Genome-wide transcriptome analysis of PAK4 inhibition/knockdown in human bladder cancer cell line VMCUB1

Using multi-omic analyses, we identified PAK4 (P21 (RAC1) Activated Kinase 4) amplification and overexpression of Kinase PAK4 in a subset of bladder cancers. We confirmed the role of PAK4 in bladder cancer cell proliferation and invasion by in vitro experiments. Furthermore, our studies showed that PAK4 inhibitor is effective in curtailing bladder cancer cell growth. In order to understand the effect of PAK4 inhibition and knockdown on bladder cancer transcriptome, we performed RNA-sequencing of PAK4 siRNA transfected and PAK4 inhibitor (PF-3758309) treated bladder cancer cells (VM-CUB1). Analyses led to identification of direct targets of PAK4 in bladder cancer and associated pathways. Overall design: Total RNA were separately isolated from a) VM-CUB1 cells treated with 5 nM PAK4 inhibitor (PF-3758309, Selleck Chemicals) and incubated for 4 days, b) VM-CUB1 cells treated with DMSO for 4 days, c) VM-CUB1 cells transfected with PAK4 siRNA using Lipofectamine RNAiMAX Reagent (Life Technologies) and b) VM-CUB1 cells transfected with non-targeting siRNA.