Targeting of epigenetic co-dependencies enhances anti-AML efficacy of Menin inhibitor in AML with MLL1-r or mutant NPM1. [ChIP-Seq]
Monotherapy with Menin inhibitor (MI), e.g., SNDX-5613, induces clinical remissions in patients with relapsed/refractory AML harboring MLL1-r or mtNPM1, but most patients either fail to respond or eventually relapse. Utilizing single cell RNA-Seq, ChiP-Seq, concordant perturbations in ATAC-Seq and RNA-Seq peaks, RPPA and CyTOF analyses, present pre-clinical studies elucidate gene-expression correlates of MI efficacy in AML cells harboring MLL1-r or mtNPM1. MI-mediated genome-wide, concordant, log2 fold-perturbations (up or down-regulation) in ATAC-Seq and RNA-Seq peaks were observed at the loci of MLL-FP target genes, with upregulation of mRNAs associated with AML differentiation. scRNA-Seq analysis of bone marrow aspirate (BMA) cells harboring MLL1-FP and FLT3 mutation revealed enrichment of gene-sets of TNFa, interferon a/?, inflammatory response and apoptosis gene-sets, but negative enrichment of the gene-set of MYC targets. Notably, MI treatment reduced the number of cells expressing the stem/progenitor cell signature. A protein domain-focused CRISPR-Cas9 screen in MLL1-r AML cells identified targetable co-dependencies with MI treatment, including BRD4, EP300, MOZ and KDM1A. Consistent with this, in vitro co-treatment with MI and BET, MOZ, LSD1 or CBP/p300 inhibitor induced synergistic loss of viability of AML cells with MLL1-r or mtNPM1. Co-treatment with MI and BET or CBP/p300 inhibitor also exerted significantly superior in vivo efficacy in xenograft models of AML with MLL1-r. These findings highlight novel, MI-based combinations that could prevent escape of AML stem/progenitor cells following MI monotherapy and could potentially prevent therapy-refractory relapse of AML with MLL1-r or mtNPM1. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27Ac in MOLM13 cells.