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Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

Nature Genetics volume 44, pages 1111–1116 (2012)Cite this article

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Abstract

Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis. Here, we obtained exome, transcriptome and copy-number alteration data from approximately 53 samples consisting of 36 primary human SCLC and normal tissue pairs and 17 matched SCLC and lymphoblastoid cell lines. We also obtained data for 4 primary tumors and 23 SCLC cell lines. We identified 22 significantly mutated genes in SCLC, including genes encoding kinases, G protein–coupled receptors and chromatin-modifying proteins. We found that several members of the SOX family of genes were mutated in SCLC. We also found SOX2 amplification in ∼27% of the samples. Suppression of SOX2 using shRNAs blocked proliferation of SOX2-amplified SCLC lines. RNA sequencing identified multiple fusion transcripts and a recurrent RLF-MYCL1 fusion. Silencing of MYCL1 in SCLC cell lines that had the RLF-MYCL1 fusion decreased cell proliferation. These data provide an in-depth view of the spectrum of genomic alterations in SCLC and identify several potential targets for therapeutic intervention.

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Figure 1: SCLC somatic mutations.
Figure 2: Significantly mutated genes in SCLC.
Figure 3: SOX2 is amplified in SCLC and drives proliferation.
Figure 4: SOX2 gene amplification and protein expression in SCLC.
Figure 5: Kinase fusions.

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References

  1. Siegel, R., Ward, E., Brawley, O. & Jemal, A. Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J. Clin. 61, 212–236 (2011).

    Article  Google Scholar 

  2. Siegel, R., Naishadham, D. & Jemal, A. Cancer statistics, 2012. CA Cancer J. Clin. 62, 10–29 (2012).

    Article  Google Scholar 

  3. Hann, C.L. & Rudin, C.M. Fast, hungry and unstable: finding the Achilles' heel of small-cell lung cancer. Trends Mol. Med. 13, 150–157 (2007).

    Article  CAS  Google Scholar 

  4. Wistuba, I.I., Gazdar, A.F. & Minna, J.D. Molecular genetics of small cell lung carcinoma. Semin. Oncol. 28, 3–13 (2001).

    Article  CAS  Google Scholar 

  5. Mori, N. et al. Variable mutations of the RB gene in small-cell lung carcinoma. Oncogene 5, 1713–1717 (1990).

    CAS  PubMed  Google Scholar 

  6. Arriola, E. et al. Genetic changes in small cell lung carcinoma. Clin. Transl. Oncol. 10, 189–197 (2008).

    Article  CAS  Google Scholar 

  7. Yokomizo, A. et al. PTEN/MMAC1 mutations identified in small cell, but not in non-small cell lung cancers. Oncogene 17, 475–479 (1998).

    Article  CAS  Google Scholar 

  8. Tatematsu, A. et al. Epidermal growth factor receptor mutations in small cell lung cancer. Clin. Cancer Res. 14, 6092–6096 (2008).

    Article  CAS  Google Scholar 

  9. Shibata, T., Kokubu, A., Tsuta, K. & Hirohashi, S. Oncogenic mutation of PIK3CA in small cell lung carcinoma: a potential therapeutic target pathway for chemotherapy-resistant lung cancer. Cancer Lett. 283, 203–211 (2009).

    Article  CAS  Google Scholar 

  10. Onuki, N. et al. Genetic changes in the spectrum of neuroendocrine lung tumors. Cancer 85, 600–607 (1999).

    Article  CAS  Google Scholar 

  11. Sher, T., Dy, G.K. & Adjei, A.A. Small cell lung cancer. Mayo Clin. Proc. 83, 355–367 (2008).

    Article  CAS  Google Scholar 

  12. Forbes, S.A. et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 38, D652–D657 (2010).

    Article  CAS  Google Scholar 

  13. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010).

    Article  CAS  Google Scholar 

  14. Ng, P.C. & Henikoff, S. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 12, 436–446 (2002).

    Article  CAS  Google Scholar 

  15. Ramensky, V., Bork, P. & Sunyaev, S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894–3900 (2002).

    Article  CAS  Google Scholar 

  16. González-Pérez, A. & Lopez-Bigas, N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am. J. Hum. Genet. 88, 440–449 (2011).

    Article  Google Scholar 

  17. Kan, Z. et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 466, 869–873 (2010).

    Article  CAS  Google Scholar 

  18. Seshagiri, S. et al. Recurrent R-spondin fusions in colon cancer. Nature published online, doi:10.1038/nature11282 (15 August 2012).

  19. Molderings, G.J. et al. Multiple novel alterations in Kit tyrosine kinase in patients with gastrointestinally pronounced systemic mast cell activation disorder. Scand. J. Gastroenterol. 42, 1045–1053 (2007).

    Article  CAS  Google Scholar 

  20. D'Angelo, S.P. & Pietanza, M.C. The molecular pathogenesis of small cell lung cancer. Cancer Biol. Ther. 10, 1–10 (2010).

    Article  CAS  Google Scholar 

  21. Medina, P.P. et al. The SRY–HMG box gene, SOX4, is a target of gene amplification at chromosome 6p in lung cancer. Hum. Mol. Genet. 18, 1343–1352 (2009).

    Article  CAS  Google Scholar 

  22. Tompkins, D.H. et al. Sox2 is required for maintenance and differentiation of bronchiolar Clara, ciliated, and goblet cells. PLoS ONE 4, e8248 (2009).

    Article  Google Scholar 

  23. Wegner, M. SOX after SOX: SOXession regulates neurogenesis. Genes Dev. 25, 2423–2428 (2011).

    Article  CAS  Google Scholar 

  24. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).

    Article  CAS  Google Scholar 

  25. Lujan, E., Chanda, S., Ahlenius, H., Sudhof, T.C. & Wernig, M. Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. Proc. Natl. Acad. Sci. USA 109, 2527–2532 (2012).

    Article  CAS  Google Scholar 

  26. Bass, A.J. et al. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat. Genet. 41, 1238–1242 (2009).

    Article  CAS  Google Scholar 

  27. Mäkelä, T.P., Saksela, K., Evan, G. & Alitalo, K. A fusion protein formed by L-myc and a novel gene in SCLC. EMBO J. 10, 1331–1335 (1991).

    Article  Google Scholar 

  28. Robinson, D.R. et al. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat. Med. 17, 1646–1651 (2011).

    Article  CAS  Google Scholar 

  29. Lu, Y. et al. Evidence that SOX2 overexpression is oncogenic in the lung. PLoS ONE 5, e11022 (2010).

    Article  Google Scholar 

  30. Gontan, C. et al. Sox2 is important for two crucial processes in lung development: branching morphogenesis and epithelial cell differentiation. Dev. Biol. 317, 296–309 (2008).

    Article  CAS  Google Scholar 

  31. Sholl, L.M., Long, K.B. & Hornick, J.L. Sox2 expression in pulmonary non-small cell and neuroendocrine carcinomas. Appl. Immunohistochem. Mol. Morphol. 18, 55–61 (2010).

    Article  CAS  Google Scholar 

  32. Güre, A.O. et al. Serological identification of embryonic neural proteins as highly immunogenic tumor antigens in small cell lung cancer. Proc. Natl. Acad. Sci. USA 97, 4198–4203 (2000).

    Article  Google Scholar 

  33. Kwak, E.L. et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N. Engl. J. Med. 363, 1693–1703 (2010).

    Article  CAS  Google Scholar 

  34. Bergethon, K. et al. ROS1 rearrangements define a unique molecular class of lung cancers. J. Clin. Oncol. 30, 863–870 (2012).

    Article  CAS  Google Scholar 

  35. Takeuchi, K. et al. RET, ROS1 and ALK fusions in lung cancer. Nat. Med. 18, 378–381 (2012).

    Article  CAS  Google Scholar 

  36. Morgan, M. et al. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25, 2607–2608 (2009).

    Article  CAS  Google Scholar 

  37. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  38. DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).

    Article  CAS  Google Scholar 

  39. Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).

    Article  CAS  Google Scholar 

  40. Martincorena, I., Seshasayee, A.S. & Luscombe, N.M. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 485, 95–98 (2012).

    Article  CAS  Google Scholar 

  41. Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685–689 (2012).

    Article  CAS  Google Scholar 

  42. Greenman, C.D. et al. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 11, 164–175 (2010).

    Article  Google Scholar 

  43. Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).

    Article  Google Scholar 

  44. Simms, E., Gazdar, A.F., Abrams, P.G. & Minna, J.D. Growth of human small cell (oat cell) carcinoma of the lung in serum-free growth factor–supplemented medium. Cancer Res. 40, 4356–4363 (1980).

    CAS  PubMed  Google Scholar 

  45. Phelps, R.M. et al. NCI–Navy Medical Oncology Branch cell line data base. J. Cell. Biochem. Suppl. 24, 32–91 (1996).

    Article  CAS  Google Scholar 

  46. Carney, D.N., Bepler, G. & Gazdar, A.F. The serum-free establishment and in vitro growth properties of classic and variant small cell lung cancer cell lines. Recent Results Cancer Res. 99, 157–166 (1985).

    Article  CAS  Google Scholar 

  47. Sarbassov, D.D., Guertin, D.A., Ali, S.M. & Sabatini, D.M. Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex. Science 307, 1098–1101 (2005).

    Article  CAS  Google Scholar 

  48. Wiederschain, D. et al. Single-vector inducible lentiviral RNAi system for oncology target validation. Cell Cycle 8, 498–504 (2009).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Genentech DNA Sequencing and Oligo groups for their help with the project. We thank M.A. Huntley and J. Degenhardt for bioinformatics support and the Pathology Core Labs for providing histology, IHC and tissue management support. This work was also supported by grants from the Burroughs Wellcome Fund, the Flight Attendant Medical Research Institute, the Johns Hopkins Specialized Programs of Research Excellence (SPORE) NCI P50CA058184 (M.V.B. and C.M.R.), the Colorado SPORE NCI P50 CA058187 (M.V.-G) and the University of Texas SPORE NCI P50CA70907 (J.D.M., A.F.G. and K.E.H.). D.D.P. is supported by the Coordenacao de Aperfeicoamento de Passoal de Nivel Superior (CAPES) Foundation and the Ministry of Education of Brazil.

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Author notes

  1. Charles M Rudin, Steffen Durinck, Eric W Stawiski, John T Poirier, Zora Modrusan and David S Shames: These authors contributed equally to this work.

Authors and Affiliations

  1. The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA

    Charles M Rudin, John T Poirier, Emily A Bergbower, James Shin, Peter B Illei & Malcolm V Brock

  2. Department of Molecular Biology, Genentech, South San Francisco, California, USA.,

    Steffen Durinck, Eric W Stawiski, Zora Modrusan, Yinghui Guan, Joseph Guillory, Celina Sanchez Rivers, Catherine K Foo, Deepali Bhatt, Jeremy Stinson, Subhra Chaudhuri, Vasantharajan Janakiraman, Bijay S Jaiswal, Chaitali Parikh, Wenlin Yuan, Frederic J de Sauvage & Somasekar Seshagiri

  3. Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, California, USA.,

    Steffen Durinck, Eric W Stawiski, Florian Gnad, Peter M Haverty, Robert Gentleman, Zemin Zhang, Thomas D Wu & Richard Bourgon

  4. Department of Oncology Biomarker Development, Genentech, South San Francisco, California, USA.,

    David S Shames & Robert L Yauch

  5. Department of Pathology, Genentech, South San Francisco, California, USA

    Hartmut Koeppen & Howard M Stern

  6. Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA

    Kenneth E Huffman, Adi F Gazdar & John D Minna

  7. Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado, USA

    Diego D Paskulin & Marileila Varella-Garcia

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Contributions

C.M.R. and S.S. conceived the study and designed the experiments. E.W.S. and S.D. performed the exome and whole-genome sequencing, RNA-seq and copy-number analysis. Z.M. and Y.G. performed validation of the fusions. Z.M. managed exome capture. J.T.P., E.A.B., S.C., V.J., B.S.J., W.Y. and C.P. performed biological validated studies. J. Shin, D.D.P., P.B.I. and M.V.-G. performed SOX2 IHC and FISH studies. K.E.H., A.F.G. and J.D.M. provided reagents and analysis support. J. Stinson, C.K.F., D.B., C.S.R. and J.G. collected sequencing data and performed mutation validation. F.G. and Z.Z. predicted the functional effects of mutations. E.W.S., P.M.H., R.B., T.D.W. and R.G. provided bioinformatics support, including the algorithm for variant calling, fusion detection and copy-number calling. R.B. and P.M.H. analyzed SNP array data. H.K., H.M.S., P.B.I., M.V.B. and A.F.G. provided pathology support. F.J.d.S., D.S.S., R.L.Y. and J.D.M. provided critical analysis and organizational support. D.S.S., E.W.S., S.D., Z.M., C.M.R. and J.T.P. wrote the manuscript, which was reviewed and edited by the other coauthors.

Corresponding authors

Correspondence to Charles M Rudin or Somasekar Seshagiri.

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Competing interests

C.M.R. has previously consulted for Genentech. P.B.I. is a consultant for Leica Microsystems, the manufacturer of a device used in this study. The terms of these arrangements are being managed by the Johns Hopkins University in accordance with its conflict of interest policies. Some of the authors, as indicated in the author affiliations, are employees of Genentech and hold shares in Roche.

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Rudin, C., Durinck, S., Stawiski, E. et al. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet 44, 1111–1116 (2012). https://doi.org/10.1038/ng.2405

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