Genome-wide screen of promoter methylation identifies novel markers in melanoma.

Y Koga, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM.

August 2009

Abstract

DNA methylation is an important component of epigenetic modifications $b a c k s l a s h$ nthat influences the transcriptional machinery and aberrant in many $b a c k s l a s h$ nhuman diseases. In this study we present the first genome-wide integrative $b a c k s l a s h$ nanalysis of promoter methylation and gene expression for the identification $b a c k s l a s h$ nof methylation markers in melanoma. Genome-wide promoter methylation $b a c k s l a s h$ nand gene expression of eight early-passage human melanoma cell strains $b a c k s l a s h$ nwere compared to newborn and adult melanocytes. We used linear mixed $b a c k s l a s h$ neffect models (LME) in combination with a series of filters based $b a c k s l a s h$ non the localization of promoter methylation relative to the transcription $b a c k s l a s h$ nstart site, overall promoter CpG content, and differential gene expression $b a c k s l a s h$ nto discover DNA methylation markers. This approach identified 76 $b a c k s l a s h$ nmarkers, of which 68 were hyper- and 8 hypo-methylated (LME P textless 0.05). $b a c k s l a s h$ nPromoter methylation and differential gene expression of five markers $b a c k s l a s h$ n(COL1A2, NPM2, HSPB6, DDIT4L, MT1G) were validated by sequencing $b a c k s l a s h$ nof bisulfite modified DNA and real-time reverse transcriptase PCR, $b a c k s l a s h$ nrespectively. Importantly, the incidence of promoter methylation $b a c k s l a s h$ nof the validated markers increased moderately in early- and significantly $b a c k s l a s h$ nin advanced-stage melanomas, employing early-passage cell strains $b a c k s l a s h$ nand snap frozen tissues (n = 18 and n = 24, respectively) compared $b a c k s l a s h$ nto normal melanocytes and nevi (n = 11 and n = 9, respectively). $b a c k s l a s h$ nOur approach allows robust identification of methylation markers $b a c k s l a s h$ nthat can be applied to other studies involving genome-wide promoter $b a c k s l a s h$ nmethylation. In conclusion, this study represents the first unbiased $b a c k s l a s h$ nsystematic effort to determine methylation markers in melanoma, and $b a c k s l a s h$ nrevealed several novel genes regulated by promoter methylation that $b a c k s l a s h$ nwere not described in cancer cells before.

Type

Journal article

Publication

Genome Research