Targeting of epigenetic co-dependencies enhances anti-AML efficacy of Menin inhibitor in AML with MLL1-r or mutant NPM1

by Selleckchem | Sep 15 2023

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, ATAC-Seq, RNA-Seq, RPPA, and mass cytometry (CyTOF) analyses, present pre-clinical studies elucidate gene-expression correlates of MI efficacy in AML cells harboring MLL1-r or mtNPM1. Notably, MI-mediated genome-wide, concordant, log2 fold-perturbations 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. MI treatment also reduced the number of AML 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, which is responsible for therapy-refractory AML relapse.

Comments:

The mentioned pre-clinical studies investigated the efficacy of monotherapy with a Menin inhibitor (MI), specifically SNDX-5613, in patients with relapsed/refractory acute myeloid leukemia (AML) harboring MLL1-r or mtNPM1 genetic abnormalities. While MI treatment induced clinical remissions in some patients, many either did not respond or eventually relapsed. To understand the gene-expression correlates of MI efficacy in AML cells, various techniques such as single-cell RNA sequencing (RNA-Seq), chromatin immunoprecipitation sequencing (ChIP-Seq), assay for transposase-accessible chromatin sequencing (ATAC-Seq), reverse phase protein array (RPPA), and mass cytometry (CyTOF) were utilized.

The results demonstrated that MI treatment led to genome-wide, concordant, log2 fold-perturbations in both ATAC-Seq and RNA-Seq peaks at the loci of MLL-FP target genes. These perturbations were associated with upregulation of mRNAs linked to AML differentiation. Additionally, MI treatment reduced the number of AML cells expressing the stem/progenitor cell signature, suggesting a potential effect on eliminating these cells.

To identify targetable co-dependencies with MI treatment, a protein domain-focused CRISPR-Cas9 screen was conducted in MLL1-r AML cells. The screen identified several genes, including BRD4, EP300, MOZ, and KDM1A, which showed co-dependencies with MI treatment. This suggests that targeting these genes in combination with MI could enhance the efficacy of treatment. In line with this, in vitro co-treatment of AML cells harboring MLL1-r or mtNPM1 with MI and inhibitors targeting BRD4, MOZ, LSD1, or CBP/p300 resulted in synergistic loss of cell viability.

Furthermore, the combination of MI with BET or CBP/p300 inhibitor demonstrated significantly superior efficacy in in vivo xenograft models of AML with MLL1-r compared to MI monotherapy. These findings highlight the potential of novel MI-based combinations to prevent the escape of AML stem/progenitor cells, which is a major contributor to therapy-refractory AML relapse.

Overall, these pre-clinical studies provide valuable insights into the gene-expression correlates of MI efficacy in AML cells harboring MLL1-r or mtNPM1 and identify potential combination strategies that could enhance the therapeutic outcomes of MI treatment in patients with relapsed/refractory AML.