Promoter hypermethylation of SFRP1 is an allele fraction-dependent prognostic biomarker in metastatic pancreatic ductal adenocarcinoma

Introduction: Metastatic pancreatic ductal adenocarcinoma (PDAC) is highly lethal. Promoter hypermethylation of SFRP1 (phSFRP1) in cell-free DNA is an established prognostic biomarker in PDAC. We used digital droplet PCR (ddPCR) to examine whether the prognostic impact of phSFRP1 was allele fraction (AF) dependent. Methods: Prospectively collected plasma samples were analyzed blinded. Dual-strand methylation ddPCR assays were designed for SFRP1, with single-strand assay for the reference gene EPHA3. Patients were stratified into unmethylated SFRP1 (umSFRP1), low phSFRP1 AF (phSFRP1^low), and high phSFRP1 AF (phSFRP1^high). Survival was assessed with Kaplan–Meier curves. The 3-, 6-, and 12-month absolute risk difference (ARD) was calculated, and performance assessed with ROC analyses. Results: Overall, 354 patients were included. Patients with umSFRP1 (n=137) had a mOS of 9.1 months compared to 7.2 months in phSFRP1^low (n=78) and 3.4 months in phSFRP1^high (n=143, P<0.01). phSFRP1^high was associated with increased mortality at 3 (ARD 26%, 95%CI: 15, 37), 6 (ARD 37%, 95%CI: 26, 48), and 12 months (ARD 23%, 95%CI: 14, 33). phSFRP1^low was associated with increased mortality at 12 months (ARD 13%, 95%CI: 2, 25) but not at 3 (ARD -3%, 95%CI: -13, 8) or 6 months (ARD 3%, 95%CI: -10, 17). phSFRP1 significantly improved performance in predicting mortality compared to only clinical variables (AUC: 0.70-0.71 vs. 0.54-0.57). Discussion: Patients with phSFRP1^high had significantly shorter survival than phSFRP1^low or umSFRP1, indicating AF-dependent prognostic effects. phSFRP1^low had a worse prognosis than umSFRP1 at only 12 months, indicating dynamic changes. This could help personalize the treatment of PDAC.