Supplementary Figure 1. Additional examples of genes most correlated (> 0.50 or <-0.50) to RUNX1 mutation type and VAF, as described in Figure 2C. Supplementary Figure 2. (a) Waterfall plot showing Pearson correlation coefficients calculated between all compounds tested in viability screen (n=5,068) and Dexamethasone. Supplementary Figure 3. Dose response curves for Flumethasone (Flu), representative of the Glucocorticoid cluster, for RUNX1mut and RUNX1wt specimens. Supplementary Figure 4. Heat map showing response profile of 32 AML cell lines to compounds of the GC cluster (n=24) and 6-thioguanine. Supplementary Figure 5. Response to GC Mometasone Furoate (MF) observed in Kasumi-1 and OCI-AML3 cells in the presence of increasing concentrations of GR full antagonist RU486. Supplementary Figure 6. (a) Infection of OCI-AML3 cells with shRNAs targeting NR3C1 (sh1 to sh4) and assessment of GR knockdown efficiency in GFP+ sorted cells by western blotting. Supplementary Figure 7. (a) Top. Expression profile of lymphoid markers and of the NR3C1 gene (encoding the GR) in AML specimens of the Leucegene cohort. Supplementary Figure 8. (a) Dose response curves and associated IC50s for Flumethasone (Flu) and Budesonide (Bude) upon RUNX1 knockdown in OCI-AML5 cells.
ARTICLE ABSTRACTPurpose: RUNX1-mutated (RUNX1mut) acute myeloid leukemia (AML) is associated with adverse outcome, highlighting the urgent need for a better genetic characterization of this AML subgroup and for the design of efficient therapeutic strategies for this disease. Toward this goal, we further dissected the mutational spectrum and gene expression profile of RUNX1mut AML and correlated these results to drug sensitivity to identify novel compounds targeting this AML subgroup.Experimental Design: RNA-sequencing of 47 RUNX1mut primary AML specimens was performed and sequencing results were compared to those of RUNX1 wild-type samples. Chemical screens were also conducted using RUNX1mut specimens to identify compounds selectively affecting the viability of RUNX1mut AML.Results: We show that samples with no remaining RUNX1 wild-type allele are clinically and genetically distinct and display a more homogeneous gene expression profile. Chemical screening revealed that most RUNX1mut specimens are sensitive to glucocorticoids (GCs) and we confirmed that GCs inhibit AML cell proliferation through their interaction with the glucocorticoid receptor (GR). We observed that specimens harboring RUNX1 mutations expected to result in low residual RUNX1 activity are most sensitive to GCs, and that coassociating mutations as well as GR levels contribute to GC sensitivity. Accordingly, acquired glucocorticoid sensitivity was achieved by negatively regulating RUNX1 expression in human AML cells.Conclusions: Our findings show the profound impact of RUNX1 allele dosage on gene expression profile and glucocorticoid sensitivity in AML, thereby opening opportunities for preclinical testing which may lead to drug repurposing and improved disease characterization. Clin Cancer Res; 23(22); 6969–81. ©2017 AACR.