Comprehensive regulatory network construction highlights lncRNA-miRNA-mRNA-TF interactions and key molecular drivers...

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent inflammation and progressive joint damage. Although numerous molecular contributors have been reported, the integrated regulatory architecture linking coding and non-coding transcripts remains incompletely defined. This study aimed to construct a multilayer lncRNA-miRNA-mRNA-transcription factor (TF) network to prioritize candidate regulators associated with RA. Publicly available RNA-sequencing datasets from RA and control samples were retrieved from the NCBI Sequence Read Archive. Differential expression analysis was performed using DESeq2. High-confidence miRNA-mRNA interactions were obtained from miRDip, miRNA-lncRNA associations from miRNet, and TF annotations from AnimalTFDB. Functional enrichment analyses were conducted to identify overrepresented biological themes. Network topology and module structure were evaluated in Cytoscape using CytoHubba and MCODE. Integration of interaction datasets identified 179 mRNAs targeted by 93 miRNAs, of which 90 miRNAs were connected to 404 annotated lncRNAs. Twenty-five TFs were incorporated into the regulatory framework. Degree-based analysis highlighted QKI, hsa-miR-497-5p, and KCNQ1OT1 as the most connected nodes within their respective categories. Module detection revealed five densely interconnected sub-networks, indicating coordinated regulatory organization. Several prioritized elements have previously been implicated in immune or inflammatory regulation, supporting the biological relevance of the network. This integrative analysis delineates a comprehensive regulatory landscape of RA and provides a ranked set of candidate molecules for future experimental validation. Among these, CCDC6 was identified as a downregulated gene positioned within a highly connected module and linked to multiple hub miRNAs and lncRNAs, suggesting potential functional importance in RA pathobiology.