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Patterns of Transposable Element Expression and Insertion in Cancer
Evan A Clayton1, Lu Wang2, Lavanya Rishishwar3
1Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA.
Frontiers in Molecular Biosciences
|December 1, 2016
Summary
Human transposable elements (TEs) are active in normal and tumor tissues, causing mutations that contribute to cancer. Increased L1 TE activity was observed in tumors, suggesting a role in tumorigenesis.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Biology
Background:
- Human transposable elements (TEs) are mobile genetic sequences implicated in various diseases, including cancer.
- The full extent of somatic TE activity and its contribution to tumorigenesis remain incompletely understood.
- Recent advancements in bioinformatics enable the analysis of TE expression and insertion from next-generation sequencing data.
Purpose of the Study:
- To investigate the patterns of TE expression and insertional activity in human cancers.
- To analyze the relationship between somatic TE activity and tumorigenesis.
- To identify specific TE-mediated mutations potentially driving cancer development.
Main Methods:
- Analysis of matched normal and tumor patient samples from The Cancer Genome Atlas (TCGA).
- Application of bioinformatics software to analyze transcriptome (RNA-seq) and whole genome (DNA-seq) data.
- Focus on Alu, SVA, and L1 families of active human TEs.
Main Results:
- High levels of somatic TE activity (Alu, SVA, L1) were detected in both normal and cancer tissues.
- An average of approximately 80 unique TE insertions per patient/tissue were identified.
- Increased L1 transcript expression and insertional activity were observed in primary tumor samples across three cancer types.
- Tumor-specific TE insertions were enriched for private mutations, suggesting a causal role in tumorigenesis.
- Specific cases of Alu and L1 insertions disrupting tumor suppressor gene expression (CBL, BAALC) were detailed.
Conclusions:
- Somatic activity of human TEs is widespread across diverse tissue types.
- TEs generate numerous insertion mutations that can contribute to tumorigenesis.
- L1 TE activity is elevated in tumors, highlighting its potential role in cancer development.
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