Biology of Human Tumors Molecular Characterization of Choroid Plexus Tumors Reveals Novel Clinically Relevant Subgroups

Purpose: To investigatemolecular alterations in choroid plexus tumors (CPT) using a genome-wide high-throughput approach to identify diagnostic and prognostic signatures that will refine tumor stratification and guide therapeutic options. Experimental Design: One hundred CPTs were obtained from a multi-institutional tissue and clinical database. Copynumber (CN), DNA methylation, and gene expression signatures were assessed for 74, 36, and 40 samples, respectively. Molecular subgroups were correlated with clinical parameters and outcomes. Results: Unique molecular signatures distinguished choroid plexus carcinomas (CPC) from choroid plexus papillomas (CPP) and atypical choroid plexus papillomas (aCPP); however, no significantly distinct molecular alterations between CPPs and aCPPswere observed. Allele-specific CNanalysis of CPCs revealed twonovel subgroups according toDNA content: hypodiploid and hyperdiploid CPCs. Hyperdiploid CPCs exhibited recurrent acquired uniparental disomy events. Somatic mutations in TP53 were observed in 60% of CPCs. Investigating the number of mutated copies of p53 per sample revealed a high-risk group of patients with CPC carrying two copies of mutant p53, who exhibited poor 5-year event-free (EFS) and overall survival (OS) compared with patients with CPC carrying one copy of mutant p53 (OS: 14.3%, 95% confidence interval, 0.71%–46.5% vs. 66.7%, 28.2%–87.8%, respectively, P 1⁄4 0.04; EFS: 0% vs. 44.4%, 13.6%–71.9%, respectively, P 1⁄4 0.03). CPPs and aCPPs exhibited favorable survival. Discussion:Our data demonstrate that differences in CN, gene expression, and DNA methylation signatures distinguish CPCs fromCPPs and aCPPs; however,molecular similarities among the papillomas suggest that these twohistologic subgroups are indeed a single molecular entity. A greater number of copies of mutated TP53 were significantly associated to increased tumor aggressiveness and a worse survival outcome in CPCs. Collectively, these findings will facilitate stratified approaches to the clinical management of CPTs. Clin Cancer Res; 21(1); 184–192. 2014 AACR.