Genome-wide CRISPR screen identifies KEAP1 as a genetic dependency of ARID1A-deficient cells

Abstract

ABSTRACTARID1A is the core DNA binding subunit of the BAF chromatin remodeling complex and is mutated in about ~8% of all cancers. The frequency of ARID1A loss varies between cancer subtypes, with clear cell ovarian carcinoma (CCOC) presenting the highest incidence at >50% of cases. Despite a growing understanding of the consequences of ARID1A-loss in cancer, there remains limited targeted therapeutic options for ARID1A-deficient cancers. Using a genome-wide CRISPR screening approach, we identify KEAP1 as a synthetic lethal partner of ARID1A in CCOC. Depletion or chemical inhibition of KEAP1 results in the selective killing of ARID1A-KO cells. While we confirm that KEAP1-NRF2 signalling is dysregulated in ARID1A-KO cells, we suggest that this synthetic lethality is not due to aberrant NRF2 signalling. Rather, we find that KEAP1 perturbation exacerbates genome instability phenotypes associated with ARID1A-deficiency. We also confirm the selective killing of ARID1A-KO cells by the KEAP1 inhibitor AI-1 in edited primary endometrial epithelial cells and organoids. Together, our findings uncover a novel therapeutic avenue for the treatment of cancers harboring ARID1A mutations.AUTHOR SUMMARYARID1A, a component of a protein complex that regulates DNA accessibility, is frequently mutated in various cancers. Ovarian clear cell carcinoma (CCOC) is particularly affected, with over 50% of cases showing ARID1A loss. Despite growing knowledge on ARID1A loss in cancer, therapeutic options for ARID1A-deficient tumors remain limited. Using high throughput CRISPR screening, we identified KEAP1 perturbation as a sensitivity of ARID1A-deficient cells in cell lines and patient-derived samples. While the exact mechanism underlying this sensitivity remains uncertain, we showed that perturbation of KEAP1 exacerbates the heightened DNA damage states associated with ARID1A-deficiency. Taking advantage of these findings, we showed that combination treatment against KEAP1 and the DNA repair protein ATR results in improved killing of ARID1A-depleted cancer cells. Ultimately, our results provide new knowledge on the consequences of ARID1A loss in cancer and suggest that KEAP1 inhibition may provide clinical benefit to selectively eliminate ARID1A-deficient tumours.