Disrupting the CBFβ-SMMHC-RUNX1 oncogenic protein–protein interaction in inv(16) AML: from fusion biology to targeted therapy

Core-binding factor (CBF) leukemias, including inv(16) AML, involve RUNX1/CBFβ chromosomal rearrangements that generate oncogenic fusion proteins. In inv(16) AML, the CBFβ-SMMHC fusion (CBFB-MYH11) dominantly perturbs RUNX1 by sequestering it in aberrant, high-affinity complexes. Structural studies reveal that CBFβ-SMMHC binds the RUNX1 Runt domain with higher affinity than wild-type CBFβ, aided by a second RUNX1-binding site in its SMMHC tail. This altered interface underlies the fusion's dominant-negative disruption of RUNX1 target-gene regulation. Chemical probes have been developed to disrupt this interface; notably, the bivalent inhibitor AI-10-49 selectively binds CBFβ-SMMHC, displacing RUNX1 and restoring RUNX1 transcriptional function. AI-10-49 delays leukemia progression in murine inv(16) models and induces apoptosis in human inv(16) AML cells. Mechanistically, uncoupling RUNX1 from CBFβ-SMMHC liberates RUNX1 to repress oncogenic programs: for example, RUNX1 rebinds distal MYC enhancers and recruits polycomb factors (RING1B) in place of SWI/SNF (BRG1) to silence MYC, triggering leukemia cell apoptosis. These chromatin and transcriptional consequences underscore how CBFβ-SMMHC sustains leukemic transcriptional programs. Importantly, combining CBFβ-SMMHC inhibitors with BET bromodomain inhibitors synergistically eradicates inv(16) leukemia in preclinical models. Together, these insights into the structural basis and functional role of the CBFβ-SMMHC-RUNX1 interface highlight protein-protein interaction disruption as a promising translational strategy in core-binding factor leukemia therapy.