SMARCA4 Inhibits Breast Tumor progression through Transcriptional Activation of GTPase Activating Factor ARHGAP29 and RHOA Suppression [RNA]

The chromatin-remodeling SWI/SNF complex emerged as a potent suppressor of tumor spheroid growth. SMARCA4 was identified as a top candidate to suppress TNBC growth in 3D tumor spheroid model using genome-wide CRISPR screen. Specifically, the loss of the SWI/SNF ATPase subunit SMARCA4 promotes tumor spheroid growth with reduced compactness, and enhanced the growth in breast primary tumors and metastasis across multiple breast cancer models. Further investigations revealed its function in inhibiting the RHOA pathway. SMARCA4 is required for the transcription of Rho GTPase activating factor ARHGAP29, achieved through direct binding to its promoter to provide DNA accessibility. The loss of SMARCA4 resulted in reduced ARHGAP29 levels and hyperactive RHOA signaling. This subsequently disrupted cell adhesion, facilitated a loose spheroid structure and promoted spheroid growth. Total RNA samples were collected from non-targeting shRNA control (NTC) and SMARCA4 knockdown derivatives (KD1 and KD2) of human triple negative breast cancer (TNBC) cell SUM159 cultured in both 2D and 3D spherioid culture system. The whole transcriptome profiling were determined using RNAseq. Three repeats of each 3D samples were profiled while single sample pair for 2D culture is used.