Impact of rs7528684 (-169T/C) on FCRL3, FOXP3, IL-35 Gene Expression and RF correlation: Insights into Rheumatoid Arthritis Pathogenesis

Background Fc Receptor-Like Protein 3 ( FCRL3 ) gene encodes for transmembrane receptor, that predominantly expressed on the surface of the Regulatory T cells (Tregs). The receptor owns two crucial motifs in its cytoplasmic domain, which downregulates the signal transduction of T - cell Receptor (TCR) mediated Tregs activation and proliferation. Single Nucleotide Polymorphism (SNP) in FCRL3 gene (rs7528684 -169 T/C) is hypothesised to enhance its expression, that leads to the loss of self-tolerance and dysfunction of Tregs. This, in turn, induces rapid proliferation of autoreactive T cells and other immune cells, exacerbating the progression of Rheumatoid Arthritis (RA) and other autoimmune diseases. Methods In the current study, we screened the FCRL3 SNP rs7528684 at -169 (T/C) position of the gene using High-Resolution Melting Analysis (HRMA) and confirmed the findings with Sanger sequencing technique to predict its link with RA in the Indian ethnicity. We further analysed the impact of SNP rs7528684 on FCRL3 , Fork head Box Protein 3 ( FOXP3) , and Interleukin − 35 ( IL-35 ) gene expression. Furthermore, we also evaluated the inflammatory biomarkers Rheumatoid Factor (RF) and C-Reactive Protein (CRP) in RA patients. Results It was observed that the FCRL3 SNP rs7528684 with C/C genotype significantly increased ( p <  0.0005) RA risk in the Indian ethnicity compared to T/T and C/T genotypes (Odd Ratio (OR) = 2.63; 95% Confidence Interval (C.I) = 1.78 to 3.86 and Relative Risk (RR) = 1.82). Moreover, the C allele frequency was significantly higher in the RA group (58.6%). Similarly, RA samples carrying C/C genotype exhibited significantly higher FCRL3 mRNA expression levels than controls ( p <  0.0072). Additionally, a downregulation of FOXP3 and IL-35 mRNA expression was observed in RA patients carrying C/C genotype. The results also exhibited a significant link between C/C genotype and RF-positive RA cases. Conclusion In summary, our findings suggest that the C/C genotype of FCRL3 SNP rs7528684 was strongly associated with RA in the Indian ethnicity. This genotype was characterised with positive RF, upregulated FCRL3 , and downregulated FOXP3 and IL-35 , a key anti-inflammatory cytokine.