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The landscape of viral expression and host gene fusion and adaptation in human cancer

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  • Ka-Wei Tang

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

  • Babak Alaei-Mahabadi

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

  • Tore Samuelsson

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

  • Magnus Lindh

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

  • Erik Larsson

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

Abstract

Viruses cause 10–15% of all human cancers. Massively parallel sequencing has recently proved effective for uncovering novel viruses and virus–tumour associations, but this approach has not yet been applied to comprehensive patient cohorts. Here we screen a diverse landscape of human cancer, encompassing 4,433 tumours and 19 cancer types, for known and novel expressed viruses based on >700 billion transcriptome sequencing reads from The Cancer Genome Atlas Research Network. The resulting map confirms and extends current knowledge. We observe recurrent fusion events, including human papillomavirus insertions in RAD51B and ERBB2. Patterns of coadaptation between host and viral gene expression give clues to papillomavirus oncogene function. Importantly, our analysis argues strongly against viral aetiology in several cancers where this has frequently been proposed. We provide a virus–tumour map of unprecedented scale that constitutes a reference for future studies of tumour-associated viruses using transcriptome sequencing data.

Suggested Citation

  • Ka-Wei Tang & Babak Alaei-Mahabadi & Tore Samuelsson & Magnus Lindh & Erik Larsson, 2013. "The landscape of viral expression and host gene fusion and adaptation in human cancer," Nature Communications, Nature, vol. 4(1), pages 1-9, December.
  • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3513
    DOI: 10.1038/ncomms3513
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    Cited by:

    1. Erik Elias & Arman Ardalan & Markus Lindberg & Susanne E. Reinsbach & Andreas Muth & Ola Nilsson & Yvonne Arvidsson & Erik Larsson, 2021. "Independent somatic evolution underlies clustered neuroendocrine tumors in the human small intestine," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    2. Liyuan Zhou & Qiongzi Qiu & Qing Zhou & Jianwei Li & Mengqian Yu & Kezhen Li & Lingling Xu & Xiaohui Ke & Haiming Xu & Bingjian Lu & Hui Wang & Weiguo Lu & Pengyuan Liu & Yan Lu, 2022. "Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Abdurrahman Elbasir & Ying Ye & Daniel E. Schäffer & Xue Hao & Jayamanna Wickramasinghe & Konstantinos Tsingas & Paul M. Lieberman & Qi Long & Quaid Morris & Rugang Zhang & Alejandro A. Schäffer & Noa, 2023. "A deep learning approach reveals unexplored landscape of viral expression in cancer," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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