PDF, English - main document Restricted access: Repository staff only until 30 November 2026. Login+Download (4MB) | Terms of use

Abstract

Human papillomavirus (HPV) causes ca. 5% of all cancer cases worldwide, including anal and oropharyngeal cancer (OPC). HPV-driven OPC usually presents with disseminated disease and requires aggressive multimodal treatment, which often has long-term negative effects on cancer survivors health. Early detection of HPV-driven OPC and optimized post-therapy surveillance could lead to better patient outcomes. HPV-driven anal cancer is rare in the general population, but people living with HIV are at a greatly increased risk. Currently there are no screening programs for HPV-driven anal cancer or OPC. Liquid biopsies, and especially cell-free DNA from blood plasma, are a minimally invasive biomaterial that could be suitable as a basis for a screening or post-therapy surveillance test for these cancers. In this thesis I describe my work on developing and applying a digital PCR (dPCR) assay for HPV cell-free DNA from blood plasma as a biomarker for HPV-driven cancer early detection and post-therapy surveillance. The workflow from blood sample collection over cfDNA purification to dPCR and data analysis has been optimized for these applications. In plasma samples from 57 HPV-driven OPC and 29 HPV-negative OPC patients, the assay had a sensitivity of 93% and a specificity of 97% for distinguishing HPV-driven and HPV-negative OPC. I also applied the assay in post-therapy surveillance to detect recurrent HPV-driven OPC. I tested blood plasma samples from HPV-driven OPC patients from different time points during and after end of therapy. Positive HPV cfDNA test results after end of therapy had a positive predictive value of 80 to 100% for recurrence of HPV-driven OPC. HPV cfDNA was predictive of HPV-driven OPC recurrence up to 8 months before diagnosis. When I applied the assay to pre-diagnostic plasma samples from HPV-driven OPC cases or anal cancer cases, it yielded positive results in 25% of anal cancer cases and 67% of OPC cases. In 5% of anal cancer cases HPV cfDNA was detected more than 4 years before diagnosis. In summary, in this thesis I have shown that HPV cfDNA detection by dPCR is a highly specific biomarker for HPV-driven cancers and can be detected before diagnosis, and therefore is a promising candidate for a screening biomarker.