Identification and characterization of the SWI/SNF complex as a novel regulator in breast cancer

Abstract

Triple-negative breast cancer (TNBC) represents a formidable challenge with breast cancers, characterized by its aggressive nature and the absence of targeted therapy. In pursuit of novel TNBC regulators, we conducted a genome-wide pooled CRISPR-knockout screen, employing both 3D tumor spheroid and 2D conventional cell culture models. This systemic approach allowed us to identify functionally pertinent gene clusters orchestrating the growth of breast tumor cells. Our results unveiled oncogene candidates under both 2D and 3D conditions, while the exclusive utility of 3D in the identification of putative tumor suppressors. Notably, the chromatin-remodeling SWI/SNF complex emerged as an unequivocal suppressor of tumor spheroid growth. We further investigated the SWI/SNF ATPase module SMARCA4 and revealed its function in maintaining cell adhesion. Specifically, SMARCA4 is required for the transcription of Rho GTPase activating factor ARHGAP29, through direct binding to its promoter to provide DNA accessibility. The loss of SMARCA4 resulted in a reduction in both ARHGAP29 mRNA and protein levels. These, in turn, led to an hyperactive RhoA signaling and subsequent disruption of cell-cell adhesion. The perturbation in adhesion facilitated a relaxed spheroid structure, permitting the oxygen and nutrient penetration to the spheroid core and promoted cell proliferation. Furthermore, in the {\it in vivo} context, loss of SMARCA4 led to augmented growth in primary breast tumors and metastasis across multiple TNBC cell lines. Collectively, our investigations underscore the instrumental role of 3D models in deciphering the mechanism of tumor regulators and provide new insights into the putative mechanisms governing the tumor-suppressive role of the SWI/SNF complex within the context of TNBC.