Cited by 35Cancer Immunotherapy and BiomarkersGenetic factors in colorectal cancerColorectal Cancer Treatments and Studies

Overexpression of transposable elements is associated with immune evasion and poor outcome in colorectal cancer

Open access
Zhu, Xiaoqiang, Fang, Hu, Gladysz, Kornelia, Barbour, Jayne A., Wong, Jason W.H.·2021·European Journal of Cancer

Published version of a preprint

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.ejca.2021.08.003

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 40

  1. Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, et al. Ten things you should know about transposable elements. Genome biology 2018;19:199.
  2. Anwar SL, Wulaningsih W, Lehmann U. Transposable Elements in Human Cancer: Causes and Consequences of Deregulation. International journal of molecular sciences 2017;18.
  3. Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nature reviews Genetics 2007;8:272-85.
  4. Roulois D, Loo Yau H, Singhania R, Wang Y, Danesh A, Shen SY, et al. DNA- Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts. Cell 2015;162:961-73.
  5. Pagès F, Mlecnik B, Marliot F, Bindea G, Ou FS, Bifulco C, et al. International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study. Lancet (London, England) 2018;391:2128-39.
  6. Galon J, Mlecnik B, Bindea G, Angell HK, Berger A, Lagorce C, et al. Towards the introduction of the 'Immunoscore' in the classification of malignant tumours. The Journal of pathology 2014;232:199-209.
  7. Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nature communications 2019;10:5228.
  8. Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 2018;173:400-16.e11.
  9. Criscione SW, Zhang Y, Thompson W, Sedivy JM, Neretti N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC genomics 2014;15:583.
  10. Jeong HH, Yalamanchili HK, Guo C, Shulman JM, Liu Z. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing 2018;23:168-79.
  11. Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 2015;160:48-61.
  12. Eo S-H, Kang HJ, Hong S-M, Cho H. K-adaptive partitioning for survival data, with an application to cancer staging. arXiv preprint arXiv:13064615 2013.
  13. Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nature medicine 2015;21:1350-6.
  14. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Yang T-HO, et al. The immune landscape of cancer. Immunity 2018;48:812-30. e14 %@ 1074-7613.
  15. Gryfe R, Kim H, Hsieh ET, Aronson MD, Holowaty EJ, Bull SB, et al. Tumor microsatellite instability and clinical outcome in young patients with colorectal cancer. The New England journal of medicine 2000;342:69-77.
  16. Romero D. TMB is linked with prognosis. Nature reviews Clinical oncology 2019;16:336.
  17. Garcia-Garijo A, Fajardo CA, Gros A. Determinants for Neoantigen Identification. Frontiers in immunology 2019;10:1392.
  18. Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene- Sanz A, et al. IntOGen-mutations identifies cancer drivers across tumor types. Nature methods 2013;10:1081-2 %@ 548-7105.
  19. Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nature biotechnology 2016;34:155-63.
  20. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 2008;9:559 %@ 1471-2105.
  21. Pugacheva EM, Teplyakov E, Wu Q, Li J, Chen C, Meng C, et al. The cancer- associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics & chromatin 2016;9:35.
  22. Yu Y. Molecular classification and precision therapy of cancer: immune checkpoint inhibitors. Frontiers of medicine 2018;12:229-35.
  23. Ribic CM, Sargent DJ, Moore MJ, Thibodeau SN, French AJ, Goldberg RM, et al. Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. The New England journal of medicine 2003;349:247-57.
  24. Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, et al. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS genetics 2010;6:e1000917.
  25. Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature genetics 2013;45:836-41.
  26. Esteller M. Epigenetics in cancer. The New England journal of medicine 2008;358:1148-59.
  27. Swets M, Zaalberg A, Boot A, van Wezel T, Frouws MA, Bastiaannet E, et al. Tumor LINE-1 Methylation Level in Association with Survival of Patients with Stage II Colon Cancer. International journal of molecular sciences 2016;18.
  28. Harada K, Baba Y, Ishimoto T, Chikamoto A, Kosumi K, Hayashi H, et al. LINE-1 methylation level and patient prognosis in a database of 208 hepatocellular carcinomas. Annals of surgical oncology 2015;22:1280-7.
  29. Terry MB, Delgado-Cruzata L, Vin-Raviv N, Wu HC, Santella RM. DNA methylation in white blood cells: association with risk factors in epidemiologic studies. Epigenetics 2011;6:828-37.
  30. Bogu GK, Reverter F, Marti-Renom MA, Snyder MP, Guigó R. Atlas of transcriptionally active transposable elements in human adult tissues. bioRxiv 2019:714212.
  31. Larouche J-D, Trofimov A, Hesnard L, Ehx G, Zhao Q, Vincent K, et al. Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues. Genome Medicine 2020;12:1-16.
  32. Burns KH. Our Conflict with Transposable Elements and Its Implications for Human Disease. Annual review of pathology 2020;15:51-70.
  33. Wylie A, Jones AE, Abrams JM. p53 in the game of transposons. BioEssays : news and reviews in molecular, cellular and developmental biology 2016;38:1111-6.
  34. Chen N, Xia P, Li S, Zhang T, Wang TT, Zhu J. RNA sensors of the innate immune system and their detection of pathogens. IUBMB life 2017;69:297-304.
  35. Schumann GG. APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition. Biochemical Society transactions 2007;35:637-42.
  36. Jones PA, Ohtani H, Chakravarthy A, De Carvalho DD. Epigenetic therapy in immune-oncology. Nature reviews Cancer 2019;19:151-61.
  37. Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science (New York, NY) 2016;351:1083-7.
  38. Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus- specific regulation of interspersed repeat expression. Nucleic acids research 2019;47:e27.
  39. Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, et al. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS computational biology 2019;15:e1006453.
  40. Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Cheetham SW, et al. Nanopore sequencing enables comprehensive transposable element epigenomic profiling. bioRxiv 2020.

Cited by

Sorted by citations

Authors
Zhu, X., Fang, H., Gladysz, K., Barbour, J. A., & Wong, J. W. H.
Affiliations
University of Hong Kong (HK)
Corresponding author
Wong, Jason W.H.
Venue
European Journal of Cancer
Publisher
Elsevier BV
Published
2021-11
Volume
157
Pages
94-107
ISSN
0959-8049 (ISSN-L)
OpenAlex
W3196957665
Cited by
35
References
7
Citations by year
2026: 9 · 2025: 8 · 2024: 7 · 2023: 6 · 2022: 3 · 2021: 2
FWCI
1.65
Type
journal article
Language
en
Open access
Locations
  • European Journal of Cancer (publishedVersion)
  • medRxiv (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
University of Hong Kong
Topics
  • Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
  • Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
  • Health Sciences › Medicine › Oncology › Colorectal Cancer Treatments and Studies
Keywords
transposable elements, colorectal cancer, immune evasion, tumor immune microenvironment, immune cell infiltration, PD-L1 expression, interferon signaling, DNA methyltransferase inhibition, microsatellite instability, tumour-associated macrophages, prognostic factors, JAK/STAT signaling
MeSH terms
DNA Transposable Elements, Humans, Immunity, Innate, Colorectal Neoplasms, Tumor Escape, DNA Methylation, Cell Line, Tumor, STAT Transcription Factors, B7-H1 Antigen

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 ›

Are you an author, or do you see a problem with this page? Request a review