RNA-Seq analysis of prostate cancer cell line PC-3 treated with siRNA control (siCont) and siELL2
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ABSTRACT:
PROVIDER: PRJNA554330 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9675830_1.fastq.gz | Fastqsanger.gz | |||
| SRR9675830_2.fastq.gz | Fastqsanger.gz | |||
| SRR9675831_1.fastq.gz | Fastqsanger.gz | |||
| SRR9675831_2.fastq.gz | Fastqsanger.gz | |||
| SRR9675826_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional profiling of the prostate adenocarcinoma cell line PC-3 comparing control cells transfected with a pool of oligonucleotides control (siControl) with cells transfected a pool of oligonucleotides specific to inhibit ARHGAP21 expression (siARHGAP21). The efficiency of the transfection was checked with quantitative PCR and western blotting. Goal was to determine the effects of ARHGAP21 silencing on global PC-3 gene expression.
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Project description:Prostate cancer is the leading type of cancer diagnosed and the third leading cause of cancer-related deaths worldwide each year in men. The limitations of the current prostate cancer screening test demands new biomarkers for early diagnosis of prostate cancer metastasis to bone. In this study, we performed a deep proteomic analysis of secreted proteins from the prostate cancer bone metastasis cell line, PC-3, and normal prostate cell line, RWPE-1. Here, we quantified 917 proteins and found 68 highly secreted in PC-3 versus RWPE-1 cells using LC-MS/MS. To characterize the highly secreted proteins in the PC-3 cell line to identify biomarker proteins, the quantifiable proteins were divided into four quantitative categories (Q1-Q4). The KEGG pathways of lysine degradation and osteoclast differentiation were enriched in Q4, the highly secreted group. Transforming growth factor (TGF) beta family proteins related to osteoclast differentiation were identified as key regulators in PC-3 cells. Among the 68 highly secreted proteins, pentraxin, follistatin, and TGF-beta family members were confirmed by immunoblots. In particular, serpin B3, modulated by TGF-beta, was detected and its selective expression and secretion in PC-3 cells was confirmed. In the present study, we suggest that serpin B3 is a novel biomarker candidate for diagnosis of prostate cancer metastasis to the bone.
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Project description:ETS gene fusions have been characterized in a majority of prostate cancers, however key molecular alterations in ETS negative cancers are unclear. Here we used an outlier meta-analysis (meta-COPA) to identify SPINK1 outlier-expression exclusively in a subset of ETS rearrangement negative cancers (~10% of total cases). We validated the mutual exclusivity of SPINK1 expression and ETS fusion status, demonstrated that SPINK1 outlier-expression can be detected non-invasively in urine and observed that SPINK1 outlier-expression is an independent predictor of biochemical recurrence after resection. We identified the aggressive 22RV1 cell line as a SPINK1 outlier-expression model, and demonstrate that SPINK1 knockdown in 22RV1 attenuates invasion, suggesting a functional role in ETS rearrangement negative prostate cancers. Keywords: Genetic Modification 22RV1 cells were infected with non-targeting siRNA or siRNA against SPINK1. For reported hybridizations, the reference channel is 22RV1 cells infected with non-targeting siRNA. Duplicate hybridizations were performed with duplicate dye flips, for a total of four arrays. Over and under-expressed signatures were generated by filtering to include only features with significant differential expression (PValueLogRatio < 0.01) in all hybridizations and Cy5/Cy3 ratios > or < 1 in all hybridizations.
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Project description:SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus SChLAP1-siRNA treatment. Goal was to determine the effect of SChLAP1 knockdown on gene expression in prostate cancer.
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Project description:BACKGROUND. Human prostate cancer LNCaP and PC-3 cell lines have been extensively used as prostate cancer cell models to study prostate cancer progression and to develop therapeutic agents. Although LNCaP and PC-3 cells are generally assumed to represent early and late stages of prostate cancer development, respectively, there is limited information regarding comprehensive gene expression patterns between these two cells lines and relating these cells to prostate cancer progression based on their gene expression. METHODS. Comprehensive gene expression analysis was performed in LNCaP and PC-3 cells. Total RNA was isolated from cultured cells and hybridized to Illumina human Ref-8 version 3 BeadChips representing 24,526 transcripts. Bioinformatics approach was applied to identify genes, their functional roles and interaction networks that are unique in either LNCaP or PC-3 cells. RESULTS. We observed large differences in gene expression between LNCaP and PC-3 cells.Using robust statistical analysis and very high significance criteria to identify tractable number of genes 115 and 188 genes were identified uniquely expressed in LNCaP and PC-3 cells, respectively. Genes uniquely expressed in LNCaP cells contained UDP-glucosyltransferases as a signature for this cell line. This cell line demonstrated upregulation of various metabolic pathways on gene expression level. Talα/β, GATA-1 and c-Myc/Max were identified by in silico analysis as possible transcription factors regulating unique LNCaP genes. PC-3 cells were characterized by cytosceleton-related genes, keratins in particular. Several other well known genes (VEGFC, IL8, TGFβ2 and others) scattered throughout literature were identified and summarized in the discussion. CONCLUSIONS. This study demonstrated that LNCaP and PC-3 cells represent two distinct prostate cancer cell lineages. LNCaP cells retain many prostate cell specific properties, whereas PC-3 cells have acquired more aggressive bone-like characteristics following bone metastasis and show little resemblance to prostate cells. Microarray studies confirmed previously published results and provided more information between these two prostate cancer cell lines. Future studies need to consider their similarities and differences in gene expression between localized and metastasized prostate cancer.
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Project description:Transcriptional profiling of the prostate adenocarcinoma cell line PC-3 comparing control cells transfected with a pool of oligonucleotides control (siControl) with cells transfected a pool of oligonucleotides specific to inhibit ARHGAP21 expression (siARHGAP21). The efficiency of the transfection was checked with quantitative PCR and western blotting. Goal was to determine the effects of ARHGAP21 silencing on global PC-3 gene expression. Two-condition experiment, siControl vs. siARHGAP21 PC-3 cells with three biological samples of PC3 cells transfected with a pool of oligonucleotides control (siControl 1, 2 and 3) and three biological samples of PC3 cells transfected with a pool of oligonucleotides specific to inhibit ARHGAP21 (siARHGAP21 1, 2 and 3). For each sample (three siControl and three siARHGAP21), two technical replicates were performed (labelled with Cy3 or Cy5).
2012-12-31 | E-GEOD-37888 | biostudies-arrayexpress