|
| Status |
Public on Mar 15, 2016 |
| Title |
Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome, and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared to commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies.
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| |
|
| Overall design |
Examination of 3 different histone modifications in 2 patient tumor and adjacent normal samples.
|
| |
|
| Contributor(s) |
Becket E, Liang G |
| Citation(s) |
26759245 |
| |
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gangning Liang |
| E-mail(s) |
gliang@usc.edu
|
| Phone |
323-865-0470
|
| Organization name |
University of Southern California
|
| Department |
Urology
|
| Lab |
Gangning Liang Laboratory
|
| Street address |
1441 Eastlake Ave, NOR 7344
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (16)
|
|
| Relations |
| BioProject |
PRJNA304737 |
| SRA |
SRP066907 |
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