Identification of the KDM4B regulated transcriptome in the ER positive breast cancer cell line MCF-7

To elucidate the KDM4B regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM4B-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. Differentially expressed genes were compared with KDM3A and FOXA1 regulated transcriptomes. We identified 229 genes co-regulated by all three enzymes and that co-regulated genes were involved in cell cycle processes. We identified that 53% and 48% of KDM4B-regulated genes were also regulated by KDM3A and FOXA1, with co-regulatory gene signatures being involved with estrogen response signatures and cell proliferation. We also identified that depletion of KDM3A and KDM4B together inhibits ER-target gene expression and ER-positive breast cancer cell growth more than depletion of either gene on its own. MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a KDM4B targeting siRNA (siKDM4B#1) using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 48 hours prior to treatment with 10 nM E2 for 4 hours before RNA extraction using TRIzol (Ambion, Life Technologies) and hybridization of duplicate samples to an Illumina HT-12 v4 BeadChip array.