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Treatment of prostate cancer cell lines DU-145 and LNCaP with zebularine

ABSTRACT: Cultures of DU-145 cells and of LNCaP cells were treated for 216 hours with 100ÂµM zebularine (SIGMA) in three independent biological experiments. Zebularine acts as a DNA methyltransferase (DNMT) inhibitor thereby upregulating genes that are inactivated by e.g. promotor hypermethylation. The experiment aimed to search for upregulated transcripts to provide new targets for biomarker development and therapeutic use. Total RNA of untreated and treated (100ÂµM zebularine) DU-145 cells (experiment HK_21_DU_145-HK_26_DU_145), and of untreated and treated (100ÂµM zebularine) LNCaP cells (experiment HK_27_LNCaP-HK_32_LNCaP), were subjected to Affymetrix array analysis to detail the overall expression changes after treatment with a DNMT inhibitor. Treated cells showed no obvious signs of zebularine-induced cytotoxicity as revealed by XTT assays.

ORGANISM(S): Homo sapiens

SUBMITTER: Hans Krause

PROVIDER: E-GEOD-51629 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Treatment of prostate cancer cell lines DU-145 and LNCaP with zebularine

Project description:Cultures of DU-145 cells and of LNCaP cells were treated for 216 hours with 100µM zebularine (SIGMA) in three independent biological experiments. Zebularine acts as a DNA methyltransferase (DNMT) inhibitor thereby upregulating genes that are inactivated by e.g. promotor hypermethylation. The experiment aimed to search for upregulated transcripts to provide new targets for biomarker development and therapeutic use.

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Project description:Transcriptomic changes in human liver cancer cell lines caused by the demethylating drug zebularine. Epigenomic changes such as aberrant hypermethylation and subsequent atypical gene silencing are characteristic features of human cancer. Here, we report a comprehensive characterization of epigenomic modulation caused by zebularine, an effective DNA methylation inhibitor, in human liver cancer. Using transcriptomic and epigenomic profiling, we identified a zebularine signature that classified liver cancer cell lines into two major subtypes with different drug-responses. In drug-sensitive cell lines, zebularine caused inhibition of proliferation coupled with increased apoptosis, whereas drug-resistant cell lines were associated with upregulation of oncogenic networks (e.g. E2F1, MYC, and TNF) driving liver cancer growth in vitro and in mice. Assessment of zebularine-based therapy in xenograft mouse models demonstrated potent therapeutic effects against tumors established from zebularine-sensitive but not zebularine-resistant liver cancer cells leading to increased survival and decreased pulmonary metastasis. Integration of zebularine gene expression and demethylation response signatures differentiated patients with HCC according to their survival and disease recurrence and identified a subclass of patients within the poor survivors likely to benefit from therapeutic agents that target the cancer epigenome. Each cell line was mock treated or treated with 100uM and 200uM zebularine for 7 days, respectively *** This Series represents the gene expression component of the study.

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Gene Expression of Prostate Cancer Cells; 22Rv1, DU-145 and LNCaP: 5-Aza-2'-deoxycytidine (DAC) Treatment vs. Control

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).

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miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines

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Revealing the transitory and local effect of the demethylation agent zebularine on plant development and proteome dynamics of Salix purpurea

Project description:DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for arboreal species, DNA methylation constitute a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach has been adopted to highlight the effects of hypomethylation on proteomic dynamics, exposing the age-specific (three weeks of in vitro culture and one month of growth in soil) and tissue-specific (shoot and root) effects following exposure to zebularine. Significant proteomic shifts were revealed in the development from in vitro to in-soil culture and, whereas zebularine treatment decreased methylation in three-weeks roots, a functionally heterogeneous subset of protein entries was differentially accumulated in shoot samples, including entries associated with cell wall dynamics, tissue morphogenesis, and hormonal regulation. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation in early plant development in willow species.

2024-01-08 | PXD045653 | Pride

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