Loss of UXS1 Selectively Depletes Pyrimidines and Induces Replication Stress in KEAP1-Mutant Lung Cancer

Abstract

Kelch-like ECH-associated protein 1 (KEAP1) is the third most commonly mutated gene in non-small cell lung cancer and is associated with poor prognosis. In this study, we investigated synthetic lethal interaction genes in KEAP1-mutated cancer cells and identified a dependency on UDP-xylose synthase 1 (UXS1), which converts UDP-glucuronic acid (UDP-GlcA) to UDP-xylose in the proteoglycan synthetic pathway. UDP-glucose dehydrogenase (UGDH), a transcriptional target of NRF2 that converts UDP-glucose to UDP-GlcA, was highly expressed in KEAP1-mutant tumors. Upon UXS1 knockdown, depletion of UDP-xylose occurred in both KEAP1-mutant and wild-type cells, whereas UDP-GlcA accumulated to a greater extent in the KEAP1-mutant setting. The resulting shortage of available UDP and other pyrimidines slowed S-phase progression and stalled DNA replication fork marks, causing cells to undergo prolonged cell-cycle exit or apoptosis. Dependency on UXS1 was rescued by knocking out UGDH to prevent UDP-GlcA accumulation and UDP depletion. DNA replication stress in UXS1-depleted cells sensitized them to clinical cell-cycle checkpoint inhibitors. Furthermore, CRISPR screening experiments identified genes that modulate UXS1 dependency. Whereas the liver had the highest normal tissue expression of UGDH, UXS1 knockout in the liver did not result in hepatotoxicity. Taken together, these data demonstrate that UXS1 is a selective dependency in KEAP1-mutant tumors, and loss of UXS1 creates additional therapeutically exploitable vulnerabilities in KEAP1-mutant tumors.

Significance: UXS1 loss in KEAP1-mutant cells causes pyrimidine nucleotide depletion, DNA replication stress induction, and ultimately cell-cycle exit that results in tumor stasis, highlighting UXS1 as a potential therapeutic target in KEAP1-mutant tumors. See related commentary by Yasseen and DeNicola, p. 4582.