E-GEOD-45266 - Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma

Status
Released on 24 April 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (29)
Array (1)
Protocols (5)
Description
The implication of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic naevus interrogating 14,495 genes using beadchip technology. This first genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C and CLDN11genes was established. Promoter methylation of MAPK13, encoding p38?, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression. Bisulphite converted genomic DNA from 5 fresh-frozen benign naevus and 24 fresh-frozen primary melanoma biopsy samples were hybridised to Illumina's Infinium HumanMethylation27 Beadchips
Experiment type
methylation profiling by array 
Contacts
Linda Gao <geo@ncbi.nlm.nih.gov>, Cornelis P Tensen, Daniel S Peeper, Els M Verdegaal, Jelle J Goeman, Joost J van den Oord, Marguerite Stas, Marjon A Smit, Nelleke A Gruis, Rein Willemze, Remco van Doorn, Samuel Beck, Sjoerd H van der Burg
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-45266.idf.txt
Sample and data relationshipE-GEOD-45266.sdrf.txt
Processed data (1)E-GEOD-45266.processed.1.zip
Array designA-GEOD-8490.adf.txt
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