Comparative diagnostic value of a blood-based three-gene DNA methylation assay and a seven-autoantibody panel for
Dong Rui1, Xunsi Liang2, Min Yi3
1Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, China.
Background:
Low-dose CT has increased pulmonary nodule detection, but noninvasively distinguishing benign from malignant nodules or early lung cancer remains difficult. Blood-based DNA methylation and tumour-associated autoantibody assays may complement imaging.
Methods:
This combined prospective and retrospective study evaluated two blood-based strategies. The prospective methylation cohort (141 participants; May 2024-April 2026) comprised 91 malignant, 22 benign-nodule, and 28 high-risk individuals, with plasma SHOX2, RASSF1A, and PTGER4 methylation measured by multiplex fluorescence PCR. The retrospective cohort (446 participants; January 2023-April 2025) comprised 193 malignant, 118 benign-nodule, and 135 high-risk individuals, with serum conventional markers (CYFRA21-1, CEA, NSE, SCC) and seven autoantibodies (p53, GAGE7, PGP9.5, CAGE, MAGEA1, SOX2, GBU4-5) analysed. Performance was assessed by positive rate, sensitivity, specificity, AUC, and Youden index.
Results:
Positive rates in the malignant versus benign versus high-risk groups were 83.52% vs 45.45% vs 10.71% for the three-methylation panel and 63.20% vs 16.95% vs 10.37% for the seven-autoantibody panel (both P < 0.05). In early-stage (I-II) disease, the methylation panel had the highest positive rate (83.87%), exceeding the autoantibody panel (67.53%) and conventional markers (37.66%; P < 0.05), whereas conventional markers were highest in advanced (III-IV) disease (93.97%). Early-stage AUCs were 0.789 for methylation (sensitivity 83.87%, specificity 74.00%), 0.771 for autoantibodies (sensitivity 67.53%, specificity 86.56%), and 0.570 for conventional markers, rising to 0.851 in advanced disease. Combining the methylation and autoantibody panels raised early-stage sensitivity to 94.75% (AUC 0.794). As additional clinically oriented validation, the methylation panel yielded an overall positive predictive value of 85.39%, negative predictive value of 71.15%, accuracy of 80.14%, positive likelihood ratio of 3.21, and negative likelihood ratio of 0.22 for malignant disease versus all controls.
Conclusions:
Both panels aided differentiation of malignant from benign pulmonary nodules; methylation gave the strongest early-stage sensitivity and autoantibodies higher specificity, both outperforming conventional markers. Combined testing may improve sensitivity but requires multicentre validation.
