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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 28, 2007 |
| Title |
Genome-wide screen for promoter methylation in NSCLC identifies novel methylation markers for multiple malignancies |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. METHODS AND FINDINGS: In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. CONCLUSIONS: By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention.
Keywords: Dose response, cell-type comparison,
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| Overall design |
We compared the gene expression changes HBEC and NSCLC cells before and after treatment with 5-aza-2'deoxycytidine.
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| Contributor(s) |
Shames DS, Girard L, Gao B, Sato M, Lewis CM, Shivapurkar N, Jiang A, Perou CM, Kim YH, Pollack JR, Fong KM, Lam C, Wong M, Shyr Y, Nanda R, Olopade OI, Gerald W, Euhus DM, Shay JW, Gazdar AF, Minna JD |
| Citation(s) |
17194187 |
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| Submission date |
Jan 09, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
David S Shames |
| E-mail(s) |
shames.david@gene.com
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| Phone |
650-225-7559
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| Organization name |
Genentech Inc
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| Department |
Oncology Biomarker Development
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| Lab |
Shames
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| Street address |
1 DNA Way
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (7)
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| GSM154495 |
H1819 Control group treatment |
| GSM154496 |
H1819 Lose dose treatment group (100 nM) |
| GSM154497 |
H1819 High dose treatment group (1000 nM) |
| GSM154498 |
HBEC2 Control group treatment |
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| Relations |
| BioProject |
PRJNA99053 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6695_RAW.tar |
59.1 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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