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Using transcriptome sequencing to identify mechanisms of drug action and resistance


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.

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Figure 1: Characterization of BI 2536–resistant clones.
Figure 2: Characterization of bortezomib-resistant clones.


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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.).

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Authors and Affiliations



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

Correspondence to Olivier Elemento or Tarun M Kapoor.

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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)

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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).

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