Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression and DNA methylation of colon cancer cell lines

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE34077: Colon Cancer cell line YB5 untreated cells vs YB5 treated 24h with Depsipeptide at 20 nM GSE34427: DNA methylation analysis of Colon Cancer cell line SW48 Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Noel Raynal

PROVIDER: E-GEOD-34429 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

DNA methylation does not stably lock gene expression but instead serves as a molecular mark for gene silencing memory.

Raynal Noël J-M NJ Si Jiali J Taby Rodolphe F RF Gharibyan Vazganush V Ahmed Saira S Jelinek Jaroslav J Estécio Marcos R H MR Issa Jean-Pierre J JP

Cancer research 20120104 5

DNA methylation is commonly thought of as a "molecular lock" that leads to permanent gene silencing. To investigate this notion, we tested 24 different histone deacetylase inhibitors (HDACi) on colon cancer cells that harbor a GFP locus stably integrated and silenced by a hypermethylated cytomegalovirus (CMV) promoter. We found that HDACi efficiently reactivated expression of GFP and many other endogenous genes silenced by DNA hypermethylation. After treatment, all promoters were marked with act ...[more]

PMID: 22219169

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Project description:Transcriptional profiling of LNCaP prostate cancer cells comparing control siRNA-treated LNCaP cells with LNCaP cells treated with siRNAs targeting Prostate Cancer Associated Transcript-1 (PCAT1), an uncharacterized long non-coding RNA. High-throughput sequencing of polyA+ RNA (RNA-Seq) in human cancer shows remarkable potential to identify both novel disease-specific markers for clinical uses and uncharacterized aspects of tumor biology, particularly non-coding RNA (ncRNA) species. To illustrate this approach, we employed RNA-Seq on a cohort of 102 prostate tissues and cells lines and found that aberrant expression profiles of novel tissue-specific ncRNAs distinguished benign, cancerous, and metastatic tumors. Among these, a novel prostate-cancer specific ncRNA (termed PCAT-1) defined a subset of aggressive cancers with low expression of the epigenetic regulator EZH2, a component of the Polycomb Repressive Complex 2 (PRC2) commonly upregulated in metastatic cancers. In vitro assays for core PRC2 genes indicated that the PRC2 complex directly binds and represses PCAT-1, and that the PCAT-1 transcript reciprocally binds PRC2, suggesting a regulatory feedback mechanism. Importantly, knockdown of PCAT-1 in cells with high levels of endogenous PCAT-1 transcript showed changes in cell proliferation and transcriptional regulation of several key biological processes, including cell cycle. Finally, we showed that ncRNA expression signatures, including PCAT-1, were effective for the non-invasive detection of prostate cancer, and that high ncRNA expression signature values correlate with high-grade histology. The findings presented herein establish the utility of RNA-Seq to comprehensively identify unannotated ncRNAs that define human disease states and characterize PCAT-1 as a novel regulator of cell proliferation mechanistically linked to PRC2 and contributory to translational clinical tests for prostate cancer. Two-condition experiment: Control-siRNA-treated versus PCAT1-siRNA-treated LNCaP cells. Biological replicates: 3 control replicates, 3 treatment replicates.

Dataset Information

Expression and DNA methylation of colon cancer cell lines

Publications

DNA methylation does not stably lock gene expression but instead serves as a molecular mark for gene silencing memory.

Similar Datasets

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