Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed after the disease has metastasized; it is among the most lethal forms of cancer. We recently described aberrant expression of an open reading frame 1 protein, ORF1p, encoded by long interspersed element-1 (LINE-1; L1) retrotransposon, in PDAC1. To test whether LINE-1 expression leads to somatic insertions of this mobile DNA, we used a targeted method to sequence LINE-1 insertion sites in matched PDAC and normal samples. We found evidence of 465 somatic LINE-1 insertions in 20 PDAC genomes, which were absent from corresponding normal samples. In cases in which matched normal tissue, primary PDAC and metastatic disease sites were available, insertions were found in primary and metastatic tissues in differing proportions. Two adenocarcinomas secondarily involving the pancreas, but originating in the stomach and duodenum, acquired insertions with a similar discordance between primary and metastatic sites. Together, our findings show that LINE-1 contributes to the genetic evolution of PDAC and suggest that somatic insertions are acquired discontinuously in gastrointestinal neoplasms.

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Figure 1: Experimental approach.
Figure 2: Somatic LINE-1 insertions in PDAC.
Figure 3: Retrotransposition (RT) events.
Figure 4: Effects of somatic LINE-1 insertions in PDAC.

References

  1. 1

    Rodic´, N. et al. Long interspersed element-1 protein expression is a hallmark of many human cancers. Am. J. Pathol. 184, 1280–1286 (2014).

    Article  Google Scholar 

  2. 2

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

    CAS  Article  Google Scholar 

  3. 3

    Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801–1806 (2008).

    CAS  Article  Google Scholar 

  4. 4

    Yachida, S. et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114–1117 (2010).

    CAS  Article  Google Scholar 

  5. 5

    Burns, K.H. & Boeke, J.D. Human transposon tectonics. Cell 149, 740–752 (2012).

    CAS  Article  Google Scholar 

  6. 6

    Beck, C.R., Garcia-Perez, J.L., Badge, R.M. & Moran, J.V. LINE-1 elements in structural variation and disease. Annu. Rev. Genomics Hum. Genet. 12, 187–215 (2011).

    CAS  Article  Google Scholar 

  7. 7

    Hancks, D.C. & Kazazian, H.H. Jr. Active human retrotransposons: variation and disease. Curr. Opin. Genet. Dev. 22, 191–203 (2012).

    CAS  Article  Google Scholar 

  8. 8

    Iskow, R.C. et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141, 1253–1261 (2010).

    CAS  Article  Google Scholar 

  9. 9

    Ewing, A.D. & Kazazian, H.H. Jr. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 20, 1262–1270 (2010).

    CAS  Article  Google Scholar 

  10. 10

    Murphy, K.M. et al. Evaluation of candidate genes MAP2K4, MADH4, ACVR1B, and BRCA2 in familial pancreatic cancer: deleterious BRCA2 mutations in 17%. Cancer Res. 62, 3789–3793 (2002).

    CAS  PubMed  Google Scholar 

  11. 11

    Jones, S. et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 324, 217 (2009).

    CAS  Article  Google Scholar 

  12. 12

    Whitcomb, D.C. et al. Hereditary pancreatitis is caused by a mutation in the cationic trypsinogen gene. Nat. Genet. 14, 141–145 (1996).

    CAS  Article  Google Scholar 

  13. 13

    Whelan, A.J., Bartsch, D. & Goodfellow, P.J. Brief report: a familial syndrome of pancreatic cancer and melanoma with a mutation in the CDKN2 tumor-suppressor gene. N. Engl. J. Med. 333, 975–977 (1995).

    CAS  Article  Google Scholar 

  14. 14

    Ostertag, E.M. & Kazazian, H.H. Jr. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35, 501–538 (2001).

    CAS  Article  Google Scholar 

  15. 15

    Ostertag, E.M. & Kazazian, H.H. Jr. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 11, 2059–2065 (2001).

    CAS  Article  Google Scholar 

  16. 16

    Goodier, J.L., Ostertag, E.M. & Kazazian, H.H. Jr. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9, 653–657 (2000).

    CAS  Article  Google Scholar 

  17. 17

    Beck, C.R. et al. LINE-1 retrotransposition activity in human genomes. Cell 141, 1159–1170 (2010).

    CAS  Article  Google Scholar 

  18. 18

    Solyom, S. et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res. 22, 2328–2338 (2012).

    CAS  Article  Google Scholar 

  19. 19

    Shukla, R. et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101–111 (2013).

    CAS  Article  Google Scholar 

  20. 20

    Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967–971 (2012).

    CAS  Article  Google Scholar 

  21. 21

    Helman, E. et al. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res. 24, 1053–1063 (2014).

    CAS  Article  Google Scholar 

  22. 22

    Tubio, J.M. et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345, 1251343 (2014).

    Article  Google Scholar 

  23. 23

    Stephens, P.J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011).

    CAS  Article  Google Scholar 

  24. 24

    Evrony, G.D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483–496 (2012).

    CAS  Article  Google Scholar 

  25. 25

    Huang, C.R. et al. Mobile interspersed repeats are major structural variants in the human genome. Cell 141, 1171–1182 (2010).

    CAS  Article  Google Scholar 

  26. 26

    Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  27. 27

    Ji, H. et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26, 1293–1300 (2008).

    CAS  Article  Google Scholar 

  28. 28

    Amikura, K., Kobari, M. & Matsuno, S. The time of occurrence of liver metastasis in carcinoma of the pancreas. Pancreatol. 17, 139–146 (1995).

    CAS  Google Scholar 

  29. 29

    Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).

    CAS  Article  Google Scholar 

  30. 30

    Mootha, V.K. et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).

    CAS  Article  Google Scholar 

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Acknowledgements

This work was started by funding from the Sol Goldman Pancreatic Cancer Research Center (K.H.B. and N.R.) and supported also by the Fred and Janet Sanfilippo Fund in the Department of Pathology at the Johns Hopkins University School of Medicine (N.R.); a Burroughs Wellcome Fund Career Award for Biomedical Scientists Program (K.H.B.); and US National Institutes of Health awards F31CA180682 (A.M.-M.), R01CA163705 (K.H.B.), R01GM103999 (K.H.B.), P50CA62924 (R.H.H. and C.A.I.-D.), R01CA179991 (C.A.I.-D.), as well as the National Institute of General Medical Sciences Center for Systems Biology of Retrotransposition P50GM107632 (K.H.B. and J.D.B.). Computational resources were provided through the National Science Foundation–funded MRI-R2 project #DBI-0959894. The authors would like to thank H. Kazazian, S. Solyom and A. Ewing for their helpful discussion. This work is dedicated to Dr. Frank Kretzer.

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N.R., R.H.H., C.A.I.-D., J.D.B. and K.H.B. conceived of the project; N.R., A.M.-M. and C.A.I.-D. obtained tissues and reviewed histology; J.P.S., A.M., P.S. and P.M. designed and performed molecular-biology assays; N.R., R.S., M.S.T. and N.J.B. performed and reviewed immunostains; Z.A.K., C.R.H. and D.A. designed and performed sequence analysis; N.R., J.P.S., J.D.B. and K.H.B. interpreted data; J.P.S. summarized data for the supplementary tables; N.R. and K.H.B. wrote the manuscript. All authors contributed edits and approved of the final manuscript.

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Correspondence to Kathleen H Burns.

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The authors declare no competing financial interests.

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Rodić, N., Steranka, J., Makohon-Moore, A. et al. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med 21, 1060–1064 (2015). https://doi.org/10.1038/nm.3919

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