Deciphering the pathogenicity of PADI4 missense variant L117M in rheumatoid arthritis: An integrated in silico and gene expression study.

Rheumatoid Arthritis (RA) is a complex autoimmune disorder characterized by chronic joint inflammation and systemic immune dysfunction. Its etiology involves genetic, environmental, and immunological factors. Among the genetic contributors, single nucleotide polymorphisms (SNPs) in the PADI4 gene encoding peptidylarginine deiminase type 4 have gained prominence. PADI4 mediates citrullination, a post-translational modification linked to RA. The missense mutation rs1748033 has been associated with increased RA susceptibility. To investigate the pathogenic role of rs1748033, an integrated computational and experimental strategy was adopted. Gene-disease association analysis was first performed using DisGeNET and Open Targets Genetics to identify nonsynonymous SNPs in PADI4. Further assessments were conducted using GeneCards, gnomAD, and Ensembl databases. PredictSNP, integrating nine algorithms, was used to predict functional effects of the identified variants. To assess structural and functional impacts of rs1748033 (L117M), molecular dynamics simulations (MDS) and PCA-based free energy landscape (FEL) analyses were conducted. Comparative evaluation of wild-type and mutant (L117M) PADI4 structures revealed notable conformational changes. Finally, real-time quantitative PCR (RT-qPCR) was used to assess PADI4 expression in RA patient samples, revealing high expression in both WT and mutant forms. This integrative study highlights the functional relevance of rs1748033, reinforcing PADI4's role as a potential therapeutic target in RA.