Extensive somatic L1 retrotransposition in colorectal tumors

Szilvia Solyom, Adam D. Ewing, Eric P. Rahrmann, Tara Doucet, Heather H. Nelson, Michael B. Burns, Reuben S. Harris, David F. Sigmon, Alex Casella, Bracha Erlanger, Sarah Wheelan, Kyle R. Upton, Ruchi Shukla, Geoffrey J. Faulkner, David A. Largaespada, Haig H. Kazazian

Research output: Contribution to journalArticle

Abstract

L1 retrotransposons comprise 17% of the human genome and are its only autonomous mobile elements. Although L1-induced insertional mutagenesis causes Mendelian disease, their mutagenic load in cancer has been elusive. Using L1-targeted resequencing of 16 colorectal tumor and matched normal DNAs, we found that certain cancers were excessively mutagenized by human-specific L1s, while no verifiable insertions were present in normal tissues. We confirmed de novo L1 insertions in malignancy by both validating and sequencing 69/107 tumor-specific insertions and retrieving both 59 and 39 junctions for 35. In contrast to germline polymorphic L1s, all insertions were severely 59 truncated. Validated insertion numbers varied from up to 17 in some tumors to none in three others, and correlated with the age of the patients. Numerous genes with a role in tumorigenesis were targeted, including ODZ3, ROBO2, PTPRM, PCM1, and CDH11. Thus, somatic retrotransposition may play an etiologic role in colorectal cancer.

Original languageEnglish (US)
Pages (from-to)2328-2338
Number of pages11
JournalGenome research
Volume22
Issue number12
DOIs
StatePublished - Dec 1 2012

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Solyom, S., Ewing, A. D., Rahrmann, E. P., Doucet, T., Nelson, H. H., Burns, M. B., Harris, R. S., Sigmon, D. F., Casella, A., Erlanger, B., Wheelan, S., Upton, K. R., Shukla, R., Faulkner, G. J., Largaespada, D. A., & Kazazian, H. H. (2012). Extensive somatic L1 retrotransposition in colorectal tumors. Genome research, 22(12), 2328-2338. https://doi.org/10.1101/gr.145235.112