|
| Status |
Public on Oct 19, 2011 |
| Title |
Epigenetic portraits of human breast cancers (various cell lines methylation data) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
|
| Summary |
Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Here we used the Infinium Methylation Platform to profile at single-CpG resolution (over 14,000 genes interrogated) the methylomes of 119 breast tumours. It emerges that many genes whose expression is linked to the ER status are epigenetically controlled (or/ we show that the two major phenotypes of breast cancers determined by ER status are widely involving epigenetic regulatory mechanisms), offering the prospect of a novel approach to treating ER-positive tumours. We have distinguished methylation-profile-based tumour clusters, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour typology. We show that methylation patterns may reflect the cellular origins of tumours. Having highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, we show that a set of immune genes have high prognostic value in specific tumour categories. By laying the ground for better understanding of breast cancer heterogeneity and improved tumour taxonomy, the precise epigenetic portraits drawn here should contribute to better management of breast cancer patients.
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| Overall design |
Gene expression profiling cell lines. Study of epigenetic variation (methylation) linked to gene expression. No replicate, no reference sample.
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| Contributor(s) |
Dedeurwaerder S, Desmedt C, Calonne E, Singhal SK, Haibe-Kains B, Luciani J, Putmans P, Lallemand F, Larsimont D, Toussaint J, Haussy S, Rothé F, Rouas G, Metzger O, Georges M, Sotiriou C, Fuks F |
| Citation(s) |
21910250 |
| |
| Submission date |
Jun 10, 2010 |
| Last update date |
Jan 02, 2015 |
| Contact name |
Benjamin Haibe-Kains |
| E-mail(s) |
[email protected]
|
| Phone |
+14165818626
|
| Organization name |
Princess Margaret Cancer Centre
|
| Department |
Princess Margaret Research
|
| Lab |
Bioinformatics and Computational Genomics
|
| Street address |
610 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2M9 |
| Country |
Canada |
| |
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| Platforms (1) |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
|
| Samples (19)
|
| GSM554400 |
Normal breast cell line MCF10A (methylation data) |
| GSM554401 |
Breast cancer cell line MCF-7 WT (methylation data) |
| GSM554402 |
Breast cancer cell line MCF-7 5-AZA (methylation data) |
| GSM554403 |
Breast cancer cell line T47D WT (methylation data) |
| GSM554404 |
Breast cancer cell line T47D 5 AZA (methylation data) |
| GSM554405 |
Breast cancer cell line SKBR3 WT (methylation data) |
| GSM554406 |
Breast cancer cell line SKBR3 5 AZA (methylation data) |
| GSM554407 |
Breast cancer cell line BT20 WT (methylation data) |
| GSM554408 |
Breast cancer cell line BT20 5 AZA (methylation data) |
| GSM554409 |
Breast cancer cell line MDA-MB-231 WT (methylation data) |
| GSM554410 |
Breast cancer cell line MDA-MB-231 5 AZA (methylation data) |
| GSM554411 |
Breast cancer cell line MDA-MB-361 WT (methylation data) |
| GSM554412 |
Breast cancer cell line MDA-MB-361 5 AZA (methylation data) |
| GSM554413 |
Breast cancer cell line ZR-75-1 WT (methylation data) |
| GSM554414 |
Breast cancer cell line ZR-75-1 5 AZA (methylation data) |
| GSM554415 |
Normal lymphoid cell line WEIS3E5 (methylation data) |
| GSM554416 |
ex vivo B lymphocytes (methylation data) |
| GSM554417 |
ex vivo T lymphocytes (methylation data) |
| GSM554418 |
Breast cancer cell line R12C9 |
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| This SubSeries is part of SuperSeries: |
| GSE20713 |
Epigenetic portraits of human breast cancers |
|
| Relations |
| BioProject |
PRJNA128711 |
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