Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions.
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.
Department of Genetics, Stanford University, Stanford, California, USA.
Kyuho
K
Han
Department of Genetics, Stanford University, Stanford, California, USA.|Program in Cancer Biology, Stanford University, Stanford, California, USA.
Edwin E
EE
Jeng
Department of Genetics, Stanford University, Stanford, California, USA.
Gaelen T
GT
Hess
Department of Genetics, Stanford University, Stanford, California, USA.
David W
DW
Morgens
Department of Genetics, Stanford University, Stanford, California, USA.
Amy
A
Li
Department of Genetics, Stanford University, Stanford, California, USA.|Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California, USA.
Michael C
MC
Bassik
D000971:Antineoplastic Combined Chemotherapy Protocols / Q000008:administration & dosage*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D004354:Drug Screening Assays, Antitumor / Q000379:methods*; D004357:Drug Synergism; D006801:Humans; D020014:K562 Cells; D009363:Neoplasm Proteins / Q000235:genetics*; D009374:Neoplasms, Experimental / Q000188:drug therapy* / Q000235:genetics*
D009363:Neoplasm Proteins