Bisulfite-free detection of DNA methylation in early-stage lung cancer with a multiplex SERS immunoassay

DNA methylation is a promising biomarker for early cancer detection; however, traditional detection methods require bisulfite treatment and nucleic acid amplification, which are costly and impractical for point-of-care use. We propose a facile method that leverages immunoassays and surface-enhanced Raman scattering (SERS) readouts for the multiplex, sensitive, and portable detection of lung cancer-related DNA methylation biomarkers. This approach employs 5-methylcytosine antibody-modified magnetic probes to enrich methylated DNA sequences and uses core–shell nanoparticles with Probe DNA as SERS nanotags for multiplex detection, eliminating the need for bisulfite treatment and nucleic acid amplification. The multiplex SERS immunoassay detects synthetic methylated SHOX2 and RASSF1A with detection limits of 0.52 pM and 0.66 pM, respectively. It shows a strong correlation with quantitative PCR results in analyzing methylated SHOX2 and RASSF1A from cell lines and formalin-fixed paraffin-embedded tissue samples (n = 35). Additionally, the random forest analysis based on methylated SHOX2 and RASSF1A expression distinguishes lung cancer from benign lung diseases with a clinical sensitivity of 96 %, specificity of 90 %, and an AUC value of 0.972. This method offers a significant advancement for DNA methylation research and clinical applications.