Integration of human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC), yet the tumorigenicity of cis genomic changes at integration sites remains largely understudied.
Combining multi-omics data from The Cancer Genome Atlas with patient-matched long-read sequencing of HPV integration sites, we developed a strategy for using HPV integration events to identify and prioritise novel candidate ICC target genes (integration-detected genes (IDGs)). Four IDGs were then chosen for in vitro functional studies employing small interfering RNA-mediated knockdown in cell migration, proliferation and colony formation assays.
PacBio data revealed 267 unique human–HPV breakpoints comprising 87 total integration events in eight tumours. Candidate IDGs were filtered based on the following criteria: (1) proximity to integration site, (2) clonal representation of integration event, (3) tumour-specific expression (Z-score) and (4) association with ICC survival. Four candidates prioritised based on their unknown function in ICC (BNC1, RSBN1, USP36 and TAOK3) exhibited oncogenic properties in cervical cancer cell lines. Further, annotation of integration events provided clues regarding potential mechanisms underlying altered IDG expression in both integrated and non-integrated ICC tumours.
HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.
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The PacBio long-read sequencing data generated in this study have been submitted to the NCBI BioProject database under accession number PRJNA640649.
All codes used to generate results presented are publicly available and cited with the first mention.
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We thank the Genomic Sciences and Precision Medicine Center (GSPMC) at the Medical College of Wisconsin for their assistance and technical support with PacBio sequencing.
This work was supported by the NCI R21CA241013 (to JSR) and the Women’s Health Research Programme in the Department of Obstetrics and Gynecology, Medical College of Wisconsin.
The authors declare no competing interests.
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The study protocol was approved by the Medical College of Wisconsin’s Institutional Review Board. All the cervical cell lines used in this study were purchased from the American Type Cell Collection (ATCC, Manassas, VA).
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Iden, M., Tsaih, SW., Huang, YW. et al. Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br J Cancer (2021). https://doi.org/10.1038/s41416-021-01545-0