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. 2022 Oct 28;12(12):2880–2905. doi: 10.1158/2159-8290.CD-21-1491

Figure 6.

Figure 6. Pharmacologic targeting of the BAF complex in vitro and in vivo mimics the biological effects of SMARCA4 depletion in H3K27M glioma. A, Schematic showing biological assessment of BRG1/BRM ATPase inhibitor– and degrader–treated H3.3K27M-glioma neurospheres for changes in chromatin accessibility by ATAC-seq, gene expression by bulk RNA sequencing (RNA-seq), and in vivo efficacy of chemical compounds in subcutaneous xenograft mouse models. B, Profile plot (top) depicting average ATAC-seq signal at BRG1 binding sites (n = 1,335) in BT869 (H3.3K27M-glioma) neurospheres after 24 hours of treatment with 1 μmol/L of BRG1/BRM inhibitors [Compound 11 (C11), Compound 14 (C14)] and degraders [JQ-dS-4 (JQ), AU-15330 (AU)] and DMSO controls. The plot shows 6.4-kb regions, centered on BRG1 peaks. Gene tracks (bottom) exemplify changes in chromatin accessibility observed at BRG1 binding sites. Displayed are BRG1 ChIP-seq signal in control BT869 cells as well as ATAC-seq data on the same cells after 24 or 48 hours of treatment with 1 μmol/L of BRG1/BRM inhibitors or degraders and DMSO controls. C, Biological processes (gene ontology analysis) enriched in regions with decreased accessibility in BT869 neurosphere cells treated for 24 hours with 1 μmol/L of Compound (Cmpd) 14, Compound 11, JQ-dS-4, or AU-15330 as determined by ATAC-seq. The number of genes is indicated by the size of the circle, and significance is depicted by the color scale. Reg., regulation of. D, Overlap of genes with reduced chromatin accessibility in drug-treated BT869 neurospheres (as determined by bulk ATAC-seq) with single-cell transcriptional metaprograms in H3K27M glioma. BT869 cells were treated with 1 μmol/L of either Compound 11 (C11), Compound 14 (C14), JQ-dS-4 (JQ), or AU-15330 (AU) for 24 hours. The color scale indicates the number of overlapping genes. E, A heat map showing z-scores of gene expression of OPC-like metaprogram marker genes with statistically significant changes upon Compound 11 or 14 treatments in BT869 neurospheres after 24 hours. Colored bars indicate z-scores of gene expression. rep, replicate.F, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)– or BRG1/BRM degrader JQ-dS-4 (50 mg/kg i.p. daily)–treated mice bearing BT869 (H3.3K27M-glioma) subcutaneous tumors as compared with vehicle controls (n = 10 mice per group). Data are shown as mean ± SEM, P < 0.0001 (unpaired t test comparing vehicle and Compound 14 groups). Kaplan–Meier survival curves (bottom) of mice treated with either Compound 14 (20 mg/kg i.p. daily) or JQ-dS-4 (50 mg/kg i.p. daily) for 60 days in a subcutaneous BT869 xenograft model (n = 10 mice per group). The P value was calculated using the log-rank (Mantel–Cox) test. Gray bars show the duration of treatment. G, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)–treated mice bearing SU-DIPGXIIIP* (H3.3K27M) subcutaneous tumors as compared with vehicle controls (n = 8 mice per group). Data are shown as mean ± SEM, P < 0.0001 (unpaired t test). Gray bar shows the duration of the treatment. Tumor volume (bottom) measured after 30 days of Compound 14 treatment compared with vehicle control in mice bearing SU-DIPGXIIIP* (H3.3K27M) subcutaneous tumors. P = 0.0017 (unpaired t test). H, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)–treated mice bearing HSJD-GBM001 (H3WT) subcutaneous tumors as compared with vehicle controls (n = 10 mice per group). Data are shown as mean ± SEM, P = 0.578 (unpaired t test). Kaplan–Meier survival curves (bottom) of mice treated with Compound 14 (20 mg/kg i.p. daily) for 30 days in a subcutaneous xenograft model of HSJD-GBM001 (n = 10 mice per group). The P value was calculated using the log-rank (Mantel–Cox) test. Gray bars show the duration of treatment.

Pharmacologic targeting of the BAF complex in vitro and in vivo mimics the biological effects of SMARCA4 depletion in H3K27M glioma. A, Schematic showing biological assessment of BRG1/BRM ATPase inhibitor– and degrader–treated H3.3K27M-glioma neurospheres for changes in chromatin accessibility by ATAC-seq, gene expression by bulk RNA sequencing (RNA-seq), and in vivo efficacy of chemical compounds in subcutaneous xenograft mouse models. B, Profile plot (top) depicting average ATAC-seq signal at BRG1 binding sites (n = 1,335) in BT869 (H3.3K27M-glioma) neurospheres after 24 hours of treatment with 1 μmol/L of BRG1/BRM inhibitors [Compound 11 (C11), Compound 14 (C14)] and degraders [JQ-dS-4 (JQ), AU-15330 (AU)] and DMSO controls. The plot shows 6.4-kb regions, centered on BRG1 peaks. Gene tracks (bottom) exemplify changes in chromatin accessibility observed at BRG1 binding sites. Displayed are BRG1 ChIP-seq signal in control BT869 cells as well as ATAC-seq data on the same cells after 24 or 48 hours of treatment with 1 μmol/L of BRG1/BRM inhibitors or degraders and DMSO controls. C, Biological processes (gene ontology analysis) enriched in regions with decreased accessibility in BT869 neurosphere cells treated for 24 hours with 1 μmol/L of Compound (Cmpd) 14, Compound 11, JQ-dS-4, or AU-15330 as determined by ATAC-seq. The number of genes is indicated by the size of the circle, and significance is depicted by the color scale. Reg., regulation of. D, Overlap of genes with reduced chromatin accessibility in drug-treated BT869 neurospheres (as determined by bulk ATAC-seq) with single-cell transcriptional metaprograms in H3K27M glioma. BT869 cells were treated with 1 μmol/L of either Compound 11 (C11), Compound 14 (C14), JQ-dS-4 (JQ), or AU-15330 (AU) for 24 hours. The color scale indicates the number of overlapping genes. E, A heat map showing z-scores of gene expression of OPC-like metaprogram marker genes with statistically significant changes upon Compound 11 or 14 treatments in BT869 neurospheres after 24 hours. Colored bars indicate z-scores of gene expression. rep, replicate.F, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)– or BRG1/BRM degrader JQ-dS-4 (50 mg/kg i.p. daily)–treated mice bearing BT869 (H3.3K27M-glioma) subcutaneous tumors as compared with vehicle controls (n = 10 mice per group). Data are shown as mean ± SEM, P < 0.0001 (unpaired t test comparing vehicle and Compound 14 groups). Kaplan–Meier survival curves (bottom) of mice treated with either Compound 14 (20 mg/kg i.p. daily) or JQ-dS-4 (50 mg/kg i.p. daily) for 60 days in a subcutaneous BT869 xenograft model (n = 10 mice per group). The P value was calculated using the log-rank (Mantel–Cox) test. Gray bars show the duration of treatment. G, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)–treated mice bearing SU-DIPGXIIIP* (H3.3K27M) subcutaneous tumors as compared with vehicle controls (n = 8 mice per group). Data are shown as mean ± SEM, P < 0.0001 (unpaired t test). Gray bar shows the duration of the treatment. Tumor volume (bottom) measured after 30 days of Compound 14 treatment compared with vehicle control in mice bearing SU-DIPGXIIIP* (H3.3K27M) subcutaneous tumors. P = 0.0017 (unpaired t test). H, Tumor volume measurements (top) in BRG1/BRM inhibitor Compound 14 (20 mg/kg i.p. daily)–treated mice bearing HSJD-GBM001 (H3WT) subcutaneous tumors as compared with vehicle controls (n = 10 mice per group). Data are shown as mean ± SEM, P = 0.578 (unpaired t test). Kaplan–Meier survival curves (bottom) of mice treated with Compound 14 (20 mg/kg i.p. daily) for 30 days in a subcutaneous xenograft model of HSJD-GBM001 (n = 10 mice per group). The P value was calculated using the log-rank (Mantel–Cox) test. Gray bars show the duration of treatment.