Nasopharyngeal swab transcriptomics identifies divergent molecular signatures in adenoid hypertrophy and allergic rhinitis comorbidity

Background: Adenoid hypertrophy (AH) frequently coexists with allergic rhinitis (AR) in children, yet the molecular mechanisms underlying this comorbidity remain unclear. Using nasopharyngeal swab-based transcriptomics-enabling inclusion of healthy pediatric controls previously precluded by ethical constraints-this study aimed to characterize the transcriptomic landscape of AH with and without AR and identify disease-specific molecular features. Methods: We performed RNA sequencing on nasopharyngeal swab samples from 24 pediatric subjects, including healthy controls (HC, n=6), children with AH (n=10), and children with AH accompanied by AR (AHAR, n=8). Weighted gene co-expression network analysis (WGCNA) was employed to identify disease-associated gene modules. Functional enrichment analysis, protein-protein interaction (PPI) network construction, and cellular deconvolution were performed to elucidate molecular mechanisms. Key findings were validated by qRT-PCR and multiplex immunohistochemistry in an independent cohort. Results: Differential expression analysis identified 276 DEGs in AH vs HC, 1,361 DEGs in AHAR vs HC, and 1,593 DEGs in AHAR vs AH. WGCNA revealed distinct modules: brown module correlated with AH, turquoise module with AR. The 168 AH-associated genes-derived from brown module and AH-associated DEGs intersection-were enriched in epithelial keratinization, IL-36 signaling, and antimicrobial peptide pathways, with SPRR family members identified as top hub genes by PPI analysis. In contrast, 854 AR-comorbidity-associated genes were predominantly enriched in ciliary assembly and motility pathways. Cellular deconvolution and multiplex immunohistochemistry consistently indicated AHAR-specific expansion of goblet cells and ciliated cells, absent in AH alone. Conclusions: This study suggests that AH is primarily characterized by epithelial barrier dysfunction and IL-36-associated innate immune activation. When AR co-occurs with AH, enhanced ciliogenesis and epithelial remodeling associated with type 2 inflammation are observed in addition to these features. This two-tier pathological model underscores the potential value of individualized therapeutic approaches tailored to distinct molecular profiles in pediatric upper airway disorders, though validation in larger cohorts including an isolated AR group would strengthen these conclusions.