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Updated: Jun 14, 2026
Pooled CRISPR-Based Genetic Screens in Mammalian Cells
Published on: September 4, 2019
CRISPR metabolic screen identifies ATM and KEAP1 as targetable genetic vulnerabilities in solid tumors
Haojian Li1,2,3, Yue Liu2,3, Yunjie Xiao1,2,3
1Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892.
Abstract:
Cancer treatments targeting DNA repair deficiencies often encounter drug resistance, possibly due to alternative metabolic pathways that counteract the most damaging effects. To identify such alternative pathways, we screened for metabolic pathways exhibiting synthetic lethality with inhibition of the DNA damage response kinase Ataxia-telangiectasia-mutated (ATM) using a metabolism-centered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 library. Our data revealed Kelch-like ECH-associated protein 1 (KEAP1) as a key factor involved in desensitizing cancer cells to ATM inhibition both in vitro and in vivo. Cells depleted of KEAP1 exhibited an aberrant overexpression of the cystine transporter SLC7A11, robustly accumulated cystine inducing disulfide stress, and became hypersensitive to ATM inhibition. These hallmarks were reversed in a reducing cellular environment indicating that disulfide stress was a crucial factor. In The Cancer Genome Atlas (TCGA) pan-cancer datasets, we found that ATM levels negatively correlated with KEAP1 levels across multiple solid malignancies. Together, our results unveil ATM and KEAP1 as new targetable vulnerabilities in solid tumors.
Insights
This study identifies Kelch-like ECH-associated protein 1 (KEAP1) as a key factor in cancer drug resistance. KEAP1 depletion sensitizes tumors to ATM kinase inhibition by causing disulfide stress, revealing new therapeutic targets.
Area of Science:
- Molecular Oncology
- Cancer Metabolism
- DNA Damage Response
Background:
- Cancer treatments targeting DNA repair deficiencies often face drug resistance.
- Alternative metabolic pathways may contribute to resistance by counteracting DNA damage effects.
- The DNA damage response kinase Ataxia-telangiectasia-mutated (ATM) is a key target in cancer therapy.
Purpose of the Study:
- To identify metabolic pathways that exhibit synthetic lethality with ATM inhibition.
- To investigate the role of Kelch-like ECH-associated protein 1 (KEAP1) in resistance to ATM inhibition.
Main Methods:
- Screened for metabolic pathways synthetic lethal with ATM inhibition using a CRISPR/Cas9 library.
- Assessed the effect of KEAP1 depletion on cancer cell sensitivity to ATM inhibition in vitro and in vivo.
- Analyzed The Cancer Genome Atlas (TCGA) pan-cancer datasets for correlations between ATM and KEAP1 levels.
Main Results:
- KEAP1 was identified as a key factor desensitizing cancer cells to ATM inhibition.
- KEAP1-depleted cells overexpressed SLC7A11, accumulated cystine, and showed increased disulfide stress, leading to hypersensitivity to ATM inhibition.
- ATM levels negatively correlated with KEAP1 levels across multiple solid tumors in TCGA datasets.
Conclusions:
- Disulfide stress, induced by KEAP1 depletion and SLC7A11 overexpression, is crucial for sensitizing cancer cells to ATM inhibition.
- ATM and KEAP1 represent novel, targetable vulnerabilities in solid tumors.
- Targeting the interplay between DNA damage response and cellular metabolism offers new therapeutic strategies.
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