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A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer

Abstract

Here we describe a conditional piggyBac transposition system in mice and report the discovery of large sets of new cancer genes through a pancreatic insertional mutagenesis screen. We identify Foxp1 as an oncogenic transcription factor that drives pancreatic cancer invasion and spread in a mouse model and correlates with lymph node metastasis in human patients with pancreatic cancer. The propensity of piggyBac for open chromatin also enabled genome-wide screening for cancer-relevant noncoding DNA, which pinpointed a Cdkn2a cis-regulatory region. Histologically, we observed different tumor subentities and discovered associated genetic events, including Fign insertions in hepatoid pancreatic cancer. Our studies demonstrate the power of genetic screening to discover cancer drivers that are difficult to identify by other approaches to cancer genome analysis, such as downstream targets of commonly mutated human cancer genes. These piggyBac resources are universally applicable in any tissue context and provide unique experimental access to the genetic complexity of cancer.

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Figure 1: A conditional piggyBac transposition system for tissue-specific mutagenesis in mice.
Figure 2: A pancreatic piggyBac cancer gene discovery screen identifies large sets of common insertion sites.
Figure 3: Exploiting QISeq data to identify patterns of mutually exclusive cancer gene insertions.
Figure 4: piggyBac insertion patterns in the transcription factor genes Foxp1, Foxp2 and Bcl6.
Figure 5: Functional validation of Foxp1.
Figure 6: Deploying piggyBac to identify cancer-relevant noncoding areas with distant cis regulatory function.
Figure 7: Deploying piggyBac to study the genetic basis of different histologic subtypes of pancreatic cancer.

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Acknowledgements

We thank the Wellcome Trust Sanger Institute Research Support Facility for excellent technical assistance as well as K. Yusa and B. Göttgens for discussions and advice. The work was supported by the Wellcome Trust (to A.B.), the German Cancer Consortium (to R.R.) and the Helmholtz Gemeinschaft (PCCC Consortium; to R.R. and D.S.).

Author information

Authors and Affiliations

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Contributions

R.R. and A.B. designed the study. R.R. wrote the paper. R.R., L.R., W.W., A. Strong, H. Ponstingl, I.F.B., M.M., K.S., J.W., M. Hieber, C.V., S.E., U.G., R.Ö., M.Z., M.B., R.M., J.C., M.F., I.V., F.C.-C., A. Sarver, B.S., J.B., E.M., A.K., U.E., M.A.Q., G.V., I.E. and D.S. performed experiments or bioinformatics or histological analyses. J.t.H., H. Prosser, M. Heikenwälder, G.S., T.K., P.R., D.A., R.G., C.P., Z.N., L.W., R.M.S., M.A.Q., P.L. and D.S. contributed biological or analytical tools.

Corresponding author

Correspondence to Roland Rad.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–22 and Supplementary Table 3 (PDF 12142 kb)

Supplementary Table 1

Tapdance analysis to identify common insertion sites in 49 pancreatic cancers. (XLS 105 kb)

Supplementary Table 2

GCK (Gaussian Kernel Convolution) analysis to identify common insertion sites in 49 pancreatic cancers. (XLSX 128 kb)

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Rad, R., Rad, L., Wang, W. et al. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer. Nat Genet 47, 47–56 (2015). https://doi.org/10.1038/ng.3164

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