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Synthetic lethal screen identification of chemosensitizer loci in cancer cells

Abstract

Abundant evidence suggests that a unifying principle governing the molecular pathology of cancer is the co-dependent aberrant regulation of core machinery driving proliferation and suppressing apoptosis1. Anomalous proteins engaged in support of this tumorigenic regulatory environment most probably represent optimal intervention targets in a heterogeneous population of cancer cells. The advent of RNA-mediated interference (RNAi)-based functional genomics provides the opportunity to derive unbiased comprehensive collections of validated gene targets supporting critical biological systems outside the framework of preconceived notions of mechanistic relationships. We have combined a high-throughput cell-based one-well/one-gene screening platform with a genome-wide synthetic library of chemically synthesized small interfering RNAs for systematic interrogation of the molecular underpinnings of cancer cell chemoresponsiveness. NCI-H1155, a human non-small-cell lung cancer line, was employed in a paclitaxel-dependent synthetic lethal screen designed to identify gene targets that specifically reduce cell viability in the presence of otherwise sublethal concentrations of paclitaxel. Using a stringent objective statistical algorithm to reduce false discovery rates below 5%, we isolated a panel of 87 genes that represent major focal points of the autonomous response of cancer cells to the abrogation of microtubule dynamics. Here we show that several of these targets sensitize lung cancer cells to paclitaxel concentrations 1,000-fold lower than otherwise required for a significant response, and we identify mechanistic relationships between cancer-associated aberrant gene expression programmes and the basic cellular machinery required for robust mitotic progression.

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Figure 1: Functional relationships among candidate paclitaxel-sensitizing siRNA targets.
Figure 2: Drug sensitivity profiles.
Figure 3: Convergence of paclitaxel and sensitizer gene function on mitotic spindle integrity.

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Acknowledgements

This work was supported by grants from the National Cancer Institute, the Robert E. Welch Foundation, the Susan G. Komen Foundation, the Department of Defense Congressionally Directed Medical Research Program and the National Cancer Institute Lung Cancer Specialized Program of Research Excellence.

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Correspondence to Michael A. White.

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Supplementary information

Supplementary Table 1

This file contains Supplementary Table 1 which shows full data set containing mean, S.D., p-values, and associated gene annotations from the genome-wide screen. (XLS 9352 kb)

Supplementary Table 2

This file contains Supplementary Table 2 which shows 5% FDR gene list. (XLS 70 kb)

Supplementary Table 3

This file contains Supplementary Table 3 which shows 2.5 percentile gene list. (XLS 68 kb)

Supplementary Table 4

This file contains Supplementary Table 4 which shows p-values and FDR values for genes described in Figure 2. (XLS 24 kb)

Supplementary Table 5

This file contains Supplementary Table 5 which shows siRNA sequences corresponding to the HC hit list. (XLS 39 kb)

Supplementary Table 6

This file contains Supplementary Table 6 which shows transfection conditions for all cell lines used in this study. (XLS 18 kb)

Supplementary Table 7

This file contains Supplementary Table 7 which shows primer sequences used for quantitative rtPCR. (XLS 19 kb)

Supplementary Information

This file contains Supplementary Figures 1-6 with Legends and Supplementary Methods (PDF 1110 kb)

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Whitehurst, A., Bodemann, B., Cardenas, J. et al. Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 446, 815–819 (2007). https://doi.org/10.1038/nature05697

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  • DOI: https://doi.org/10.1038/nature05697

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