Abstract A10: Higher incidence of epigenomic alterations on BRAF and NRAS wild type melanoma brain metastases
Authors: Marzese Diego M. , Huynh Jamie L. , Huang Sharon K. , Barkhoudarian Garni , Kelly Daniel F. , Hoon Dave S.B. 
Published: May 2016

Combined BRAF and NRAS gene mutations (mt) account for 70-80% of metastatic melanomas. Patients with BRAFmt benefit from novel targeted therapies; however, patients without this mutation lack effective targeted therapies. We have recently demonstrated that epigenetic alterations are alternative melanoma brain metastasis (MBM) drivers. Here, we propose that identifying epigenome-wide alterations on patients with MBM BRAF and NRAS wild type can identify novel epigenetic drug-based therapies. We performed targeted sequencing to cover the complete exon coverage of mutations of the BRAF and NRAS genes. Firstly, this analysis revealed a mutual exclusivity between BRAFmt and NRASmt. Of the 79% (100/127) of MBMs that carried BRAF or NRAS mutations, 57.5% (73/127) were BRAFmt and 21.2% (27/127) were NRASmt. The remaining 21.2% (27/127) were double wild type (BRAFwt/NRASwt). To identify genome-wide DNA methylation differences between MBMs harboring BRAFmt, NRASmt, or BRAFwt/NRASwt, we generated methylome maps of each MBM type using the Human methylation 450K BeadChip. BRAFwt/NRASwt MBMs presented a significantly higher methylation level (mean = 51% methylation level) than MBMs with NRASmt (mean = 48%) or BRAFmt (mean = 47% methylation level; P&lt;0.001), suggesting a higher influence of epigenetic alterations. 1,598 CpG sites were significantly differentially methylated in BRAFwt/NRASwt MBMs (FDR-corrected P&lt;0.05). Among the most affected genes, we identified significant enrichment on gene networks involved in oncogenic and pro-metastatic functions. These gene networks include apoptosis cascade, adhesion molecules, autophagy regulation, cell cycle regulation, ganglioside metabolism, homeotic and paralog genes (mainly from HOXA gene cluster, PAX6 and PAX7 genes), invasion mechanisms (including multiple metalloproteinase genes), oncogenic growth signaling (including BRAF, PI3K, RAC, and NOTCH pathways, among others), major master transcription factors (including MITF, SOX2, and SOX8), key tumor suppressor genes (including APC, ATM, BRCA1, RB1, and RUNX3, among others), and key epigenome regulatory factors, including DNA methyltransferases (DNMT3B and DNMT3L genes), histone deacetylases (HDAC2, HDAC3, HDAC4, HDAC5 genes) and lysine demethylases (KDM2A, KDM2B, KDM3A, KDM4B, KDM6B genes). Our study suggests the existence of a larger epigenomic alteration influence in double wild type (BRAFwt/NRASwt) MBMs than MBMs with driver mutations on BRAF or NRAS genes and provides the basis for the identification of novel and alternative epigenome-targeted therapies for melanoma patients with MBMs that cannot benefit from current targeted therapies.

Citation Format: Diego M. Marzese, Jamie L. Huynh, Sharon K. Huang, Garni Barkhoudarian, Daniel F. Kelly, and Dave S.B. Hoon. Higher incidence of epigenomic alterations on BRAF and NRAS wild type melanoma brain metastases. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr A10.