The emerging role of cell-free DNA as a molecular marker for cancer management

Abstract

An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.

Dynamics of tumor‐specific cfDNA in response to therapy in multiple myeloma patients

“…We observed high intra‐ and inter‐patient variability (range 1.75‐405.6 ng per mL of serum), which is consistent with previous studies among MM patients and other malignancies . A wide range of biological and physiological factors, including tumor burden, disease stage or even half‐life of cfDNA can influence release and clearance of tumor‐specific fraction of total cfDNA and play a role in this variability . As a result, scarce amounts of cfDNA are isolated in some cases in which target molecules may be under‐represented causing false‐negative results .…”

“…28 A wide range of biological and physiological factors, including tumor burden, disease stage or even half-life of cfDNA can influence release and clearance of tumor-specific fraction of total cfDNA and play a role in this variability. 42 As a result, scarce amounts of cfDNA are isolated in some cases in which target molecules may be under-represented causing false-negative results. 6,43 This at least partially explains why some patients were found cfDNA negative at diagnosis and put emphasis on standardization of preanalytical factors which can be influenced.…”

Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer

“…To address this challenge, we reconstructed tumor phylogenies from genome and exome sequencing of tissue in order to select alleles representing the major subclones that would be present at the time of surgery and further mediate relapse. Prior to executing these experiments, we developed and tested a bespoke patient-specific, allele-specific sequencing assay that satisfied requirements for reproducibility, accuracy, sensitivity, and specificity [16,30,31]. This assay consistently detected spiked-in alleles and showed 100% concordance to unbiased whole exome sequencing of the same sample at very high coverage.…”

Tumor microenvironment complexity and therapeutic implications at a glance

“…It consists of very short (< 200 bp) double-stranded DNA fragments obtained at very low concentrations [193][194][195]. In cancerous conditions, cfDNA is derived not only from the cancer cells but also from TME and other noncancer cells, e.g., endothelial and immune cells [196,197]. Nevertheless, cancerous conditions that are marked with the increased cfDNA concentration and a significant amount of cfDNA are likely to be derived from the tumor, hence offering diagnostic evidence (Fig.…”

“…Notably, cfDNA fragments are able to enter neighboring/ distal cells and are capable of altering the biology of recipient cells. In the context of cancer, they are involved in horizontal gene transfer and oncogenic transformation of normal cells as well as in the metastasis development [197]. Although there is no clear mechanistic evidence for their oncogenic potential, several proposals include (ii) overexpression of several pro-metastatic genes through the tolllike receptor 9 (TLR9)/ myeloid differentiation primary response 88 (MYD88) independent pathway [198]; (ii) transposable elements [199] and finally the cellular uptake of exosomes [200,201].…”