Acquired MEN1 mutations mediate resistance to Menin inhibition [RNA-seq]

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.