Search

In urothelial bladder cancer accurate identification of grade and stage is critical for optimal treatment to achieve robust disease control and long-term survival. However, among the initially superficial tumors, which are non-invasive and highly treatable, 20 to 25 % recur, progress to invasive tumors, and metastasize during the patients’ lifetime. Thus, the challenge is to provide risk stratification during the initial diagnosis in order to identify those patients who are unlikely to progress while offering radical therapy to those who are at risk. To address this issue, the field has heavily focused on the discovery of few mutations in potential driver genes. However, recent findings indicate that deregulation of enhancers can play a major role in cancer progression. In this study, we employed DNase-Seq to detect enhancer activities genome-wide in 16 bladder cancer cell lines (BLCs) that included three lineages (T24, UMUC3, 253J lineages) with different tumorigenic and metastatic potentials, and thus represent models of cancer progression and metastasis development. We analyzed the gain and loss of enhancer activity in each BLC lineages as well as in metastatic cell lines relative to non-metastatic cell lines. Our analysis in the T24 lineage revealed a striking feature, a dramatic loss of intronic and distal DHSs (DNase I Hypersensitive sites), during the initial transition to tumorigenic type. During metastatic progression, new enhancer classes emerged and there was an enrichment for association with target organ-specific genes. The analysis of differential DHSs between metastatic and non-metastatic BLCs identified an enhancer signature enriched with lost DHSs in metastatic BLCs where nearby genes were associated with cellular movement/invasion functions. Lost DHSs were also present near key factors such as PPARG, RXRA, FOXA1, TP63, and GATA3, which play a role in urothelial development and differentiation, and the transcription activity of those genes were correlated with the change of enhancer activity. This study identified a set of DHSs that are associated with cancer progression in bladder cancer, and provides a potential clinical application for developing prognostic markers to predict the risk of developing aggressive disease. Citation Format: Sohyoung Kim, Lyuba Varticovski, Qizong Lao, Songjoon Baek, Michael L. Nickerson, Myong-Hee Sung, Lars Grontved, Thompson Bethtrice, Dan Theodorescu, Piyush K. Agarwal, Michael Dean, Gordon Hager. Genome-wide enhancer identify signature predictive of metastatic phenotypes in bladder cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3352. doi:10.1158/1538-7445.AM2017-3352

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