Genome-wide promoter analysis uncovers portions of the cancer methylome.
DNA methylation has a role in mediating epigenetic silencing of CpG island genes in cancer and other diseases. Identification of all gene promoters methylated in cancer cells "the cancer methylome" would greatly advance our understanding of gene regulatory networks in tumorigenesis. We previously described a new method of identifying methylated tumor suppressor genes based on pharmacologic unmasking of the promoter region and detection of re-expression on microarray analysis. In this study, we modified and greatly improved the selection of candidates based on new promoter structure algorithm and microarray data generated from 20 cancer cell lines of 5 major cancer types. We identified a set of 200 candidate genes that cluster throughout the genome of which 25 were previously reported as harboring cancer-specific promoter methylation. The remaining 175 genes were tested for promoter methylation by bisulfite sequencing or methylation-specific PCR (MSP). Eighty-two of 175 (47%) genes were found to be methylated in cell lines, and 53 of these 82 genes (65%) were methylated in primary tumor tissues. From these 53 genes, cancer-specific methylation was identified in 28 genes (28 of 53; 53%). Furthermore, we tested 8 of the 28 newly identified cancer-specific methylated genes with quantitative MSP in a panel of 300 primary tumors representing 13 types of cancer. We found cancer-specific methylation of at least one gene with high frequency in all cancer types. Identification of a large number of genes with cancer-specific methylation provides new targets for diagnostic and therapeutic intervention, and opens fertile avenues for basic research in tumor biology.
Hoque
Mohammad Obaidul
MO
Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland 21231, USA.
Kim
Myoung Sook
MS
Ostrow
Kimberly Laskie
KL
Liu
Junwei
J
Wisman
G Bea A
GB
Park
Hannah Lui
HL
Poeta
Maria Luana
ML
Jeronimo
Carmen
C
Henrique
Rui
R
Lendvai
Agnes
A
Schuuring
Ed
E
Begum
Shahnaz
S
Rosenbaum
Eli
E
Ongenaert
Maté
M
Yamashita
Keishi
K
Califano
Joseph
J
Westra
William
W
van der Zee
Ate G J
AG
Van Criekinge
Wim
W
Sidransky
David
D
D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D019921:Biotinylation; D001973:Bromodeoxyuridine / Q000494:pharmacology; D045744:Cell Line, Tumor; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic
D000964:Antimetabolites, Antineoplastic; D001973:Bromodeoxyuridine