DNA methylation subgroups in melanoma are associated with proliferative and immunological processes

BACKGROUND: DNA methylation at CpG dinucleotides is modified in tumorigenesis with potential impact on transcriptional activity. METHODS: We used the Illumina 450 K platform to evaluate DNA methylation patterns of 50 metastatic melanoma tumors, with matched gene expression data. RESULTS: We identified three different methylation groups and validated the groups in independent data from The Cancer Genome Atlas. One group displayed hypermethylation of a developmental promoter set, genome-wide demethylation, increased proliferation and activity of the SWI/SNF complex. A second group had a methylation pattern resembling stromal and leukocyte cells, over-expressed an immune signature and had improved survival rates in metastatic tumors (p < 0.05). A third group had intermediate methylation levels and expressed both proliferative and immune signatures. The methylation groups corresponded to some degree with previously identified gene expression phenotypes. CONCLUSIONS: Melanoma consists of divergent methylation groups that are distinguished by promoter methylation, proliferation and content of immunological cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12920-015-0147-4) contains supplementary material, which is available to authorized users.