A map of mobile DNA insertions in the NCI-60 human cancer cell panel

John G. Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P. Gnanakkan, Toby C. Cornish, Jef D. Boeke, Kathleen Burns

Research output: Contribution to journalArticle

Abstract

Background: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. Method: We used Transposon Insertion Profiling by microarray (TIP-chip) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. We focused this discovery effort on annotated Cancer Gene Index loci. Results: We catalogued a total of 749 and 2,100 loci corresponding to candidate LINE-1 and Alu insertion sites, respectively. As expected, these numbers encompass previously known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. We also conducted association analyses relating individual insertions to a variety of cellular phenotypes. Conclusions: These data provide a resource for investigators with interests in specific cancer gene loci or mobile element insertion effects more broadly. Our data underscore that significant genetic variation in cancer genomes is owed to LINE-1 and Alu retrotransposons. Our findings also indicate that as large numbers of cancer genomes become available, it will be possible to associate individual transposable element insertion variants with molecular and phenotypic features of these malignancies.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalMobile DNA
Volume7
Issue number1
DOIs
StatePublished - Oct 31 2016

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National Cancer Institute (U.S.)
DNA
Neoplasm Genes
Neoplasms
Genome
Long Interspersed Nucleotide Elements
Exome
Karyotyping
Retroelements
DNA Transposable Elements
Nucleic Acid Repetitive Sequences
Tumor Cell Line
Epigenomics
Cell Biology
Research Personnel
RNA
Phenotype
Cell Line

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Zampella, J. G., Rodić, N., Yang, W. R., Huang, C. R. L., Welch, J., Gnanakkan, V. P., ... Burns, K. (2016). A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mobile DNA, 7(1), 1-11. https://doi.org/10.1186/s13100-016-0078-4

A map of mobile DNA insertions in the NCI-60 human cancer cell panel. / Zampella, John G.; Rodić, Nemanja; Yang, Wan Rou; Huang, Cheng Ran Lisa; Welch, Jane; Gnanakkan, Veena P.; Cornish, Toby C.; Boeke, Jef D.; Burns, Kathleen.

In: Mobile DNA, Vol. 7, No. 1, 31.10.2016, p. 1-11.

Research output: Contribution to journalArticle

Zampella, JG, Rodić, N, Yang, WR, Huang, CRL, Welch, J, Gnanakkan, VP, Cornish, TC, Boeke, JD & Burns, K 2016, 'A map of mobile DNA insertions in the NCI-60 human cancer cell panel', Mobile DNA, vol. 7, no. 1, pp. 1-11. https://doi.org/10.1186/s13100-016-0078-4
Zampella JG, Rodić N, Yang WR, Huang CRL, Welch J, Gnanakkan VP et al. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mobile DNA. 2016 Oct 31;7(1):1-11. https://doi.org/10.1186/s13100-016-0078-4
Zampella, John G. ; Rodić, Nemanja ; Yang, Wan Rou ; Huang, Cheng Ran Lisa ; Welch, Jane ; Gnanakkan, Veena P. ; Cornish, Toby C. ; Boeke, Jef D. ; Burns, Kathleen. / A map of mobile DNA insertions in the NCI-60 human cancer cell panel. In: Mobile DNA. 2016 ; Vol. 7, No. 1. pp. 1-11.
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