HPV: viral DNA integration in anal cancer

Nathalie Boissière
At Institut Curie, a cross-disciplinary group of experts is focusing on analyzing the process by which the human papillomavirus genome is integrated into anal squamous cell carcinoma cells. The findings of their research were published in the science journal Cancers, and demonstrate that the signatures the viral genome left may be used as a prognostic indicator.

The role played by human papillomavirus (HPV) in some cancers such as cervical cancer is well documented. Studies are currently underway to better understand the mechanisms induces by this virus on the formation of different types of cancer. Research shows that this is related to the role played by viral proteins and the manner in which its DNA can be integrated into the genome of host cells, meaning patients’ pre-tumorous cells.

Depending on the way in which the virus’ DNA is inserted into the genome, the viral load and the existence of mutations, we were able to draw links with cancer severity

Drawing on the Curie model in which researchers and doctors work together, particularly within the context of the medical-scientific program (MSP), a ‘HPV integration’ working group has been set up, bringing together doctors, pathologists, biologists and bioinformatics experts from Institut Curie’s Hospital Group and Research Center. The team is working to uncover the various mechanisms at play and the sites at which HPV DNA is inserted into human genomes. The results of a first clinical/biological research study, in collaboration with Hôpital européen Georges-Pompidou (HEGP) in Paris, conducted on one type of cancer (rectal carcinoma) in conjunction with HPV (first cohort) have been published in the science journal Cancers (November 22, 2019). “We were able to assess prognosis in a large number of patients with anal cancer infected by HPV in long-term treatment,” explains Dr. Cindy Neuzillet, Institut Curie digestive oncologist. “Using the same approach, we rolled this viral DNA integration in human genomes analysis out to the prospective cervical cancer cohort from the European RAIDs project (findings scheduled for the next AACR congress in 2020), as well as head and neck cancer cohorts,” adds Maud Kamal (PhD), head of the transversal scientific coordination cell at the D3i (Department of Drug Development and Innovation) early-phase trial department at Institut Curie.

For this first study, 96 HPV-positive tumor biopsy samples taken from 93 patients treated between 1993 and 2017 at the Institut Curie hospital for anal squamous cell carcinomas were retrospectively extracted from the institute’s Biological resource center directed by Odette Mariani (PhD).

“We analyzed these tumoral biopsies than the DNA was sequenced via the Institut Curie NGS platform coordinated by Sylvain Baulande (PhD), thereby allowing us to determine the viral sub-type and to identify recurring molecular signatures for viral genome integration,” continues head of the Institut Curie Hospital Group’s pharmacogenomics unit, Ivan Bièche.

Then, “we were able to set up a HPV dedicated analysis pipeline in order to precisely determine the exact insertion sites into patients’ cancer cell,” say Nicolas Servant (PhD), joint managing director of the Research Center’s bioinformatics platform and Marc Deloger (PhD), bioinformatics chief project.

Different viral insertions identified

“Depending on the way in which the virus’ DNA is inserted into the cells’ genome, and depending on the viral load and the existence or lack of mutations, we were able to draw links with cancer severity indexed to patient survival. This means that drawing on our analytical method, it may now be possible to provide clinical prognosis,” according to the authors. The sequencing tool used in this clinical trial comes from an early originator development trial conducted by Sonia Lameiras as part of the research team headed up by Alain Nicolas (PhD) (CNRS UMR 3244/Institut Curie).

This new method developed at Institut Curie to analyse cervical tumors* uses high rate DNA sequencing technology ; it allows the determination of all HPV variants genotypes, its presence in variable numbers of copies, and its free nature or different integrated ways in the carcinoma cellular genome.

Published in this month’s issue of Cancers, the study confirms the reliability of this pioneer technology called Capt-HPV in a translationnal research or even clinical context.

In order to truly determine whether HPV integration signatures and status have a prognostic impact on HPV-triggered anal squamous cell carcinomas, researchers will now need to conduct studies on a larger number of patient biopsy samples.

*Holmes A. et al., NPJ Genom Med. 2016

Patient participation in clinical research remains vital in this area. For many years now, Institut Curie has been leading awareness-building campaigns and educational initiatives to help get patients involved. The Clip2 label (early-phase trial labeled center) was awarded for the third consecutive time, and will remain valid until 2024. This certification allows the D3i early-phase trial department to give a growing number of patients the opportunity to take part in clinical trials, thus providing them with access to innovative treatment. In 2018, 17.2% of patients took part in a clinical trial.

Source/DOI : Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas.