IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v4y2013i1d10.1038_ncomms3513.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms3513
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms3513?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3513. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.