Abstract 4103: MLL4/COMPASS dysfunction in cancer and treatment

Epigenetic status-altering mutations in chromatin-modifying enzymes are a feature of human diseases, including many cancers. We investigated cellular dependencies, or vulnerabilities, that arise when enhancer function is compromised by loss of the frequently mutated COMPASS family members MLL3 (KMT2C) and MLL4 (KMT2D). We performed a CRISPR dropout screen that revealed a targetable metabolic dependency arising from epigenetic factor deficiency, identifying potential therapies for cancers with epigenetic alterations secondary to MLL3/4-COMPASS dysfunction. We identified strong evidence that there is an internal balance between promoter and enhancer usage dictated by MLL1- versus MLL4-COMPASS, and this equilibrium is subject to disruption during cancer. Using an autochthonous carcinogen model of bladder cancer, we demonstrate that truncated, cytoplasmic MLL4 predicts response to targeted metabolic inhibition therapy for bladder cancer and could be developed as a biomarker for KMT2D-mutated cancers. We also highlight the broader potential for prognosis, patient stratification and treatment decision-making based on KMT2D mutation status in MLL4 truncation-relevant diseases, including human cancers and Kabuki Syndrome. Due to the high prevalence of loss-of-function mutations affecting MLL4 or its COMPASS partner UTX (KDM6A) in bladder cancer, we hypothesized that KMT2D mutation status may predict responsiveness to purine-targeting therapy, including methotrexate and pemetrexed. Our study found that KMT2D mutant bladder cancer cells were selectively dependent on TYMS and showed heightened sensitivity to pemetrexed, a drug that inhibits TYMS, DHFR, and GART. This suggests that targeting multiple enzymes within the one-carbon metabolism and de novo purine synthesis pathway could be promising for the treatment of MLL4/UTX-COMPASS mutant bladder cancer. Based on our previous and current findings, a clinical trial using pemetrexed in MLL4/UTX-COMPASS mutant solid tumors is being launched at Northwestern Medicine. Citation Format: Zibo Zhao, Sarah Gold, Yuki Aoi, Khyati A. Meghani, Luke St John, Rukkia Liaqat, Carolyn Moloney, Yanni Yu, Jun Qian, Issam Ben-Sahra, Rintaro Hashizume, Devalingam Mahalingam, Joshua Meeks, Ali Shilatifard. MLL4/COMPASS dysfunction in cancer and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4103.