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Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements
Open accessAbstract
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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“Intriguingly, a prior study uncovered the presence of tumor-specific antigens originating from certain repetitive sequences in various cancers, potentially eliciting immune responses25.”
From Multi-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity (2025) · cites this paper as [25]
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Metadata
- Authors
- Shah, N. M., Jang, H. J., Liang, Y., Maeng, J. H., Tzeng, S.-C., Wu, A., Basri, N. L., Qu, X., Fan, C., Li, A., Katz, B., Li, D., Xing, X., Evans, B. S., & Wang, T.
- Affiliations
- Washington University in St. Louis (US)
- Van Andel Institute (US)
- Donald Danforth Plant Science Center (US)
- Corresponding author
- Wang, Ting
- ORCID
- Venue
- Nature Genetics
- Published
- 2023-03-27
- Volume
- 55
- Issue
- 4
- Pages
- 631-639
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC13152471
- OpenAlex
- W4360999762
- Cited by
- 175
- References
- 70
- Citations by year
- 2026: 40 · 2025: 61 · 2024: 46 · 2023: 27
- FWCI
- 22.95
- Type
- journal article
- Language
- en
- Open access
- green
- pmc.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG007175, U01HG009391)
- National Institute of General Medical Sciences (T32GM007067)
- National Institute of Environmental Health Sciences (U24ES026699)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- transposable elements, cryptic promoter, tumor-specific antigens, cancer immunotherapy, membrane proteins, pan-cancer analysis, cancer cell lines
- MeSH terms
- Adult, Antigens, Neoplasm, Cell Line, DNA Transposable Elements, Humans, Neoplasms, Promoter Regions, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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