Global gene expression changes following ELF3 knockdown in prostate epithelial cell lines
ABSTRACT: This study aimed to elucidate the role of ELF3, an epithelia-specific member of the ETS family, in normal prostate development and prostate cancer. Four comparisons (untreated, mock-transfected, scrambled siRNA, and targeted siRNA) were performed in two prostate epithelial cell lines BPH-1 (benign) and PC3 (malignant). Global gene expression arrays were performed for each combination.
Project description:This study aimed to elucidate the role of ELF3, an epithelia-specific member of the ETS family, in normal prostate development and prostate cancer. Four comparisons (untreated, mock-transfected, scrambled siRNA, and targeted siRNA) were performed in two prostate epithelial cell lines BPH-1 (benign) and PC3 (malignant). Global gene expression arrays were performed for each combination.
Project description:This study aimed to elucidate the role of ELF3, an ETS family member in normal prostate growth and prostate cancer. Silencing ELF3 in both benign prostate (BPH-1) and prostate cancer (PC3) cell lines resulted in decreased colony-forming ability, inhibition of cell migration and reduced cell viability due to cell cycle arrest, establishing ELF3 as a cell cycle regulator. Increased ELF3 expression in more advanced prostate tumours was shown by immunostaining of tissue microarrays and from analysis of gene expression and genetic alteration studies. This study indicates that ELF3 functions not only as a part of normal prostate epithelial growth but also as a potential oncogene in advanced prostate cancers.
Project description:Purpose:The present study aims to investigate the role of ELF3-AS1 in oral squamous cell carcinoma (OSCC). Patients and methods:A total of 112 patients with OSCC were admitted in Guangdong Provincial Stomatological Hospital from March 2016 to March 2019. RT-qPCR, cells and transient transfections, cell proliferation rate measurements and Western blots were carried out to analyze the samples. Results:In the present study, we showed that ELF3-AS1 and glucose transporter 1 (GLUT1) were both upregulated in OSCC tissues, and those two factors were positively correlated. In OSCC cells, ELF3-AS1 overexpression resulted in upregulation, while ELF3-AS1 siRNA silencing caused downregulated expression of GLUT1 and glucose uptake. ELF3-AS1 and GLUT1 overexpression resulted in increased rate of OSCC cells, while ELF3-AS1 and GLUT1 siRNA silencing resulted in decreased proliferation rate of OSCC cells. In addition, GLUT1 siRNA silencing attenuated the effects of ELF3-AS1 overexpression. Conclusion:Therefore, ELF3-AS1 promotes the proliferation of OSCC cells by reprogramming glucose metabolism.
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. Two-condition experiment: non-targeting siRNA versus SChLAP1 siRNA treated cells. Biological replicates: 1 control replicate, 2 treatment replicates. Technical replicates: 3 replicates per SChLAP1 siRNA. Cell lines: 22Rv1 and LNCaP.
Project description:Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus siRNAs targeting SWI/SNF complex proteins (SMARCA2, SMARCA4, and SMARCB1). Goal was to determine the effect of SWI/SNF knockdown on gene expression in prostate cancer. Two-condition experiment: non-targeting siRNA versus SWI/SNF-siRNA treated cells. Three SWI/SNF proteins were targeted: SMARCA2, SMARCA4, and SMARB1. Biological replicates: 1 control replicate, 2 treatment replicates per SWI/SNF protein. Technical replicates: 1 replicate per SWI/SNF protein. Cell lines: 22Rv1 and LNCaP.
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.
Project description:The objective of this study was to evaluate the consequences of Ago1 knockdown in metastatic prostate cancer cells PC3. To this end we profiled RNA from PC3 cells 72 hours following the transfection with a scramble siRNA (siGL3) and a siRNA targeting Ago1 (siAgo1). We profiled RNA from PC3 cells 72 hours following the transfection with a scramble siRNA (siGL3) and a siRNA targeting Ago1 (siAgo1). siAgo1 vs siGL3 gene expression profiling, two technical replicates with dye swap labeling scheme.
Project description:We are interested in the role of NOTCH1 and Shear Stress in Aortic Valve Endothelium. Primary human aortic valve endothelium was subjected to 4 conditions in vitro. 1) Control siRNA, No shear stress. 2) NOTCH1 siRNA, No shear stress. 3) Control siRNA, 15 dynes/cm2 shear stress. 4) NOTCH1 siRNA, 15 dynes/cm2 shear stress. Triplicates of each condition were pooled for library perp and sequencing
Project description:The purpose of our study was to examine the function of BMI1 in fusion positive and fusion negative rhabdomyosarcoma cell lines and validate these findings in patient tissue. RD and RH30 cell lines were treated with control-siRNA or BMI1-siRNA and the RNA was subsequently sequenced on a HiSeq2500. The resultant sequencing data was used for Gene Set Enrichment Analysis and pathway analysis.