Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br J Cancer 2021 Nov;125(10):1408-1419
Date
09/17/2021Pubmed ID
34526665Pubmed Central ID
PMC8575955DOI
10.1038/s41416-021-01545-0Scopus ID
2-s2.0-85115169639 (requires institutional sign-in at Scopus site) 19 CitationsAbstract
BACKGROUND: 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.
METHODS: 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.
RESULTS: 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.
CONCLUSIONS: HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.
Author List
Iden M, Tsaih SW, Huang YW, Liu P, Xiao M, Flister MJ, Rader JSAuthors
Janet Sue Rader MD Chair, Professor in the Obstetrics and Gynecology department at Medical College of WisconsinShirng-Wern Tsaih Research Scientist II in the Obstetrics and Gynecology department at Medical College of Wisconsin
MESH terms used to index this publication - Major topics in bold
AlphapapillomavirusCell Line, Tumor
Cell Movement
Cell Proliferation
DNA-Binding Proteins
Female
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
HeLa Cells
Humans
Papillomavirus Infections
Survival Analysis
Transcription Factors
Ubiquitin Thiolesterase
Uterine Cervical Neoplasms
Virus Integration
Whole Genome Sequencing
