HPV integration profiling using nanopore sequencing and association with cervical precancerous lesion

Hou, Ying; Ni, Shoufeng; Liu, Xin; Liu, Xingyu; Wang, Nan; Xu, Fuqiang; Gao, Jianyong; Li, Yanmei; Zhou, Yuxiang; Huadong, Tang; Bian, Meina; Li, Xiulan; Zhang, Lili; Wang, Weiwei; Liu, Qing

doi:10.3389/fmicb.2025.1522550

ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Systems Microbiology

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1522550

This article is part of the Research Topic Infectious disease control in the microbial functional genomics era View all articles

HPV integration profiling using nanopore sequencing and association with cervical precancerous lesion

Provisionally accepted

Ying Hou ¹

Shoufeng Ni ² Xin Liu

Xin Liu ¹

Xingyu Liu ²

Nan Wang ¹

Fuqiang Xu ¹

Jianyong Gao ²

Yanmei Li ¹

Yuxiang Zhou ¹

Tang Huadong ¹

Meina Bian ¹

Xiulan Li ¹

Lili Zhang ²

Weiwei Wang ²

Qing Liu ^1*

¹ Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
² Geneis (Beijing) Co. Ltd, Beijing, China

The final, formatted version of the article will be published soon.

Objectives: HPV infection and HPV DNA integration can lead to cervical cancer, but the relationship with lesion severity is unclear. This study aimed to investigate the correlation between HPV integration profile and cervical lesion extent. Materials and methods: Twenty patients representing cervicitis, CIN I, CIN II, and CIN III underwent nanopore sequencing for HPV genotype and integration site analysis. HPV integration profiles were correlated with lesion severity. Gene Ontology (GO) and KEGG analysis were used to identify stage-specific genes and pathways. Results: HPV integration rates were 60%, 60%, 100%, and 100% for cervicitis, CIN I, CIN II, and CIN III, respectively, with varying numbers of integrated genes. Each group had specific stage-related genes, with 83 shared genes linked to neuron development and cell-cell processes. CIN II and CIN III displayed more cancer-related pathway enrichment than earlier stages. Conclusion: A positive correlation exists between HPV integration frequency and cervical lesion stage. Late-stage lesions showed heightened enrichment in cancer-related pathways through specific HPV-integrated genes.

Keywords: Human papillomavirus, cervical lesions, cervical cancer, nanopore sequencing, Virus Integration

Received: 04 Nov 2024; Accepted: 10 Feb 2025.

Copyright: © 2025 Hou, Ni, Liu, Liu, Wang, Xu, Gao, Li, Zhou, Huadong, Bian, Li, Zhang, Wang and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Qing Liu, Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China

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