Deciphering the LncRNA-Mediated Gene Regulatory Network and Pathogenic Cascades in Thyroid-Associated Ophthalmopathy

Objective To identify key genes and long noncoding RNAs (lncRNAs) involved in the pathogenesis of thyroid-associated ophthalmopathy (TAO) and investigate the expression patterns of the IL-17 and IL-23, and their downstream signaling pathways in TAO. Methods We conducted transcriptome sequencing (RNA-seq) to measure the expression difference of lncRNAs and mRNAs among healthy controls (control), active TAO patients (active TAO), and inactive TAO patients (quiescent TAO) samples by bioinformatics tools, including Lasso regression, random forest (RF), and weighted gene co-expression network analysis (WGCNA). Finally, enzyme-linked immunosorbent assay (ELISA) and reverse transcription and quantitative polymerase chain reaction (RT-qPCR) were used to measure the levels of key proteins in the three groups. Results ELISA revealed the elevated expression of IL-23 and IL-17A in the active TAO group compared to the control and inactive TAO groups. RT-qPCR confirmed differential expression of inflammatory cytokines (IL-17A, IL-17F, CCR6, IL-23A, IL-26), with higher levels in active TAO group. RNA-seq analyses identified 256 differentially expressed genes (DEGs) in the active group that were enriched in immune and inflammatory response pathways. Lasso and RF analyses identified three core genes ( ADRB1, MYH15, LEPR ) as potential peripheral blood biomarkers for TAO. WGCNA highlighted the module containing six immune-related genes ( CR2, LTBP3, TRBV5-1, TRBV24-1, TRAV12-1, TRAV12-3 ) with higher expression level in active TAO group. We also identified 77 Differentially Expressed lncRNAs (DElncRNAs) between Active TAO vs. control, and 112 DElncRNAs between Active TAO vs. quiescent TAO. Co-expression analysis revealed 72 lncRNAs interacting with 128 DEGs. Notable lncRNAs (LEF1-AS1, LINC01259, LMNTD2-AS1, and ENSG00000288960) may enhance transcriptional activity of immune-related genes in active TAO group. Conclusion The IL-17/IL-23 pathway and key genes (e.g., ADRB1, MYH15, LEPR ) play critical roles in TAO pathogenesis. The identified lncRNAs and immune-related genes may serve as biomarkers or therapeutic targets, particularly in active TAO stages.