|
| Status |
Public on Oct 03, 2018 |
| Title |
Integrative epigenetic taxonomy of primary prostate cancer [ChIP-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. To comprehensively study the epigenetic landscape, we complemented RNA-seq with ChIP-seq for AR and histone modification marks (H3K27ac, H3K4me3, H3K27me3) in 100 primary prostate carcinomas. Integrative molecular subtyping of the five data streams revealed three major subtypes of which two were clearly TMPRSS2-ERG dictated. Importantly, a third novel subtype was identified, with low AR chromatin binding and activity, even though the receptor was clearly expressed. While positive for neuroendocrine-hallmark genes, these tumors were copy number-neutral with low mutation burden, significantly depleted for genes characteristic of poor-outcome associated luminal B-subtype. We present a rich novel resource on transcriptional and epigenetic control in prostate cancer, revealing a tight control of gene regulation differentially dictated by AR over the three subtypes.
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| |
|
| Overall design |
AR, H3K27ac, H3K4me3 and H3K27me3 ChIP-seq data for primary prostate carcinomas
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| |
|
| Contributor(s) |
Zwart W, Stelloo S, Kim Y, Nevedomskaya E |
| Citation(s) |
30464211 |
| |
| Submission date |
Oct 02, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Suzan Stelloo |
| E-mail(s) |
Stelloo@science.ru.nl
|
| Organization name |
Radboud University
|
| Department |
Molecular Biology
|
| Street address |
Geert Grooteplein Zuid 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (312)
|
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| This SubSeries is part of SuperSeries: |
| GSE120742 |
Integrative epigenetic taxonomy of primary prostate cancer |
|
| Relations |
| BioProject |
PRJNA494344 |
| SRA |
SRP163171 |
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