Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer

Nikolaos M. R. Lykoskoufis (), Evarist Planet, Halit Ongen, Didier Trono and Emmanouil T. Dermitzakis ()
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Nikolaos M. R. Lykoskoufis: University of Geneva Medical School
Evarist Planet: Ecole Polytechnique Fédérale de Lausanne (EPFL)
Halit Ongen: University of Geneva Medical School
Didier Trono: Ecole Polytechnique Fédérale de Lausanne (EPFL)
Emmanouil T. Dermitzakis: University of Geneva Medical School

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Transposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 normal colon and 276 colorectal cancer samples from the SYSCOL cohort, discovering 10,231 and 5,199 TE-expression quantitative trait loci (eQTLs) in normal and tumor tissues, respectively, of which 376 are colorectal cancer specific eQTLs, likely due to methylation changes. Tumor-specific TE-eQTLs show greater enrichment of transcription factors, compared to shared TE-eQTLs suggesting specific regulation of their expression in tumor. Bayesian networks reveal 1,766 TEs as mediators of genetic effects, altering the expression of 1,558 genes, including 55 known cancer driver genes and show that tumor-specific TE-eQTLs trigger the driver capability of TEs. These insights expand our knowledge of cancer drivers, deepening our understanding of tumorigenesis and presenting potential avenues for therapeutic interventions.

Date: 2024
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DOI: 10.1038/s41467-023-42405-0

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