Abstract 3560: Genome and RNA sequencing identifies fusion transcripts in bladder cancer
Authors: Iver K. Nordentoft, Karin Birkenkamp-Demtroder, Philippe Lamy, Thomas Reinert, Søren Vang, Jakob Hedegaard, Kasper Thorsen, Lars Dyrskjøt, Jakob Skou Pedersen, Torben Falck Ørntoft
Journal: Cancer Research (2014)

Abstract Urothelial cell carcinoma of the bladder (UCC) is a common malignancy with the highest prevalence rates found in Europe and United States where it rate as the fifth and fourth most common malignancy respectively. Bladder cancer is divided into two clinically divergent groups, non-muscle invasive (NMIBC) and muscle invasive bladder tumors (MIBC) accounting at diagnosis for 75% and 25% respectively and necessitates very different treatments. NMIBC have recurrence rate of 50-70% and often requires lifelong surveillance, however the prognosis is relatively good. In contrast MIBC often progresses and develop systemic disease. The aim of this study was to identify genomic rearrangements producing fusion transcripts in bladder cancer. Translocations in coding regions are known to be associated with malignancy. Especially in liquid tumors translocations are frequent; however the increased throughput in sequencing now identifies translocation associated with many solid tumors. In this study we used next generation sequencing to annotate genomic rearrangements in paired bladder cancer tumors (&amp;gt;90% tumor cells) presenting as Ta tumors and progressed to T1 or T2. Tumors were sequenced to 40-50x whole genome read depth (blood to &amp;gt;50x) and 65 million paired end reads of whole transcriptome RNAseq. Combining DNA and RNAseq, genomic rearrangements leading to expressed fusion transcript were identified (nFUSE, McPherson AW et. al. Genome Res. 2012 Jun 28). Approximately 25% of the predicted fusions could be validated using Sanger sequencing of cDNA. Importantly more than 80% of the fusions were only present in one of the paired tumors and primarily in the advanced tumor. Most of the fusions were out of frame and created truncated proteins. Two examples are truncation of metastasis suppressor 1 (MTSS1) and polymerase beta (POLB) both frequently mutated in cancer. As an interesting example of in frame fusions we found CTNNBL1 (Beta-Catenin-Like Protein 1) to be fused to FAM110A (family with sequence similarity 110, member A). Importantly the fusion places the promoter of CTNNBL1 in front of FAM110A and because the reading frame is preserved it is likely that both the start codon of CTNNBL1 and FAM110A can serve as translation start giving rise to nearly identical proteins. Furthermore, expression analysis showed significant increase of FAM110A expression in the affected tumor pair sample. Little is known about the FAM110 gene family, however they are shown to localizes to centrosomes and spindle poles and could potentially play an essential role in chromosome segregation and thereby cancer development. All sequencing was performed on the Illumina HiSeq platform. Citation Format: Iver K. Nordentoft, Karin Birkenkamp-Demtroder, Philippe Lamy, Thomas Reinert, Søren Vang, Jakob Hedegaard, Kasper Thorsen, Lars Dyrskjøt, Jakob Skou Pedersen, Torben Falck Ørntoft. Genome and RNA sequencing identifies fusion transcripts in bladder cancer. [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 3560. doi:10.1158/1538-7445.AM2014-3560