confirm massive reprogramming of regulatory networks. Many of these sites were unique for each stage of tumor progression and have potential clinical application. Specific chromatin modifications were found in NFkB and inflammatory pathways. Thus, in the tumorigenic stage, these cells acquired not only the capacity for tumor formation, but also some of the characteristics associated with metastasis. Combination of exome sequencing with the gene expression and unbiased analysis of global chromatin landscape provided valuable new information on bladder cancer biology and tumor progression. Citation Format: Lyuba Varticovski, Sohyoung Kim, Michael L. Nickerson, Bethtrice Thompson, Qizong Lao, Lars Grøntved, Songjoon Baek, Myong-Hee Sung, Dan Theodorescu, Michael Dean, Gordon L. Hager. Novel molecular markers of bladder cancer progression identified by global chromatin profiling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4783. doi:10.1158/1538-7445.AM2015-4783