Therapeutic targeting of metabolic vulnerabilities in cancers with MLL3/4-COMPASS epigenetic regulator mutations
Zibo Zhao, … , Issam Ben-Sahra, Ali Shilatifard
Zibo Zhao, … , Issam Ben-Sahra, Ali Shilatifard
Published May 30, 2023
Citation Information: J Clin Invest. 2023;133(13):e169993. https://doi.org/10.1172/JCI169993.
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Research Article Genetics Metabolism

Therapeutic targeting of metabolic vulnerabilities in cancers with MLL3/4-COMPASS epigenetic regulator mutations

Abstract

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.

Authors

Zibo Zhao, Kaixiang Cao, Jun Watanabe, Cassandra N. Philips, Jacob M. Zeidner, Yukitomo Ishi, Qixuan Wang, Sarah R. Gold, Katherine Junkins, Elizabeth T. Bartom, Feng Yue, Navdeep S. Chandel, Rintaro Hashizume, Issam Ben-Sahra, Ali Shilatifard

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Figure 1

Genome-wide Screen Identifies Purine and Pyrimidine Synthesis Pathways as Essential for viability in MLL3/4-KO mESCs.

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Genome-wide Screen Identifies Purine and Pyrimidine Synthesis Pathways a...
(A) Flowchart showing CRISPR KO-based dropout screening in WT and KO cells. (B) GO biological process pathway analysis (using MAGeCK) of the top 300 negatively selected genes in MLL3/4-KO cells. (C) Rank plot showing the distribution of negative RRA score with the scores of the 12 genes involved in purine/pyrimidine synthesis that were identified as essential in MLL3/4 KO. (D) β scores of gene essentiality were calculated for WT and KO cells. The 12 screen-identified genes involved in purine/pyrimidine synthesis are shown in the 9-square view. Orange, genes selectively essential in KO not WT; light purple, genes selectively essential in WT not KO; green, genes depletion of which enhanced survival in KO not WT; dark purple, genes depletion of which enhanced survival in WT not KO. (E) Distribution of sgRNA read counts (normalized) of the 2 representative genes Ppat and Mthfd1 in WT and KO cells at different time points. The four colors represent the four distinct sgRNAs in the Brie CRISPR library.