Project description:Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated three PCa cell lines, 22Rv1, DU-145 and LNCap with the demethylating agent 5-aza 2’–deoxycitidine (DAC) and examined gene expression changes using a custom microarray (GPL16604). These data were integrated with gene methylation status (GEO Pending) in PCa cell lines and further combined with patient tumor data to identify potential novel biomarkers for PCa patients. In order to identify genes that are methylated in PCa, we employed a genome-wide gene expression profiling approach and compared cells treated with 5-aza 2’–deoxycitidine (DAC) to untreated cells. 22Rv1, DU-145 and LNCaP PCa cell lines were incubated in culture medium with 2 μg/mL DAC for 4 days with medium change every 2 days. Total RNA was extracted and gene expression was analyzed using a custom microarray (GPL16604).
Project description:Transcriptional silencing associated with aberrant promoter hypermethylation is a common mechanism of inactivation of tumor suppressor genes in cancer cells. To profile the genes silenced by hypermethylation in prostate cancer, we screened an expression microarray for genes reactivated in the LNCaP, DU-145, PC-3 and MDA2b prostate tumor cell lines after treatment with the demethylating drug 5-aza-2 deoxycytidine (5Aza-dC) and histone deacetylation inhibiting drug trichostatin A (TSA).
Project description:Transcriptional profiling of DU-145 cells treated with 5-Aza for 72 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs. Two-condition experiment, 5-Aza-treated vs. untreated DU-145 cells. Biological replicates: 2. Technical replicates: 2.
Project description:miRNA expression profiling of prostate cancer cell lines, PC-3, DU145, LAPC-4, VCaP, LNCaP, 22rv1, and normal prostate epithelial cells, PrECs, was done after treating the cells with DNA demethylating agent 5-aza-2'-deoxycytidine (5azadC; Sigma-Aldrich, St. Louis, MO) and histone deacetylase inhibitor trichostatin A (TSA; Sigma-Aldrich). These treatments relieve epigenetic modifications, and thus reveal potentially epigenetically silenced miRNAs amongst the miRNAs with increased expression after the treatments.
Project description:MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. This series is meant to identify miRNAs deregulated in prostate cancer (PCa) by comparing the PCa cell lines LNCaP, PC3 and Du-145 to the normal prostate epithelial cell line RWPE-1. We analyzed three arrays each for LNCaP, PC3, Du-145 and RWPE-1 cell lines
Project description:Gene expression of 5 prostate cancer cell lines (LNCaP, VCaP, DU-145, PC-3, DuCaP) in standard culture conditions, harvested during exponential growth phase.
Project description:We aimed to investigate gene expression associated with radiosensitisation of normoxic and hypoxic prostate cancer cells by the class I/II histone deacetylase inhibitor (HDACi) vorinostat. A pronounced deregulation of DNA repair and chromatin organization genes by vorinostat in DU 145 than in PC-3 or 22Rv1 was found and was a likly mechanism underlying radiosensitisation of DU 145. Expression of these genes was generally not affected by hypoxia and was altered by vorinostat in DU 145 towards the baseline levels of PC-3 and 22Rv1. A 56-gene expression signature associated with radiosensitisation under normoxia and hypoxia, including 8 genes with baseline expression characteristic of the radiosensitising effect was generated. These findings propose a hypoxia independent expression signature to predict the radiosensitising effect of vorinostat.
Project description:Human prostate cancer cells, LNCaP (AR+) and DU-145 (AR-), were treated with C-1311 to identify the transcriptomic profile and functionally relevant androgen-dependent and independent genes using RNA sequencing.
Project description:Neuroendocrine transdifferentiation (NED) of prostate cancer cells and aberrant activation of survival pathways involved in tumorigenesis are among the events that lead to the development of resistance to anti-androgen therapy and are associated with poor prognosis in patients with castration resistance prostate cancer (CRPC). Most of these molecular events appear to be mediated by epigenetic mechanisms, in particular DNA methylation. In this study, we evaluated the antitumor activity and epigenetic modulation of two epigenetic drugs, 5-aza-2’-deoxycytidine (AZA) and S-adenosylmethionine (SAM) in two human CRPC cell lines with NED (NED-CRPC), DU-145 and PC-3. The effects of AZA and SAM on the cell growth proliferation, cell cycle, apoptosis, migration and genome-wide DNA methylation profiling have been evaluated through MTT assay, DNA flow cytometry with propidium iodide, and Annexin V-FITC/propidium iodide staining, wound-healing assay and Infinium450k microarray, respectively. Both epigenetic drugs showed a prominent antitumor activity in NED-CRPC cell line exerted through perturbation of cell cycle progression, induction of apoptosis and migration arrest. AZA and SAM reversed NED in DU-145 and PC-3, respectively. Moreover, AZA treatment profoundly modified DNA methylation pattern, sustaining a pervasive hypomethylation of the genome, with a relevant effect on several pathways involved in regulation of cell migration, cell proliferation and apoptosis. Among these, the Wnt/beta-catenin signaling appeared to be the most directly involved. In conclusion, both AZA and SAM showed a relevant antitumor activity on NED-CRPC cell lines. This opens a new scenario in the therapy of this lethal variant of prostate cancer.
Project description:Withaferin A (WA), a major chemical component of an Indian herb Withania somnifera, induces cell death (apoptosis/necrosis) in a variety of tumor cells, but its molecular mechanism remains elusive. We report that WA induces cell death selectively in high-grade prostate (PC-3 and DU-145) and tongue (SAS) cancer cells but not in normal human fibroblast (TIG-1) and low-grade prostate cancer (LNCaP) cells. To identify genes whose expression levels were up- or down-regulated in prostate cancer cells following WA treatment, we examined the transcriptome profiles of mRNA prepared from TIG-1, LNCaP, PC-3 and DU-145 cells using Agilent’s Whole Human Genome Microarray.
