Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett’s esophagus

Abstract

We report a biomarker-based non-endoscopic method for detecting Barrett’s esophagus (BE), based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma (EAC). Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve (AUC)=0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals, who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 minutes. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.

Early detection and therapeutics

“…Given the costs associated with endoscopy‐based screening modalities, there is increasing interest in non‐endoscopic cell collection devices (Lao‐Sirieix et al ., ; Moinova et al ., ). This technology has been used previously in the context of OSCC screening but has failed as a result of a reliance on cytological assessment of atypia.…”

“…Methylation or miRNAs are alternative biomarkers that could avoid the paraffin embedding and manual pathology review steps required for TFF‐3 (Chettouh et al ., ). Moreover, some potential biomarkers could stratify patients with Barrett's into low‐ and high‐risk groups for malignant progression using a combination of biomarkers including TP53 (Moinova et al ., ).…”

Role of TFF3 as an adjunct in the diagnosis of Barrett's esophagus using a minimally invasive esophageal sampling device—The CytospongeTM

“…In a pilot study of 10 patients with known BE, none of the samples obtained contained identifiable goblet cells, 16 whilst in a larger study of 63 patients with known BE, 83% of samples contained columnar epithelium however the cell yield was low and goblet cells were only identified in 24% of cases overall. 18 Initial analysis of esophageal brushing samples identified aberrant cytosine methylation at the CCNA1 locus as a potential biomarker for BE, dysplasia and EAC. 18 Initial analysis of esophageal brushing samples identified aberrant cytosine methylation at the CCNA1 locus as a potential biomarker for BE, dysplasia and EAC.…”

“…18 Initial analysis of esophageal brushing samples identified aberrant cytosine methylation at the CCNA1 locus as a potential biomarker for BE, dysplasia and EAC. 18 Balloonbased esophageal sampling combined with the methylation biomarkers was then undertaken in a cohort of 156 patients with a sampling success rate of 82% and high patient tolerance. 18 Balloonbased esophageal sampling combined with the methylation biomarkers was then undertaken in a cohort of 156 patients with a sampling success rate of 82% and high patient tolerance.…”

Molecular landscape of esophageal cancer: implications for early detection and personalized therapy

“…Some of these studies identified different mutation, DNA methylation, and SCNA patterns among the progressing and nonprogressing types of BE suggesting a window of opportunity for early detection with multiomics approach . A couple of recent reports using molecular biomarker‐based nonendoscopic method (Table ) enables an efficient, well‐tolerated, sensitive, and specific method of screening at‐risk populations for BE . Moreover, exposure‐associated genetic and epigenetic changes may prove instrumental in evaluating the cancer risk in heavily exposed individuals.…”