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:Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of tumour suppressor inactivation in cancer, including malignant brain tumours. To identify targets of epigenetic silencing mediated by CpG island methylation in paediatric ependymoma, we used a pharmacological unmasking approach through treatment with the demethylating agent 5-Aza-2M-bM-^@M-^Y-deoxycytidine followed by global expression microarray analysis. Three short-term ependymoma cell cultures were used for whole genome expression analysis following treatment with the demethylating agent 5-Aza-dC (5 M-BM-5mol/L) or mock-treated with DMSO (M-bM-^IM-$0.1% v/v) for 96-hrs.
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:Purpose: To use reduced representation bisulfite sequencing and RNA-seq to identify demethylated promoters of genes that were derepressed following treatment with demethylating agent, 5-Aza-2'-deoxycytidine (5aCdR, CAS# 2353-33-5).
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.
Project description:A neuroblastoma cell line, NB-1, was treated with mock, a DNA demethylating agent (5-aza-2'-deoxycytidine: 5-aza-dC), a synthetic retinoic acid (tamibarotene: TBT), and the combination of 5-aza-dC and TBT. A genome-wide gene expression analysis was performed using SurePrint G3 Human Gene Expression 8 x 60K v2 Microarray.
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.
