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Series GSE51820 Query DataSets for GSE51820
Status Public on Dec 31, 2014
Title DNA methylation profiles of primary ovarian cancers
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Targeted approaches have revealed frequent epigenetic alterations in ovarian cancer, but the scope and relation of these changes to histologic subtype of disease is unclear. Genome-wide methylation and expression data for 14 clear cell carcinoma (CCC), 32 non-CCC, and 4 corresponding normal cell lines were generated to determine how methylation profiles differ between cells of different histological derivations of ovarian cancer. Consensus clustering showed that CCC is epigenetically distinct. Inverse relationships between expression and methylation in CCC were identified, suggesting functional regulation by methylation, and included 22 hypomethylated (UM) genes and 276 hypermethylated (HM) genes. Categorical and pathway analyses indicated that the CCC-specific UM genes were involved in response to stress and many contain hepatocyte nuclear factor (HNF) 1 binding sites, while the CCC-specific HM genes included members of the estrogen receptor alpha (ERalpha) network and genes involved in tumor development. We independently validated the methylation status of 17 of these pathway-specific genes, and confirmed increased expression of HNF1 network genes and repression of ERalpha pathway genes in CCC cell lines and primary cancer tissues relative to non-CCC specimens. Treatment of three CCC cell lines with the demethylating agent Decitabine significantly induced expression for all five genes analyzed. Coordinate changes in pathway expression were confirmed using two primary ovarian cancer datasets (p<0.0001 for both). Our results suggest that methylation regulates specific pathways and biological functions in CCC, with hypomethylation influencing the characteristic biology of the disease while hypermethylation contributes to the carcinogenic process.
Overall design This study included 96 total samples, including 53 serous ovarian cancers, 11 endometrioid ovarian cancers, 13 clear cell ovarian cancers, 8 mucinous ovarian cancers, 4 fallopian tube epithelium specimens, 4 ovarian surface epithelium specimens, 1 universally methylated DNA sample, 1 normal human lymphocyte sample, and 1 50:50 mixture of the normal human lymphocyte DNA and universally methylated DNA samples.
Contributor(s) Murphy SK, Andrew B, Yamaguchi K, Huang Z
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Submission date Oct 28, 2013
Last update date Mar 22, 2019
Contact name Susan K. Murphy
Organization name Duke University Medical Center
Department Obstetrics and Gynecology
Street address B226 LSRC B Wing, Research Drive, Box 91012
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (96)
GSM1253201 1444-01A_860
GSM1253202 1444-01B_1605
GSM1253203 1444-01C_3107
BioProject PRJNA225585

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE51820_RAW.tar 183.1 Mb (http)(custom) TAR
GSE51820_non_normalized.txt.gz 226.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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