Genome-wide DNA methylation profiling identifies ionizing radiation-induced hypomethylated genes with clinical significance in oral squamous cell carcinoma

ABSTRACT: Background: The epigenetic consequences of ionizing radiation (IR), particularly its effects on DNA methylation, remain poorly understood. Here, we investigated whether IR induces genome-wide DNA methylation changes in OSCC cells and examined whether IR-induced hypomethylated candidate genes correspond to epigenetically silenced loci in oral cancer patient tumors, and whether their methylation status influences clinical outcomes. Methods: OSCC cells were treated with IR or 5-aza-2'-deoxycytidine (5-aza-dC) and subjected to genome-wide DNA methylation profiling using the Illumina HumanMethylationEPIC BeadChip. Candidate hypomethylated genes were validated by qRT-PCR and quantitative methylation-specific PCR (qMSP). DNMT1 promoter occupancy was assessed by chromatin immunoprecipitation (ChIP). Clinical relevance was evaluated using the TCGA-HNSCC dataset. Results: IR significantly reduced DNMT1 and DNMT3b protein levels in OSCC cells, indicating IR-induced global DNA hypomethylation. Genome-wide profiling identified three candidate genes, MLPH, BMP4, and MYO5A, showing concordant promoter demethylation and transcriptional upregulation following IR treatment, with ChIP analysis confirming reduced DNMT1 occupancy at their promoters. Importantly, TCGA-HNSCC analysis revealed that BMP4 and MLPH are hypermethylated and transcriptionally silenced in untreated HNSCC tumors, a finding mechanistically complementary to our experimental data, suggesting that IR reverses tumor-associated epigenetic silencing through DNMT1-mediated passive demethylation. Consistently, BMP4 hypermethylation was associated with poor overall survival, and BMP4-hypermethylated patients receiving radiotherapy survived longer than those receiving chemotherapy. Conclusions: This study provides the first evidence that IR induces genome-wide DNA hypomethylation in OSCC through DNMT1 and DNMT3b downregulation, reactivating epigenetically silenced genes including MLPH, BMP4, and MYO5A. These findings suggest that IR-induced epigenetic reactivation of tumor-silenced genes may represent a clinically meaningful mechanism of radiotherapy response, and that BMP4 methylation status may serve as a potential predictive biomarker in oral cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE335152 | GEO | 2026/07/10

REPOSITORIES: GEO