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Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer

Author

Listed:
  • Liyuan Zhou

    (Zhejiang University School of Medicine)

  • Qiongzi Qiu

    (Zhejiang University School of Medicine)

  • Qing Zhou

    (Zhejiang University School of Medicine)

  • Jianwei Li

    (Zhejiang University School of Medicine)

  • Mengqian Yu

    (Zhejiang University School of Medicine)

  • Kezhen Li

    (Huazhong University of Science and Technology)

  • Lingling Xu

    (Zhejiang University School of Medicine)

  • Xiaohui Ke

    (Wenzhou Central Hospital)

  • Haiming Xu

    (Zhejiang University)

  • Bingjian Lu

    (Zhejiang University School of Medicine
    Zhejiang University)

  • Hui Wang

    (Zhejiang University School of Medicine
    Zhejiang University)

  • Weiguo Lu

    (Zhejiang University
    Zhejiang University School of Medicine)

  • Pengyuan Liu

    (Zhejiang University School of Medicine
    Zhejiang University
    Zhejiang University School of Medicine
    Medical College of Wisconsin)

  • Yan Lu

    (Zhejiang University School of Medicine
    Zhejiang University
    Zhejiang University School of Medicine)

Abstract

Integration of human papillomavirus (HPV) DNA into the human genome is considered as a key event in cervical carcinogenesis. Here, we perform comprehensive characterization of large-range virus-human integration events in 16 HPV16-positive cervical tumors using the Nanopore long-read sequencing technology. Four distinct integration types characterized by the integrated HPV DNA segments are identified with Type B being particularly notable as lacking E6/E7 genes. We further demonstrate that multiple clonal integration events are involved in the use of shared breakpoints, the induction of inter-chromosomal translocations and the formation of extrachromosomal circular virus-human hybrid structures. Combined with the corresponding RNA-seq data, we highlight LINC00290, LINC02500 and LENG9 as potential driver genes in cervical cancer. Finally, we reveal the spatial relationship of HPV integration and its various structural variations as well as their functional consequences in cervical cancer. These findings provide insight into HPV integration and its oncogenic progression in cervical cancer.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30190-1
    DOI: 10.1038/s41467-022-30190-1
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    References listed on IDEAS

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    1. Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
    2. Yilong Li & Nicola D. Roberts & Jeremiah A. Wala & Ofer Shapira & Steven E. Schumacher & Kiran Kumar & Ekta Khurana & Sebastian Waszak & Jan O. Korbel & James E. Haber & Marcin Imielinski & Joachim We, 2020. "Patterns of somatic structural variation in human cancer genomes," Nature, Nature, vol. 578(7793), pages 112-121, February.
    3. Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    4. 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.
    5. Akinyemi I. Ojesina & Lee Lichtenstein & Samuel S. Freeman & Chandra Sekhar Pedamallu & Ivan Imaz-Rosshandler & Trevor J. Pugh & Andrew D. Cherniack & Lauren Ambrogio & Kristian Cibulskis & Bjørn Bert, 2014. "Landscape of genomic alterations in cervical carcinomas," Nature, Nature, vol. 506(7488), pages 371-375, February.
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