Fig. 8: An allosteric CBF-inhibitor mimics RUNX1 depletion suggesting a targeted treatment for B-ALL. | Nature Communications

Fig. 8: An allosteric CBF-inhibitor mimics RUNX1 depletion suggesting a targeted treatment for B-ALL.

From: Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability

Fig. 8: An allosteric CBF-inhibitor mimics RUNX1 depletion suggesting a targeted treatment for B-ALL.

a Growth curves for the indicated cell lines following transduction with CBFb- or non-targeting shRNA. Data presented as mean ± SD, n = 3 biologically independent samples. b Ventral and dorsal bioluminescence, at weeks 2 and 4 (end point), of mice engrafted with shGFP+Luc+ and competitor GFP−Luc− NALM-6 cells. Control: non-targeting shRNA; CBFb - CBFb-targeting shRNA. c Endpoint analysis of competitive engraftment (% GFP+ within human CD45+CD19+) of indicated patient samples transduced with CBFb- or non-targeting shRNA. Data presented as mean ± SD, n = 3 biologically independent samples. d Heatmap and average profiles of ChIP-seq signal across RUNX1 and ETV6-RUNX1 binding sites in a 3 kb window centered on peak summits from control (DMSO) or CBFi (AI-14-91) treated Reh following immunoprecipitation with RUNX1, ETV6 or control (IgG) antibodies. GSEA plots for indicated Hallmark gene sets (e) and label-retaining cell (LRC) signature (f) against genes ranked from most significantly up- to most significantly down-regulated following CBFb knockdown. g Heatmap showing cell death (relative Celltox Green) in response to increasing concentrations of AI-14-91 (CBFi) in the indicated cell lines after 72 h. h Mass cytometry analysis for B-ALL cell lines, t(12;21) (control: 72782 cells, CBFi: 71610 cells), t(1;19) (control: 292097 cells, CBFi: 143778 cells) and t(4;11) (control: 192338 cells, CBFi: 274718 cells) treated with 15uM CBFi (AI-14-91) or DMSO (control) for 48 h. UMAP projections based on cell cycle and viability/apoptosis markers, colors represent manually annotated SOM clusters. Barplots show proportion of live cells in the indicated cell cycle phases and the proportion of dead/apoptotic cells. Two-tailed, unpaired t-test revealed a significant reduction in engraftment following CBFb knock-down, ****p < 0.0001 (c). Two sided, 5-sample test for given proportions revealed that cell cycle distribution in AI-14-91 samples differed significantly from control in t(12;21) (Chi-squared = 29551, df = 5, p < 2.2e−16), t(1;19) (Chi-squared = 142822, df = 5, p < 2.2e−16), and t(4;11) (Chi-squared = 99804, df = 5, p < 2.2e−16) (h). Source data are provided as a Source Data file.

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