Diagnosis of Early-Stage Non-Small Cell Lung Cancer Using DNA Methylation in Tissue and Plasma

Background: To explore the diagnostic value of DNA methylation in early-stage lung cancer using tissue and plasma. Methods: A tissue cohort (n=100) and a plasma cohort (n=146) of patients diagnosed with lung cancer and benign diseases were enrolled and randomly divided into training and validation groups. Methylation profiles were compared to select lung cancer-specific methylation markers. Diagnostic prediction models were constructed using these markers. Their efficacies were estimated by sensitivity, specificity, and AUC. Findings: Diagnostic models were developed to differentiate lung cancer from benignity. In the tissue cohort, 276 markers were significantly differentially methylated in lung cancer (FDR<0.05). A diagnostic prediction model of 6 markers from these achieved outstanding performances in both training cohort (Sensitivity 90%, Specificity 97%, AUC 0.988) and validation cohort (Sensitivity 92%, Specificity 94%, AUC 0.977). These markers were not significantly differentially methylated in the plasma samples. Thus, another 15 markers were selected independently in the plasma samples, yielding a sensitivity of 98% and a specificity of 100% (AUC 0.998) in the training cohort and a sensitivity of 81% and a specificity of 59% (AUC 0.797) in the validation cohort. Analysis based on the methylation haplotype was also conducted, identifying 1,222 differentially methylated regions in tissue samples (FDR<0.05) that were enriched in DNA replication-related pathways. Correlations between DNA methylation and clinical characteristics revealed significant differential methylation patterns between smokers and nonsmokers (FDR<0.05) in both tissue and plasma. Interpretation: Both tissue and ctDNA methylation can potentially be used as biomarkers for the early diagnosis of lung cancer. Funding: National Natural Science Foundation of China (81871890, 91859203). Declaration of Interest: The authors declare no potential conflicts of interest. Ethical Approval: The clinical protocol was approved by the Ethics Committee of West China Medical Center, and written informed consent was provided by all participants in this research.