Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

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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.

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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.

Author information

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.

Correspondence to Kathleen H Burns.

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The authors declare no competing financial interests.

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Supplementary Tables 1–6 (XLSX 185 kb)

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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) doi:10.1038/nm.3919

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