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

•Multiplexed SERS assay for methylated DNA marker detection without any pretreament.•SERS results show good correlation with qPCR results in analyzing clinical samples.•Multiplexed SERS assay combined with random forest identifies early-stage lung cancer. DNA methylation is a promising biomarker for...

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Bibliographic Details
Published in:Chemical engineering journal (Lausanne, Switzerland : 1996) Switzerland : 1996), 2025-01, Vol.503, Article 158491
Main Authors: Lu, Dechan, Chen, Yanping, Ke, Longfeng, Huang, Zufang, Lu, Yudong, Wang, Jing
Format: Article
Language:English
Subjects:
Biosensor
DNA methylation
Lung cancer
Multiplex assay
SERS immunoassay
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Summary:•Multiplexed SERS assay for methylated DNA marker detection without any pretreament.•SERS results show good correlation with qPCR results in analyzing clinical samples.•Multiplexed SERS assay combined with random forest identifies early-stage lung cancer. 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.
ISSN:1385-8947
DOI:10.1016/j.cej.2024.158491