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A comprehensive overview of genomic imprinting in breast and its deregulation in cancer

Author

Listed:
  • Tine Goovaerts

    (Ghent University)

  • Sandra Steyaert

    (Ghent University)

  • Chari A. Vandenbussche

    (Ghent University)

  • Jeroen Galle

    (Ghent University)

  • Olivier Thas

    (Ghent University
    Bioinformatics Institute Ghent - from Nucleotides to Networks (BIG N2N), Ghent University
    Cancer Research Institute Ghent (CRIG), Ghent University)

  • Wim Van Criekinge

    (Ghent University
    Bioinformatics Institute Ghent - from Nucleotides to Networks (BIG N2N), Ghent University
    Cancer Research Institute Ghent (CRIG), Ghent University)

  • Tim De Meyer

    (Ghent University
    Bioinformatics Institute Ghent - from Nucleotides to Networks (BIG N2N), Ghent University
    Cancer Research Institute Ghent (CRIG), Ghent University)

Abstract

Genomic imprinting plays an important role in growth and development. Loss of imprinting (LOI) has been found in cancer, yet systematic studies are impeded by data-analytical challenges. We developed a methodology to detect monoallelically expressed loci without requiring genotyping data, and applied it on The Cancer Genome Atlas (TCGA, discovery) and Genotype-Tissue expression project (GTEx, validation) breast tissue RNA-seq data. Here, we report the identification of 30 putatively imprinted genes in breast. In breast cancer (TCGA), HM13 is featured by LOI and expression upregulation, which is linked to DNA demethylation. Other imprinted genes typically demonstrate lower expression in cancer, often associated with copy number variation and aberrant DNA methylation. Downregulation in cancer frequently leads to higher relative expression of the (imperfectly) silenced allele, yet this is not considered canonical LOI given the lack of (absolute) re-expression. In summary, our novel methodology highlights the massive deregulation of imprinting in breast cancer.

Suggested Citation

  • Tine Goovaerts & Sandra Steyaert & Chari A. Vandenbussche & Jeroen Galle & Olivier Thas & Wim Van Criekinge & Tim De Meyer, 2018. "A comprehensive overview of genomic imprinting in breast and its deregulation in cancer," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06566-7
    DOI: 10.1038/s41467-018-06566-7
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