Extended Data Fig. 3: Base-editor screening as a tool to identify point mutants in MEN1.
From: MEN1 mutations mediate clinical resistance to menin inhibition
a) Schematic depicting the workflow of the MEN1-base editor screen performed in MOLM13 (MLL::AF9) and MV4;11 (MLL::AF4) cells. The schematic in a was created using BioRender (https://biorender.com). b) Dot-plot showing the results of a CRISPR-Cas9 base-editor screen in MV4;11 cells aiming to identify point mutations that cause resistance to Menin inhibitor treatment. Each dot represents a single guide RNA. Along the x-axis guide RNAs are sorted by their targeting location relative to the Menin-coding sequence. The y-axis shows differential CRISPR-beta-scores (DMSO-score subtracted from the VTP-50469-treatment score). Outstanding hits are marked in red and targeted amino acid residues are labeled. c) X-ray co-crystal structure of revumenib bound to WT-Menin (PDB: 7UJ4). The hydrogen bonds between sulfonamide oxygen of revumenib and indole nitrogen of W346 or sulfonamide nitrogen of revumenib and backbone carbonyl oxygen of M327 are indicated with black dashed lines. Non polar hydrogens are shown for revumenib and the W346. d) X-ray co-crystal structure of Menin in complex with MLL14–15 peptide (PDB: 4GQ6). View corresponds to Extended Data Fig. 3c. Recurrently mutated amino acids are labeled in red. The W346 residue that builds up a strong hydrogen bond with revumenib to stabilize binding of the molecule is marked in blue. e) Alignment of the Menin bound revumenib (PDB: 7UJ4) with Menin bound MLL14–15 peptide (PDB: 4GQ6). Recurrently mutated amino acids are labeled in red. The W346 residue that builds up a strong hydrogen bond with revumenib to stabilize binding of the molecule is marked in blue.
