Abstract 1133: Combined inhibition of cKIT and Lysine-Specific Demethylase 1 as a therapeutic strategy in acute myeloid leukemia

Responses to kinase inhibitors in AML are short-lived with the inevitable development of resistance. Combination therapy with agents from distinct functional classes is one strategy to overcome this resistance. Using AML cell lines and primary patient samples harboring oncogenic cKIT mutations we demonstrate that inhibition of the epigenetic regulator Lysine-Specific Demethylase 1 (LSD1) markedly augments the cytotoxic effect of the KIT inhibitor avapritinib. Transcriptomic and epigenetic profiling revealed synergistic suppression of Myc activity accompanied by a global loss of acetylation and decreased expression of key leukemia cell cycle genes. This epigenetic reorganization results from disruption of key transcription factor networks responsible for maintaining leukemia cell self-renewal and survival. These findings demonstrate that combined KIT and LSD1 inhibition is an exciting new therapeutic avenue for KIT mutant AML. Previously, we have shown targeting the leukemic epigenome as a possible mechanism to augment the efficacy of kinase inhibitors. Thus, we hypothesize that targeting both the cKIT and CBF mutations with combination therapy will result in a deeper molecular response. Kasumi-1 cells harbor mutant cKIT, making an ideal model to study this combination. We observed a synergistic response to a clinically available KIT inhibitor, avapritinib, and two different LSD1 inhibitors, ORY-1001 and GSK-LSD1. Colony formation of healthy CD34+ cells and cell growth of cKIT WT cells were not significantly altered by the combination, thus showing the specificity of this combination by targeting mutant KIT. Bulk RNA-seq and master regulator analysis revealed greater suppression of Myc target genes with dual inhibition of KIT and LSD1. Using Cleavage Under Targets and Tagmentation (CUT&Tag), we observed synergistic loss of H3K27Ac at the promoters of genes necessary for cell proliferation. Additionally, we used Cleavage Under Targets and Release Using Nuclease (CUT&RUN) to interrogate Myc localization, and found a greater loss of Myc binding with dual inhibition, overlapping with the loss of acetylation at these loci. This study demonstrates the synergistic efficacy of combination therapy and identifies key biomarkers for drug activity, namely loss of histone acetylation and Myc binding. Collectively, combined KIT and LSD1 inhibition may be an effective therapeutic approach for cKIT mutant AML. Citation Format: Brittany M. Smith, Daniel J. Coleman, Lauren M