Monitoring dynamic cytotoxic chemotherapy response in castration-resistant prostate cancer using plasma cell-free DNA (cfDNA)

Abstract

Objective Cell-free DNA (cfDNA) is an attractive cancer biomarker, as it is thought to reflect a component of the underlying genetic makeup of the tumor and is readily accessible in serial fashion. Because chemotherapy regimens are expected to act rapidly on cancer and cfDNA is cleared from the blood within minutes, we hypothesized that cfDNA would reflect immediate effects of treatment. Here, we developed a method for monitoring long cfDNA fragments, and report dynamic changes in response to cytotoxic chemotherapy. Results Peripheral blood was obtained from 15 patients with metastatic castration-resistant prostate cancer (CRPC) immediately before and after cytotoxic chemotherapy infusion. cfDNA was extracted and quantified for long interspersed nuclear elements (LINE1; 297 bp) using qPCR. Targeted deep sequencing was performed to quantify the frequency of mutations in exon 8 of the androgen receptor (AR), a mutational hotspot region in CRPC. Single nucleotide mutations in AR exon 8 were found in 6 subjects (6/15 = 40%). Analytical variability was minimized by pooling independent PCR reactions for each library. In 5 patients, tumor-derived long cfDNA levels were found to change immediately after infusion. Detailed analysis of one subject suggests that cytotoxic chemotherapy can produce rapidly observable effects on cfDNA. Electronic supplementary material The online version of this article (10.1186/s13104-019-4312-2) contains supplementary material, which is available to authorized users.

On-treatment measurements of circulating tumor DNA during FOLFOX therapy in patients with colorectal cancer

“…Instead, we invariably observed a pattern of ctDNA mAF decrease in all cases. Interestingly, that decreased ctDNA levels at the end of a therapy may indicate therapy response was also suggested in the abovementioned NSCLC and prostate cancer studies 22,23 . In our study, patients with progressive disease showed a trend towards a ctDNA mAF increase between T5 and T9 ( Figs.…”

“…In patients with non-small-cell lung cancer (NSCLC), one study analyzed daily kinetic changes of EGFR mutation levels in urine from nine patients 21 and another study quantified EGFR and KRAS mutations in three patients over defined time periods, but only in one on a daily basis, i.e., every 24 h 22 . A further study analyzed pre- and postchemotherapy samples in five patients with metastatic prostate cancer within 1 h of chemotherapy infusion 23 .…”

Microfluidic Technologies for cfDNA Isolation and Analysis

“…RT-qPCR, which consists of TaqMan and ARMS assays, is the most commonly used way to quantify cfDNA in tubes with large sample volume [65,66], with the limit of detection (LOD) of ~0.02 pg [67]. The TaqMan probe, which contains a fluorophore and a quencher, is complementary to part of PCR product.…”

Kinetics of plasma cfDNA predicts clinical response in non-small cell lung cancer patients

“…cfDNA, on the other hand, is relatively abundant and easier to quantify in circulating blood. Though the majority of cfDNA is often not of cancerous origin, preliminary studies suggest that cfDNA level and kinetics may still be used to assist in cancer diagnosis, treatment response or prognostic prediction 27 – 32 .…”