Transcriptomes change differerntly in differernt cancer cells upon EPZ-6438 treatment

Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to find out the difference between EZH2 inhibitor treatment and DMSO group in each cancer cell line, and find the relationship between transcriptomes change and drug sensivitity. Methods: mRNA profiles of cell lines were generated using Illumina PE150, then GSEA was used for cellular pathways analysis Results: The result showed 53 common oncogenic signatures were enriched in RNA-seq data. For example, KRAS.300_UP.V1_UP, MEK_UP.V1_UP were statistically enriched in the RNA-seq data. In addition, some oncogenic signatures were only enriched in certain cancer cell lines. For example, 101 and 12 signatures from the RNA-seq were statistically enriched in U2932 and SMMC-7721, respectively. Conclusions: Our study systematically examined the cellular transcriptomes affected by EPZ-6438, with biologic replicates, generated by RNA-seq technology. EZH2 inhibition results in the transcriptional activation of multiple onco-pathways in a cell-context dependent manner, which may underline the resistance to EZH2 inhibition. mRNA profiles of 3 cancer cell lines treated with 1 μM EPZ-6348 or DMSO for 6 days, using NEBNext® UltraTM RNA Library Prep it for Illumina® (NEB, USA).