Somatic retrotransposition is infrequent in glioblastomas

Pragathi Achanta, Jared P. Steranka, Zuojian Tang, Nemanja Rodić, Reema Sharma, Wan Rou Yang, Sisi Ma, Mark Grivainis, Cheng Ran Lisa Huang, Anna M. Schneider, Gary L Gallia, Gregory J Riggins, Alfredo Quinones-Hinojosa, David Fenyö, Jef D. Boeke, Kathleen Burns

Research output: Contribution to journalArticle

Abstract

Background: Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals. Results: We found and PCR validated one somatically acquired tumor-specific insertion in a case of secondary GBM. No LINE-1 insertions present in primary GBM oncosphere cultures were missing from corresponding blood samples. However, several copies of the element (11) were found in genomic DNA from blood and not in the oncosphere cultures. SNP 6.0 microarray analysis revealed deletions or loss of heterozygosity in the tumor genomes over the intervals corresponding to these LINE-1 insertions. Conclusions: These findings indicate that LINE-1 retrotransposon can act as an infrequent insertional mutagen in secondary GBM, but that retrotransposition is uncommon in these central nervous system tumors as compared to other neoplasias.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalMobile DNA
Volume7
Issue number1
DOIs
StatePublished - Nov 11 2016

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Glioblastoma
Neoplasms
High-Throughput Nucleotide Sequencing
Central Nervous System Neoplasms
Retroelements
DNA Transposable Elements
Loss of Heterozygosity
DNA
Mutagens
Microarray Analysis
Brain Neoplasms
Glioma
Single Nucleotide Polymorphism
Genome
Biopsy
Cell Line
Polymerase Chain Reaction

Keywords

  • Cancer
  • Glioblastoma
  • LINE-1
  • Retrotransposition

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Achanta, P., Steranka, J. P., Tang, Z., Rodić, N., Sharma, R., Yang, W. R., ... Burns, K. (2016). Somatic retrotransposition is infrequent in glioblastomas. Mobile DNA, 7(1), 1-9. https://doi.org/10.1186/s13100-016-0077-5

Somatic retrotransposition is infrequent in glioblastomas. / Achanta, Pragathi; Steranka, Jared P.; Tang, Zuojian; Rodić, Nemanja; Sharma, Reema; Yang, Wan Rou; Ma, Sisi; Grivainis, Mark; Huang, Cheng Ran Lisa; Schneider, Anna M.; Gallia, Gary L; Riggins, Gregory J; Quinones-Hinojosa, Alfredo; Fenyö, David; Boeke, Jef D.; Burns, Kathleen.

In: Mobile DNA, Vol. 7, No. 1, 11.11.2016, p. 1-9.

Research output: Contribution to journalArticle

Achanta, P, Steranka, JP, Tang, Z, Rodić, N, Sharma, R, Yang, WR, Ma, S, Grivainis, M, Huang, CRL, Schneider, AM, Gallia, GL, Riggins, GJ, Quinones-Hinojosa, A, Fenyö, D, Boeke, JD & Burns, K 2016, 'Somatic retrotransposition is infrequent in glioblastomas', Mobile DNA, vol. 7, no. 1, pp. 1-9. https://doi.org/10.1186/s13100-016-0077-5
Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR et al. Somatic retrotransposition is infrequent in glioblastomas. Mobile DNA. 2016 Nov 11;7(1):1-9. https://doi.org/10.1186/s13100-016-0077-5
Achanta, Pragathi ; Steranka, Jared P. ; Tang, Zuojian ; Rodić, Nemanja ; Sharma, Reema ; Yang, Wan Rou ; Ma, Sisi ; Grivainis, Mark ; Huang, Cheng Ran Lisa ; Schneider, Anna M. ; Gallia, Gary L ; Riggins, Gregory J ; Quinones-Hinojosa, Alfredo ; Fenyö, David ; Boeke, Jef D. ; Burns, Kathleen. / Somatic retrotransposition is infrequent in glioblastomas. In: Mobile DNA. 2016 ; Vol. 7, No. 1. pp. 1-9.
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AU - Boeke, Jef D.

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