Overcoming menin inhibitor resistance in AML cells with combinations including BET proteins and a dual BRG1/BRM inhibitor

Menin inhibitors (MI) disrupt the binding of menin to mixed-lineage leukemia 1 (MLL1), leading to the repression of MLL1 or MLL1-fusion protein target genes, including reduced levels of HOXA9 and MEIS1 in acute myeloid leukemia (AML) with mutant NPM1 (mtNPM1) or MLL1 rearrangement (MLL1-r). Although MI are relatively well tolerated and induce clinical remissions, they are often short-lived due to the development of resistance followed by AML relapse. Through repeated shocks with the MI SNDX-50469, a precursor tool compound to revumenib, followed by recovery, we developed MI-resistant (MITR) AML MV4-11 and OCI-AML3 cells. Present studies show that compared with MI-sensitive parental cells, MITR cells exhibit an altered epigenome, transcriptome, and proteome, without menin mutations. Through a CRISPR screen, novel druggable MI coenrichments were identified and targeted, including BRD4, SMARCA4, and CREBBP. Cotreatment with the MI and the SMARCA4/SMARCA2 (BRG1/BRM) inhibitor FHD-286 or the BET proteins inhibitor OTX015 (birabresib) synergistically induced in vitro lethality in MITR and MI-resistant AML cells expressing the mutant menin (M327I), as well as in patient-derived (PD) AML cells with MLL1-r or mtNPM1 that exhibited ex vivo resistance to MI. Compared with each drug alone, cotreatment with SNDX-5613 (revumenib) and FHD-286 or OTX015 and FHD-286 significantly reduced the in vivo AML burden and improved survival of the immune-depleted mice, without inducing significant toxicity, in the xenograft models of MITR and MI-resistant PD MLL1-r AML cells. These findings highlight novel, targeted, drug combinations that overcome MI resistance in AML cells with MLL1-r or mtNPM1.