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Series GSE16079 Query DataSets for GSE16079
Status Public on May 13, 2009
Title Promoter methylation profiles for ectopic vs. eutopic endometrium in SUP, VES and OME
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Several lines of evidence indicate that endometriosis could be partially due to epigenetic dysregulations. Hypermethylation of some key gene promoters, such as progesterone receptor or aromatase, has been reported to be associated with silencing of these genes. However, it is unknown whether global alterations in DNA methylation are a hallmark of endometriosis and to what extent they are involved in its pathogenesis. We conducted a whole-genome scanning of methylation status in more than 25,000 promoters using a combination of methylated DNA immunoprecipitation with hybridization to promoter microarray. We detailed a methylation profile for each subtype of the disease (superficial endometriosis, endometrioma and deep infiltrating endometriosis) and compared them to the profile obtained for the endometrium. Our results indicate that global methylation patterns are strongly correlated between the different disease subtypes, showing regions consistently hyper- or hypomethylated (more than 1.5-times) and others specific to one given subtype. However, there was no systematic correlation between promoter methylation and the expression of nearby genes, except for 35 that have never been previously associated to endometriosis and might be of outstanding importance in the disease development. Also, the distribution of hypermethylated regions appears located at the ends of the chromosomes whereas hypomethylation appears to be located randomly all over the chromosomes. This is a unique observation in a human disease, providing potential new insights into the understanding of endometriosis’ pathogenesis: we hypothesize that it might be a new mechanism that could confer protection against malignancy.

Keywords: Promoter microarrays
Overall design We performed four hybridizations on Affymetrix GeneChip® Human Promoter 1.0R Arrays, with immunoprecipitated DNA, extracted from superficial endometriosis (SUP), endometrioma (OME), vesical endometriosis (VES) and eutopic endometrium (E), prepared from 5-patients pools, where the same patients providing the ectopic endometrium also provided the eutopic endometrium.
Contributor(s) Borghese B, Barbaux S, Mondon F, Pierre G, Chapron C, Vaiman D
Citation(s) 20685852
Submission date May 12, 2009
Last update date Jan 21, 2015
Contact name Bruno Borghese
Organization name Institut Cochin
Department Genetics and Development
Lab Team 21
Street address 24, rue du Faubourg Saint-Jacques
City Paris
ZIP/Postal code 75014
Country France
Platforms (1)
GPL5082 [Hs_PromPR] Affymetrix Human Promoter 1.0R Array
Samples (4)
GSM402515 eutopic endometrium
GSM402516 ectopic endometrium (endometrioma)
GSM402517 ectopic endometrium (superficial endometriosis)
BioProject PRJNA115507

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
GSE16079_Intervals_ActiveRegions_Annotations.txt.gz 91.6 Kb (ftp)(http) TXT
GSE16079_RAW.tar 162.5 Mb (http)(custom) TAR (of BAR, CEL)
GSE16079_README.txt 747 b (ftp)(http) TXT
Processed data provided as supplementary file
Processed data are available on Series record

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