Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Resource
  • Published:

Genomic landscape of carcinogen-induced and genetically induced mouse skin squamous cell carcinoma

Nature Medicine volume 21, pages 946–954 (2015)Cite this article

Subjects

An Erratum to this article was published on 04 February 2016

This article has been updated

Abstract

Mouse models of cancers are routinely used to study cancer biology. However, it remains unclear whether carcinogenesis in mice is driven by the same spectrum of genomic alterations found in humans. Here we conducted a comprehensive genomic analysis of 9,10-dimethyl-1,2-benzanthracene (DMBA)-induced skin cancer, the most commonly used skin cancer model, which appears as benign papillomas that progress into squamous cell carcinomas (SCCs). We also studied genetically induced SCCs that expressed G12D mutant Kras (Kras G12D) but were deficient for p53. Using whole-exome sequencing, we uncovered a characteristic mutational signature of DMBA-induced SCCs. We found that the vast majority of DMBA-induced SCCs presented recurrent mutations in Hras, Kras or Rras2 and mutations in several additional putative oncogenes and tumor-suppressor genes. Similar genes were recurrently mutated in mouse and human SCCs that were from different organs or had been exposed to different carcinogens. Invasive SCCs, but not papillomas, presented substantial chromosomal aberrations, especially in DMBA-induced and genetically induced Trp53-mutated SCCs. Metastasis occurred through sequential spreading, with relatively few additional genetic events. This study provides a framework for future functional cancer genomic studies in mice.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mutational signature of DMBA-TPA–induced msSCCs.
Figure 2: Recurrent somatic mutations in DMBA-induced msSCCs.
Figure 3: Recurrent CNAs in DMBA-induced and genetically induced msSCC.
Figure 4: Histological heterogeneity of DMBA-induced msSCCs.
Figure 5: Clonal evolution in primary and metastatic DMBA-induced msSCC.

Similar content being viewed by others

Accession codes

Primary accessions

ArrayExpress

Change history

  • 06 August 2015

    In the published article, the format was listed as Article, but this is a Resource. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Luch, A. Nature and nurture —lessons from chemical carcinogenesis. Nat. Rev. Cancer 5, 113–125 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Poirier, M.C. Chemical-induced DNA damage and human cancer risk. Nat. Rev. Cancer 4, 630–637 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Abel, E.L., Angel, J.M., Kiguchi, K. & DiGiovanni, J. Multi-stage chemical carcinogenesis in mouse skin: fundamentals and applications. Nat. Protoc. 4, 1350–1362 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Balmain, A., Ramsden, M., Bowden, G.T. & Smith, J. Activation of the mouse cellular Harvey-ras gene in chemically induced benign skin papillomas. Nature 307, 658–660 (1984).

    Article  CAS  PubMed  Google Scholar 

  5. Quintanilla, M., Brown, K., Ramsden, M. & Balmain, A. Carcinogen-specific mutation and amplification of Ha-ras during mouse skin carcinogenesis. Nature 322, 78–80 (1986).

    Article  CAS  PubMed  Google Scholar 

  6. Bizub, D., Wood, A.W. & Skalka, A.M. Mutagenesis of the Ha-ras oncogene in mouse skin tumors induced by polycyclic aromatic hydrocarbons. Proc. Natl. Acad. Sci. USA 83, 6048–6052 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ruggeri, B. et al. Alterations of the p53 tumor suppressor gene during mouse skin tumor progression. Cancer Res. 51, 6615–6621 (1991).

    CAS  PubMed  Google Scholar 

  8. Kemp, C.J., Donehower, L.A., Bradley, A. & Balmain, A. Reduction of p53 gene dosage does not increase initiation or promotion but enhances malignant progression of chemically induced skin tumors. Cell 74, 813–822 (1993).

    Article  CAS  PubMed  Google Scholar 

  9. Aldaz, C.M., Trono, D., Larcher, F., Slaga, T.J. & Conti, C.J. Sequential trisomization of chromosomes 6 and 7 in mouse skin premalignant lesions. Mol. Carcinog. 2, 22–26 (1989).

    Article  CAS  PubMed  Google Scholar 

  10. Quigley, D.A. et al. Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility. Genome Biol. 12, R5 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lapouge, G. et al. Identifying the cellular origin of squamous skin tumors. Proc. Natl. Acad. Sci. USA 108, 7431–7436 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  12. White, A.C. et al. Defining the origins of Ras/p53-mediated squamous cell carcinoma. Proc. Natl. Acad. Sci. USA 108, 7425–7430 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Beck, B. et al. A vascular niche and a VEGF-Nrp1 loop regulate the initiation and stemness of skin tumours. Nature 478, 399–403 (2011).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Dipple, A., Pigott, M., Moschel, R.C. & Costantino, N. Evidence that binding of 7,12-dimethylbenz(a)anthracene to DNA in mouse embryo cell cultures results in extensive substitution of both adenine and guanine residues. Cancer Res. 43, 4132–4135 (1983).

    CAS  PubMed  Google Scholar 

  16. Cai, Y., Patel, D.J., Broyde, S. & Geacintov, N.E. Base sequence context effects on nucleotide excision repair. J. Nucleic Acids 2010, 174252 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Westcott, P.M. et al. The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature 517, 489–492 (2015).

    Article  CAS  PubMed  Google Scholar 

  18. Bos, J.L. ras oncogenes in human cancer: a review. Cancer Res. 49, 4682–4689 (1989).

    CAS  PubMed  Google Scholar 

  19. Saez, R., Chan, A.M., Miki, T. & Aaronson, S.A. Oncogenic activation of human R-ras by point mutations analogous to those of prototype H-ras oncogenes. Oncogene 9, 2977–2982 (1994).

    CAS  PubMed  Google Scholar 

  20. Schramek, D. et al. Direct in vivo RNAi screen unveils myosin IIa as a tumor suppressor of squamous cell carcinomas. Science 343, 309–313 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chu, W.K. & Hickson, I.D. RecQ helicases: multifunctional genome caretakers. Nat. Rev. Cancer 9, 644–654 (2009).

    Article  CAS  PubMed  Google Scholar 

  22. Nicolas, M. et al. Notch1 functions as a tumor suppressor in mouse skin. Nat. Genet. 33, 416–421 (2003).

    Article  CAS  PubMed  Google Scholar 

  23. Laczmanska, I. et al. Copy number alterations of chromosomal regions enclosing protein tyrosine phosphatase receptor-like genes in colorectal cancer. Pathol. Res. Pract. 210, 893–896 (2014).

    Article  CAS  PubMed  Google Scholar 

  24. Provost, E. et al. The tumor suppressor rpl36 restrains KRAS(G12V)-induced pancreatic cancer. Zebrafish 11, 551–559 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. The Cancer Genome Atlas Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576–582 (2015).

  26. Cohen-Dvashi, H. et al. Navigator-3, a modulator of cell migration, may act as a suppressor of breast cancer progression. EMBO Mol. Med. 7, 299–314 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dickinson, R.E. et al. Epigenetic inactivation of SLIT3 and SLIT1 genes in human cancers. Br. J. Cancer 91, 2071–2078 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hase, K. et al. AP-1B-mediated protein sorting regulates polarity and proliferation of intestinal epithelial cells in mice. Gastroenterology 145, 625–635 (2013).

    Article  CAS  PubMed  Google Scholar 

  29. Yu, J. et al. Kibra functions as a tumor suppressor protein that regulates Hippo signaling in conjunction with Merlin and Expanded. Dev. Cell 18, 288–299 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pogue-Geile, K.L. et al. Palladin mutation causes familial pancreatic cancer and suggests a new cancer mechanism. PLoS Med. 3, e516 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lee, C.S. et al. Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nat. Genet. 46, 1060–1062 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. South, A.P. et al. NOTCH1 mutations occur early during cutaneous squamous cell carcinogenesis. J. Invest. Dermatol. 134, 2630–2638 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Pickering, C.R. et al. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin. Cancer Res. 20, 6582–6592 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Li, Y.Y. et al. Genomic analysis of metastatic cutaneous squamous cell carcinoma. Clin. Cancer Res. 21, 1447–1456 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157–1160 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Agrawal, N. et al. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333, 1154–1157 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519–525 (2012).

  38. Song, Y. et al. Identification of genomic alterations in oesophageal squamous cell cancer. Nature 509, 91–95 (2014).

    Article  CAS  PubMed  Google Scholar 

  39. Lin, D.C. et al. Genomic and molecular characterization of esophageal squamous cell carcinoma. Nat. Genet. 46, 467–473 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. India Project Team of the International Cancer Genome Consortium. Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nat. Commun. 4, 2873 (2013).

  41. Ojesina, A.I. et al. Landscape of genomic alterations in cervical carcinomas. Nature 506, 371–375 (2014).

    Article  CAS  PubMed  Google Scholar 

  42. Lin, D.C. et al. The genomic landscape of nasopharyngeal carcinoma. Nat. Genet. 46, 866–871 (2014).

    Article  CAS  PubMed  Google Scholar 

  43. Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107–1120 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wu, W. et al. HERC2 is an E3 ligase that targets BRCA1 for degradation. Cancer Res. 70, 6384–6392 (2010).

    Article  CAS  PubMed  Google Scholar 

  45. Toll, A. et al. MYC gene numerical aberrations in actinic keratosis and cutaneous squamous cell carcinoma. Br. J. Dermatol. 161, 1112–1118 (2009).

    Article  CAS  PubMed  Google Scholar 

  46. Al Bashir, S. et al. Cysteine-rich secretory protein 3 (CRISP3), ERG and PTEN define a molecular subtype of prostate cancer with implication to patients' prognosis. J. Hematol. Oncol. 7, 21 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Quintana, R.M. et al. A transposon-based analysis of gene mutations related to skin cancer development. J. Invest. Dermatol. 133, 239–248 (2013).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Dudgeon, C. et al. The evolution of thymic lymphomas in p53 knockout mice. Genes Dev. 28, 2613–2620 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Hennings, H. et al. FVB/N mice: an inbred strain sensitive to the chemical induction of squamous cell carcinomas in the skin. Carcinogenesis 14, 2353–2358 (1993).

    Article  CAS  PubMed  Google Scholar 

  51. Lapouge, G. et al. Skin squamous cell carcinoma propagating cells increase with tumour progression and invasiveness. EMBO J. 31, 4563–4575 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Miller, S.J. et al. Mouse skin is particularly susceptible to tumor initiation during early anagen of the hair cycle: possible involvement of hair follicle stem cells. J. Invest. Dermatol. 101, 591–594 (1993).

    Article  CAS  PubMed  Google Scholar 

  53. Blanpain, C., Lowry, W.E., Geoghegan, A., Polak, L. & Fuchs, E. Self-renewal, multipotency, and the existence of two cell populations within an epithelial stem cell niche. Cell 118, 635–648 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Albers, C.A. et al. Dindel: accurate indel calls from short-read data. Genome Res. 21, 961–973 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Dees, N.D. et al. MuSiC: identifying mutational significance in cancer genomes. Genome Res. 22, 1589–1598 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Farkash-Amar, S. et al. Global organization of replication time zones of the mouse genome. Genome Res. 18, 1562–1570 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. & Chan, A.P. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7, e46688 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Risso, D., Schwartz, K., Sherlock, G. & Dudoit, S. GC-content normalization for RNA-Seq data. BMC Bioinformatics 12, 480 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).

    Article  PubMed  Google Scholar 

  67. Gao, J. et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 6, pl1 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665–1674 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. USA 104, 20007–20012 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Carter, S.L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

C.B. is an investigator at Walloon Excellence in Life Sciences and Biotechnology (WELBIO). D.N. and M.L. are supported by Télévie and an EMBO long-term fellowship, respectively. The computational resources and services used in this work were provided by the Flemish Supercomputer Center (VSC), funded by the Hercules Foundation and the Flemish Government, Department of Economy, Science and Innovation (EWI). This work was supported by Fonds de la Recherche Scientifique (FNRS), Télévie, the Interuniversity Attraction Program (PAI), a research grant and an infrastructure grant from Fondation Contre le Cancer/Stichting tegen Kanker, Fondation ULB, Fond Yvonne Boël, Fond Gaston Ithier, the the Baillet Latour Foundation and the European Research Council (ERC).

Author information

Author notes

  1. Dany Nassar, Mathilde Latil and Bram Boeckx: These authors contributed equally to this work.

  2. Diether Lambrechts and Cédric Blanpain: These authors jointly directed this work.

Authors and Affiliations

  1. Institut de recherche interdisciplinaire en biologie humaine et moléculaire (IRIBHM), Université libre de Buxelles (ULB), Brussels, Belgium

    Dany Nassar, Mathilde Latil & Cédric Blanpain

  2. Vesalius Research Center, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium

    Bram Boeckx & Diether Lambrechts

  3. Department of Oncology, Laboratory for Translational Genetics, Katholieke Universiteit Leuven (KUL), Leuven, Belgium

    Bram Boeckx & Diether Lambrechts

  4. WELBIO, Brussels, Belgium

    Cédric Blanpain

Authors
  1. Dany Nassar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mathilde Latil
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bram Boeckx
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Diether Lambrechts
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Cédric Blanpain
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.B., D.N. and D.L. designed the experiments. B.B. and D.L. performed bioinformatic analysis. D.N. and M.L. performed biological experiments. All authors performed data analysis. C.B., D.L. and D.N. wrote the manuscript.

Corresponding authors

Correspondence to Diether Lambrechts or Cédric Blanpain.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 (PDF 6667 kb)

Supplementary Data

Sequencing data and analysis (XLSX 8166 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nassar, D., Latil, M., Boeckx, B. et al. Genomic landscape of carcinogen-induced and genetically induced mouse skin squamous cell carcinoma. Nat Med 21, 946–954 (2015). https://doi.org/10.1038/nm.3878

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nm.3878

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer