Perivascular epithelial remodeling is reflected in circulating cfDNA methylation signals as detection markers for early esophageal tumorigenesis

Early detection of esophageal squamous cell carcinoma (ESCC) is hindered by a lack of noninvasive biomarkers for precancerous lesions. Here, we report a circulating cell-free DNA (cfDNA) methylation approach for early esophageal neoplasia detection. In prospective community screening, the assay achieved standardized sensitivity of 78% at 79% specificity for the clinically actionable endpoint of high-grade intraepithelial neoplasia (HGIN) or ESCC, with stage-specific sensitivities of 76% for HGIN and 86% for ESCC. Genome-wide methylation profiling reveals HGIN as an early epigenetic reprogramming stage. Integrative spatial and single-cell RNA sequencing reveals pronounced remodeling of the endothelial-proximal epithelial cell population, whose methylation signatures are detected in cfDNA. Guided by these findings, we develop an 11-gene cfDNA methylation panel that shows robust discrimination of early-stage ESCC across three retrospective case-control sets and an independent screening-derived case-control set. Together, these results demonstrate that our cfDNA methylation panel has promising utility for early ESCC detection.