Document resource
Introduction Barrett’s oesophagus (BO) is a precursor to oesophageal adenocarcinoma (OAC). Patients with BO undergo regular endoscopic surveillance with biopsies to detect dysplasia at an early stage. However, this is invasive and expensive, dysplasia may be missed by biopsies, and there is variability between pathologists in assessing dysplasia. There is an urgent need for novel risk-stratification biomarkers. Altered DNA methylation can occur early in neoplastic transformation, making it attractive as a potential biomarker. Few studies have compared methylation in baseline non-dysplastic BO biopsies between patients who later progressed to OAC and those who did not.Methods Through the Northern Ireland Barrett’s Register, a cohort of 42 progressor/non-progressor pairs was identified, matched on age, sex, and year of Barrett’s diagnosis (n = 84). Progressors were defined as patients who progressed from non-dysplastic BO to high-grade dysplasia or OAC, whilst non-progressors did not progress beyond non-dysplastic BO. DNA was extracted from the baseline non-dysplastic Barrett’s formalin-fixed paraffin-embedded biopsies. These biopsies were obtained 1 to 5 years before progression, or before the corresponding matched timepoint for non-progressors.Methylation profiling was performed using the Twist Human Methylome Panel targeting ~4 million CpG sites. Differential methylation analysis was conducted using the RnBeads Bioconductor package with limma-based modelling, with significance defined as false discovery rate (FDR)-adjusted p-value < 0.05. Differentially methylated CpG sites were mapped to genes based on genomic location.Results We identified 25 significantly differentially methylated CpG sites (FDR < 0.05). All significant CpG sites were hypermethylated in progressors compared to non-progressors. Beta-value differences (Δβ) ranged from 0.033 to 0.262, with a mean of 0.143.These 25 CpG sites were mapped to 13 genes, with 3 genes (IGDCC3, GJC1, GNG4) harbouring multiple differentially methylated CpG sites. The genes identified include proto-oncogenes (FGFR1, ADRA1B) and genes involved in cell adhesion (IGDCC3, GJC1, CDH22, COL19A1), cell signalling (GNG4, GNB4), cell proliferation (HDGFL3), and immune regulation (THEMIS2). Methylation of GJC1, GNB4, ELOVL5, and ADRA1B has been previously implicated in gastrointestinal cancers. Overall, these 13 genes are involved in biological processes relevant to BO progression.Conclusions We detected 25 CpG sites which were hypermethylated in BO progressors compared to matched non-progressors, in baseline non-dysplastic biopsy samples taken 1 to 5 years before progression. These sites map to genes involved in biological processes relevant to oesophageal carcinogenesis. These hypermethylated sites represent candidate biomarkers for risk stratification in BO, and warrant validation in independent cohorts.