Genome-wide CRISPR screen identifies AraC-Dauno-Eto (ADE) response modulators that predicts outcome in pediatric AML

• Combining CRISPR drug screens and outcome in pediatric AML (pAML) reveals genetic modulators that predict repsonse in pAML.

• BCL2, CLIP2, and VAV3 were identified as ADE-resistant genes and unfavorable biomarkers in pAML treated with ADE.

Cytarabine, daunorubicin, and etoposide (ADE) have been the standard backbone of induction chemotherapy regimens for acute myeloid leukemia (AML) patients for over five decades. However, chemoresistance is still a major concern, and a significant proportion of AML becomes resistant to ADE treatment leading to relapse and poor survival. Therefore, there is a significant need to identify mechanisms mediating drug resistance to overcome chemoresistance. Herein, we performed genome-wide synthetic lethal CRISPR/Cas9 screens using araC, daunorubicin and etoposide. We further integrated significant findings from the CRISPR screen with outcome in pAML patients treated with standard ADE regimen on 3 independent clinical trials to identify drug response biomarkers of prognostic significance. We identified seveal mediators that would represent clinically and biologically significant genes for ADE treatment, such as BCL2, CLIP2, and VAV3, which are resistant genes with high expression associated with poor outcomes in pAML treated with ADE, and GRPEL1, HCFC1, and TAF10, which are sensitive genes with high expression showing beneficial outcomes. Notably, knockdowns of the BCL2, CLIP2, and VAV3 genes sensitize the ADE component in AML cell lines, suggesting that these genes should be further studied as potential therapeutic targets to overcome chemoresistance.