Detection of LINE-1 hypomethylation in cfDNA of Esophageal Adenocarcinoma Patients

Abstract

DNA methylation plays an important role in cancer development. Cancer cells exhibit two types of DNA methylation alteration: site-specific hypermethylation at promoter of oncosuppressor genes and global DNA hypomethylation. This study evaluated the methylation patterns of long interspersed nuclear element (LINE-1) sequences which, due to their relative abundance in the genome, are considered a good surrogate indicator of global DNA methylation. LINE-1 methylation status was investigated in the cell-free DNA (cfDNA) of 21 patients, 19 with esophageal adenocarcinoma (EADC) and 2 with Barrett’s esophagus (BE). The two BE patients and one EADC patient were also analyzed longitudinally. Methylation status was analyzed using restriction enzymes and DNA amplification. This methodology was chosen to avoid bisulfite conversion, which we considered inadequate for cfDNA analysis. Indeed, cfDNA is characterized by poor quality and low concentration, and bisulfite conversion might worsen these conditions. Results showed that hypomethylated LINE-1 sequences are present in EADC cfDNA. Furthermore, longitudinal studies in BE suggested a correlation between methylation status of LINE-1 sequences in cfDNA and progression to EADC. In conclusion, our study indicated the feasibility of our methodological approach to detect hypomethylation events in cfDNA from EADC patients, and suggests LINE-1 methylation analysis as a new possible molecular assay to integrate into patient monitoring.

Epigenetic Alterations from Barrett’s Esophagus to Esophageal Adenocarcinoma

“…The findings of this study reveal the heterogeneity of DNA methylation patterns in BE and EAC and their impact on gene expression and genomic stability, providing evidence for the involvement of DNA methylation changes in EAC development [74]. Boldrin et al stated that LINE-1 hypomethylation could be used as a biomarker not only to monitor EAC prognosis but also as an indicator in BE surveillance [76]. In a study examining the whole genome methylation of progressive and nonprogressive nondysplastic BE patients, 44 methylation profiles were found to be different between the two groups; particularly, hypomethylation at the OR3A4 position was identified as a differentiator between progressive and nonprogressive patients [13].…”

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

“…Recently, an analysis of methylation patterns of long interspersed nuclear element (LINE‐1) sequences, a good surrogate indicator of global DNA methylation, showed that hypomethylation of these sequences was present in cfDNA in 19 EAC patients [84]. Also, longitudinal studies on 2 BE patients suggested an association between methylation status of LINE‐1 sequences in cfDNA and progression to EAC [77]. Although further studies are needed, these results suggest a potential method for early EAC detection.…”

“…Methylation of cytosine adjacent to guanine (CpG sites) is important for cell type-specific gene regulation and is a hallmark of cell identity [75]. Cancer cells exhibit two types of DNA methylation alteration: site-specific hypermethylation at the promoter of oncosuppressor genes and global DNA hypomethylation [76,77]. Interestingly, DNA methylation patterns detected in cfDNA are highly concordant with those found in matched primary tumor tissues [78,79].…”

SMAD3 Hypomethylation as a Biomarker for Early Prediction of Colorectal Cancer

“…This indicates that SMAD3 is a specific biomarker in Taiwanese esophageal cancer. In esophageal adenocarcinoma, cfDNA LINE-1 hypomethylation is considered a possible molecular assay [ 34 ]. Therefore, further investigation to confirm the hypomethylation level of ccfDNA SMAD3 in esophageal cancer is encouraged.…”