|
| Status |
Public on May 22, 2021 |
| Title |
RNA-seq access dataset for epigenomics landscape of colorectal cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Enhancer aberrations are beginning to emerge as a key feature of colorectal cancers, however, we have limited understanding of epigenomic patterns that distinguish tumors and underlying heterogeneity between tumors. Here, using epigenomic profiling of colorectal tumors, adenomas and normal colon tissues, we identify unique pattern of regulatory elements in colorectal cancer, which could reliably distinguish tumors from normal colon specimens. We define shared and unique enhancer elements during colorectal cancer progression using normal adjacent colon, adenomas and adenocarcinomas. We validate the functional nature of tumor-specific enhancers for important oncogenes such as ASCL2 and Fzd10. NMF clustering identified 4 epigenetic (EPIC) subtypes in colorectal cancer, which mimics consensus molecular subtypes (CMS)1, with an advantage of introducing a novel epigenetically-identifiable subtype with poor prognosis and survival. Based on this correlation, we defined and validated a combination therapeutic strategy of enhancer-blocking BETi with pathway specific inhibitor for 3 CMS subtypes. In conclusion, by comprehensive characterization of chromatin state patterns in colorectal tumors, we define epigenomic patterns during tumor evolution, heterogeneity of enhancers among patients and a combination therapy strategy for CMS-subgroups.
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| Overall design |
There are 12 samples with 7 tumor samples and 5 normal samples.
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| |
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| Contributor(s) |
Orouji E, Raman AT, Singh AK, Rai K |
| Citation(s) |
34059508 |
| |
| Submission date |
Aug 29, 2019 |
| Last update date |
Jun 02, 2021 |
| Contact name |
Ayush T Raman |
| E-mail(s) |
aayushraman09@gmail.com
|
| Organization name |
Broad Institute of MIT and Harvard
|
| Department |
Epigenomics Program
|
| Street address |
75 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (12)
|
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| This SubSeries is part of SuperSeries: |
| GSE136889 |
Epigenomics landscape of colorectal cancer |
|
| Relations |
| BioProject |
PRJNA562898 |
| SRA |
SRP219837 |
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