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Nat Biotechnol. 2017 May;35(5):463-474. doi: 10.1038/nbt.3834. Epub 2017 Mar 20.

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions.

Author information

1
Department of Genetics, Stanford University, Stanford, California, USA.
2
Program in Cancer Biology, Stanford University, Stanford, California, USA.
3
Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California, USA.

Abstract

Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs. We applied CDKO to generate a large-scale human GI map, comprising 490,000 double-sgRNAs directed against 21,321 pairs of drug targets in K562 leukemia cells and identified synthetic lethal drug target pairs for which corresponding drugs exhibit synergistic killing. These included the BCL2L1 and MCL1 combination, which was also effective in imatinib-resistant cells. We further validated this system by identifying known and previously unidentified GIs between modifiers of ricin toxicity. This work provides an effective strategy to screen synergistic drug combinations in high-throughput and a CRISPR-based tool to dissect functional GI networks.

PMID:
28319085
PMCID:
PMC5557292
DOI:
10.1038/nbt.3834
[Indexed for MEDLINE]
Free PMC Article

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