Similar Datasets
Project description:PCa-LINES: Ribo-minus RNA-seq of 4 patient samples and 2 PCa cell lines
| EGAS00001004613 | EGA
Project description:PCa-LINES: rRNA-minus RNA-seq of PCa cell-lines (VCaP & PC346c) and 4 additional patient samples
| EGAD00001006366 | EGA
Project description:Withaferin A (WA) is a lactone extracted from Withania somnifera commonly known as Ashwagandha. WA has several therapeutic benefits. The current study was aimed to identify biomarkers that could be targeted by WA in prostate cancer (PCA) cells. We have used SILAC approach to identify WA-regulated proteins at 4 h and 24 time points in three PCA cell lines such as LNCaP, 22Rv1 and DU-145. Ontology prediction suggested that WA treatment can upregulate stress-responsive pathways and shutdown translation and cell metabolism to conserve energy. The cytoprotective stress granule (SG) protein G3BP1 showed upregulation in all the three tested cell lines in response to WA treatment, and subsequently, SGs formed at a higher rate in the WA treated cells. Knockdown (KD) of G3BP1 blocked WA-induced SG formation and reduced the cell survival. We speculate that the activation of G3BP1 and the formation of SGs might constitute a mechanism by which PCA cells induce cell protection after WA- treatment. Knock down of SG proteins such as G3BP1 could help to evade the cytoprotective effects of WA and to assist in the sensitization of cells.
2021-07-21 | PXD016759 | Pride
Project description:In this study, we knockdown the expression of CTCF in EL4 cells by shRNA, followed by single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells. Principal component analysis (PCA) of single cell RNA-seq data showed that WT cells and CTCF-KD cells essentially concentrated in two different clusters on the PCA projection, indicating gene expression profiles of CTCF-KD cells and WT cells were systematically different. We further found the cells’ CTCF expression levels were correlated with the cell’s positioning on PCA projection. Interestingly, GO terms including regulation of transcription, DNA binding, Zinc finger and transcription factor binding are significantly enriched in CTCF-KD specific highly variable genes, indicating tissue specific genes such as transcription factors were highly sensitive to CTCF-KD level and showed strongly increased variation. While the housekeeping genes including rRNA processing, DNA repair and tRNA processing are significantly enriched in WT specific highly variable genes, potentially indicating cell-to-cell variation of cell activity in WT cells is higher than that of CTCF-KD cells. We found CTCF-KD cell specific highly variable genes were significantly enriched in CTCF-KD specific down-regulated genes, indicating knockdown of CTCF simultaneously reduced expression levels and increased gene expression noises of its target genes. In summary, analysis of genome-wide cell-to-cell variation in this study showed CTCF-medicated promoter-enhancer interaction not only important for maintaining the expression of its target genes, but also played important roles in reducing the expression noise of its target genes.
2020-01-08 | GSE135769 | GEO
Project description:We profiled the proteomics of prostate cancer (PCa) cell lines.
2024-12-06 | PXD058635 |
Project description:Transcriptional profiling of human WT-PTECs, SETD2-KD PTECs, PBRM1-KD PTECs, and 10 different ccRCC derived cell lines. ccRCC derived cell lines showed distict expression signatures as compared to PTECs, some of them also present in SETD2-KD PTECs, and/or PBRM1-KD PTECs.
2017-11-01 | GSE89214 | GEO
Project description:Prostate cancer (PCa) is the second most prevalent cancer and leading causes of death among men worldwide. Androgen deprivation is the first line of treatment for locally advanced and metastatic PCa. For men who develop metastatic castration-resistant PCa (mCRPC), survival is limited. Thus, there is a need to identify synergistic pathways to either prevent or re-sensitize the castration-resistant phenotype. PCa has a long natural history of development and there is a significant correlation between age, diet, metabolism and progress of PCa. We have previously reported that treating PCa cells with fatty acid oxidation inhibitors (FAOi) sensitizes them to androgen blockade. Here we set out to evaluate how the two disparate pathways: AR signaling and FAO, influence one another hoping to identify new therapeutic vulnerabilities. We used CRPC cell models (LNCaP-MDV-resistant, and LNCaP-C4-2), as well as the FAOi (etomoxir and ranolazine) and the antiandrogen enzalutamide (MDV3100). Cells were treated for 48 hours, followed by gene expression, androgen signaling and growth analysis. Both FAOi strongly suppressed the androgen response hallmark in MDV-res cells, and this was associated with a significant upregulation of the ATF3 gene. Interestingly, knockdown (KD) of ATF3 with shRNAs resulted in differential responses to FAOi in these genetically-related cells. In the MDV-resistant cells, ATF3 KD resulted in increased PSA expression with FAOi treatment. On the other hand, in the C4-2 cells, ATF3 KD resulted in decreased PSA expression with FAOi treatment. These results suggested that ATF3 is a convergent point for AR and FAO pathways and that is cell-context dependent, and its expression status could be exploited to sensitize PCa cells to MDV3100 and/or the FAOi. Cell growth and apoptosis assays confirmed that the LNCaP-derived ATF3 KD were more sensitive to MDV3100 and FAOi compared to control cells. Examination of patient databases revealed an inverse correlation between AR and ATF3, a low expression of ATF3 in advanced cancers and better disease-free survival in patients with high ATF3 expression. These data support the role for FAOi to re-sensitize CRPC to endocrine therapies. In conclusion, we have identified ATF3 as a modulator of FAO and AR signaling that has predictive value for clinical outcomes using FAOi in CRPC.
2022-04-01 | GSE124971 | GEO
Project description:Prostate cancer (PCa) is the most common malignant carcinoma that develops in men in Western countries. Up to 30% of patients continue to suffer from disease progression following radical prostatectomy. Therefore, better prognostic markers and molecular targets for cancer treatment are needed. MicroRNA (miRNA) has the potential to be used as biomarkers and as a therapeutic target for the treatment of various cancers, including PCa. Here, to determine how miRNA is involved in PCa progression, we investigated the miRNA expression profiles of 3 PCa cell lines, namely PC3, DU145, and LNCaP, and 2 normal prostate cell lines, namely RWPE-1 and PrSc, using miRNA microarrays.
2013-09-01 | GSE40026 | GEO
Project description:Resistant to immune checkpoint blockade (ICB) therapy, especially in a few solid tumor types including advanced prostate cancer (PCa), represents a formidable clinical challenge. In this study, we developed a series of ICB-resistant PCa cell lines from an ICB-sensitive PCa cell line previously developed from the PB-Cre+ PtenL/L p53L/L Smad4L/L mouse model of metastatic PCa. These four cell lines were profiled with RNAseq.
2024-02-13 | GSE252986 | GEO