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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Schenone, M., Dancik, V., Wagner, B.K. & Clemons, P.A. Nat. Chem. Biol. 9, 232–240 (2013).
Titov, D.V. & Liu, J.O. Bioorg. Med. Chem. 20, 1902–1909 (2012).
Bassik, M.C. et al. Cell 152, 909–922 (2013).
Shalem, O. et al. Science 343, 84–87 (2014).
Wang, T., Wei, J.J., Sabatini, D.M. & Lander, E.S. Science 343, 80–84 (2014).
Weiss, W.A., Taylor, S.S. & Shokat, K.M. Nat. Chem. Biol. 3, 739–744 (2007).
Wacker, S.A., Houghtaling, B.R., Elemento, O. & Kapoor, T.M. Nat. Chem. Biol. 8, 235–237 (2012).
Stratton, M.R., Campbell, P.J. & Futreal, P.A. Nature 458, 719–724 (2009).
Cong, L. et al. Science 339, 819–823 (2013).
Mali, P. et al. Science 339, 823–826 (2013).
Bergnes, G., Brejc, K. & Belmont, L. Curr. Top. Med. Chem. 5, 127–145 (2005).
Rath, O. & Kozielski, F. Nat. Rev. Cancer 12, 527–539 (2012).
Sakowicz, R. et al. Cancer Res. 64, 3276–3280 (2004).
Mayer, T.U. et al. Science 286, 971–974 (1999).
Mardin, B.R. et al. Dev. Cell 25, 229–240 (2013).
Sturgill, E.G. & Ohi, R. Curr. Biol. 23, 1280–1290 (2013).
Schwank, G. et al. Cell Stem Cell 13, 653–658 (2013).
Guschin, D.Y. et al. Methods Mol. Biol. 649, 247–256 (2010).
Talapatra, S.K., Anthony, N.G., Mackay, S.P. & Kozielski, F. J. Med. Chem. 56, 6317–6329 (2013).
Adams, J. Cancer Cell 5, 417–421 (2004).
Cole, D.G., Saxton, W.M., Sheehan, K.B. & Scholey, J.M.A. J. Biol. Chem. 269, 22913–22916 (1994).
Holmes, D. Nat. Med. 18, 842–843 (2012).
Glaros, T.G. et al. Cancer Chemother. Pharmacol. 70, 207–212 (2012).
Shendure, J. & Ji, H. Nat. Biotechnol. 26, 1135–1145 (2008).
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.
Author information
Authors and Affiliations
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
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Results, Supplementary Figures 1–12 and Supplementary Tables 1–13. (PDF 3069 kb)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nchembio.1551
This article is cited by
-
Target identification of small molecules: an overview of the current applications in drug discovery
BMC Biotechnology (2023)
-
Targeting pan-essential pathways in cancer with cytotoxic chemotherapy: challenges and opportunities
Cancer Chemotherapy and Pharmacology (2023)
-
Chemical strategies to overcome resistance against targeted anticancer therapeutics
Nature Chemical Biology (2020)
-
Discovering and validating cancer genetic dependencies: approaches and pitfalls
Nature Reviews Genetics (2020)
-
CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML
Nature Chemical Biology (2019)