Epigenomic liquid biopsy-based biomarkers of platinum and PARP inhibitor response in patients with germ line BRCA-associated PDAC: A pilot study

Background: Despite favorable overall response, pancreatic ductal adenocarcinoma (PDAC) patients with germline BRCA mutations show varied response to platinum-based chemotherapy and PARP inhibitor treatment. While some patients demonstrate long term response, others develop acquired resistance after an initial durable response and a third group are refractory to first-line platinum-based therapy. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell-free DNA (cfDNA) of PDAC patients present a non-invasive approach to investigate treatment response biomarkers. Here, we investigated 5hmC profiles of plasma-derived cfDNA obtained from PDAC patients prior to treatment and while on treatment. Additionally, samples were evaluated for response by CA19-9 measurements and the Avantect Pancreatic Cancer Test (Avantect, a non-invasive, blood-based assay designed to detect PDAC using epigenomics and genomics biomarkers. Methods: A total of 80 blood samples were collected in EDTA tubes from 32 PDAC patients pre-treatment or while on-treatment, with 2-5 timepoints for each patient. Blood samples were processed to obtain plasma. Cell-free DNA extracted from plasma were analyzed using Avantect. Germline BRCA1 / 2 mutations were confirmed for all study subjects. Results: Of the 32 patients included in the study, 6 were refractory, 14 developed acquired resistance and 12 were long term responders to platinum/PARP-inhibitor treatment. Differential 5hmC analysis at the earliest available timepoint for each patient revealed refractory patients to have distinct cfDNA profiles relative to both acquired resistance and long-term responders. Analysis with Avantect showed that the refractory group exhibited the highest cancer scores when compared to the acquired resistance and long-term responder groups (p value 0.001). Stratification of stage IV patients according to Avantect test results revealed that cancer signal-detected patients have poor overall survival relative to cancer signal not-detected patients (9.3 months vs 25.9 months, Hazard ratio 4.17, p = 0.017). Furthermore, evaluation of on-treatment timepoints demonstrated that Avantect detected disease progression in 78.6% (11/14) of PDAC patients who developed acquired resistance. Conclusions: cfDNA 5hmC analysis revealed clear differences between long-term responders and patients with resistance, highlighting potential blood-based biomarkers of treatment durability and mechanisms of resistance.​ Cancers with worse response to therapy were detected at a higher rate by the Avantect test. These findings suggest that larger studies using Avantect can be performed to identify patient subpopulations with limited treatment response and to monitor treatment response.