Gene Set: HOQUE_METHYLATED_IN_CANCER

Standard name HOQUE_METHYLATED_IN_CANCER
Systematic name M19948
Brief description Genes whose DNA was methylated both in primary tumors and across a panel of cancer cell lines.
Full description or abstract 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.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 18413733   Authors: Hoque MO,Kim MS,Ostrow KL,Liu J,Wisman GB,Park HL,Poeta ML,Jeronimo C,Henrique R,Lendvai A,Schuuring E,Begum S,Rosenbaum E,Ongenaert M,Yamashita K,Califano J,Westra W,van der Zee AG,Van Criekinge W,Sidransky D
Exact source Table 2S
Related gene sets (show 14 gene sets from the same authors)
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Organism Homo sapiens
Contributed by Jessica Robertson (Broad Institute)
Source platform SEQ_ACCESSION
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.0: First introduced

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