Epigenetic liquid biopsies for minimal residual disease, what's around the corner?

Abstract

Liquid biopsy assays for minimal residual disease (MRD) are used to monitor and inform oncological treatment and predict the risk of relapse in cancer patients. To-date, most MRD assay development has focused on targeting somatic mutations. However, epigenetic changes are more frequent and universal than genetic alterations in cancer and circulating tumor DNA (ctDNA) retains much of these changes. Here, we review the epigenetic signals that can be used to detect MRD, including DNA methylation alterations and fragmentation patterns that differentiate ctDNA from noncancerous circulating cell-free DNA (ccfDNA). We then summarize the current state of MRD monitoring; highlight the advantages of epigenetics over genetics-based approaches; and discuss the emerging paradigm of assaying both genetic and epigenetic targets to monitor treatment response, detect disease recurrence, and inform adjuvant therapy.

Keywords: DNA methylation; MRD; cancer; ccfDNA (circulating cell-freeDNA); ctDNA (circulating tumor DNA); epigenetics; fragmentomics; liquid biopsy.

Figure 1

Minimal residual disease (MRD) epigenetic assays and their use across a cancer patient journey. (A) Establishing the molecular targets for MRD assays can be performed prior to treatment initiation. A decline in the level of the assayed biomarker suggests efficacious treatment and reduced tumor burden. (B) The continued presence of a tumor biomarker after curative intent treatment, accompanied by no visible signs of a tumor, indicates the presence of MRD. (C) Tracking with an MRD assay over time is useful for early detection of cancer recurrence, as the level of the assayed biomarker will increase as a tumor remerges. (D) Liquid biopsies can be performed on a variety of bodily fluids including blood, urine, saliva, lymph, and cerebrospinal fluid. Circulating tumor DNA (ctDNA) contains epigenetic alterations that can separate it from the cancer’s normal tissue counterpart and circulating cell-free DNA (ccfDNA) derived from noncancerous sources. Cancer-specific epigenetic alterations include: (E) aberrant DNA methylation, and (F) altered fragmentomic signals (i.e., changes in ctDNA fragment lengths, end sequences, and nucleosome-associated genomic positioning).