# Elucidating Alterations in Viral and Human Gene Expression Due to Human Papillomavirus Integration by Using Multimodal RNA Sequencing

## TL;DR

This study uses RNA sequencing to show how HPV integration into human DNA affects gene expression, revealing patterns that could help treat cervical cancer.

## Contribution

The study identifies specific transcriptional patterns and cancer-related genes activated near HPV integration sites using multimodal RNA sequencing.

## Key findings

- HPV-derived transcripts were detected in 17 of 20 clinical samples.
- Chimeric RNAs were identified in 13 of 17 samples, revealing 16 viral integration sites.
- Upregulation of 12 cancer-related genes near integration sites was observed, including MAGI1-AS1 and MMP12.

## Abstract

Human papillomavirus (HPV) infection is a primary driver of cervical cancer. Integration of HPV into the human genome causes persistent expression of viral oncogenes E6 and E7, which promote carcinogenesis and disrupt host genomic function. However, the impact of integration on host gene expression remains incompletely understood. We used multimodal RNA sequencing, combining total RNA-seq and Cap Analysis of Gene Expression (CAGE), to clarify virus–host interactions after HPV integration. HPV-derived transcripts were detected in 17 of 20 clinical samples. In most specimens, transcriptional start sites (TSSs) showed predominant early promoter usage, and transcript patterns differed with detectable E4 RNA region. Notably, the high RNA expressions of E4 region and viral-human chimeric RNAs were mutually exclusive. Chimeric RNAs were identified in 13 of 17 samples, revealing 16 viral integration sites (ISs). CAGE data revealed two patterns of TSS upregulation centered on the ISs: a two-sided pattern (43.8%) and a one-sided pattern (31.3%). Total RNA-seq showed upregulation of 12 putative cancer-related genes near ISs, including MAGI1-AS1, HAS3, CASC8, BIRC2, and MMP12. These findings indicate that HPV integration drives transcriptional activation near ISs, enhancing expression of adjacent oncogenes. Our study deepens understanding of HPV-induced carcinogenesis and informs precision medicine strategies for cervical cancer.