Discovery and validation of methylation signatures in circulating cell-free DNA for early detection of esophageal cancer: a case-control study

Guibin Qiao,Haiyu Zhou,Guoqiang Wang,Rixin Chen,Shangli Cai,Weitao Zhuang,Dongkun Zhang,Gang Chen,Dan Tian,Jiayue Xu,Xiaosong Ben,Chengcheng Li,Xiaofang Wen,Bo Dong,Jing Zhao,Yuzi Zhang,Yu Xu,Liang Xie,Zihao Zhou,Weiqi Nian,Zhihong Zhang,Bingsi Li,Ruiqing Shi,Jiming Tang,Yu Qi

doi:10.1186/s12916-021-02109-y

Abstract

BackgroundPlasma cell-free DNA (cfDNA) methylation has shown promising results in the early detection of multiple cancers recently. Here, we conducted a study to investigate the performance of cfDNA methylation in the early detection of esophageal cancer (ESCA).MethodsSpecific methylation markers for ESCA were identified and optimized based on esophageal tumor and paired adjacent tissues (n = 24). Age-matched participants with ESCA (n = 85), benign esophageal diseases (n = 10), and healthy controls (n = 125) were randomized into the training and test sets to develop a classifier to differentiate ESCA from healthy controls and benign esophageal disease. The classifier was further validated in an independent plasma cohort of ESCA patients (n = 83) and healthy controls (n = 98).ResultsIn total, 921 differentially methylated regions (DMRs) between tumor and adjacent tissues were identified. The early detection classifier based on those DMRs was first developed and tested in plasma samples, discriminating ESCA patients from benign and healthy controls with a sensitivity of 76.2% (60.5–87.9%) and a specificity of 94.1% (85.7–98.4%) in the test set. The performance of the classifier was consistent irrespective of sex, age, and pathological diagnosis (P > 0.05). In the independent plasma validation cohort, similar performance was observed with a sensitivity of 74.7% (64.0–83.6%) and a specificity of 95.9% (89.9–98.9%). Sensitivity for stage 0–II was 58.8% (44.2–72.4%).ConclusionWe demonstrated that the cfDNA methylation patterns could distinguish ESCAs from healthy individuals and benign esophageal diseases with promising sensitivity and specificity. Further prospective evaluation of the classifier in the early detection of ESCAs in high-risk individuals is warranted.

Highlights

Plasma cell-free DNA methylation has shown promising results in the early detection of multiple cancers recently
We demonstrated that the cell-free DNA (cfDNA) methylation patterns could distinguish esophageal cancer (ESCA) from healthy individuals and benign esophageal diseases with promising sensitivity and specificity
We aimed to identify ESCA-specific differentially methylated regions (DMRs) and evaluate the potential performance of cfDNA methylation markers in the early detection of ESCA through four welldesigned stages: panel design, marker selection, model development, and model validation

Summary

Introduction

Plasma cell-free DNA (cfDNA) methylation has shown promising results in the early detection of multiple cancers recently. We conducted a study to investigate the performance of cfDNA methylation in the early detection of esophageal cancer (ESCA). Circulating cell-free DNA (cfDNA)-based liquid biopsy has shown potential to revolutionize the early detection of cancers by enabling minimally invasive molecular testing of solid tumors [6]. Genetic aberrations such as mutations, small insertions and deletions, copy number variations, and epigenetic alterations shed by tumors can be detected in cfDNA using next-generation sequencing (NGS) [7]. There are nearly 30 million methylation sites across the human genome, making them a ubiquitous and rich signal to detect cancer even with a low concentration of cfDNA [8]

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