Epigenetic profiling of CDH1 and NISCH promoter methylation in plasma-derived cell-free DNA for potential diagnosis of lung cancer

Abstract

Background: DNA methylation is an epigenetic phenomenon in which DNA methyltransferases (DNMTs) add methyl groups at CpG islands of gene promoter regions, and abnormalities in methylation alter gene expression without changing the DNA sequence. The CDH1 and NISCH genes encode tumor suppressor proteins whose promoter hypermethylation has been implicated in lung carcinogenesis. Blood-derived circulating cell-free DNA (cfDNA) offers a minimally invasive substrate for detecting such epigenetic alterations. Methods: Blood samples were collected from 40 newly diagnosed lung cancer patients (24 NSCLC, 16 SCLC) and 40 age matched healthy controls after ethical approval (IEC: 140th ECM 2A/P5). cfDNA was extracted from plasma, bisulfite-converted, and analyzed for CDH1 and NISCH promoter methylation using methylation-specific PCR (MSP). Statistical analysis was performed using the chi-square test (GraphPad Prism 5.0; P < 0.05). Results: CDH1 and NISCH promoter methylation frequencies in lung cancer patients were 50% and 47.5%, respectively, compared to 22.5% and 35% in healthy controls. No significant association were identified between CDH1 and NISCH promoter methylation and evaluated demographic characteristics of lung cancer patients. CDH1 represented moderate diagnostic performance AUC ≈ 0.64 with higher specificity (77.5%). Conclusion: CDH1 and NISCH promoter methylation in blood-derived cfDNA highlights the innovation of non-invasive approach alternative to tissue biopsy, with potential to complement existing screening modalities such as low-dose CT by improving molecular level detection and reducing false-positive rates. However, larger scale validation required before clinical translation.