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DrugTargetSeqR: a genomics- and CRISPR-Cas9–based method to analyze drug targets

Abstract

To identify physiological targets of drugs and bioactive small molecules, we developed an approach, named DrugTargetSeqR, which combines high-throughput sequencing, computational mutation discovery and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9–based genome editing. We applied this approach to ispinesib and YM155, drugs that have undergone clinical trials as anticancer agents, and uncovered mechanisms of action and identified genetic and epigenetic mechanisms likely to cause drug resistance in human cancer cells.

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Figure 1: Characterization of ispinesib-resistant clones.
Figure 2: Identification of high-frequency resistance-conferring mutations.

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Acknowledgements

We are grateful to US National Institutes of Health (GM98579 to T.M.K.) and Starr Cancer Consortium (I6-A618 to O.E. and T.M.K.). C.K. was supported by the Louis and Rachel Rudin Foundation and a Medical Scientist Training Program grant (NIGMS T32GM007739) to the Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program. We are grateful to L. Marraffini (Rockefeller University) for assistance with genome editing.

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Authors and Affiliations

Authors

Contributions

C.K. carried out all experiments except cDNA library preparation and sequencing. O.E. conducted bioinformatics analysis. T.M.K. and O.E. directed experiments. T.M.K., O.E. and C.K. wrote the manuscript.

Corresponding author

Correspondence to Tarun M Kapoor.

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Competing interests

The authors declare no competing financial interests.

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Supplementary Results, Supplementary Figures 1–12 and Supplementary Tables 1–13. (PDF 3069 kb)

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Kasap, C., Elemento, O. & Kapoor, T. DrugTargetSeqR: a genomics- and CRISPR-Cas9–based method to analyze drug targets. Nat Chem Biol 10, 626–628 (2014). https://doi.org/10.1038/nchembio.1551

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  • DOI: https://doi.org/10.1038/nchembio.1551

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