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Updated: Aug 5, 2025

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR
Published on: February 1, 2013
Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements
Nakul M Shah1,2, H Josh Jang1,2,3, Yonghao Liang1,2
1Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
Abstract:
Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We performed a comprehensive screen for these TE exaptation events in 33 TCGA tumor types, 30 GTEx adult tissues and 675 cancer cell lines, and identified 1,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Whole-lysate and HLA-pulldown mass spectrometry data confirmed that TS-TEAs are presented on the surface of cancer cells. In addition, we highlight tumor-specific membrane proteins transcribed from TE promoters that constitute aberrant epitopes on the extracellular surface of cancer cells. Altogether, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that could potentially be therapeutically exploited and targeted.
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