title: Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma.
abstract: 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.
authors.affiliation: Oncogenomics Laboratory, Queensland Institute of Medical Research, Herston, QLD 4006, Australia.
authors.forename: Vanessa F
authors.initials: VF
authors.lastname: Bonazzi
authors.forename: Darryl
authors.initials: D
authors.lastname: Irwin
authors.forename: Nicholas K
authors.initials: NK
authors.lastname: Hayward
mesh_terms: D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D002352:Carrier Proteins / Q000378:metabolism; D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics; D018899:CpG Islands / Q000187:drug effects; D019175:DNA Methylation; D000077209:Decitabine; D004938:Esophageal Neoplasms / Q000235:genetics; D020869:Gene Expression Profiling; D020868:Gene Silencing; D016147:Genes, Tumor Suppressor; D005910:Glioma / Q000235:genetics; D006360:Heat-Shock Proteins / Q000378:metabolism; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology; D047908:Intracellular Signaling Peptides and Proteins; D008545:Melanoma / Q000235:genetics*; D008565:Membrane Proteins / Q000378:metabolism; D008840:Microfilament Proteins / Q000378:metabolism; D009479:Neuropeptides / Q000378:metabolism; D009687:Nuclear Proteins / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010749:Phosphoprotein Phosphatases / Q000378:metabolism; D011401:Promoter Regions, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D002352:Carrier Proteins; D006360:Heat-Shock Proteins; D006877:Hydroxamic Acids; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D008840:Microfilament Proteins; D009479:Neuropeptides; D009687:Nuclear Proteins; C491294:PPP1R3C protein, human; C452562:RARRES1 protein, human; C429767:TP53INP1 protein, human; C112302:ectodermal-neural cortex 1 protein; C012589:trichostatin A; D000077209:Decitabine; D010749:Phosphoprotein Phosphatases; D001374:Azacitidine