Abstract 933: Copy number changes are associated with BRAF and NRAS mutations and response to treatment with carboplatin, paclitaxel and sorafenib
Authors: Wilson Melissa A. , Zhao Fengmin , Khare Sanika , Letrero Richard , D'Andrea Kurt , Rimm David L. , Kirkwood John M. , Kluger Harriet M. , Lee Sandra J. , Schuchter Lynn M. , Flaherty Keith T. , Nathanson Katherine L. 
Published: May 2015

Abstract
Copy number alterations, both gains and losses, have been shown to be involved in melanoma pathogenesis and may provide novel targets for treatment. Previous observations have additionally suggested that specific copy number profiles may be associated with BRAF, NRAS and WT/WT status. The randomized, phase III clinical trial E2603: carboplatin, paclitaxel, +/- sorafenib (CP vs. CPS) offers the largest available collection of tumor samples from patients with well annotated clinical outcome to evaluate these associations. We evaluated copy number variants (CNVs) using array Comparative Genomic Hybridization in melanoma tumor samples from patients treated on this trial. Genomic DNA was hybridized on SurePrint G4 human CGH microarrays 2 x 440 K (Agilent). Copy number gains and losses were ≥ 0.3 or ≤ -0.3 on a log2 scale, respectively (Nexus BioDiscovery, Inc). In 119 melanoma tumor samples, 45% had BRAF mutations, 24% NRAS mutations, and 24% without either (designated WT), CNVs were evaluated in an initial set of 26 genes known to be involved in melanoma pathogenesis. Overall genomic instability, as measured by number of genes with CNVs, was associated with poor ECOG performance status (P=0.007) and marginally significant for more organs with metastatic involvement (P=0.06), and is consistent with other studies suggesting that genomic instability is a predictor of worsened outcome. We further explored the association between copy number and somatic mutation status. Not surprisingly, BRAF gene amplification was observed in 91% of BRAF mutant melanoma tumor samples (P&lt;0.001, as compared to 66% of NRAS/WT samples). The average value of BRAF copy number was higher in tumor samples with BRAF V600K mutations compared to samples with BRAF V600E mutations (1.11 v 0.55, P&lt;0.001). MET, also on chr 7, was found to be amplified in 59% of BRAF mutated melanoma tumor samples. The average value of MET copy number was also higher in BRAF V600K mutant compared to BRAF V600E mutant melanoma (0.53 v 0.27, P=0.04), which may contribute to the differing clinical behaviors of melanomas with the two mutations. Patients with BRAF copy number gain had a trend towards lower overall response rate to either treatment compared to diploid (15.2% v 29.6%, OR=0.37, P=0.08). Patients with NRAS copy number gain receiving CPS had significantly improved overall survival compared to patients receiving CP alone (HR=0.35, P=0.03) in multivariable Cox model. We had previously found a trend suggesting an improved clinical response and PFS in patients with NRAS mutant melanoma treated with CPS as compared to CP. Our present study demonstrates an association between CNVs and treatment response to CP or CPS, as well as an association with somatic mutations. In addition, distinct cooperating genomic events identified in somatic mutation cohorts, such as MET and BRAF V600K gain, may contribute to the pathogenesis of melanoma tumors.
Citation Format: Melissa A. Wilson, Fengmin Zhao, Sanika Khare, Richard Letrero, Kurt D'Andrea, David L. Rimm, John M. Kirkwood, Harriet M. Kluger, Sandra J. Lee, Lynn M. Schuchter, Keith T. Flaherty, Katherine L. Nathanson. Copy number changes are associated with BRAF and NRAS mutations and response to treatment with carboplatin, paclitaxel and sorafenib. [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 933. doi:10.1158/1538-7445.AM2014-933