Identification of Candidate Tumor Suppressor Genes Inactivated by Promoter Methylation in Melanoma

Tumor suppressor genes (TSGs) are sometimes inactivated by transcriptional silencing through promoter hypermethylation. To identify novel methylated TSGs in melanoma, we carried out global mRNA expression proling on a panel of 12 melanoma cell lines treated with a combination of 5-Aza-2-deoxycytidine (5AzadC) and an inhibitor of histone deacetylase, Trichostatin A. Reactivation of gene expression after drug treatment was assessed using Illumina whole-genome microarrays. After qRT-PCR conrmation, we followed up 8 genes (AKAP12, ARHGEF16, ARHGAP27, ENC1, PPP1R3C, PPP1R14C, RARRES1, and TP53INP1) by quantitative DNA methylation analysis using mass spectrometry of base-specic cleaved amplication products in panels of melanoma cell lines and fresh tumors. PPP1R3C, ENC1, RARRES1, and TP53INP1, showed reduced mRNA expression in 3559% of the melanoma cell lines compared to melanocytes and which was correlated with a high proportion of promoter methylation (>4060%). The same genes also showed extensive promoter methylation in 625% of the tumor samples, thus conrming them as novel candidate TSGs in melanoma.

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Bonazzi VF, Irwin D, Hayward NK