Landscape of Somatic Retrotransposition in Human Cancers
Open accessAbstract
Movement in the Cancer Genome: Transposable elements are genetic sequences that can replicate and move within the genome. The factors that make an element mobile are unknown but are generally considered rare in mammals. Lee et al. (p. 967 , published online 28 June) analyzed five cancer types occurring among several individuals and found that three types of epithelial tumors exhibited high rates of element movement relative to brain and blood cancers. Furthermore, these somatically acquired, tumor-specific elements targeted genes in colorectal cancer that, when disrupted, impact gene expression and thus may be a factor in the progression of the cancers.
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Cancer is characterized by genomic instability and in many cases increased expression of L1 elements.
“Cancer is characterized by genomic instability and in many cases increased expression of L1 elements86.”
From The role of retrotransposable elements in ageing and age-associated diseases (2021) · cites this paper as [86]
The indexed copy (section labelled Abstract; page unavailable) describes genomic alterations in cancer, including somatic L1 insertions and a colorectal tumor with microsatellite instability. It also says DNA methylation suppresses TE RNA expression and is disrupted in cancers, but it does not report that L1 expression itself is increased in many cancer cases. Insertion frequency is not a measure of expression. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMultiple de novo somatic insertions and associated rearrangements have been identified in human cancers, in some cases numbering in the hundreds for an individual tumor.
“Subsequent efforts identified multiple de novo somatic insertions and associated rearrangements in human cancers, in some cases numbering in the hundreds for an individual tumor86–89.”
From The role of retrotransposable elements in ageing and age-associated diseases (2021) · cites this paper as [86]
The passages labeled Abstract report 194 somatic transposable-element insertions across 43 patients, including 106 in one colorectal tumor (CR3518). That supports multiple insertions and a count exceeding one hundred in an individual tumor, but the paper does not report associated rearrangements; 106 also does not clearly support the plural phrasing “in the hundreds.” No page numbers are provided in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measuredGenome sequencing approaches that revealed novel somatic LINE-1 integrations failed to find HERV integration consistent with re-infection.
“Furthermore, genome sequencing approaches that have revealed novel somatic long interspersed nuclear element (LINE-1) integrations, failed to find HERV integration that would be consistent with re-infection 80.”
From Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis (2013) · cites this paper as [80]
L1 activity has been implicated in a variety of age-related disorders, including cancer and neurodegeneration.
“L1 activity has been implicated in a variety of age-related disorders12, including cancer7,13 and neurodegeneration14,15.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [13]
The corrected RC-seq retrotransposition rate is consistent with the absence of significant somatic L1 insertions in brain tumors.
“and is consistent with the absence of significant somatic L1 insertions in brain tumors (Helman et al., 2014; Iskow et al., 2010; Lee et al., 2012).”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Lee et al., 2012
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Mir, A. A., Philippe, C., & Cristofari, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1043 · Cited by 62 · see citing works
Genome-Wide Methylation Analyses in Glioblastoma Multiforme
Lai, R. K., Chen, Y., Guan, X., Nousome, D., Sharma, C., Canoll, P., Bruce, J., Sloan, A. E., Cortes, E., Vonsattel, J.-P., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089376 · Cited by 54 · see citing works
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Li, J.-L., Mazar, J., Zhong, C., Faulkner, G. J., Govindarajan, S. S., Zhang, Z., Dinger, M. E., Meredith, G., Adams, C., Zhang, S., et al. (2013) · Scientific Reports · doi:10.1038/srep02962 · Cited by 21 · see citing works
- Authors
- Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., Wheeler, D. A., Gibbs, R. A., Kucherlapati, R., Lee, C., Kharchenko, P. V., Park, P. J., & The Cancer Genome Atlas Research Network
- Affiliations
- Brigham and Women's Hospital (US)
- Harvard University (US)
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute (US)
- Washington University in St. Louis (US)
- Baylor College of Medicine (US)
- Boston Children's Hospital (US)
- Corresponding author
- Kharchenko, Peter V.
- Park, Peter J.
- ORCID
- Venue
- Science
- Published
- 2012-08-24
- Volume
- 337
- Issue
- 6097
- Pages
- 967-971
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3656569
- OpenAlex
- W2045807857
- Cited by
- 762
- References
- 46
- Citations by year
- 2026: 22 · 2025: 42 · 2024: 26 · 2023: 42 · 2022: 51 · 2021: 54 · 2020: 61 · 2019: 64 · 2018: 59 · 2017: 60 · 2016: 65 · 2015: 71 · 2014: 69 · 2013: 65 · 2012: 10
- FWCI
- 78.97
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute on Aging (F32AG039979, K25AG037596)
- National Human Genome Research Institute (U54HG003273, U01HG005209, U01HG005725, RC1HG005482)
- National Cancer Institute (U24CA144025, T32CA009172)
- National Institute of General Medical Sciences (R01GM082798)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- somatic retrotransposition, transposable elements, LINE-1 retrotransposons, DNA hypomethylation, tumor-specific mutations, carcinogenesis, epithelial tumors
- MeSH terms
- Base Sequence, Cell Transformation, Neoplastic, Female, Glioblastoma, Humans, Male, Molecular Sequence Data, Multiple Myeloma, Mutation, Ovarian Neoplasms, Prostatic Neoplasms, Colorectal Neoplasms, Genome, Human, Gene Expression Regulation, Neoplastic, Mutagenesis, Insertional, Sequence Analysis, DNA, Retroelements, DNA Methylation, Long Interspersed Nucleotide Elements, Genes, Neoplasm, Microsatellite Instability, Molecular Sequence Annotation
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.
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