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.

中文翻译：

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人乳头瘤病毒整合位点的多组学作图阐明了新的宫颈癌靶基因

背景

人乳头瘤病毒 (HPV) 整合到宿主基因组中是浸润性宫颈癌 (ICC) 的主要特征，但整合位点的顺式基因组变化的致瘤性在很大程度上仍未得到充分研究。

方法

将来自癌症基因组图谱的多组学数据与 HPV 整合位点的患者匹配长读长测序相结合，我们开发了一种策略，使用 HPV 整合事件来识别和优先考虑新的候选 ICC 靶基因（整合检测基因 (IDG)） . 然后选择四个 IDG 进行体外功能研究，在细胞迁移、增殖和集落形成测定中采用小干扰 RNA 介导的敲低。

结果

PacBio 数据揭示了 267 个独特的人类-HPV 断点，包括八个肿瘤中的 87 个总整合事件。根据以下标准筛选候选 IDG：(1) 接近整合位点，(2) 整合事件的克隆表现，(3) 肿瘤特异性表达（Z评分）和 (4) 与 ICC 存活的关联。根据它们在 ICC 中的未知功能（BNC1、RSBN1、USP36和TAOK3）确定优先级的四个候选物在宫颈癌细胞系中表现出致癌特性。此外，整合事件的注释提供了有关整合和非整合 ICC 肿瘤中 IDG 表达改变的潜在机制的线索。

结论

HPV 整合事件可以指导新型 IDG 的鉴定，以进一步研究宫颈癌变并作为推定的治疗靶点。