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Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

Nature Genetics volume 43, pages 1202–1209 (2011)Cite this article

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Abstract

The evolution of colorectal cancer suggests the involvement of many genes. To identify new drivers of intestinal cancer, we performed insertional mutagenesis using the Sleeping Beauty transposon system in mice carrying germline or somatic Apc mutations. By analyzing common insertion sites (CISs) isolated from 446 tumors, we identified many hundreds of candidate cancer drivers. Comparison to human data sets suggested that 234 CIS-targeted genes are also dysregulated in human colorectal cancers. In addition, we found 183 CIS-containing genes that are candidate Wnt targets and showed that 20 CISs-containing genes are newly discovered modifiers of canonical Wnt signaling. We also identified mutations associated with a subset of tumors containing an expanded number of Paneth cells, a hallmark of deregulated Wnt signaling, and genes associated with more severe dysplasia included those encoding members of the FGF signaling cascade. Some 70 genes had co-occurrence of CIS pairs, clustering into 38 sub-networks that may regulate tumor development.

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Figure 1: Sleeping Beauty transposon mobilization increases morbidity and tumor burden of Apc-deficient mice.
Figure 2: Comparison of Sleeping Beauty insertions in the K-Ras, p53 and TGFβ signaling pathways.
Figure 3: Cross-species comparison implicates CISs irrespective of rank position.
Figure 4: Identification of new Wnt targets with tumorigenic potential.
Figure 5: Co-occurring CISs can be grouped into interacting networks.

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Acknowledgements

We thank the Cambridge Research Institute core service Biological Resources and Histopathology, and the Sanger Institute sequencing services for their vital contributions to this study. We are grateful to V. Theodorou for critical reading of the manuscript. H.N.M., A.G.R., N.A.W., M.E., R.K., M.J.A., L.v.d.W., D.J.W. and D.J.A. are supported by Cancer Research-UK. D.J.A. is also supported by the Wellcome Trust and L.v.d.W. by the Kay Kendall Leukemia Foundation. A.G.U., L.W., J.t.H. and J.d.R. are supported by the Netherlands Organization for Scientific Research (NWO) Genomics program and the Netherlands Genomics Initiative. J.d.R. was also supported by the BioRange program of the Netherlands Bioinformatics Centre, which is supported by a BSIK grant through the Netherlands Genomics Initiative. A.U. is also supported by the Cancer Genomics Centre through the Netherlands Genomics Initiative.

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Authors and Affiliations

  1. Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK

    H Nikki March, Matthew Eldridge, Richard Kemp & Douglas J Winton

  2. Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

    Alistair G Rust, Louise van der Weyden & David J Adams

  3. Histopathology Unit, London Research Institute, Cancer Research UK, London, UK

    Nicholas A Wright

  4. Bioinformatics and Statistics Group, Netherlands Cancer Institute, Amsterdam, The Netherlands

    Jelle ten Hoeve, Jeroen de Ridder & Lodewyk F A Wessels

  5. Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands

    Jeroen de Ridder & Lodewyk F A Wessels

  6. Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands

    Anton Berns, Jules Gadiot & Anthony Uren

  7. Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK

    Mark J Arends

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Contributions

H.N.M. performed the majority of the experiments. D.J.W., L.v.d.W. and R.K. assisted with sample processing and analysis of transposon mobilization. A.G.R., J.t.H., J.d.R., L.F.A.W. and M.E. performed data analysis and algorithm development. A.U., J.G. and A.B. provided targeted embryonic stem cells carrying the conditional Sleeping Beauty transposon allele. N.A.W. performed the majority of the histopathological analysis with assistance from M.J.A. The study was jointly designed and supervised by D.J.W. and D.J.A., who contributed to some of the experiments. H.N.M., D.J.W. and D.J.A. wrote the paper with input from some of the other authors.

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Correspondence to Douglas J Winton.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–12, and Supplementary Tables 1, 3, 4, 6–19 and 21. (PDF 2426 kb)

Supplementary Table 2

Catalog of CIS regions (XLS 3547 kb)

Supplementary Table 5

Catalog of tumor by gene insertions (XLSX 4442 kb)

Supplementary Table 20

Firestein Wnt candidates (XLS 134 kb)

Supplementary Data 1

Transposon insertion site data file (TXT 9791 kb)

Supplementary Data 2

30 kb kernel convolution CIS data file (TXT 25250 kb)

Supplementary Data 3

120 kb kernel convolution CIS data file (TXT 6337 kb)

Supplementary Data 4

Merged 30kb and 120kb kernel convolution CIS data file (TXT 122 kb)

Supplementary Data 5

Monte Carlo peaks and regions data file (TXT 3862 kb)

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March, H., Rust, A., Wright, N. et al. Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis. Nat Genet 43, 1202–1209 (2011). https://doi.org/10.1038/ng.990

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