Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.
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.
Gallagher
William M
WM
Department of Pharmacology, University College Dublin, Ireland. william.gallagher@ucd.ie
Bergin
Orla E
OE
Rafferty
Mairin
M
Kelly
Zoë D
ZD
Nolan
Ilse-Maria
IM
Fox
Edward J P
EJ
Culhane
Aedin C
AC
McArdle
Linda
L
Fraga
Mario F
MF
Hughes
Linda
L
Currid
Caroline A
CA
O'Mahony
Fiona
F
Byrne
Aileen
A
Murphy
Alison A
AA
Moss
Catherine
C
McDonnell
Susan
S
Stallings
Raymond L
RL
Plumb
Jane A
JA
Esteller
Manel
M
Brown
Robert
R
Dervan
Peter A
PA
Easty
David J
DJ
D000818:Animals; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology / Q000627:therapeutic use; D014408:Biomarkers, Tumor; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D000077209:Decitabine; D018450:Disease Progression; D004791:Enzyme Inhibitors / Q000494:pharmacology / Q000627:therapeutic use; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008546:Melanoma, Experimental / Q000235:genetics* / Q000378:metabolism / Q000517:prevention & control; D051379:Mice; D008819:Mice, Nude; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000378:metabolism; D012334:RNA, Neoplasm / Q000378:metabolism; D012878:Skin Neoplasms / Q000235:genetics* / Q000517:prevention & control / Q000556:secondary; D014183:Transplantation, Heterologous; D014407:Tumor Cells, Cultured
D014408:Biomarkers, Tumor; D018797:Cell Cycle Proteins; D004791:Enzyme Inhibitors; D012333:RNA, Messenger; D012334:RNA, Neoplasm; C497749:TSPY1 protein, human; D000077209:Decitabine; D015254:DNA Modification Methylases; D001374:Azacitidine