Methylated Cell-Free DNA Sequencing (MeD-seq) of LpnPI Digested Fragments to Identify Early Progression in Metastatic Renal Cell Carcinoma Patients on Watchful Waiting

SIMPLE SUMMARY: A subset of patients with an intermediate risk for renal cell carcinoma have an indolent disease course. For these patients, the initiation of treatment for metastatic disease can be safely delayed by entering a watchful waiting period. At present, we are not able to identify those patients with indolent disease and the minor group of patients with rapidly progressive disease requiring earlier initiation of systemic treatment. In this study, we investigate whether cell-free DNA (cfDNA) can be used as a blood-based biomarker to identify those patients with rapid progression. Methylated cfDNA profiles were used as a proxy for tumor load in blood. cfDNA methylation patterns were associated with the time to radiological progression, but not with the watchful waiting time. The results of this study do not provide definite proof that cfDNA methylation patterns are associated with WW time. ABSTRACT: According to the current guidelines, watchful waiting (WW) is a feasible option for patients with good or intermediate prognosis renal-cell carcinoma (RCC). However, some patients rapidly progress during WW, requiring the initiation of treatment. Here, we explore whether we can identify those patients using circulating cell-free DNA (cfDNA) methylation. We first defined a panel of RCC-specific circulating methylation markers by intersecting differentially methylated regions from a publicly available dataset with known RCC methylation markers from the literature. The resulting RCC-specific methylation marker panel of 22 markers was subsequently evaluated for an association with rapid progression by methylated DNA sequencing (MeD-seq) in serum from 10 HBDs and 34 RCC patients with a good or intermediate prognosis starting WW in the IMPACT-RCC study. Patients with an elevated RCC-specific methylation score compared to HBDs had a shorter progression-free survival (PFS, p = 0.018), but not a shorter WW-time (p = 0.15). Cox proportional hazards regression showed that only the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) criteria were significantly associated with WW time (HR 2.01, p = 0.01), whereas only our RCC-specific methylation score (HR 4.45, p = 0.02) was significantly associated with PFS. The results of this study suggest that cfDNA methylation is predictive of PFS but not WW.