Role of Liquid Biopsies in HPV-associated Cancer Treatment Monitoring

Although the cancers associated with human papillomavirus (HPV) infection are currently almost entirely preventable, a significant part of the Czech population suffers from these diseases. The most common HPV-associated cancers are cervical cancer (CC) and oropharyngeal cancer (OPC). In these, the severe problem is successful monitoring of the treatment effectiveness and early disease recurrence detection. It is, therefore, necessary to find a non-invasive method that could specifically and timely identify patients at risk of recurrence and thus enable patients with quality and less burdensome medical care. The use of liquid biopsies (LB), which the study focuses on, looks most promising.

This study is divided into two arms, with each arm including both prospective and retrospective parts. Into prospective parts will be enrolled only newly diagnosed CC/HSIL (high-grade cervical intraepithelial lesions) or OPC patients. In contrast, the retrospective part will enroll patients in post-treatment follow-up. In both study arms, fresh tumor tissues will be sampled from patients in prospective parts before treatment, and archived Formalin Fixed Paraffin Embedded (FFPE) tissue samples will be obtained from patients of retrospective parts.

Regarding the liquid biopsies, pre \& post-treatment sampling of LB will be performed. Subsequently, regular sample acquisition will be performed during follow-up according to the standard medical practice in both prospective and retrospective parts. Oropharyngeal swabs, gargle lavage,exhaled breath condensate (EBC), and blood samples will be collected from OPC patients. Blood collection and self-sampling of cervicovaginal swabs will be performed in patients with CC/HSIL. All samples, excluding blood samples, will be tested for the presence of the most prevalent high-risk and low-risk HPV genotypes. The circulating tumor (ct) HPV DNA will be monitored in blood samples. Additionally, the mutation profile of the primary tumors will be examined in fresh and FFPE samples.

The dynamics of HPV DNA will be monitored throughout all follow-up samples and correlated with the obtained clinical data. A created panel of frequently altered genes will be used for alterations monitoring in liquid biopsies. In the final analysis of laboratory and clinical results, we assume a finding of a clinically usable algorithm that could predict the risk of disease recurrence for a particular patient.