DNA methylation changes following rapid maxillary expansion in children

Rapid maxillary expansion (RME) is a widely used orthodontic intervention for correcting transverse maxillary deficiencies. By mechanically separating the midpalatal suture, RME improves occlusal relationships and induces tissue repair processes similar to fracture healing. Inflammation and bone regeneration following fracture are regulated by epigenetic mechanisms, such as DNA methylation. However, the effects of RME-induced mechanical stimulation on epigenetic dynamics in humans remain unclear. We evaluated genome-wide DNA methylation changes in saliva associated with RME treatment. Twenty patients undergoing orthodontic treatment with RME and four untreated controls were enrolled. Saliva samples were collected before (T0) and after treatment (T1), and genome-wide DNA methylation profiling was performed using the Illumina Infinium HumanMethylationEPIC v2.0 BeadChip. Differential methylation analysis was conducted using linear models accounting for within-subject correlations. In the RME group, 164 CpG sites were differentially methylated between T0 and T1 (false discovery rate < 0.05), whereas no significant changes were observed in controls. The differentially methylated CpG sites were annotated to genes associated with biological responses to RME, including inflammatory pathways and metabolic processes. RME may be associated with measurable changes in salivary DNA methylation, suggesting epigenetic responses detectable in saliva and providing a basis for future mechanistic investigations.