1: Neoplasia. 2005 Aug;7(8):748-60. 

Survey of differentially methylated promoters in prostate cancer cell lines.

Wang Y, Yu Q, Cho AH, Rondeau G, Welsh J, Adamson E, Mercola D, McClelland M.

Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA.

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.

PMID: 16207477 [PubMed - in process]


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