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Carcinogenesis Advance Access published online on October 14, 2004
Carcinogenesis, doi:10.1093/carcin/bgh310
© 2004 by Oxford University Press
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Received July 15, 2004
Revised October 1, 2004
Accepted October 5, 2004

CARCINOGENESIS

High throughput screening of methylation status of genes in prostate cancer using oligonucleotide methylation array

Yan Ping Yu 1, Shirish Paranjpe 1, Joel Nelson 2, Sydney Finkelstein 1, Baoguo Ren 1, Demetrius Kokkinakis 1, George Michalopoulos 1, and Jian-Hua Luo 1*

1 Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261
2 Department of Urology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261

* To whom correspondence should be addressed. E-mail: luoj{at}msx.upmc.edu.


  Abstract

Recent work using high-throughput microarray technology has discovered altered expression of a large number of genes in prostate cancer. Many of these alterations may be the consequence of the changes in methylation status in the CpG islands of promoter or exon 1 regions of these genes. In order to screen the methylation status of large number of genes and ESTs, we combined the principle of match/mismatch hybridization with the techniques of whole genome labeling to develop a highly specific oligonucleotide based methylation microarray. Using this array, we analyzed the methylation status of 105 genes and ESTs in three prostate cancer cell lines. Thirty-two to 47% of these genes and ESTs were methylated in these cell lines. By correlating the methylation status of this array with the results of Affymetrix expression arrays of three prostate cancer cell lines, we determined that methylation of genes played a significant role (37%) in down regulating certain gene expression in prostate cancer. We also tested this array on a number of primary prostate tissue samples. Our results indicated that a subset of genes in this microarray (25/105) were methylated throughout all prostate cancer samples but not in normal prostate, suggesting potential significance of alterations in methylation status of certain genes in developing prostate cancer.


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