Whole transcriptome analysis reveals ELK3 as a key driver of metastasis through regulation of 3D migration and stemness in triple-negative breast cancer cells

To investigate the key mechanisms regulated by the transcription factor ELK3 relevant for cancer metastasis, we emplyed whole-genome microarray expression profiling as a discovery tool to identify the signaling networks affected by ELK3 knockdown. MDA231 breast cancer cells with ELK3 knockdown (ELK3-KD) were generated by lentiviral mediated transduction. ELK3-KD significantly altered the expression of 2.156 genes (p<0.05), among which 740 showed a fold regulation (FR) greater than |±1.3|. ELK3 inhibition impacted key cancer-related functional signaling networks, including cellular movement, cell cycle regulation, cell death and survival, as well as cell-to-cell communication, and structural organization. MDA231 breast cancer cells with ELK3 knockdown and corresponding mock controls were generated by lentiviral mediated transduction in 4 biological relpicates. More then 95% of cells for all biological replicates were geneticaly modified after transduction. The whole transcriptome analysis was implemented on all four biological replicates in ELK3-KD vs. CTR-KD cells.