Methylation-sensitive restriction endonuclease-based amplification assay for detecting DNA methylation in colorectal cancer: a cross-sectional study

Abstract Background This study evaluates the clinical utility of combined SDC2 and ADHFE1 methylation analysis for colorectal cancer (CRC) detection using a methylation-sensitive restriction endonuclease (MSRE)-based assay. Methods Leveraging the specificity of MSRE, we developed a streamlined amplification assay that directly analyzes methylation status of SDC2 and ADHFE1 after mixing nucleic acids with PCR reagent. A cohort of 274 participants was stratified into six groups: CRC ( n = 117), advanced adenoma (AA, n = 22), polyps ( n = 30), intestinal disease control (IDC, n = 39), other gastrointestinal disease control (OGDC, n = 24), and healthy controls (HC, n = 42). SDC2 and ADHFE1 methylation levels in fecal samples were assessed, and diagnostic performance was evaluated using receiver operating characteristic (ROC) curve analysis. Results The CRC group exhibited significantly higher SDC2 and ADHFE1 methylation positivity rates compared to all comparator groups, including AA, polyps, IDC, OGDC, and HC ( P < 0.01). No significant differences were observed in the methylation positivity rates of SDC2, ADHFE1 or their combination across different TNM stages and levels of tumor differentiation. Joint SDC2 and ADHFE1 analysis increased sensitivity for CRC detection to 82.9% (vs. 64.1% and 65.0% for ADHFE1 and SDC2) with an AUC of 0.865 (95% CI: 0.817–0.913). For early-stage CRC (stages I + II), the dual-gene panel achieved an AUC of 0.872. However, the ability to discriminate between AA and HC (AUC: 0.693) or IDC (AUC: 0.615) remained limited in our dual-gene assay. Conclusions The combined SDC2/ADHFE1 MSRE-based assay significantly improves diagnostic sensitivity for CRC, demonstrating superior differentiation of CRC from benign intestinal pathologies and precancerous lesions (AA and polyps). This non-invasive approach shows promise as a supplementary tool for CRC screening.