Abstract 3153: Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer.
Authors: Nordentoft Iver K. , Birkenkamp-Demtroder Karin , Lamy Philippe , Reinert Thomas , Fristrup Niels , Skou Pedersen Jakob , Vang Søren , Hedegaard Jakob , Thorsen Kasper , Borre Michael , Dyrskjøt Lars , Falck Ørntoft Torben 
Published: August 2014

Abstract
Bladder cancer (BC) is a common malignancy with the highest incidence rates found in Europe and United
States where it rates as the fifth and fourth most common malignancy, respectively. There are two clinically distinct groups of BC, non-muscle invasive (NMIBC) and muscle invasive bladder tumors (MIBC) accounting at diagnosis for 75% and 25%, respectively, and demanding very different treatments. NMIBC have the highest cancer recurrence rate observed (50-70%) and often necessitates lifelong surveillance, however the prognosis is relatively good. MIBC in contrast often progresses and develop systemic disease. To improve the treatment of BC it is essential to understand the disease biology and to be able to predict disease progression. In this study we applied the advance of next generation sequencing technology to annotate genomic mutations and genomic rearrangements to base pair resolution in four metachronous BC cases (&gt;90% tumor cells) progressing from
Ta to T1 or T2, and matching blood. Furthermore, we explored clonal relationship among the initial tumor and the progressing tumor. Each sample was sequenced to 40-50 x whole genome coverage, 200 x targeted Exome sequencing, and 65 million paired end reads of whole transcriptome RNA-seq. Eight normal urothelium biopsies from BPH patients were used as reference for the RNA-seq. Notably we identified genetic high impact alterations in KDMA6A, PIK3CA, ZNF233, FGFR3, UBE3C, TMEM128, HOXA11,
HOXA2, ELF3, TP53, KAT2B and DYRK3 (corrected for background mutation rate). We annotated a total of 559 unique deletions, translocations, insertions and inversions. In total, 120 of these DNA breaks were selected for validation with
PCR and Sanger sequencing (80% validation rate). Ingenuity pathway analysis identified 19 canonical pathways significantly affected in four out of 8 samples. Currently we are validating the SNV findings in 50 BC samples using
Exome-Seq and RNA-seq. Furthermore, protein expression of selected genes are validated by immunohistochemistry on FFPE tissue sections from the discovery samples and on a tissue microarray containing 290 cores from Ta and T1 tumors in order to correlate protein expression to disease specific survival. All sequencing was performed on the Illumina HiSeq platform. The results reveal promising descriptive and potentially predictive knowledge that may help determine the genomic fingerprint facilitating progression of NMIBC to MIBC.
Citation Format: Iver K. Nordentoft, Karin Birkenkamp-Demtroder, Philippe Lamy, Thomas Reinert, Niels Fristrup, Jakob Skou Pedersen, Søren Vang, Jakob Hedegaard, Kasper Thorsen, Michael Borre, Lars Dyrskjøt, Torben Falck Ørntoft. Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3153. doi:10.1158/1538-7445.AM2013-3153