Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma
Article first published online: 19 SEP 2008
Copyright © 2008 Wiley-Liss, Inc.
Genes, Chromosomes and Cancer
Volume 48, Issue 1, pages 10–21, January 2009
How to Cite
Bonazzi, V. F., Irwin, D. and Hayward, N. K. (2009), Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma. Genes Chromosom. Cancer, 48: 10–21. doi: 10.1002/gcc.20615
- Issue published online: 3 NOV 2008
- Article first published online: 19 SEP 2008
- Manuscript Accepted: 9 AUG 2008
- Manuscript Received: 20 MAY 2008
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 profiling 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 confirmation, we followed up 8 genes (AKAP12, ARHGEF16, ARHGAP27, ENC1, PPP1R3C, PPP1R14C, RARRES1, and TP53INP1) by quantitative DNA methylation analysis using mass spectrometry of base-specific cleaved amplification products in panels of melanoma cell lines and fresh tumors. PPP1R3C, ENC1, RARRES1, and TP53INP1, showed reduced mRNA expression in 35–59% of the melanoma cell lines compared to melanocytes and which was correlated with a high proportion of promoter methylation (>40–60%). The same genes also showed extensive promoter methylation in 6–25% of the tumor samples, thus confirming them as novel candidate TSGs in melanoma. © 2008 Wiley-Liss, Inc.