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Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

Abstract

The proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. Although the identification of specific oncogenes has led to the development of clinically effective, molecularly targeted therapies in some cases, KRAS has remained refractory to this approach. A complementary strategy for targeting KRAS is to identify gene products that, when inhibited, result in cell death only in the presence of an oncogenic allele1,2. Here we have used systematic RNA interference to detect synthetic lethal partners of oncogenic KRAS and found that the non-canonical IκB kinase TBK1 was selectively essential in cells that contain mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression. In these cells, TBK1 activated NF-κB anti-apoptotic signals involving c-Rel and BCL-XL (also known as BCL2L1) that were essential for survival, providing mechanistic insights into this synthetic lethal interaction. These observations indicate that TBK1 and NF-κB signalling are essential in KRAS mutant tumours, and establish a general approach for the rational identification of co-dependent pathways in cancer.

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Figure 1: Meta-analysis of RNAi screens identifying KRAS synthetic lethals.
Figure 2: TBK1 synthetic lethality with oncogenic KRAS.
Figure 3: Oncogenic KRAS -induced NF-κB signalling involves TBK1.
Figure 4: TBK1 regulates c-Rel and BCL-XL in KRAS mutant cells.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All microarray data are available from the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo) under accession codes GSE17671, GSE17672 and GSE17643.

References

  1. Hartwell, L. H., Szankasi, P., Roberts, C. J., Murray, A. W. & Friend, S. H. Integrating genetic approaches into the discovery of anticancer drugs. Science 278, 1064–1068 (1997)

    ADS  CAS  Article  Google Scholar 

  2. Kaelin, W. G. The concept of synthetic lethality in the context of anticancer therapy. Nature Rev. Cancer 5, 689–698 (2005)

    CAS  Article  Google Scholar 

  3. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006)

    CAS  Article  Google Scholar 

  4. Malo, N., Hanley, J. A., Cerquozzi, S., Pelletier, J. & Nadon, R. Statistical practice in high-throughput screening data analysis. Nature Biotechnol. 24, 167–175 (2006)

    CAS  Article  Google Scholar 

  5. Gould, J., Getz, G., Monti, S., Reich, M. & Mesirov, J. P. Comparative gene marker selection suite. Bioinformatics 22, 1924–1925 (2006)

    CAS  Article  Google Scholar 

  6. Luo, B. et al. Highly parallel identification of essential genes in cancer cells. Proc. Natl Acad. Sci. USA 105, 20380–20385 (2008)

    ADS  CAS  Article  Google Scholar 

  7. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005)

    ADS  CAS  Article  Google Scholar 

  8. Lundberg, A. S. et al. Immortalization and transformation of primary human airway epithelial cells by gene transfer. Oncogene 21, 4577–4586 (2002)

    CAS  Article  Google Scholar 

  9. Wislez, M. et al. Inhibition of mammalian target of rapamycin reverses alveolar epithelial neoplasia induced by oncogenic K-ras. Cancer Res. 65, 3226–3235 (2005)

    CAS  Article  Google Scholar 

  10. Chien, Y. et al. RalB GTPase-mediated activation of the IκB family kinase TBK1 couples innate immune signaling to tumor cell survival. Cell 127, 157–170 (2006)

    CAS  Article  Google Scholar 

  11. Häcker, H. & Karin, M. Regulation and function of IKK and IKK-related kinases. Sci. STKE 2006, re13 (2006)

    Article  Google Scholar 

  12. Bild, A. H. et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439, 353–357 (2006)

    ADS  CAS  Article  Google Scholar 

  13. Hinata, K., Gervin, A. M., Jennifer Zhang, Y. & Khavari, P. A. Divergent gene regulation and growth effects by NF-κB in epithelial and mesenchymal cells of human skin. Oncogene 22, 1955–1964 (2003)

    CAS  Article  Google Scholar 

  14. Boehm, J. S. et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 129, 1065–1079 (2007)

    CAS  Article  Google Scholar 

  15. Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008)

    ADS  CAS  Article  Google Scholar 

  16. Takeuchi, T. et al. Expression profile-defined classification of lung adenocarcinoma shows close relationship with underlying major genetic changes and clinicopathologic behaviors. J. Clin. Oncol. 24, 1679–1688 (2006)

    CAS  Article  Google Scholar 

  17. Andersen, J., VanScoy, S., Cheng, T. F., Gomez, D. & Reich, N. C. IRF-3-dependent and augmented target genes during viral infection. Genes Immun. 9, 168–175 (2008)

    CAS  Article  Google Scholar 

  18. Singh, A. et al. A gene expression signature associated with “K-Ras addiction” reveals regulators of EMT and tumor cell survival. Cancer Cell 15, 489–500 (2009)

    CAS  Article  Google Scholar 

  19. Mayo, M. W. et al. Requirement of NF-κB activation to suppress p53-independent apoptosis induced by oncogenic Ras. Science 278, 1812–1815 (1997)

    ADS  CAS  Article  Google Scholar 

  20. Brown, K., Gerstberger, S., Carlson, L., Franzoso, G. & Siebenlist, U. Control of IκB-α proteolysis by site-specific, signal-induced phosphorylation. Science 267, 1485–1488 (1995)

    ADS  CAS  Article  Google Scholar 

  21. Harris, J. et al. Nuclear accumulation of cRel following C-terminal phosphorylation by TBK1/IKKε. J. Immunol. 177, 2527–2535 (2006)

    CAS  Article  Google Scholar 

  22. Mercurio, F., DiDonato, J. A., Rosette, C. & Karin, M. p105 and p98 precursor proteins play an active role in NF-κB-mediated signal transduction. Genes Dev. 7, 705–718 (1993)

    CAS  Article  Google Scholar 

  23. Owyang, A. M. et al. c-Rel is required for the protection of B cells from antigen receptor-mediated, but not Fas-mediated, apoptosis. J. Immunol. 167, 4948–4956 (2001)

    CAS  Article  Google Scholar 

  24. Scholl, C. et al. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 137, 821–834 (2009)

    CAS  Article  Google Scholar 

  25. Luo, J. et al. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 137, 835–848 (2009)

    CAS  Article  Google Scholar 

  26. Ngo, V. N. et al. A loss-of-function RNA interference screen for molecular targets in cancer. Nature 441, 106–110 (2006)

    ADS  CAS  Article  Google Scholar 

  27. Rottmann, S., Wang, Y., Nasoff, M., Deveraux, Q. L. & Quon, K. C. A. TRAIL receptor-dependent synthetic lethal relationship between MYC activation and GSK3β/FBW7 loss of function. Proc. Natl Acad. Sci. USA 102, 15195–15200 (2005)

    ADS  CAS  Article  Google Scholar 

  28. Silva, J. M. et al. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319, 617–620 (2008)

    CAS  Article  Google Scholar 

  29. Zhang, J. Powerful goodness-of-fit tests based on the likelihood ratio. J. R. Stat. Soc. Series B Stat. Methodol. 64, 281–294 (2002)

    MathSciNet  Article  Google Scholar 

  30. Sos, M. L. et al. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J. Clin. Invest. 119, 1727–1740 (2009)

    CAS  Article  Google Scholar 

  31. Bhattacharjee, A. et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl Acad. Sci. USA 98, 13790–13795 (2001)

    ADS  CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported in part by grants from the US National Cancer Institute (R33 CA128625, R01 CA130988) (W.C.H.) and NIH T32 CA09172-33 (D.A.B., S.E.M.), the Starr Cancer Consortium (I1-A11; W.C.H., D.G.G.), the Susan Madden Fund and an ASCO YIA (D.A.B.), a Department of Defense Prostate Cancer Postdoctoral Fellowship (S.Y.K.), a Brain Science Foundation Fellowship (I.F.D.), the Deutsche Krebshilfe (grant 107954) (R.K.T.), the Fritz-Thyssen-Stiftung (grant 10.08.2.175; R.K.T.) and the NGFNplus-program of the German Ministry of Science and Education (BMBF, grant 01GS08100; R.K.T.). We thank C. Yu, G. Wei and members of the Hahn laboratory for discussions. High-throughput RNAi screening was conducted at the RNAi Platform of the Broad Institute of MIT and Harvard.

Author Contributions D.A.B., J.S.B., S.Y.K., S.E.M. and W.C.H. designed the experiments. D.A.B. and P.T. performed computational analyses. S.Y.K., I.F.D., A.C.S., P.S., C.S., S.F., P.B.G., J.H.R., Q.S. and R.C.W. performed primary RNAi screens; S.J.S., S.H., B.S.W., C.M. and B.A.W. assisted with data analysis. D.A.B. performed secondary screen with help from H.L. S.E.M. performed tumour xenograft experiments. E.M. performed experiments with murine cell lines. D.A.B., J.S.B., E.M.C., M.L.S., K.M. and R.K.T. performed expression-profiling experiments. S.R., D.M.L., D.M.S., E.S.L., D.G.G., T.J. and D.E.R. supervised RNAi screens; M.M. and J.P.M. supervised data analysis. D.A.B. and W.C.H. wrote the manuscript. W.C.H. coordinated all aspects of the project. All authors discussed results and edited the manuscript.

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Correspondence to William C. Hahn.

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W.C.H., M.M. and D.M.L. are consultants for Novartis Pharmaceuticals, Inc.

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Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108–112 (2009). https://doi.org/10.1038/nature08460

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