DNA Methylation of COX‐2, IFN‐γ, TNF‐α, and LINE‐1 in Clinically Stable Periodontal Tissues Following Periodontal Therapy

ABSTRACT Background Epigenetic modifications such as DNA methylation play a crucial role in the regulation of gene expression in inflammatory diseases, including periodontitis. While previous studies have examined methylation changes during active disease or shortly after treatment, little is known about the epigenetic landscape of periodontal tissues that have remained clinically stable over the long term after Supportive Periodontal Therapy (SPT). Methods We collected gingival tissue samples from 40 individuals, including 20 with a history of periodontitis currently under long‐term SPT and 20 periodontally healthy controls. DNA methylation levels of LINE‐1 (a marker of global methylation) and inflammation‐related genes COX‐2 ( PTGS2 ), IFN‐γ ( IFNG ), and TNF‐α ( TNF ) were analyzed using bisulfite pyrosequencing. Results The LINE‐1 methylation percentage was significantly higher in the periodontitis group than in the healthy group (66.5% ± 2.0 vs. 63.9% ± 4.0; p = 0.03). However, this significance was lost after adjusting for age and gender. No significant differences were observed between groups for COX‐2 , IFN‐γ , or TNF‐α . Genomic context analysis using the Encyclopedia of DNA Elements annotations revealed that the CpG sites analyzed for PTGS2 , IFNG , and TNF are in distal regulatory regions enriched with enhancer‐like elements, histone modifications, and predicted NFKB1 binding motifs. Conclusions These findings suggest that LINE‐1 methylation in clinically stable gingival tissues may reflect long‐term epigenetic memory from previous chronic inflammation. Motif‐level analysis highlighted potential regulatory input from NFKB1 at the three loci ( PTGS2 , IFNG , and TNF ). Notably, no significant epigenetic differences were observed in the inflammation‐related genes COX‐2 , IFN‐γ , and TNF‐α , suggesting that periodontal disease can be effectively treated and that certain inflammatory markers may return to levels comparable to those seen in individuals who have never had the disease. These results highlight the importance of examining DNA methylation dynamics not only during active disease but also during long‐term remission.