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PMID: 28319085 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

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

Nature biotechnology ·Vol. 35 ·No. 5 ·2017-00-00 ·Pages 463-474

Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC

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.

MeSH Terms
Antineoplastic Combined Chemotherapy Protocols/administration & dosage Clustered Regularly Interspaced Short Palindromic Repeats/genetics Drug Screening Assays, Antitumor/methods Drug Synergism Humans K562 Cells Neoplasm Proteins/genetics Neoplasms, Experimental/drug therapy,genetics
Chemicals
Neoplasm Proteins
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Han Kyuho
Department of Genetics, Stanford University, Stanford, California, USA.
Jeng Edwin E
Department of Genetics, Stanford University, Stanford, California, USA. | Program in Cancer Biology, Stanford University, Stanford, California, USA.
Hess Gaelen T
Department of Genetics, Stanford University, Stanford, California, USA.
Morgens David W
Department of Genetics, Stanford University, Stanford, California, USA.
Li Amy
Department of Genetics, Stanford University, Stanford, California, USA.
Bassik Michael C
Department of Genetics, Stanford University, Stanford, California, USA. | Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California, USA.
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.3834
Published
2017-00-00
Epub
2017-00-20
Pages
463-474
Language
English
Region
United States
NLM ID
9604648
PMCID
PMC5557292
Subset
IM
Grants
NICHD NIH HHS · DP2 HD084069 · United States
NCI NIH HHS · T32 CA009302 · United States
NHGRI NIH HHS · T32 HG000044 · United States
NCI NIH HHS · U01 CA199216 · United States
Corrections
CommentIn
PMID: 28366937
CommentIn
PMID: 28417987
External Links
PubMed source DOI: 10.1038/nbt.3834 PMC Full Text View journal details
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