Methylation status and long‐fragment cell‐free DNA are prognostic biomarkers for gastric cancer

Abstract

Background Circulating tumor DNA (ctDNA) detected before surgery disappears after complete surgical resection of the cancer. Residual ctDNA indicates minimal residual disease (MRD), which is a cause of recurrence. The presence of long‐fragment circulating cell‐free DNA (cfDNA) or methylated cfDNA also implies the presence of cancer. In this study, we evaluated the prognostic value of cfDNA methylation and long‐fragment cfDNA concentration in gastric cancer patients undergoing curative surgery Methods Ninety‐nine gastric cancer patients were included. Peripheral blood samples were collected before and 1 month after surgery. In patients administered chemotherapy, samples were collected before starting chemotherapy. qPCR was performed to detect long‐ and short‐fragment LINE‐1. A plasma HELP (HpaII tiny fragment Enrichment by Ligation‐mediated PCR) assay to determine the concentration of HpaII small fragments was performed using ligation‐mediated PCR and HpaII was quantified as the HpaII:MspI ratio to detect methylation levels of cfDNA. Results Overall survival (OS) of patients with low methylation levels before starting treatment was significantly worse than that of patients with high methylation levels ( P = 0.006). In the 90 patients who underwent curative surgery, recurrence‐free survival (RFS) and OS of patients with low methylation levels before surgery were worse than those with high methylation levels (P=0.08 and P = 0.11, respectively). RFS and OS of patients with high concentrations of long‐fragment LINE‐1 after surgery were significantly worse than those with low concentrations of long‐fragment LINE‐1 ( P = 0.009, P = 0.04). Conclusions Pre‐surgical low methylation levels of LINE‐1 are a negative prognostic factor. Post‐surgical high concentrations of long‐fragment LINE‐1 indicate MRD and a high risk of recurrence.

The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies

“…ALU cfDNA levels were significantly decreased after the third cycle of chemotherapy compared with baseline levels in patients with breast cancer [ 49 ]. In gastric cancer, post-surgical high concentrations of LINE-1 were found to be indicative of minimal residual disease and recurrence risk [ 50 ]. In prostate cancer, LINE-1-based cfDNA measurement was found to be useful in determining dynamic changes in response to cytotoxic chemotherapy [ 93 ].…”

“…Additionally, LINE-1 hypomethylation was associated with a trend for non-response to chemotherapy with the FOLFOX regime [ 53 ]. In gastric cancer, pre-surgical low methylation levels of LINE-1 were found to be a negative prognostic factor, whereas post-surgical high concentrations of LINE-1 were indicative of minimal residual disease (MRD) and a high risk of recurrence [ 50 ]. In HCC, multivariate analyses showed that serum LINE-1 hypomethylation was a significant and independent prognostic factor of OS in patients with HCC [ 54 ].…”

DNA Methylation: An Important Biomarker and Therapeutic Target for Gastric Cancer

“…The overall survival (OS) of patients with low methylation levels before starting treatment was significantly worse than those with high methylation levels. But methylation level before surgery had no effect on recurrence-free survival (RFS) and OS (Ko et al, 2021). However, another study showed that the methylation status of LINE-1 in leukocyte DNA was not an independent prognostic factor of GC (Tahara et al, 2018).…”

Is Cell-Free DNA Testing in Pancreatic Ductal Adenocarcinoma Ready for Prime Time?

“…A study in patients with gastric cancer demonstrated that genes that are initially methylated pre-operatively become demethylated after surgical resection, and that this demethylation correlates with favorable prognosis [ 113 ]. Furthermore, low levels of hypermethylated cfDNA post-operatively are correlated with improved OS and PFS in gastric cancers [ 114 ]. Similarly, methylation of IKZF1 and BCAT1 detected in cfDNA from patients with colorectal cancer who underwent colectomy was found to indicate a greater risk of residual disease and recurrence [ 115 ].…”