Extended Data Fig. 7: CRISPR screen shows that LSD1 inhibition creates positive pressure for deleting ncBAF complex components.
a, Gene ranks based on the differences of the beta (selection) scores between the treatment (GSK-LSD1, 20 days, IC30–1.5 nM) and control (DMSO 20 days) screens show the positively and negatively selected mSWI/SNF components genes including the ncBAF complex components BRD9, GLTSCR1, SMARCA2, SMARCD1, and SMARCC1 (Supplementary Tables 18–20). The rank list contains all the previously reported mSWI/SNF components. b, BRD9 binds to SMARCA4 (BRG1) and GLTSCR1 (BICRA) in MKL-1. IP using a BRD9 antibody followed by western blotting was performed to determine interactions among BRD9, GLTSCR1, and SMARCA4. The experiment was performed at least three times. See Unprocessed Gels Extended Data Fig. 7. c, BRD9 degradation restores the loss of cell viability caused by LSD1 inhibition in MCC. MKL-1 cells were treated with varying doses of the dBRD9 and LSD1 inhibitor (GSK-LSD1) for six days. The XTT assay measured relative cell viability. d, dBRD9 degrades BRD9 efficiently. MKL-1 cells were treated with GSK-LSD1 (0.1 μM), dBRD9 (0.1 μM), or both for three days and harvested for western blotting. The experiment was performed at least three times. See Unprocessed Gels Extended Data Fig. 7. e, The PCA plot shows that the degradation of BRD9 by dBRD9 partially rescues the global gene expression changes caused by LSD1 inhibition. n = 2 independent biological replicates were used for analysis. f, BRD9 depletion by shRNAs rescues gene expression changes caused by LSD1 depletion. MKL-1 cells were transduced with an LSD1-targeting shRNA either with a control shRNA or two distinct BRD9-targeting shRNAs for six days and harvested for western blotting. The experiment was performed at least three times. See Unprocessed Gels Extended Data Fig. 7.
