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Nat Biotechnol. 2015 Jun;33(6):661-7. doi: 10.1038/nbt.3235. Epub 2015 May 11.

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

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1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.


CRISPR-Cas9 genome editing technology holds great promise for discovering therapeutic targets in cancer and other diseases. Current screening strategies target CRISPR-Cas9-induced mutations to the 5' exons of candidate genes, but this approach often produces in-frame variants that retain functionality, which can obscure even strong genetic dependencies. Here we overcome this limitation by targeting CRISPR-Cas9 mutagenesis to exons encoding functional protein domains. This generates a higher proportion of null mutations and substantially increases the potency of negative selection. We also show that the magnitude of negative selection can be used to infer the functional importance of individual protein domains of interest. A screen of 192 chromatin regulatory domains in murine acute myeloid leukemia cells identifies six known drug targets and 19 additional dependencies. A broader application of this approach may allow comprehensive identification of protein domains that sustain cancer cells and are suitable for drug targeting.

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