CRISPR-Cas9 base editor screening identifies the spectrum of MEN1 mutations impacting menin inhibitors in clinical trials [RNA-Seq]

Menin inhibitors have entered clinical trials for KMT2A-rearranged and NPM1 mutant acute leukemias and are demonstrating promising activity. CRISPR-Cas9 base editor screening previously predicted several MEN1 mutations that have arisen in patients receiving SNDX-5613 and confer menin inhibitor resistance. The extent to which MEN1 mutations will impact each menin inhibitor is currently unknown. We leveraged advances in CRISPR-Cas9 base editing technology to predict the MEN1 mutation profile that will impact five different menin inhibitors in clinical trials. We found key similarities (M327) and differences (C334, E368, V372) in the profile of MEN1 mutations that affect each compound. The co-crystal structure of menin bound to each compound suggests resistance mechanisms related to how each menin inhibitor binds in the KMT2A binding pocket of menin. Our in vitro and in vivo validation suggests that the MEN1 mutations identified and validated with this approach are likely to arise and impact all menin inhibitors. Overall design: A patient derived xenograft model was established from a patient who had AML with a KMT2A::EPS15 gene rearrangement. In the current experiment, two mice received vehicle control therapy, two mice received VTP-50469 (SNDX-5613 pre-clinical analogue) at a dose of 0.03% chow, and two mice received VTP-50469 0.1% chow. After 4 weeks of treatment of treatment, mice were euthanized, leukemia cells were obtained, and the mice were euthanized and RNA-sequencing was performed.