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| Status |
Public on May 20, 2011 |
| Title |
Identification and functional analysis of epigenetically silenced microRNAs in colorectal cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
|
| Summary |
Abnormal miRNA expression has been linked to the development and progression of human cancers, and such dysregulation can result from aberrant DNA methylation. We combined the analysis of miRNA expression data deposited with empirical DNA methylation data in HCT116 and DKO colon cancer cells (SRA accession# SRP001414) to identify novel DNA methylation regulated miRNAs.
ABSTRACT:
Abnormal microRNA (miRNA) expression has been linked to the development and progression of several human cancers, and such dysregulation can result from aberrant DNA methylation. While a small number of miRNAs is known to be regulated by DNA methylation, we postulated that such epigenetic regulation is more prevalent. By combining MBD-isolated Genome Sequencing (MiGS) to evaluate genome-wide DNA methylation patterns and microarray analysis to determine miRNA expression levels, we systematically searched for candidate miRNAs regulated by DNA methylation in colorectal cancer cell lines. We found 64 miRNAs to be robustly methylated in HCT116 cells and/or DNMT-1 and 3B doubleknock cells (DKO); eighteen of them were located in imprinting regions or already reported to be regulated by DNA methylation. In the remaining
46 miRNAs, expression levels of 18 were consistent with their DNA methylation status. Finally, 10 miRNAs were up-regulated by 5-aza-2'-deoxycytidine treatment and identified to be novel miRNAs regulated by DNA methylation. Moreover, we demonstrated the functional relevance of these epigenetically silenced miRNAs by ectopically expressing select candidates, which resulted in inhibition of growth and migration of cancer cells. Our study also provides a reliable strategy to identify DNA methylation-regulated miRNAs by combining DNA methylation profiles and expression data.
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| Overall design |
[miRNA expression]: Total RNA was extracted from 3 biological replicate sets of HCT116 and DMNT-1 and 3B double knock out HCT116 (DKO) colorectal cancer cells.
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| Contributor(s) |
Ting AH |
| Citation(s) |
21698188 |
| |
| Submission date |
Jan 24, 2011 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Angela Ting |
| E-mail(s) |
tinga@ccf.org
|
| Organization name |
Cleveland Clinic
|
| Department |
Genomic Medicine
|
| Street address |
9500 Euclid Ave/NE50
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL8179 |
Illumina Human v2 MicroRNA expression beadchip |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA136017 |
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