Identification of NEDD9 regulated genes in VCaP prostate cancer cells

NEDD9 gene (Neural precursor Expressed, Developmentally Down-regulated 9) encodes a member of the Cas family of signaling transduction molecules, which is a non-catalytic focal adhesion protein phosphorylated by FAK and Src and functions as a signaling hub to regulate downstream signaling, such as the AKT pathway. In cancers, NEDD9 regulates cell migration, epithelial-mesenchymal transition (EMT), invasion, and metastasis. Gene amplification of NEDD9 is commonly found in the advanced metastatic castration-resistant PCa (~3%) and neuroendocrine PCa (~15%), suggesting NEDD9 may play an important role in PCa progression. In order to characterize the global functions of NEDD9 in PCa cells, we performed RNA-seq analyses in VCaP cells (containing NEDD9 gene amplification) stably infected with shRNA against NEDD9 or non-targeting control (NTC). RNA-seq analyses were performed to examine gene expressions altered by silencing NEDD9 in VCaP cells. The stable cells were generated by stably infecting VCaP cells with shRNA against NEDD9 (shNEDD9) versus non-targeting control (shNTC). These stable cells were grown in the medium containing 10% FBS. The experiments were done in biological triplicates.