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Series GSE29886 Query DataSets for GSE29886
Status Public on Jul 28, 2011
Title LNCaP Prostate Cancer Cells: Control vs. siRNA-PCAT1 Treated
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
Overall design Two-condition experiment: Control-siRNA-treated versus PCAT1-siRNA-treated LNCaP cells. Biological replicates: 3 control replicates, 3 treatment replicates.
Contributor(s) Iyer MK, Prensner J, Chinnaiyan AM, Cao X, Jing X
Citation(s) 21804560
Submission date Jun 10, 2011
Last update date Feb 22, 2018
Contact name Matthew Iyer
Phone 7346154503
Organization name University of Michigan
Department Michigan Center for Translational Pathology
Lab Chinnaiyan Lab
Street address 5316 CCGC 0940 1400 E. Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48109-0940
Country USA
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (9)
GSM740115 LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 1
GSM740116 LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 2
GSM740117 LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 3
This SubSeries is part of SuperSeries:
GSE31728 Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
BioProject PRJNA155331

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29886_RAW.tar 133.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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