Abstract 4846: Genomic analysis of high grade bladder cancer: Defining genetic subtypes and therapeutic targets
Authors: Iyer Gopa , Al-Ahmadie Hikmat , Taylor Barry S. , Janakiraman Manickam , Lin Oscar , Socci Nicholas D. , Heguy Adriana , Viale Agnes , Bochner Bernard , Bajorin Dean , Milowsky Matthew , Solit David 
Published: June 2012

Abstract
Background: Genomic instability, as manifested by copy number alteration (CNA) and mutation, is a hallmark of cancer. We sought to characterize the spectrum of CNAs in 97 high-grade bladder tumors (HGBT) using high-resolution comparative genomic hybridization (CGH). We then performed an integrated analysis of CNA and targeted mutation testing to construct a comprehensive profile of genomic alterations in these tumors and to identify any correlation with clinical outcome.
Methods: Genomic DNA from 97 frozen HGBTs (tumor content&gt;70% or greater) and commercially available normal human DNA (Roche) were labeled with cyanine-based fluorescent dyes and hybridized onto a one-million oligonucleotide microarray (Agilent) followed by scanning and image analysis. High-throughput Sanger sequencing of select genes was performed with validation of hotspot oncogene mutations using a mass spectrometry based multiplex Sequenom assay.
Results: We found that 47% of HGBT samples possessed a high degree of CNA with widespread amplifications and deletions while 53% contained markedly fewer numbers of events. A non-overlapping pattern of mutations and amplifications was observed when events were grouped within the context of specific signal transduction or cell cycle pathways. Preliminary survival analysis suggests that patients in the high CNA group have a worse prognosis than those in the low CNA group: fifteen out of 46 patients (33%) in the high CNA group have died of their disease vs. 9 of 51 (18%) in the low CNA group. Highly focal amplification events were noted within HER2 (5% of samples), E2F3 (11%), and CCND1 (10%). Immunohistochemistry (IHC) confirmed 3+ overexpression of HER2 in 5 of 5 samples exhibiting genetic amplification. Deletion events were most frequent in CDKN2A (13%). A subset of 11 tumors with small-cell histologic features was included within the samples analyzed and 45% of these tumors possessed E2F3 amplification vs. only 8% within the non-small cell tumor set. Targeted sequencing of select genes revealed that the majority of mutation events occurred within the high-CNA HGBTs.
Conclusions: Distinct genetic subsets exist within HGBT and can be classified based on CNA and mutational analysis. The finding of focal amplification events within genes known to drive tumorigenesis in other contexts, such as HER2, underscores the need for global genomic approaches in identifying targets for therapy in bladder cancer. Small-cell bladder cancer may possess a distinct genetic signature characterized by E2F3 amplification. The non-overlapping pattern of CNAs and mutations seen within specific mitogenic pathways suggests that focal driver lesions can be identified for targeted therapies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4846. doi:10.1158/1538-7445.AM2011-4846