Integrative GWAS and Mendelian randomization study of rheumatoid arthritis based on the 2019 UK Biobank questionnaire

Rheumatoid arthritis (RA) is the most prevalent autoimmune inflammatory joint disorder worldwide. We aimed to identify the genetic variants contributing to RA and investigate the potential influence of related diseases on RA risk.

We performed genome-wide association studies (GWAS) on RA using the 2019 UK Biobank pain questionnaire. We conducted a primary GWAS (9,389 RA cases; 132,108 controls) and separate sex-stratified GWAS for females (4,832 cases; 75,184 controls) and males (4,557 cases; 56,924 controls). We incorporated 12 phenotypes from downstream analyses, such as genetic correlation analyses, transcriptome-wide association studies (TWAS), phenome-wide association studies (PheWAS), and Mendelian randomization (MR) studies to determine causal relationships with RA.

Two loci reached genome-wide significance in the primary GWAS. The top SNP, rs35139284 (p = 3.67 × 10^-25) in the HLA-DRB1 gene on chromosome 6, exhibited a robust replication. Another locus, harboring the top SNP rs539837 (p = 6.26 × 10^-9) near the LINC01680 gene on chromosome 1, also showed a significant association. In the female-specific GWAS, rs35139284 (p = 1.91 × 10^-22) remained the top signal, whereas the male-specific GWAS revealed a suggestive significance at rs9267989 (p = 5.28 × 10^-8) in TSBP1-AS1. TWAS and tissue specificity studies pointed to the spleen, lung, and small intestine as key tissues implicated in RA. PheWAS and MR analyses highlighted asthma and eosinophils associated with RA.

Our findings confirmed an RA locus at chromosome 6 and highlighted associations between RA and a spectrum of immune-related and inflammatory phenotypes. Further analyses may provide greater insights into the genetic architecture of RA. Key Points • Leveraging the 2019 UK Biobank pain questionnaire, our genome-wide association studies (GWAS) confirmed a risk locus on chromosome 6 associated with rheumatoid arthritis (RA). • Sex-stratified analyses revealed significant differences in RA susceptibility between males and females, paving the way for personalized therapeutic strategies by demonstrating sex-specific genetic risks. • Mendelian randomization underscored the associations of both asthma and eosinophils with RA while identifying key hub genes, thereby deepening our understanding of RA's underlying molecular mechanisms and suggesting potential targets for future interventions.