Mechanistic signatures of HPV insertions in cervical carcinomas.

Allyson Holmes,Laurent Castera,Yannick Marie,Sonia Lameiras,Alain Nicolas,Xavier Sastre-Garau,Emmanuelle Jeannot

doi:10.1038/npjgenmed.2016.4

Abstract

To identify new personal biomarkers for the improved diagnosis, prognosis and biological follow-up of human papillomavirus (HPV)-associated carcinomas, we developed a generic and comprehensive Capture-HPV method followed by Next Generation Sequencing (NGS). Starting from biopsies or circulating DNA samples, this Capture-NGS approach rapidly identifies the HPV genotype, HPV status (integrated, episomal or absence), the viral-host DNA junctions and the associated genome rearrangements. This analysis of 72 cervical carcinomas identified five HPV signatures. The first two signatures contain two hybrid chromosomal–HPV junctions whose orientations are co-linear (2J-COL) or non-linear (2J-NL), revealing two modes of viral integration associated with chromosomal deletion or amplification events, respectively. The third and fourth signatures exhibit 3–12 hybrid junctions, either clustered in one locus (MJ-CL) or scattered at distinct loci (MJ-SC) while the fifth signature consists of episomal HPV genomes (EPI). Cross analyses between the HPV signatures and the clinical and virological data reveal unexpected biased representation with respect to the HPV genotype, patient age and disease outcome, suggesting functional relevance(s) of this new classification. Overall, our findings establish a facile and comprehensive rational approach for the molecular detection of any HPV-associated carcinoma and definitive personalised sequence information to develop sensitive and specific biomarkers for each patient.

Highlights

Each year, 4500,000 individuals are diagnosed worldwide with human papillomavirus (HPV) associated cancers.1 HPV is a hallmark of most cervical cancers but is associated with anal and head and neck carcinomas
From frozen biopsies and blood samples were extracted and the HPV-containing regions enriched using a double-capture method. Both rounds of capture consist of hybridisation with an exhaustive set of 22,000 single-stranded biotinylated HPV probes (Supplementary Table S1) in order to enrich for the small targeted viral sequences, which represent less than 8 kb of DNA out of 46 Gb of human DNA
The probes were designed to detect the entire length of the HPV genomes from 4200 HPV genotypes or variants, allowing an exhaustive and unbiased method to capture any chromosomally integrated, or episomally non-integrated HPV DNA sequence

Summary

Introduction

4500,000 individuals are diagnosed worldwide with human papillomavirus (HPV) associated cancers. HPV is a hallmark of most cervical cancers but is associated with anal and head and neck carcinomas. Long-term infections of the cervical mucosa, oncogenic HPVs can cause high-grade cervical intraepithelial neoplasias (CINs), that without ablative treatment, may develop into invasive carcinomas.. Better understanding of HPV biology has permitted major advances in the development of prophylactic vaccines and in the detection of HPV-associated diseases. Cervical carcinomas remain frequent worldwide and their prognosis is poor, in advanced stages and in cases of relapse.. It is of major importance to acquire molecular biomarkers that will facilitate the early diagnosis of cervical cancer, the detection of precocious tumour relapses and offer optimal biological follow-ups of the disease, upon and after treatment. Efforts to facilitate the diagnosis of HPV-associated cancers, elucidate the mechanisms driving HPV oncogenicity and develop cost-efficient and precise monitoring tools to improve clinical oncology, are needed

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Results

Conclusion