Long-read sequencing reveals oncogenic mechanism of HPV-human fusion transcripts in cervical cancer

  • Author Footnotes
    1 Equal contribution.
    Min Liu
    1 Equal contribution.
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Author Footnotes
    1 Equal contribution.
    Zhiqiang Han
    1 Equal contribution.
    Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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  • Yong Zhi
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Yetian Ruan
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Guangxu Cao
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Guangxue Wang
    Research Center for Translational Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Xinxin Xu
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Jianbing Mu
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
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  • Jiuhong Kang
    Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
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  • Fangping Dai
    Genome-decoding Biomedical Technology Co., Ltd, Nantong, China
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  • Xuejun Wen
    Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA
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  • Qingfeng Zhang
    Reprint requests: Qingfeng Zhang, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University; 1239 Siping Road, Shanghai 200092, China
    Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai, China
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  • Fang Li
    Reprint requests: Fang Li, Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University; 150 Jimo Road, Shanghai 200120, China
    Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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  • Author Footnotes
    1 Equal contribution.
Published:October 09, 2022DOI:
      Integration of high-risk human papillomavirus (HPV) into the host genome is a crucial event for the development of cervical cancer, however, the underlying mechanism of HPV integration-driven carcinogenesis remains unknown. Here, we performed long-read RNA sequencing on 12 high-grade squamous intraepithelial lesions (HSIL) and cervical cancer patients, including 3 pairs of cervical cancer and corresponding para-cancerous tissue samples to investigate the full-length landscape of cross-species genome integrations. In addition to massive unannotated isoforms, transcriptional regulatory events, and gene chimerism, more importantly, we found that HPV-human fusion events were prevalent in HPV-associated cervical cancers. Combined with the genome data, we revealed the existence of a universal transcription pattern in these fusion events, whereby structurally similar fusion transcripts were generated by specific splicing in E6 and a canonical splicing donor site in E1 linking to various human splicing acceptors. Highly expressed HPV-human fusion transcripts, eg, HPV16 E6*I-E7-E1SD880-human gene, were the key driver of cervical carcinogenesis, which could trigger overexpression of E6*I and E7, and destroy the transcription of tumor suppressor genes CMAHP, TP63 and P3H2. Finally, evidence from in vitro and in vivo experiments demonstrates that the novel read-through fusion gene mRNA, E1-CMAHP (E1C, formed by the integration of HPV58 E1 with CMAHP), existed in the fusion transcript can promote malignant transformation of cervical epithelial cells via regulating downstream oncogenes to participate in various biological processes. Taken together, we reveal a previously unknown mechanism of HPV integration-driven carcinogenesis and provide a novel target for the diagnosis and treatment of cervical cancer.


      APA (Alternative polyadenylation positions sites), AS (Alternative splicing), ATSS (Alternative transcription start sites), DEGs (Differentially expressed genes), E1C (E1-CMAHP), Ect1_E1C (The stable Ect1/E6E7 cell line overexpressing E1-CMAHP), Ect1_NC (The stable Ect1/E6E7 cell line with control plasmid), EMT (Epithelial-to-mesenchymal transition), HR-HPV (High-risk human papillomavirus), HSIL (High-grade squamous intraepithelial lesions), PacBio Iso-Seq (Pacific Biosciences Isoform sequencing), RNA-seq (RNA sequencing), SCC (Squamous cell carcinoma), TCGA (The Cancer Genome Atlas)
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