Frequent copy number increase of CCND1 or CDK4 in melanomas without mutations in BRAF and RAS genes

1671 The major etiologic factor for malignant melanoma is UV light. However, melanoma most commonly affects intermittently rather than chronically sun-exposed skin, and can also be found in sites that are substantially or completely sun-protected. We hypothesized that this variability could be explained by the existence of biologically and genetically distinct types of melanoma with different etiologic susceptibility to UV-light. We compared the DNA copy number status using array CGH and mutational status in BRAF and RAS genes of 126 primary melanomas arising in four UV exposure groups: skin with (n=30) and without (n=40) chronic sun damage; palms, soles and subungual (acral) sites (n=36); and mucosa (n=20). Using a supervised methodology we found significant differences in the frequencies of regional DNA copy number changes and mutation frequencies in BRAF between the four groups. Based on the copy number changes alone samples could be correctly classified into the four groups with 70% overall accuracy. In two-way comparisons, melanomas arising on skin with and without signs of chronic sun-damage could be correctly classified with 84% accuracy. Similarly acral could be distinguished from mucosal melanoma with 89% accuracy. Mutation in RAS genes occurred exclusively in samples without BRAF mutation and most commonly affected NRAS. Whereas 81% of melanomas on skin without chronic sun-damage had mutations in either BRAF or NRAS, the majority of melanomas in the other groups had mutations in neither gene (acral;67%, mucosal; 84%, CSD; 67%). Melanomas that were wild-type for BRAF and RAS genes showed common copy number increases by array CGH targeting down-stream components of the RAS-BRAF pathway such as CDK4 or CCND1. Amplifications of CDK4 and CCND1 were exclusive of each other. In addition we observed that BRAF but not RAS mutations were frequently paralleled by loss of PTEN, confirming the notion that activation of the PI3-Kinase pathway via PTEN loss or RAS mutation is an independent somatic target in primary melanoma. The divergent patterns of genetic alterations in melanomas of different anatomic sites and sun exposure patterns indicate distinct genetic pathways to melanoma with implications for the design of future clinical and experimental studies. The demonstration of the strong complimentarity of genetic alterations in BRAF, NRAS, CDK4 and CCND1 implicates CDK4 and CCND1 as independent oncogenes in melanomas wild-type for BRAF and NRAS.