Project description:Chromatin-binding proteins are critical regulators of cell state in haematopoiesis1,2. Acute leukaemias driven by rearrangement of the mixed lineage leukaemia 1 gene (KMT2Ar) or mutation of the nucleophosmin gene (NPM1) require the chromatin adapter protein menin, encoded by the MEN1 gene, to sustain aberrant leukaemogenic gene expression programs3-5. In a phase 1 first-in-human clinical trial, the menin inhibitor revumenib, which is designed to disrupt the menin-MLL1 interaction, induced clinical responses in patients with leukaemia with KMT2Ar or mutated NPM1 (ref. 6). Here we identified somatic mutations in MEN1 at the revumenib-menin interface in patients with acquired resistance to menin inhibition. Consistent with the genetic data in patients, inhibitor-menin interface mutations represent a conserved mechanism of therapeutic resistance in xenograft models and in an unbiased base-editor screen. These mutants attenuate drug-target binding by generating structural perturbations that impact small-molecule binding but not the interaction with the natural ligand MLL1, and prevent inhibitor-induced eviction of menin and MLL1 from chromatin. To our knowledge, this study is the first to demonstrate that a chromatin-targeting therapeutic drug exerts sufficient selection pressure in patients to drive the evolution of escape mutants that lead to sustained chromatin occupancy, suggesting a common mechanism of therapeutic resistance.
Project description:Acute leukemias driven by rearrangements of the Mixed Lineage Leukemia gene (MLLr) or mutants of Nucleophosmin (NPM1c) require the chromatin adapter protein Menin, encoded by the MEN1 gene, to sustain aberrant gene expression programs and maintain stem-like properties. In a phase I first-in-human clinical trial, the Menin-inhibitor SNDX-5613, designed to disrupt the Menin-MLL1 interaction, induced promising clinical responses in leukemia patients6. However, acquired drug resistance was observed in some cases. Here we characterized MEN1 variants that arise on therapy and mediate resistance to Menin inhibition in patients, xenograft models, and a base-editor screen. We show that resistance was associated with emergence of novel MEN1 mutations. These mutants blunted response by impairing drug-target binding, thereby preventing the eviction of Menin-MLL1 complexes from chromatin. Structural modeling revealed a unique interaction mode of the affected residues with the drug, providing the basis for structure-guided development of second-generation compounds. These studies are the first to demonstrate that a small molecule targeting a chromatin-binding protein exerts sufficient selection pressure to drive evolution of a narrow spectrum of escape mutants leading to sustained chromatin occupancy as a novel mechanism of drug resistance in cancer.
Project description:Acute leukemias driven by rearrangements of the Mixed Lineage Leukemia gene (MLLr) or mutants of Nucleophosmin (NPM1c) require the chromatin adapter protein Menin, encoded by the MEN1 gene, to sustain aberrant gene expression programs and maintain stem-like properties. In a phase I first-in-human clinical trial, the Menin-inhibitor SNDX-5613, designed to disrupt the Menin-MLL1 interaction, induced promising clinical responses in leukemia patients6. However, acquired drug resistance was observed in some cases. Here we characterized MEN1 variants that arise on therapy and mediate resistance to Menin inhibition in patients, xenograft models, and a base-editor screen. We show that resistance was associated with emergence of novel MEN1 mutations. These mutants blunted response by impairing drug-target binding, thereby preventing the eviction of Menin-MLL1 complexes from chromatin. Structural modeling revealed a unique interaction mode of the affected residues with the drug, providing the basis for structure-guided development of second-generation compounds. These studies are the first to demonstrate that a small molecule targeting a chromatin-binding protein exerts sufficient selection pressure to drive evolution of a narrow spectrum of escape mutants leading to sustained chromatin occupancy as a novel mechanism of drug resistance in cancer.
