Epigenetic status-altering mutations in
chromatin-modifying
enzymes are a feature of human diseases, including many
cancers. However, the functional outcomes and cellular dependencies arising from these mutations remain unresolved. In this study, we investigated cellular dependencies, or vulnerabilities, that arise when enhancer function is compromised by loss of the frequently mutated COMPASS family members MLL3 and MLL4. CRISPR dropout screens in MLL3/4-depleted mouse embryonic stem cells (mESCs) revealed synthetic lethality upon suppression of
purine and
pyrimidine nucleotide synthesis pathways. Consistently, we observed a shift in metabolic activity toward increased
purine synthesis in MLL3/4-KO mESCs. These cells also exhibited enhanced sensitivity to the
purine synthesis inhibitor
lometrexol, which induced a unique gene expression signature.
RNA-Seq identified the top MLL3/4 target genes coinciding with suppression of
purine metabolism, and tandem mass tag proteomic profiling further confirmed upregulation of
purine synthesis in MLL3/4-KO cells. Mechanistically, we demonstrated that compensation by MLL1/COMPASS was underlying these effects. Finally, we demonstrated that
tumors with MLL3 and/or MLL4 mutations were highly sensitive to
lometrexol in vitro and in vivo, both in culture and in animal models of
cancer. Our results depicted a targetable metabolic dependency arising from epigenetic factor deficiency, providing molecular insight to inform
therapy for
cancers with epigenetic alterations secondary to MLL3/4 COMPASS dysfunction.