O008

Friday, November 14th, 2025 16:53 – 17:01
Speaker Óscar Rapado-González

Genome-wide discovery and validation of novel DNA methylation markers for oral cancer detection using saliva

Objective: To develop a saliva-based DNA methylation signature for the early detection of OC.

Methods: Genome-wide discovery of DNA methylation markers was performed on DNA extracted from tissue (tumor and adjacent non-tumor mucosa) and saliva samples from 19 OC patients, as well as saliva from 15 healthy controls, using the Infinium Human Methylation 850K BeadChip. Following bioinformatic analysis, candidate promoter hypermethylation markers were selected for further validation by quantitative methylation-specific PCR (qMSP) in a large multicenter cohort of saliva samples, including 157 oral cancer patients, 28 individuals with oral potentially malignant disorders, and 112 healthy controls. The diagnostic performance of individual and combined DNA methylation markers was assessed using receiver operating characteristic (ROC) curve analysis.

Results: In the discovery phase, focusing on gene promoter regions, we identified 2,752 differentially methylated CpGs (DMCpGs) between tumor and adjacent non-tumor tissues, and 12,984 DMCpGs in tumor versus normal saliva. In the validation phase, significant promoter hypermethylation of seven genes was detected in saliva samples from OC patients compared with healthy controls (p < 0.0001), with individual AUROC values greater than 0.80. The combination of two hypermethylated CpGs yielded the best diagnostic performance for distinguishing OC (accuracy 88.85%, sensitivity 89.17%, specificity 88.39%) and early OC (accuracy 88.62%, sensitivity 87.27%, specificity 89.29%) from healthy controls. In addition, this two-gene methylation panel discriminated oral epithelial dysplasia/OC from non-disease oral conditions with an accuracy of 87.21%, sensitivity of 87.95%, and specificity of 86.26%.

Conclusion: We developed a novel, sensitive, saliva-based DNA methylation diagnostic assay as a promising tool for non-invasive screening and early detection of OC.