Genome-wide methylation profiling identified methylated KCNA3 and OTOP2 as promising diagnostic markers for esophageal squamous cell carcinoma

Background:Early detection of esophageal squamous cell carcinoma(ESCC)can considerably improve the prognosis of patients.Aberrant cell-free DNA(cfDNA)methylation signatures are a promising tool for detecting ESCC.However,available markers based on cell-free DNA methylation are still inadequate.This study aimed to identify ESCC-specific cfDNA methylation markers and evaluate the diagnostic performance in the early detection of ESCC.Methods:We performed whole-genome bisulfite sequencing(WGBS)for 24 ESCC tissues and their normal adjacent tissues.Based on the WGBS data,we identified 21,469,837 eligible CpG sites(CpGs).By integrating several methylation datasets,we identified several promising ESCC-specific cell-free DNA methylation markers.Finally,we developed a dual-marker panel based on methylated KCNA3 and OTOP2,and then,we evaluated its performance in our training and validation cohorts.Results:The ESCC diagnostic model constructed based on KCNA3 and OTOP2 had an AUC of 0.91[95%CI:0.85-0.95],and an optimal sensitivity and specificity of 84.91%and 94.32%,respectively,in the training cohort.In the independent validation cohort,the AUC was 0.88[95%CI:0.83-0.92],along with an optimal sensitivity of 81.5%and specificity of 92.9%.The model sensitivity for stage I-II ESCC was 78.4%,which was slightly lower than the sensitivity of the model(85.7%)for stage III-IV ESCC.Conclusion:The dual-target panel based on cfDNA showed excellent performance for detecting ESCC and might be an alternative strategy for screening ESCC.