Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies

• Published in: Carcinogenesis (New York) Vol. 26; no. 11; pp. 1856 - 1867
• Main Authors: Gallagher, William M., Bergin, Orla E., Rafferty, Mairin, Kelly, Zoë D., Nolan, Ilse-Maria, Fox, Edward J.P., Culhane, Aedin C., McArdle, Linda, Fraga, Mario F., Hughes, Linda, Currid, Caroline A., O'Mahony, Fiona, Byrne, Aileen, Murphy, Alison A., Moss, Catherine, McDonnell, Susan, Stallings, Raymond L., Plumb, Jane A., Esteller, Manel, Brown, Robert, Dervan, Peter A., Easty, David J.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.11.2005; Oxford Publishing Limited (England)
• Subjects: 2′-deoxy-5-azacytidine; 5-methylcytosine; 5mC; Animals; Azacitidine - analogs & derivatives; Azacitidine - pharmacology; Azacitidine - therapeutic use; Biological and medical sciences; Biomarkers, Tumor; Carcinogenesis, carcinogens and anticarcinogens; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; CGH; COBRA; combined restriction bisulfite restriction analysis; comparative genomic hybridization; DAC; Disease Progression; DNA Methylation; DNA Modification Methylases - antagonists & inhibitors; DNA Modification Methylases - genetics; DNA Modification Methylases - metabolism; Enzyme Inhibitors - pharmacology; Enzyme Inhibitors - therapeutic use; Epigenesis, Genetic; Female; FISH; fluorescence in situ hybridization; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; LDA; low density array; Medical sciences; Melanoma, Experimental - genetics; Melanoma, Experimental - metabolism; Melanoma, Experimental - prevention & control; Mice; Mice, Nude; Oligonucleotide Array Sequence Analysis; radial growth phase; RGP; RNA, Messenger - metabolism; RNA, Neoplasm - metabolism; Skin Neoplasms - genetics; Skin Neoplasms - prevention & control; Skin Neoplasms - secondary; Transplantation, Heterologous; Tumor Cells, Cultured; Tumors; vertical growth phase; VGP; Biological marker; Methylation; DNA; Tumor progression
• ISSN: 0143-3334; 1460-2180
• DOI: 10.1093/carcin/bgi152

The incidence of melanoma is increasing rapidly, with advanced lesions generally failing to respond to conventional chemotherapy. Here, we utilized DNA microarray-based gene expression profiling techniques to identify molecular determinants of melanoma progression within a unique panel of isogenic human melanoma cell lines. When a poorly tumorigenic cell line, derived from an early melanoma, was compared with two increasingly aggressive derivative cell lines, the expression of 66 genes was significantly changed. A similar pattern of differential gene expression was found with an independently derived metastatic cell line. We further examined these melanoma progression-associated genes via use of a tailored TaqMan Low Density Array (LDA), representing the majority of genes within our cohort of interest. Considerable concordance was seen between the transcriptomic profiles determined by DNA microarray and TaqMan LDA approaches. A range of novel markers were identified that correlated here with melanoma progression. Most notable was TSPY, a Y chromosome-specific gene that displayed extensive down-regulation in expression between the parental and derivative cell lines. Examination of a putative CpG island within the TSPY gene demonstrated that this region was hypermethylated in the derivative cell lines, as well as metastatic melanomas from male patients. Moreover, treatment of the derivative cell lines with the DNA methyltransferase inhibitor, 2′-deoxy-5-azacytidine (DAC), restored expression of the TSPY gene to levels comparable with that found in the parental cells. Additional DNA microarray studies uncovered a subset of 13 genes from the above-mentioned 66 gene cohort that displayed re-activation of expression following DAC treatment, including TSPY, CYBA and MT2A. DAC suppressed tumor cell growth in vitro. Moreover, systemic treatment of mice with DAC attenuated growth of melanoma xenografts, with consequent re-expression of TSPY mRNA. Overall, our data support the hypothesis that multiple genes are targeted, either directly or indirectly, by DNA hypermethylation during melanoma progression.