Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing Technologies

TL;DR

This review explains how long-read sequencing improves detection of human papillomavirus genome integration into host DNA, offering new insights into cancer development.

Contribution

The paper highlights the use of long-read sequencing and T2T reference genome for analyzing viral integration in previously inaccessible genomic regions.

Findings

Long-read sequencing enables high-resolution mapping of complex HPV integration events in repeat-rich genomic regions.

HPV types 16 and 18 are responsible for over 70% of cervical, anal, and oropharyngeal cancers.

LR-Seq combined with the T2T reference genome reveals integration patterns in centromeres and structurally complex loci.

Abstract

High-risk human papillomaviruses (HR-HPVs), especially types 16 and 18, contribute to the development of various cancers by integrating their genomes into the host DNA, activating oncogenes or disrupting tumor suppressor genes. This review discusses the limitations of short-read sequencing (SR-Seq) for integration analyses and emphasizes the importance of using long-read sequencing (LR-Seq) technologies, which enable high-resolution mapping of complex integration events, including those previously inaccessible for analysis, i.e., repeat-rich genomic regions. This review highlights recent findings from LR-Seq studies on HPV integration and compares its mechanisms with those used by other viruses.

Human papillomaviruses (HPVs), like many other viruses, are able to integrate their genomes into the host cellular genome. This integration can activate viral oncogenes or alter the function of cellular oncogenes and tumor suppressor genes, thereby increasing the likelihood of HPV-associated tumor development. In particular, HPV types 16 and 18 are responsible for over 70% of all cervical, anal, and oropharyngeal cancers worldwide, with rising incidence. Even more, high-resolution mapping of preferred integration sites using LR-Seq technologies offers deep insights into the molecular mechanisms of HPV integration. LR-Seq enables the detection of complex integration patterns, where the viral genome can be replicated and amplified into virus–host concatemers, including events within large structural variations or highly repetitive genomic regions. Furthermore, aligning LR-Seq data to the latest T2T reference genome (hs1) is necessary to provide new information about viral integration in genomic regions that were previously inaccessible, such as centromeres and other structurally complex repeat-rich loci. In this review, we provide insights into HPV genomic integration revealed by LR-Seq technologies, with a particular focus on how the use of the complete T2T reference genome enhances the detection of integration events in previously uncharacterized, repeat-rich regions of the human genome.

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