ArticleFrontiers in molecular biosciences2016
Patterns of Transposable Element Expression and Insertion in Cancer.
Article in Frontiers in molecular biosciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Review
- Article
- Hsa-miR-422a Originated from Short Interspersed Nuclear Element IncreasesMolecules and cells · 2022Article
- Article
- Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants.International journal of molecular sciences · 2022Review
- The insertion and dysregulation of transposable elements in osteosarcoma and their association with patient event-free survival.Scientific reports · 2022Article
- An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data.Frontiers in bioinformatics · 2022Article
- The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease.International journal of molecular sciences · 2020Review
- An atlas of transposable element-derived alternative splicing in cancer.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Transposable element expression in tumors is associated with immune infiltration and increased antigenicity.Nature communications · 2019Article
- Article
- Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90.Clinical immunology (Orlando, Fla.) · 2018Article
- Transposable Element Expression in Acute Myeloid Leukemia Transcriptome and Prognosis.Scientific reports · 2018Article
- Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity.Cellular and molecular life sciences : CMLS · 2018Review
- Identification of transposable elements fused in the exonic region of the olive flounder genome.Genes & genomics · 2018Article
- Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes.Frontiers in microbiology · 2017Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the
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