Somatic alterations in circulating cell-free DNA of oesophageal carcinoma patients during primary staging are indicative for post-surgical tumour recurrence

Abstract

Oesophageal cancer (OC) has high mortality. This study aims at determining the feasibility of liquid biopsies for genomic profiling in early stage OC, comparing two different technologies for mutational analysis in circulating cell -free DNA (ccfDNA) and evaluating the clinical impact of these somatic alterations during primary staging. In 25 patients with locally advanced OC, endoscopic tumour biopsies and simultaneous blood samples were taken during primary staging. Genomic DNA from biopsies and ccfDNA were analysed for mutations using a 12 gene panel next-generation sequencing (NGS) assay as well as digital droplet PCR (ddPCR). Genetic data was correlated with patients’ outcome. In 21 of the tested biopsies (84%) at least one somatic mutation was detected by NGS. Mutations detected by NGS were detectable by ddPCR with similar allele frequencies. In three out of the 21 patients with proven mutations, the same mutations were also detectable in ccfDNA using NGS (14%). In contrast, ddPCR detected mutations in ccfDNA of five additional patients (8/21, 38%). Post-surgical outcome analysis was performed for those patients who had received complete tumour resection (n = 16). Five of them suffered from an early relapse within the first year after surgery, including four with detectable somatic mutations in ccfDNA during primary staging. Taken together, we showed a higher sensitivity for ddPCR compared to NGS in detecting mutated ccfDNA in OC. Detection of somatically altered ccfDNA during primary staging seems to be indicative for post-surgical tumour recurrence.

Circulating tumor DNA as an emerging liquid biopsy biomarker for early diagnosis and therapeutic monitoring in hepatocellular carcinoma

“…It also took a precondition that objective mutation sites must be certainly known in advance. In other words, NGS is more suitable for primary gene profiling on multi-gene panels [22].…”

“…The increase of cfDNA level and copy number in tumor patients are explained by the raised number of apoptotic and necrotic carcinoma cells. It has been proven in liver cancer, oesophageal cancer, breast cancer, and pancreatic cancer [22,52,53]. Recently, Yan L et al clearly showed that the cfDNA concentration in plasma was significantly higher in HCC patients compared to patients with liver fibrosis or healthy individuals [25].…”

Liquid biopsy for esophageal cancer: Is detection of circulating cell‐free DNA as a biomarker feasible?

“…ddPCR detects mutations in cfDNA with high sensitivity, but it is only suitable when the mutations are already known from previous tumor tissue‐based analyses [42]. Also, the location of somatic mutations in EC‐related driver genes span large regions of the genome [43], which are difficult to track by PCR‐based methods.…”

Precision medicine for gastrointestinal cancer: Recent progress and future perspective

“…Clinically relevant biomarkers are genetic, epigenetic, proteinic, or cellular alterations that are intrinsic to cancer cells. These biomarkers can be used to predict patients' responses to Huang et al [50] , 2017 Pasternack et al [112] , 2018 Kakiuchi et al [42] , 2014 Yoshida et al [113] , 2019 Nagahashi et al [39] , 2016…”

“…TP53 was commonly implicated in all references except 28035762, 30297788 and 30523343 (PMID) [50,112,117] . EC: Esophageal cancer; GC: Gastric cancer; CRC: Colorectal cancer; NGS: Next-generation sequencing; FFPE: Formalin-fixed paraffin-embedded; N/A: Not available; EBV: Epstein-Barr virus; MSI: Microsatellite instability; NGS: Next-generation sequencing.…”