Gene expression profiling of MDA_MB_231 cell line in response to treatment with Dexamethasone and SH4-54

To determine how the transcription factors GR and STAT3 cooperate to regulate gene expression, the MDA-MB-231 breast cancer cell line was treated with dexamethasone (1µM for 24 hours) and the STAT3 inhibitor SH4-54 (8µM for 24 hours) alone and in combination. A multivariate linear model with a GR:STAT3 interaction term was used to identify genes that are differentially expressed when both TFs are fully active in the nucleus. Overall design: MDA-MB-231 cells were plated in 6-well plates at ~300,000 cells in 4ml of media per well and grown for 24 hours. Three replicates wells were treated for 24 hours with 1µM of Dexamethasone (DEX), 8µM SH4-54, no treatment, or a combination of DEX and SH4-54. The cells were lysed using Qiagen RLT buffer and 1% BME.