Integrated Methylome–Transcriptome Analysis Reveals Epigenomic Remodeling and Rho GTPase –Linked Immune–Epithelial Crosstalk in Atopic Dermatitis

Background Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by immune dysregulation and epithelial barrier dysfunction. Although transcriptional changes in AD skin are increasingly well characterized, DNA methylation patterns remain less well understood. Methods Here, we present an integrated analysis of matched DNA methylomes, transcriptomes, and microbiomes from lesional ( n = 40), adjacent non‐lesional ( n = 38), and healthy control ( n = 40) skin, using complementary cell‐type‐adjusted models. Results We identified thousands of differentially methylated regions (DMRs) across all pairwise contrasts (lesional vs. healthy: n = 13,514; lesional vs. non‐lesional: n = 4591; non‐lesional vs. healthy: n = 1716), including both hyper‐ and hypo‐methylated regions with balanced effect sizes. A core subset of DMRs persisted after methylation‐based adjustment, whereas the extensive lesional vs. non‐lesional set was largely composition‐driven. Integration with transcriptomic co‐expression networks linked DMRs to immune–epithelial modules, and 225 DMR–gene pairs showed significant anti‐correlation (FDR < 0.05). Lesional skin with dominant Staphylococcus aureus colonization differed at 92 DMRs compared with absent‐colonized skin, of which 70 also overlapped with local severity. Pathway analyses consistently highlighted Rho GTPase and actin–junctional programs across analytic layers, suggesting that Rho GTPase signaling is a central integrator of immune, epithelial, and microbial interactions in AD. Conclusions Our study underscores the importance of epigenomic remodeling in AD and highlights potential avenues for precision intervention in chronic inflammatory skin disease.