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Updated: Jul 28, 2025
Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes
Published on: May 23, 2025
The genomic landscape of sensitivity to arsenic trioxide uncovered by genome-wide CRISPR-Cas9 screening
Jun-Zhu Chen1, Li-Na Wang1, Xue-Qun Luo1
1Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Introduction:
Arsenic trioxide (ATO) is a promising anticancer drug for hematological malignancy. Given the dramatic efficacy of acute promyelocytic leukemia (APL), ATO has been utilized in other types of cancers, including solid tumors. Unfortunately, the results were not comparable with the effects on APL, and the resistance mechanism has not been clarified yet. This study intends to identify relevant genes and pathways affecting ATO drug sensitivity through genome-wide CRISPR-Cas9 knockdown screening to provide a panoramic view for further study of ATO targets and improved clinical outcomes.
Methods:
A genome-wide CRISPR-Cas9 knockdown screening system was constructed for ATO screening. The screening results were processed with MAGeCK, and the results were subjected to pathway enrichment analysis using WebGestalt and KOBAS. We also performed protein-protein interaction (PPI) network analysis using String and Cytoscape, followed by expression profiling and survival curve analysis of critical genes. Virtual screening was used to recognize drugs that may interact with the hub gene.
Results:
We applied enrichment analysis and identified vital ATO-related pathways such as metabolism, chemokines and cytokines production and signaling, and immune system responses. In addition, we identified KEAP1 as the top gene relating to ATO resistance. We found that KEAP1 expression was higher in the pan-cancer, including ALL, than in normal tissue. Patients with acute myeloid leukemia (AML) with higher KEAP1 expression had worse overall survival (OS). A virtual screen showed that etoposide and eltrombopag could bind to KEAP1 and potentially interact with ATO.
Discussion:
ATO is a multi-target anticancer drug, and the key pathways regulating its sensitivity include oxidative stress, metabolism, chemokines and cytokines, and the immune system. KEAP1 is the most critical gene regulating ATO drug sensitivity, which is related to AML prognosis and may bind to some clinical drugs leading to an interaction with ATO. These integrated results provided new insights into the pharmacological mechanism of ATO and potentiate for further applications in cancer treatments.
Insights
Arsenic trioxide (ATO) shows promise in treating cancers, but resistance mechanisms are unclear. Genome-wide screening identified KEAP1 as a key gene in ATO resistance, suggesting new therapeutic targets for improved cancer treatment outcomes.
Area of Science:
- Oncology
- Pharmacology
- Genomics
Background:
- Arsenic trioxide (ATO) is effective against acute promyelocytic leukemia (APL) but shows limited efficacy in solid tumors.
- Mechanisms of ATO resistance in various cancers remain largely undefined.
- Identifying genes and pathways influencing ATO sensitivity is crucial for optimizing its clinical use.
Purpose of the Study:
- To identify genes and pathways affecting arsenic trioxide (ATO) drug sensitivity using genome-wide CRISPR-Cas9 screening.
- To elucidate the molecular mechanisms underlying ATO resistance in cancer.
- To provide insights for developing novel therapeutic strategies and improving clinical outcomes.
Main Methods:
- Genome-wide CRISPR-Cas9 knockdown screening was employed to identify genes affecting ATO sensitivity.
- Bioinformatic analyses including MAGeCK, WebGestalt, KOBAS, and String/Cytoscape were used for data processing and network analysis.
- Virtual screening was performed to identify potential drug interactions with identified key genes.
Main Results:
- Enrichment analysis revealed key ATO-related pathways: metabolism, chemokines/cytokines, and immune responses.
- KEAP1 was identified as the top gene associated with ATO resistance, with higher expression in pan-cancer tissues compared to normal tissues.
- Elevated KEAP1 expression correlated with worse overall survival in acute myeloid leukemia (AML) patients, and etoposide/eltrombopag showed potential binding to KEAP1.
Conclusions:
- ATO is a multi-target drug, with sensitivity influenced by oxidative stress, metabolism, and immune pathways.
- KEAP1 is a critical regulator of ATO drug sensitivity and impacts AML prognosis.
- These findings offer new perspectives on ATO's pharmacological mechanisms and potential for broader cancer treatment applications.
