BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML
MECOM rearrangement (r) in AML involves either inv(3)(q21;q26.2) or t(3;3)(q21;q26.2), where the dislocated GATA2 enhancer drives overexpression of the transcriptional regulator EVI1, causes concomitant GATA2 repression, and promotes AML progression, aggressive phenotype and therapy refractoriness. Treatment with BET protein inhibitor (BETi) induces in vitro and in vivo efficacy in 3q26.2-r AML cells (Leukemia 38:545-556,2024). Here, utilizing an unbiased, high-throughput drug screen, focused on mechanistically annotated drugs (NCATS Mechanism Interrogation Plates [MIPE 5.0], we identified BRD4, PIK3CA, mTOR and XIAP as dependencies in the 3q26.2-r AML cells. Monotherapy with mivebresib (BETi), dactolisib (PI3K/mTORi) and LCL161 (IAPi) dose-dependently induced greater lethality in PD 3q26.2-r versus non-3q26.2-r AMLs cells (p < 0.01). RNA-Seq and/or mass spectrometry analyses revealed that treatment with mivebresib or dactolisib downregulated MYC-targets and cell cycle gene-sets whereas CyTOF and Western analyses also demonstrated reduction in the protein levels of EVI1, c-Myb, c-Myc in 3q26.2-r AML cells. Combination of mivebresib with dactolisib or LCL161 synergistically induced apoptosis as well as reduced AML burden and increased survival of the NSG mice engrafted with the luciferized PD 3q26.2-r AML cells (p < 0.05).  In a separate 3q26.2-r AML PDX model, mivebresib-based combination with dactolisib or LCL161, was superior to each agent alone or vehicle control in reducing AML burden and increasing mouse survival (p < 0.05). These findings highlight that combined therapy with a BETi and PIK3CA/mTOR or IAP inhibitor exerts superior in vitro and in vivo efficacy in the 3q26.2-r AML cell models and underscore further evaluation of these BETi-based combinations. Overall design: Paired end RNA Seq of MECOM rearranged AML191 and AML194 cells treated with 500 nM of BET inhibitor mivebresib for 16 hours.