Letter | Published:

The mutational landscapes of genetic and chemical models of Kras-driven lung cancer

Nature volume 517, pages 489492 (22 January 2015) | Download Citation


Next-generation sequencing of human tumours has refined our understanding of the mutational processes operative in cancer initiation and progression, yet major questions remain regarding the factors that induce driver mutations and the processes that shape mutation selection during tumorigenesis. Here we performed whole-exome sequencing on adenomas from three mouse models of non-small-cell lung cancer, which were induced either by exposure to carcinogens (methyl-nitrosourea (MNU) and urethane) or by genetic activation of Kras (KrasLA2). Although the MNU-induced tumours carried exactly the same initiating mutation in Kras as seen in the KrasLA2 model (G12D), MNU tumours had an average of 192 non-synonymous, somatic single-nucleotide variants, compared with only six in tumours from the KrasLA2 model. By contrast, the KrasLA2 tumours exhibited a significantly higher level of aneuploidy and copy number alterations compared with the carcinogen-induced tumours, suggesting that carcinogen-induced and genetically engineered models lead to tumour development through different routes. The wild-type allele of Kras has been shown to act as a tumour suppressor in mouse models of non-small-cell lung cancer. We demonstrate that urethane-induced tumours from wild-type mice carry mostly (94%) Kras Q61R mutations, whereas those from Kras heterozygous animals carry mostly (92%) Kras Q61L mutations, indicating a major role for germline Kras status in mutation selection during initiation. The exome-wide mutation spectra in carcinogen-induced tumours overwhelmingly display signatures of the initiating carcinogen, while adenocarcinomas acquire additional C > T mutations at CpG sites. These data provide a basis for understanding results from human tumour genome sequencing, which has identified two broad categories of tumours based on the relative frequency of single-nucleotide variations and copy number alterations1, and underline the importance of carcinogen models for understanding the complex mutation spectra seen in human cancers.

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The raw .bam files have been deposited in the European Nucleotide Archive under accession number ERP001454.


  1. 1.

    et al. Emerging landscape of oncogenic signatures across human cancers. Nature Genet. 45, 1127–1133 (2013)

  2. 2.

    , & The cancer genome. Nature 458, 719–724 (2009)

  3. 3.

    et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013)

  4. 4.

    et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013)

  5. 5.

    et al. Somatic activation of the K-ras oncogene causes early onset lung cancer in mice. Nature 410, 1111–1116 (2001)

  6. 6.

    , , , & Activation of the Ki-ras protooncogene in spontaneously occurring and chemically induced lung tumours of the strain A mouse. Proc. Natl Acad. Sci. USA 86, 3070–3074 (1989)

  7. 7.

    , & A comprehensive survey of Ras mutations in cancer. Cancer Res. 72, 2457–2467 (2012)

  8. 8.

    et al. Analysis of lung tumour initiation and progression using conditional expression of oncogenic K-ras. Genes Dev. 15, 3243–3248 (2001)

  9. 9.

    et al. Wildtype Kras2 can inhibit lung carcinogenesis in mice. Nature Genet. 29, 25–33 (2001)

  10. 10.

    et al. Kras regulatory elements and exon 4A determine mutation specificity in lung cancer. Nature Genet. 40, 1240–1244 (2008)

  11. 11.

    et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 150, 1121–1134 (2012)

  12. 12.

    Mechanisms of lung tumourigenesis by ethyl carbamate and vinyl carbamate. Drug Metab. Rev. 42, 355–378 (2010)

  13. 13.

    , , , & Molecular analysis of point mutations in a barley genome exposed to MNU and gamma rays. Mutat. Res. 738–739, 52–70 (2012)

  14. 14.

    Mutagenesis at methylated CpG sequences. Curr. Top. Microbiol. Immunol. 301, 259–281 (2006)

  15. 15.

    et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 150, 264–278 (2012)

  16. 16.

    et al. Ras interaction with two distinct binding domains in Raf-1 may be required for Ras transformation. J. Biol. Chem. 271, 233–237 (1996)

  17. 17.

    , , , & Dynamic properties of the Ras switch I region and its importance for binding to effectors. Proc. Natl Acad. Sci. USA 98, 4944–4949 (2001)

  18. 18.

    et al. Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer. Proc. Natl Acad. Sci. USA 110, 12426–12431 (2013)

  19. 19.

    et al. Cancer genome landscapes. Science 339, 1546–1558 (2013)

  20. 20.

    et al. Mutation analysis of the 8p22 candidate tumour suppressor gene ATIP/MTUS1 in hepatocellular carcinoma. Mol. Cell. Endocrinol. 252, 207–215 (2006)

  21. 21.

    et al. Copy number variant in the candidate tumour suppressor gene MTUS1 and familial breast cancer risk. Carcinogenesis 28, 1442–1445 (2007)

  22. 22.

    et al. Down-regulation of MTUS1 in human colon tumours. Oncol. Rep. 23, 183–189 (2010)

  23. 23.

    et al. Reduced expression of MTUS1 mRNA is correlated with poor prognosis in bladder cancer. Oncol Lett 4, 113–118 (2012)

  24. 24.

    et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nature Med. 14, 822–827 (2008)

  25. 25.

    et al. Progressive genomic instability in the FVB/KrasLA2 mouse model of lung cancer. Mol. Cancer Res. 9, 1339–1345 (2011)

  26. 26.

    , , , & Transduction of interleukin-2 antiapoptotic and proliferative signals via Akt protein kinase. Proc. Natl Acad. Sci. USA 94, 3627–3632 (1997)

  27. 27.

    et al. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell 156, 1298–1311 (2014)

  28. 28.

    , & Specific Ki-ras codon 61 mutations may determine the development of urethan-induced mouse lung adenomas or adenocarcinomas. Mol. Carcinog. 3, 287–295 (1990)

  29. 29.

    et al. Identification of Fat4 and Tsc22d1 as novel candidate genes for spontaneous pulmonary adenomas. Cancer Res. 71, 5779–5791 (2011)

  30. 30.

    , , , & Interactions between wild-type and mutant Ras genes in lung and skin carcinogenesis. Oncogene 32, 4028–4033 (2013)

  31. 31.

    et al. K-ras is an essential gene in the mouse with partial functional overlap with N-ras. Genes Dev. 11, 2468–2481 (1997)

  32. 32.

    et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469, 539–542 (2011)

  33. 33.

    & Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

  34. 34.

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

  35. 35.

    et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213–219 (2013)

  36. 36.

    et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)

  37. 37.

    , & ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010)

  38. 38.

    et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945–D950 (2011)

  39. 39.

    et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011)

  40. 40.

    et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012)

  41. 41.

    et al. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27, 268–269 (2011)

  42. 42.

    et al. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res. 66, 7466–7472 (2006)

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This work was supported by National Cancer Institute (NCI) grants R01 CA111834, U01 CA84244, U01 CA141455 and UO1 CA176287 (to A.B.), and partly funded by the Bonnie Addario Foundation. P.M.K.W. was supported by the National Institutes of Health (NIH) training grant T32 GM007175 and a National Science Foundation GRFP award, and is currently supported by an NCI F31 NRSA award. K.D.H. was supported by the NIH training grant T32 GM007175, and is currently supported by an NCI F31 NRSA award. D.J.A. is supported by Cancer Research UK and the Wellcome Trust. We are appreciative of help and comments from our colleagues in refining this study and manuscript. We would also like to thank S. Busch for assistance with animal studies, and S. Green, T. Yuan and M. McMahon for providing the K493.1 cell line.

Author information


  1. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA

    • Peter M. K. Westcott
    • , Kyle D. Halliwill
    • , Minh D. To
    • , Reyno Delrosario
    • , David A. Quigley
    •  & Allan Balmain
  2. Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA

    • Peter M. K. Westcott
    •  & Kyle D. Halliwill
  3. Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK

    • Mamunur Rashid
    • , Alistair G. Rust
    • , Thomas M. Keane
    •  & David J. Adams
  4. Department of Pathology, University of California San Francisco, San Francisco, California 94143, USA

    • Kuang-Yu Jen
  5. Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA

    • Kay E. Gurley
    •  & Christopher J. Kemp
  6. Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm 171 21, Sweden

    • Erik Fredlund
  7. Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, USA

    • Allan Balmain


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P.M.K.W., K.D.H., M.D.T., D.J.A. and A.B. contributed to the overall study design. P.M.K.W. carried out most of the experiments, with help from M.D.T. R.D. was responsible for all of the animal studies. Sequencing and Sequenom were performed at the Sanger Institute under the supervision of D.J.A., and data processing was carried out by K.D.H., M.R., A.G.R. and T.M.K. SNV and CNA calling were carried out by K.D.H. Data analysis was carried out primarily by P.M.K.W. and K.D.H., with help from E.F. and D.A.Q. K.-Y.J. made histological assessments of all tumours. Adenomas and adenocarcinomas from the A/J mice were provided by C.J.K. and K.E.G. The manuscript was written primarily by P.M.K.W. and A.B., with contributions from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Allan Balmain.

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    Supplementary Information

    This file contains Supplementary Table 1 and 3-8.

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    Supplementary Data

    VCF file of all SNVs called in the 82 lung adenomas.

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    Supplementary Data

    VCF file of all SNVs called in the 22 lung adenocarcinomas.

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    Supplementary Data

    Sample to ID key file.

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