DNA methylation features and diagnostic model establishment of MET amplification in lung adenocarcinoma

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Background: Accurate detection of MET amplification is essential for guiding targeted therapy in lung adenocarcinoma (LUAD). Conventional methods such as FISH are limited by tissue availability, and ctDNA-based liquid biopsy shows limited sensitivity for amplification detection. DNA methylation profiling offers a promising alternative. Objectives: To identify MET amplification-associated DNA methylation features and develop a diagnostic model for MET amplification detection in LUAD. Design: A retrospective cohort study. Methods: Targeted DNA methylation sequencing (Illumina TruSeq Methyl Capture EPIC) was performed on 38 LUAD tissue samples at our institution. MET amplification was defined based on NGS-derived copy number (CN) using two thresholds: CN3 and CN5. DNA methylation data from 443 LUAD cases in TCGA were integrated with the institutional cohort to identify high-confidence differentially methylated positions (DMPs). Random Forest models were constructed and validated internally and in the TCGA cohort. Subgroup analyses were performed by EGFR mutation status and sample type. GO and KEGG analyses were conducted for functional relevance. Results: A total of 20,661 (CN3) and 13,303 (CN5) DMPs were identified, of which 241 and 107, respectively, overlapped with TCGA-derived DMPs. The CN3-based model achieved AUCs of 0.92 (95% CI: 0.84-1.00) in the test cohort and 0.69 (95% CI: 0.64-0.74) in the TCGA cohort, whereas the CN5-based model yielded AUCs of 0.93 (95% CI: 0.81-1.00) and 0.77 (95% CI: 0.70-0.84), respectively. A simplified CN5-based model using the top five DMPs maintained comparable performance (AUC 0.89, 95% CI: 0.72-1.00). Diagnostic performance remained stable in EGFR-mutant patients and in biopsy specimens. Functional enrichment analyses indicated that DMPs were significantly involved in kinase regulation and MET downstream signaling pathways, including the PI3K-Akt signaling pathway. A hypermethylated MET amplification-associated DMP at Chr7:116367600 was consistently observed under both CN thresholds in the institutional cohort. Conclusion: This study identifies MET amplification-associated DNA methylation features in LUAD. The CN5-based diagnostic model demonstrated promising accuracy. These findings suggest a novel approach for predicting NGS-defined MET amplification and warrant further validation in larger cohorts and prospective liquid biopsy studies.

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