Abstract
Determining mechanisms of drug action in human cells remains a major challenge. Here we describe an approach in which multiple-drug-resistant clones are isolated and transcriptome sequencing is used to find mutations in each clone. Further analysis of mutations common to more than one clone can identify a drug's physiological target and indirect resistance mechanisms, as indicated by our proof-of-concept studies of the cytotoxic anticancer drugs BI 2536 and bortezomib.
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
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Chan, J.N., Nislow, C. & Emili, A. Trends Pharmacol. Sci. 31, 82–88 (2010).
Giaever, G. et al. Nat. Genet. 21, 278–283 (1999).
Ho, C.H. et al. Nat. Biotechnol. 27, 369–377 (2009).
Walker, G.M. J. Gen. Microbiol. 128, 61–71 (1982).
Ong, S.E. et al. Proc. Natl. Acad. Sci. USA 106, 4617–4622 (2009).
Rix, U. & Superti-Furga, G. Nat. Chem. Biol. 5, 616–624 (2009).
Weiss, W.A., Taylor, S.S. & Shokat, K.M. Nat. Chem. Biol. 3, 739–744 (2007).
Gorre, M.E. et al. Science 293, 876–880 (2001).
Azam, M., Latek, R.R. & Daley, G.Q. Cell 112, 831–843 (2003).
Lénárt, P. et al. Curr. Biol. 17, 304–315 (2007).
Teraishi, F. et al. Cancer Res. 65, 6380–6387 (2005).
Glaab, W.E. & Tindall, K.R. Carcinogenesis 18, 1–8 (1997).
Girdler, F. et al. Chem. Biol. 15, 552–562 (2008).
Kothe, M. et al. Chem. Biol. Drug Des. 70, 540–546 (2007).
Scutt, P.J. et al. J. Biol. Chem. 284, 15880–15893 (2009).
Yusuf, R.Z., Duan, Z., Lamendola, D.E., Penson, R.T. & Seiden, M.V. Curr. Cancer Drug Targets 3, 1–19 (2003).
Chen, D., Frezza, M., Schmitt, S., Kanwar, J. & Dou, Q.P. Curr. Cancer Drug Targets 11, 239–253 (2011).
Lü, S. et al. J. Pharmacol. Exp. Ther. 326, 423–431 (2008).
Oerlemans, R. et al. Blood 112, 2489–2499 (2008).
Groll, M., Berkers, C.R., Ploegh, H.L. & Ovaa, H. Structure 14, 451–456 (2006).
Skoufias, D.A. et al. J. Biol. Chem. 281, 17559–17569 (2006).
Rickert, K.W. et al. Arch. Biochem. Biophys. 469, 220–231 (2008).
Wood, K.W. et al. Proc. Natl. Acad. Sci. USA 107, 5839–5844 (2010).
Acknowledgements
We thank the Genomics Resources Core Facility of Weill Cornell Medical College for conducting the RNA-seq and D. Soong (Weill Cornell Medical College) for providing custom analysis software. This work was supported by the US National Science Foundation CAREER grant 1054964 (O.E.) and US National Institutes of Health GM98579 and GM65933 (T.M.K.).
Author information
Authors and Affiliations
Contributions
S.A.W. carried out all experiments other than the selection of BI 2536–resistant clones, which was done by B.R.H. O.E. conducted bioinformatics analysis. T.M.K. conceived the project, and T.M.K. and O.E. directed the project.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Methods and Supplementary Results (PDF 782 kb)
Supplementary Dataset 1
Upregulated Genes in BI 2536-resistant Clones, values are log2 ratios between clone RPKM and HCT-116 RPKM (XLS 93 kb)
Supplementary Dataset 2
Downregulated Genes in BI 2536-resistant Clones, values are log2 ratios between clone RPKM and HCT-116 RPKM (XLS 89 kb)
Supplementary Dataset 3
Upregulated Genes in Bortezomib-resistant Clones, values are log2 ratios between clone RPKM and HCT-116 RPKM (XLS 182 kb)
Supplementary Dataset 4
Downregulated Genes in Bortezomib-resistant Clones, values are log2 ratios between clone RPKM and HCT-116 RPKM (XLS 148 kb)
Rights and permissions
About this article
Cite this article
Wacker, S., Houghtaling, B., Elemento, O. et al. Using transcriptome sequencing to identify mechanisms of drug action and resistance. Nat Chem Biol 8, 235–237 (2012). https://doi.org/10.1038/nchembio.779
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nchembio.779
This article is cited by
-
Targeting pan-essential pathways in cancer with cytotoxic chemotherapy: challenges and opportunities
Cancer Chemotherapy and Pharmacology (2023)
-
The Critical Biomarkers Identification of Insulin Signaling Involved in Initiating cAMP Signaling Mediated Salivary Secretion in Sjogren Syndrome: Transcriptome Sequencing in NOD Mice Model
Biological Procedures Online (2022)
-
Chemical strategies to overcome resistance against targeted anticancer therapeutics
Nature Chemical Biology (2020)
-
Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity
Acta Pharmacologica Sinica (2020)
-
Discovering and validating cancer genetic dependencies: approaches and pitfalls
Nature Reviews Genetics (2020)