Effect of Trichostatin A on CNE2 Nasopharyngeal Carcinoma Cells - Genome-wide DNA Methylation Alteration

Abstract

Trichostatin A (TSA) is a histone deacetylase (HDAC) inhibitor. We here investigated its effects on proliferation and apoptosis of the CNE2 carcinoma cell line, and attempted to establish genome-wide DNA methylation alteration due to differentially histone acetylation status. After cells were treated by TSA, the inhibitory rate of cell proliferation was examined with a CCK8 kit, and cell apoptosis was determined by flow cytometry. Compared to control, TSA inhibited CNE2 cell growth and induced apoptosis. Furthermore, TSA was found to induce genome-wide methylation alteration as assessed by genome-wide methylation array. Overall DNA methylation level of cells treated with TSA was higher than in controls. Function and pathway analysis revealed that many genes with methylation alteration were involved in key biological roles, such as apoptosis and cell proliferation. Three genes (DAP3, HSPB1 and CLDN) were independently confirmed by quantitative real-time PCR. Finally, we conclude that TSA inhibits CNE2 cell growth and induces apoptosis in vitro involving genome-wide DNA methylation alteration, so that it has promising application prospects in treatment of NPC in vivo. Although many unreported hypermethylated/hypomethylated genes should be further analyzed and validated, the pointers to new biomarkers and therapeutic strategies in the treatment of NPC should be stressed.

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“…Methylation scores represented as β values were generated for each site using Illumina Genome Studio Methylation module v1.8 (Illumina Inc., USA) and were computed based on the ratio of methylated to methylated plus ummethylated signal outputs. Control panel in the BeadStudio analytical software showed excellent intensity for staining, clear clustering for the hybridization probes, good target removal intensity and satisfactory bisulfite conversion [ 44 ].…”

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“…The hypermethylated genes, namely, DLC1 , PEG10 , and the hypomethylated genes, namely, ABCC5 , CHFR , ERBB2 , and GSTP1 , were identified and confirmed as downregulated and upregulated, respectively, in the resistant cells. Yang and colleagues [ 24 ] also applied the microchip containing ~27 k CpG loci covering more than 14,000 genes at single-nucleotide resolution to evaluate the effect of trichostatin A, one of the most potent HDAC inhibitors, on genome-wide DNA methylation pattern of a NPC cell line CNE2. Their data showed that the DNA methylation in trichostatin A-treated cells appeared to be higher in total compared to the controls.…”