HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples

Sonja Lagström,Alexander Hesselberg Løvestad,Sinan Uğur Umu,Ole Herman Ambur,Mari Nygård,Trine B Rounge,Irene Kraus Christiansen

doi:10.1016/j.tvr.2021.200221

Abstract

Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration.We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5).Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.

Highlights

1 INTRODUCTION1.1 Human papillomavirus and cancerHuman papillomavirus (HPV) causes nearly 5% of all cancers worldwide [1]
This thesis aimed to characterise HPV genomic variation at the minor nucleotide level and chromosomal integration, and to explore HPV genomic events contributing to HPV-induced carcinogenesis
We developed a unique deep-sequencing protocol TaME-seq for deep analysis of HPV genomic variation and integration; we have filed a patent application for the method

Summary

Introduction

1 INTRODUCTION1.1 Human papillomavirus and cancerHuman papillomavirus (HPV) causes nearly 5% of all cancers worldwide [1]. Human papillomavirus (HPV) is the most common sexually transmitted infection worldwide [1] and persistent infection with an oncogenic HPV type is required, but not sufficient, for the development of cervical cancer [2]. Objectives: The objective of this study was to investigate HPV16 genome variation at the minor variant level on persisting HPV16 cervical infections from a population of young Dutch women. We identify a number of MNVs that have previously been associated with higher incidence of high-grade lesions (CIN3+) in a population study. These findings may provide a starting point for future studies exploring causality between emerging HPV minor genomic variants and cancer development

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