Fig. 6: Combination treatment with PU.1 inhibitor DB2313 in ALL.
A Left: Schematic of PU.1 motif that is most responsive to DB2313 treatment (DB-sensitive) and showed PU.1 binding loss after DB2313 treatment54. Right: log-odds ratio for enrichments of DB-sensitive PU.1 motif in GR-LSOs (n = 1510) and non-GR-LSOs (n = 10707). Statistics were performed using receiver operating characteristics (ROC) analysis. B PU.1 ChIP-seq profiles and heatmap plots (DeepTools) at LSOs in a B-ALL cell line (kopn8) exposed to DEX (Dex, 1 μM) alone or a combination treatment of 1 μM Dex and 1 μM of a PU.1 inhibitor DB2313 (DB) for 16 h in vitro. C ATAC-seq analysis of Nalm6 and ALL-54S cells treated with DEX ± DB2313 for 48 h in vitro. Upper left panel normalized ATAC-seq intensity at LSOs. Gene-set enrichment analysis was performed using the “RHEIN ALL GLUCOCORTICOID THERAPY UP55” gene set (RAGTU, lower left panel) and the top activated signaling pathways (right panel) comparing Dex + DB with Dex-treated Nalm6 cells. See the Methods section for statistics. D RNA transcriptional activities in Nalm6 treated with DEX ± DB2313 for 48 h in vitro. The data are presented as normalized transcript counts across TSS to TES of genes associated with LSOs (LSO-related Genes), GR-LSOs (GR-LSO Genes), GR-LSOs with PU.1 Loss (PU.1 Loss at GR-LSOs), RAGTU gene set, and differentially expressed genes comparing Dex treatment and control Nalm6 cells (DEG). E Time course study of DEX ± DB2313 induced gene expression in Nalm6 cells. Cells were exposed to DEX (1 μM) ± DB2313 (1 μM). GILZ is a direct target of GR and was used as a positive control. F Cytotoxicity assays of DEX (1 μM) ± DB2313 (1 μM) in two ALL cell lines (Nalm6 and 697) and two ALL PDXs (RJ-1 and RJ-10) treated for 72 h in vitro. G Cytotoxicity assay to determine synergistic effects of DEX and DB in inducing cell death of Nalm6 Cells. Interactive analysis is performed using SynergyFinder. A synergy score >10 is considered significant. Data in E, F, and G are presented as the mean ± SEM of three biological replicates. P value was calculated using two-sided student t-test. See also Supplementary Fig. 5–7. Source data are provided as a Source Data file.
