Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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

References

  1. 1

    Schenone, M., Dancik, V., Wagner, B.K. & Clemons, P.A. Nat. Chem. Biol. 9, 232–240 (2013).

    CAS  Article  Google Scholar 

  2. 2

    Titov, D.V. & Liu, J.O. Bioorg. Med. Chem. 20, 1902–1909 (2012).

    CAS  Article  Google Scholar 

  3. 3

    Bassik, M.C. et al. Cell 152, 909–922 (2013).

    CAS  Article  Google Scholar 

  4. 4

    Shalem, O. et al. Science 343, 84–87 (2014).

    CAS  Article  Google Scholar 

  5. 5

    Wang, T., Wei, J.J., Sabatini, D.M. & Lander, E.S. Science 343, 80–84 (2014).

    CAS  Article  Google Scholar 

  6. 6

    Weiss, W.A., Taylor, S.S. & Shokat, K.M. Nat. Chem. Biol. 3, 739–744 (2007).

    CAS  Article  Google Scholar 

  7. 7

    Wacker, S.A., Houghtaling, B.R., Elemento, O. & Kapoor, T.M. Nat. Chem. Biol. 8, 235–237 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8

    Stratton, M.R., Campbell, P.J. & Futreal, P.A. Nature 458, 719–724 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Cong, L. et al. Science 339, 819–823 (2013).

    CAS  Article  Google Scholar 

  10. 10

    Mali, P. et al. Science 339, 823–826 (2013).

    CAS  Article  Google Scholar 

  11. 11

    Bergnes, G., Brejc, K. & Belmont, L. Curr. Top. Med. Chem. 5, 127–145 (2005).

    CAS  Article  Google Scholar 

  12. 12

    Rath, O. & Kozielski, F. Nat. Rev. Cancer 12, 527–539 (2012).

    CAS  Article  Google Scholar 

  13. 13

    Sakowicz, R. et al. Cancer Res. 64, 3276–3280 (2004).

    CAS  Article  Google Scholar 

  14. 14

    Mayer, T.U. et al. Science 286, 971–974 (1999).

    CAS  Article  Google Scholar 

  15. 15

    Mardin, B.R. et al. Dev. Cell 25, 229–240 (2013).

    CAS  Article  Google Scholar 

  16. 16

    Sturgill, E.G. & Ohi, R. Curr. Biol. 23, 1280–1290 (2013).

    CAS  Article  Google Scholar 

  17. 17

    Schwank, G. et al. Cell Stem Cell 13, 653–658 (2013).

    CAS  Article  Google Scholar 

  18. 18

    Guschin, D.Y. et al. Methods Mol. Biol. 649, 247–256 (2010).

    CAS  Article  Google Scholar 

  19. 19

    Talapatra, S.K., Anthony, N.G., Mackay, S.P. & Kozielski, F. J. Med. Chem. 56, 6317–6329 (2013).

    CAS  Article  Google Scholar 

  20. 20

    Adams, J. Cancer Cell 5, 417–421 (2004).

    CAS  Article  Google Scholar 

  21. 21

    Cole, D.G., Saxton, W.M., Sheehan, K.B. & Scholey, J.M.A. J. Biol. Chem. 269, 22913–22916 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Holmes, D. Nat. Med. 18, 842–843 (2012).

    Article  Google Scholar 

  23. 23

    Glaros, T.G. et al. Cancer Chemother. Pharmacol. 70, 207–212 (2012).

    CAS  Article  Google Scholar 

  24. 24

    Shendure, J. & Ji, H. Nat. Biotechnol. 26, 1135–1145 (2008).

    CAS  Article  Google Scholar 

Download references

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

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.

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

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

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

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing