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Transposon mutagenesis identifies genes and evolutionary forces driving gastrointestinal tract tumor progression

Nature Genetics volume 47, pages 142–150 (2015)Cite this article

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Abstract

To provide a more comprehensive understanding of the genes and evolutionary forces driving colorectal cancer (CRC) progression, we performed Sleeping Beauty (SB) transposon mutagenesis screens in mice carrying sensitizing mutations in genes that act at different stages of tumor progression. This approach allowed us to identify a set of genes that appear to be highly relevant for CRC and to provide a better understanding of the evolutionary forces and systems properties of CRC. We also identified six genes driving malignant tumor progression and a new human CRC tumor-suppressor gene, ZNF292, that might also function in other types of cancer. Our comprehensive CRC data set provides a resource with which to develop new therapies for treating CRC.

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Figure 1: Tumor formation was accelerated and mouse survival times were shortened by SB-mediated mutagenesis.
Figure 2: Cohort and cross-species comparisons.
Figure 3: Apc is the primary gatekeeper mutation in Apcmut:SB, KrasG12D:SB and p53R172H:SB tumors but not in Smad4KO:SB tumors.
Figure 4: Different genes are selectively mutated during gastrointestinal tract tumor formation depending on the nature of the initiating mutation.
Figure 5: Genes involved in malignant gastrointestinal tract tumor progression.

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Acknowledgements

We thank K. Rogers, S. Rogers and the Institute of Molecular and Cell Biology histopathology core for performing the histopathological analysis; M.M. Taketo (Kyoto University) for supplying Smad4KO mice and S. Robin (Institute Curie) for supplying Vil1-creERT2 mice; Y. Ito for helpful discussions and encouragement; and P. Goh, P. Cheok, N. Lim, D. Chen and C. Wee for monitoring mice and animal technical assistance. The Biomedical Research Council, Agency for Science, Technology and Research (A-STAR), Singapore, and the Cancer Prevention Research Institute of Texas (CPRIT) supported this research. N.G.C. and N.A.J. are both CPRIT Scholars in Cancer Research. D.J.A. and A.G.R. are supported by Cancer Research UK and the Wellcome Trust.

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Authors and Affiliations

  1. Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore

    Haruna Takeda, Hideto Koso, Christopher Chin Kuan Yew, Michael B Mann, Jerrold M Ward, Neal G Copeland & Nancy A Jenkins

  2. Department of Oncologic Pathology, School of Medicine, Kanazawa Medical University, Ishikawa, Japan

    Haruna Takeda

  3. Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA

    Zhubo Wei, Michael B Mann, Neal G Copeland & Nancy A Jenkins

  4. Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan

    Hideto Koso

  5. Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK

    Alistair G Rust & David J Adams

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  1. Haruna Takeda
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Contributions

H.T., N.G.C. and N.A.J. designed the research. H.T., N.G.C. and N.A.J. wrote the manuscript. H.T., Z.W. and H.K. performed the experiments. H.T., H.K., M.B.M., C.C.K.Y., D.J.A. and A.G.R. performed the statistical analysis. D.J.A. and A.G.R. performed the sequencing. J.M.W. diagnosed tumor grade.

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Correspondence to Nancy A Jenkins.

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Integrated supplementary information

Supplementary Figure 1 Lineage tracing using the R26R3 LacZ reporter line and Villin-CreERT2 mice showed that Villin-CreERT2 marks intestinal stem cells.

(a) Villin-CreERT2:R26R double–compound mutant mice were administrated 2 mg of tamoxifen by intraperitoneal injection for 3 d each beginning at 4 weeks of age. On day 60 after tamoxifen injection, X-Gal staining was performed using whole-mount intestinal tissue. (b) More than 95% of the villi in the duodenum, (c) ~90% in the jejunum, (d) ~60% in the ileum and (e) 20–30% in the colon showed LacZ staining. Scale bars, 50 μm. The presence of blue-stained cells 60 d after Cre induction shows that Villin-CreERT2 is expressed in intestinal stem cells.

Supplementary Figure 2 Comparison of survival curves and the location of tumors.

SB mutagenesis shortened the lifespan of (a) ApcMin, (b) KrasG12D, (c) Smad4KO and (d) wt mice but not p53R172H mice (e). Polyps developed mainly in the duodenum and jejunum. (f) The polyp number in the colon was significantly higher in the KrasG12D cohort compared to the Smad4KO and p53R172H cohorts (t test, P < 0.05). Duo, duodenum; Jej, jejunum; Ile, ileum; Col, colon.

Supplementary Figure 3 Histopathology of intestinal tumors in KrasG12D:SB, Smad4KO:SB, p53R172H:SB and ApcMin:SB mice.

(a) A polypoid KrasG12D:SB adenoma and (b,c) two invasive KrasG12D:SB adenocarcinomas. (d) A low-magnification image of a Smad4KO:SB sessile adenoma and (e) an invasive Smad4KO:SB mucinous adenocarcinoma. (f) High-power magnification of e shows that tumor cells have invaded the tunica muscularis. (g) Invasive Smad4KO:SB mucinous tumor cells reaching the serosa. (h) An invasive Smad4KO:SB adenocarcinoma containing signet ring cells. (i) Smad4KO:SB tumor cells along with Paneth cells can be seen invading the tunica muscularis. (j) A p53R172H:SB sessile adenoma and (k,l) two invasive p53R172H:SB adenocarcinomas. (m) A primary intestinal adenocarcinoma that (n) metastasized to the lymph node. (o) A second case of lymph node metastasis. (p,q) Two ApcMin:SB adenomas. Scale bars, (a,k) 0.5 mm, (d,e j p,q) 200 μm, (b,c,f,g,l–n) 100 μm, (h,i,o) 50 μm.

Supplementary Figure 4 Trunk driver analysis shows CIS genes with high read counts.

(a) ApcMin:SB, (b) KrasG12D:SB, (c) Smad4KO:SB and (d) p53R172H:SB.

Supplementary Figure 5 Characterization of SB-Smad4 and SB-Rspo2 fusion transcripts.

(a) A chromatogram showing the partial sequence of an SB-Smad4 fusion tumor transcript. The transcript contains Smad4 exon2, which was replaced with the PGK-neo expression cassette in the knockout allele. This shows that the transposon is inserted in the wild-type Smad4 allele. (b) Primer design used to amplify by RT-PCR SB-Rspo2 fusion tumor transcripts. Black arrows denote primers. (c) A chromatogram showing a partial sequence of the SB-Rspo2 fusion transcript. Note that the transposon splice donor (SD) site is spliced to Rspo2 exon 2, which contains the ATG initiation codon. Full-length Rspo2 protein is thus overexpressed following SB insertion upstream of Rspo2. ex, exon.

Supplementary Figure 6 CRCs that overexpress RSPO1, RSPO2 or RSPO3 and lack APC mutations have decreased expression or an increased number of mutations in SMAD4.

(a) Five CRC cases (highlighted by asterisks) out of seven CRC cases, which showed RSPO1 or RSPO2 overexpression but carried no mutations in APC, had decreased SMAD4 expression and/or mutations in SMAD4 (ref. 4). (b) Six of seven CRC cases, which showed RSPO2 or RSPO3 overexpression but carried no APC mutations, showed deregulation of SMAD4 (modified from Supplementary Figure 21 in ref. 5).

Supplementary Figure 7 Hamming dendrogram shows biological independence of transposon insertions in KrasG12D:SB tumors.

Supplementary Figure 8 Hamming dendrogram shows biological independence of transposon insertions in Smad4KO:SB tumors.

Supplementary Figure 9 Hamming dendrogram shows biological independence of transposon insertions in p53R172H:SB tumors.

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Supplementary Figures 1–9 and Supplementary Note. (PDF 10489 kb)

Supplementary Tables 1–23

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Takeda, H., Wei, Z., Koso, H. et al. Transposon mutagenesis identifies genes and evolutionary forces driving gastrointestinal tract tumor progression. Nat Genet 47, 142–150 (2015). https://doi.org/10.1038/ng.3175

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