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Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

Author

Listed:
  • Arghavan Ashouri

    (Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg)

  • Volkan I. Sayin

    (New York University School of Medicine)

  • Jimmy Van den Eynden

    (Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg)

  • Simranjit X. Singh

    (New York University School of Medicine)

  • Thales Papagiannakopoulos

    (New York University School of Medicine)

  • Erik Larsson

    (Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg)

Abstract

Thousands of long non-coding RNAs (lncRNAs) lie interspersed with coding genes across the genome, and a small subset has been implicated as downstream effectors in oncogenic pathways. Here we make use of transcriptome and exome sequencing data from thousands of tumours across 19 cancer types, to identify lncRNAs that are induced or repressed in relation to somatic mutations in key oncogenic driver genes. Our screen confirms known coding and non-coding effectors and also associates many new lncRNAs to relevant pathways. The associations are often highly reproducible across cancer types, and while many lncRNAs are co-expressed with their protein-coding hosts or neighbours, some are intergenic and independent. We highlight lncRNAs with possible functions downstream of the tumour suppressor TP53 and the master antioxidant transcription factor NFE2L2. Our study provides a comprehensive overview of lncRNA transcriptional alterations in relation to key driver mutational events in human cancers.

Suggested Citation

  • Arghavan Ashouri & Volkan I. Sayin & Jimmy Van den Eynden & Simranjit X. Singh & Thales Papagiannakopoulos & Erik Larsson, 2016. "Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events," Nature Communications, Nature, vol. 7(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13197
    DOI: 10.1038/ncomms13197
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