Abstract A10: Higher incidence of epigenomic alterations on BRAF and NRAS wild type melanoma brain metastases

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<0.001), suggesting a higher influence of epigenetic alterations. 1,598 CpG sites were significantly differentially methylated in BRAFwt/NRASwt MBMs (FDR-corrected P<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.

Brain metastasis is predetermined in early stages of cutaneous melanoma by CD44v6 expression through epigenetic regulation of the spliceosome

Melanoma brain metastasis (MBM) is frequent and has a very poor prognosis with no current predictive factors or therapeutic molecular targets. Our study unravels the molecular alterations of cell-surface glycoprotein CD44 variants during melanoma progression to MBM. High expression of CD44 splicing variant 6 (CD44v6) in primary melanoma (PRM) and regional lymph node metastases from AJCC Stage IIIC patients significantly predicts MBM development. The expression of CD44v6 also enhances the migration of MBM cells by hyaluronic acid and hepatocyte growth factor exposure. Additionally, CD44v6-positive MBM migration is reduced by blocking with a CD44v6-specific monoclonal antibody or knocking down CD44v6 by siRNA. ESRP1 and ESRP2 splicing factors correlate with CD44v6 expression in PRM, and ESRP1 knockdown significantly decreases CD44v6 expression. However, an epigenetic silencing of ESRP1 is observed in metastatic melanoma, specifically in MBM. In advanced melanomas, CD44v6 expression correlates with PTBP1 and U2AF2 splicing factors, and PTBP1 knockdown significantly decreases CD44v6 expression. Overall, these findings open a new avenue for understanding the high affinity of melanoma to progress to MBM, suggesting CD44v6 as a potential MBM-specific factor with theranostic utility for stratifying patients.

DNA methylation and gene deletion analysis of brain metastases in melanoma patients identifies mutually exclusive molecular alterations

BACKGROUND

The brain is a common target of metastases for melanoma patients. Little is known about the genetic and epigenetic alterations in melanoma brain metastases (MBMs). Unraveling these molecular alterations is a key step in understanding their aggressive nature and identifying novel therapeutic targets.

METHODS

Genome-wide DNA methylation analyses of MBMs (n = 15) and normal brain tissues (n = 91) and simultaneous multigene DNA methylation and gene deletion analyses of metastatic melanoma tissues (99 MBMs and 43 extracranial metastases) were performed. BRAF and NRAS mutations were evaluated in MBMs by targeted sequencing.

RESULTS

MBMs showed significant epigenetic heterogeneity. RARB, RASSF1, ESR1, APC, PTEN, and CDH13 genes were frequently hypermethylated. Deletions were frequently detected in the CDKN2A/B locus. Of MBMs, 46.1% and 28.8% had BRAF and NRAS missense mutations, respectively. Compared with lung and liver metastases, MBMs exhibited higher frequency of CDH13 hypermethylation and CDKN2A/B locus deletion. Mutual exclusivity between hypermethylated genes and CDKN2A/B locus deletion identified 2 clinically relevant molecular subtypes of MBMs. CDKN2A/B deletions were associated with multiple MBMs and frequently hypermethylated genes with shorter time to brain metastasis.

CONCLUSIONS

Melanoma cells that colonize the brain harbor numerous genetically and epigenetically altered genes. This study presents an integrated genomic and epigenomic analysis that reveals MBM-specific molecular alterations and mutually exclusive molecular subtypes.

Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis

Melanoma brain metastasis (MBM) represents a frequent complication of cutaneous melanoma. Despite aggressive multi-modality therapy, patients with MBM often have a survival rate of <1 year. Alteration in DNA methylation is a major hallmark of tumor progression and metastasis; however, it remains largely unexplored in MBM. In this study, we generated a comprehensive DNA methylation landscape through the use of genome-wide copy number, DNA methylation and gene expression data integrative analysis of melanoma progression to MBM. A progressive genome-wide demethylation in low CpG density and an increase in methylation level of CpG islands according to melanoma progression were observed. MBM-specific partially methylated domains (PMDs) affecting key brain developmental processes were identified. Differentially methylated CpG sites between MBM and lymph node metastasis (LNM) from patients with good prognosis were identified. Among the most significantly affected genes were the HOX family members. DNA methylation of HOXD9 gene promoter affected transcript and protein expression and was significantly higher in MBM than that in early stages. A MBM-specific PMD was identified in this region. Low methylation level of this region was associated with active HOXD9 expression, open chromatin and histone modifications associated with active transcription. Demethylating agent induced HOXD9 expression in melanoma cell lines. The clinical relevance of this finding was verified in an independent large cohort of melanomas (n = 145). Patients with HOXD9 hypermethylation in LNM had poorer disease-free and overall survival. This epigenome-wide study identified novel methylated genes with functional and clinical implications for MBM patients.

Identification of functional DNA methylation aberrations associated with outcome in melanoma patients with brain metastasis

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Background: Brain metastasis (MBM) represents one of the most significant causes of death in melanoma patients. Identification of clinically relevant markers is necessary to recognize patients with high risk of MBM development. Alterations in DNA methylation patterns have been recognized as a major epigenetic hallmark of metastasis initiation and progression. Methods: To generate a comprehensive genomic DNA methylation landscape of MBM, we performed genome-wide data integrative analyses examining the DNA methylation (Illumina HumanMethylation 450K), gene expression (Affymetrix HumanExon 1.0), and genotype (Affymetrix SNP 6.0) of specimens related to melanoma progression from normal to MBM (n=65). Results: We observed significant genome-wide hypomethylation and CpG island hypermethylation according to melanoma progression to the brain. To identify significant differentially methylated CpG sites between lymph node metastasis and MBM, we applied a strict statistical threshold (β-value difference >0.3 and FDR-corrected p <0.005). We identified the homeobox D (HOXD) gene family members amongst the most significantly affected genes. The influence on gene expression and the frequency of HOXD hypermethylation were verified using integrative analysis of publicly available data generated from 168 melanoma specimens. In a cohort of clinically annotated melanoma patients (n = 159), we demonstrated that hypermethylation of a genomic region in the HOXD gene cluster was significantly associated with shorter disease-free survival (p = 0.004) and overall survival (p = 0.002).Multivariate analysis confirmed the association with poorer survival (p = 0.01 and HR = 2.8; CI95%: 1.3-6.1). Conclusions: The use of genome-wide DNA methylation, gene expression, and genotyping integrative analyses allowed the identification of novel markers with functional and clinical implications for melanoma patients with brain metastasis.