Integrated m6A methylome and transcriptome profiling of mRNAs and lncRNAs in nasal mucosal epithelial cells of allergic rhinitis patients undergoing allergen-specific immunotherapy

Allergic rhinitis (AR) affects 10–25% of the global population, with nasal epithelial cell (NEC) dysfunction acting as a central driver of its pathogenesis. Allergen-specific immunotherapy (AIT) is the sole disease-modifying treatment for AR; however, its optimization is hindered by the lack of validated predictive biomarkers. N6-methyladenosine (m6A) is a pivotal epitranscriptomic regulator of immune and epithelial homeostasis. This study aims to delineate the m6A modification landscape in NECs during AIT to identify candidate genes associated with clinical efficacy and elucidate the underlying molecular mechanisms. We performed methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) on NECs from house dust mite (HDM)-sensitized AR patients who completed a 3-year AIT course and severity-matched non-AIT controls. Bioinformatics analyses, including Gene Set Enrichment Analysis (GSEA), were conducted to explore biological functions and signaling pathways. Key differentially methylated and expressed mRNAs and lncRNAs were validated using qRT-PCR and MeRIP-qPCR in an independent cohort (n = 12). Clinical relevance was assessed via correlation with the Total Nasal Symptom Score (TNSS). MeRIP-Seq revealed distinct m6A topographies, identifying 1,455 hypermethylated and 4,636 hypomethylated mRNAs, alongside 267 hypermethylated and 799 hypomethylated lncRNAs in the AIT group. Integrated multi-omics analysis and GSEA demonstrated that AIT significantly downregulates pro-inflammatory cascades (e.g., PI3K-Akt, MAPK, and Ras signaling) while upregulating pathways related to cell adhesion and apoptotic regulation. We identified and validated four key mRNAs (KANK2, DBI, IL18, and TNFRSF10A) exhibiting inverse correlations between m6A modification and gene expression, which also correlated with the patients’ TNSS. Furthermore, 28.7% of differentially m6A-methylated lncRNAs were chromatin-associated. Notably, within this subset, the m6A methylation level of LUCAT1 was positively correlated with the patients’ TNSS, suggesting its potential role in epigenetic regulation during AIT. This study delineates the m6A epitranscriptomic landscape in NECs following AIT, revealing its critical role in orchestrating epithelial barrier restoration and immune microenvironment homeostasis. The identified candidate mRNAs (KANK2, DBI, IL18, TNFRSF10A) and chromatin-associated lncRNAs (e.g., LUCAT1) offer novel mechanistic insights into epitranscriptomic remodeling and serve as promising molecular candidates for future therapeutic or diagnostic development in precision AR management.