Survey of differentially methylated promoters in prostate cancer cell lines.
DNA methylation and copy number in the genomes of three immortalized prostate epithelial and five cancer cell lines (LNCaP, PC3, PC3M, PC3M-Pro4, and PC3M-LN4) were compared using a microarray-based technique. Genomic DNA is cut with a methylation-sensitive enzyme HpaII, followed by linker ligation, polymerase chain reaction (PCR) amplification, labeling, and hybridization to an array of promoter sequences. Only those parts of the genomic DNA that have unmethylated restriction sites within a few hundred base pairs generate PCR products detectable on an array. Of 2732 promoter sequences on a test array, 504 (18.5%) showed differential hybridization between immortalized prostate epithelial and cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, there were eight (CD44, CDKN1A, ESR1, PLAU, RARB, SFN, TNFRSF6, and TSPY) previously observed in prostate cancer and 13 previously known methylation targets in other cancers (ARHI, bcl-2, BRCA1, CDKN2C, GADD45A, MTAP, PGR, SLC26A4, SPARC, SYK, TJP2, UCHL1, and WIT-1). The majority of genes that appear to be both differentially methylated and differentially regulated between prostate epithelial and cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, and GG2-1, representing a rich new source of candidate genes used to study the role of DNA methylation in prostate tumors.
Wang
Yipeng
Y
Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA.
Yu
Qiuju
Q
Cho
Ann H
AH
Rondeau
Gaelle
G
Welsh
John
J
Adamson
Eileen
E
Mercola
Dan
D
McClelland
Michael
M
D045744:Cell Line, Tumor; D019175:DNA Methylation; D004273:DNA, Neoplasm; D015257:DNA-Cytosine Methylases; D004847:Epithelial Cells / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism; D012334:RNA, Neoplasm / Q000378:metabolism
D004273:DNA, Neoplasm; D012334:RNA, Neoplasm; C029641:DNA modification methylase HpaII; D015257:DNA-Cytosine Methylases