Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma

Genes Chromosomes Cancer. 2009 Jan;48(1):10-21. doi: 10.1002/gcc.20615.


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.

MeSH terms

  • Azacitidine / analogs & derivatives
  • Azacitidine / pharmacology
  • Carrier Proteins / metabolism
  • Cell Line, Tumor
  • Colonic Neoplasms / genetics
  • CpG Islands / drug effects
  • DNA Methylation*
  • Decitabine
  • Esophageal Neoplasms / genetics
  • Gene Expression Profiling
  • Gene Silencing*
  • Genes, Tumor Suppressor*
  • Glioma / genetics
  • Heat-Shock Proteins / metabolism
  • Humans
  • Hydroxamic Acids / pharmacology
  • Intracellular Signaling Peptides and Proteins
  • Melanoma / genetics*
  • Membrane Proteins / metabolism
  • Microfilament Proteins / metabolism
  • Neuropeptides / metabolism
  • Nuclear Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Phosphoprotein Phosphatases / metabolism
  • Promoter Regions, Genetic*
  • Reverse Transcriptase Polymerase Chain Reaction


  • Carrier Proteins
  • Heat-Shock Proteins
  • Hydroxamic Acids
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • Microfilament Proteins
  • Neuropeptides
  • Nuclear Proteins
  • PPP1R3C protein, human
  • RARRES1 protein, human
  • TP53INP1 protein, human
  • ectodermal-neural cortex 1 protein
  • trichostatin A
  • Decitabine
  • Phosphoprotein Phosphatases
  • Azacitidine