Transcriptomic analysis of human cancer cell lines treated with the histone deacetylase inhibitor romidepsin

Global gene expression analysis was performed on 8 cancer cell lines after treatment with romidepsin for 6h, or 6h treatment followed by 12 h incubation with drug free medium. The cell lines were selected based on their response spectrum to romidepsin, and included HUT78, LOXIMVI, M14, A549, MDA231, ACHN, MiaPaca2 and PC3. Differentially expressed genes (DEG) included genes involved in DNA damage repair (DDR) pathways. The Affymetrix Human Genome U133 Plus 2.0 platform was used for the gene expression profiling. 57 samples were analyzed in triplicate. All 8 cell lines were treated with romidepsin (46 nm/ 25 ng/ml) for 6 hours, or 6h followed by 12 hours incubation in drug-free medium (18h). The romidepsin effect was evaluated against DMSO treated controls