Somatic Copy Number Alterations by Whole Exome Sequencing Reveals YWHAZ and PTK2 as Potential Therapeutic Targets in Castration Resistant Prostate Cancer
Kerstin Ruenauver, Roopika Menon, Mario Deng, Friedrich Kunze, Diana Bohm, Wenzel Vogel, Veit Scheble, Falko Fend, Glen Kristiansen, Nicolas Wernert, Nicole Oberbeckmann, Saskia Biskup, Mark Rubin, Zaki Shaikhibrahim, Sven Perner. Institute of Pathology, University Hospital of Bonn, Bonn, Germany; University Hospital of Tuebingen, Tuebingen, Germany; CeGaT GmbH, Tuebingen, Germany; Weill Cornell Medical College of Cornell University, New York, NY; Institute of Pathology, University Hospital of Tuebingen, Tuebingen, Germany
Background: Castration resistant prostate cancer (CRPC) is the most aggressive form of prostate cancer (PCa) with a poor prognosis and remains a therapeutic challenge. The key to the development of novel therapeutic targets for CRPC is to decipher the molecular alterations underlying this lethal disease. The aim of our study was to identify therapeutic targets for CRPC by assessing somatic copy number alterations (SCNA) by whole exome sequencing on five CRPC/normal paired formalin fixed paraffin embedded (FFPE) samples.
Design: Genomic DNA was extracted from 5 CRPC/normal paired FFPE samples and sequenced using the SOLiD4 next generation sequencing (NGS) platform. Data were validated using fluorescence in-situ hybridization (FISH) on a PCa progression cohort containing 352 PCa samples. Gene copy number amplification status, mRNA and protein expression were determined in selected PCa cell lines. In vitro functional assays were performed with specific inhibition or siRNA knockdown in PCa cell lines.
Results: Among a set of known amplified/deleted genes in PCa (PTEN, AR, cMYC, NKX3.1), whole exome sequencing identified the 8q12.2-24.22 region including PTK2 and YWHAZ to be amplified. FISH analysis of this region showed an increasing amplification frequency of PTK2 and YWHAZ with disease progression. PTK2 was amplified in 1% of the localized PCa and 35% of CRPC samples. YWHAZ was amplified in 4% of the localized PCa and 48% of the CRPC samples. High level amplification of PTK2/YWHAZ in PC3 cells was revealed by FISH analysis. PTK2 inhibition using the specific inhibitor TAE226 and YWHAZ siRNA knockdown significantly reduced proliferation and migration in PC3 cells.
Conclusions: Our findings suggest that inhibition of PTK2 and YWHAZ could delay disease progression in CRPC patients harbouring amplification of the latter genes. The validated sequencing data show that FFPE tissue could be a promising alternative for SCNA screening using NGS technologies.
Category: Genitourinary (including renal tumors)
Monday, March 4, 2013 1:00 PM
Poster Session II # 148, Monday Afternoon