Integrative multi-omics analyses identify PKD1 and SLC2A4 as genetically supported glycolysis-related candidate genes for rheumatoid arthritis

Xinyu A^1,2Pengfei Xin³Lin Zheng⁴Bo Xu⁴Jianye Wang^1,2Songtao Sun⁴Jun Xie⁴Chenxin Gao⁴Peijun Pan⁴Guowei Qiu⁴Lang Jin⁴Jun Shen⁴Xirui Xu⁴Yiwei Cheng^1,2Shaoqiang Pei^1,2Lei Ran^2,4*Yanqin Bian^2,4*Lianbo Xiao^2,4*

• ¹Shanghai University of Traditional Chinese Medicine, Shanghai, China
• ²The Research Institute for Joint Diseases, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
• ³Jiangxi University of Traditional Chinese Medicine Affiliated Hospital, Nanchang, China
• ⁴Shanghai Guanghua Hospital of Integrative Medicine, Shanghai, China

Glycolytic reprogramming has been implicated in rheumatoid arthritis (RA) pathogenesis, yet the underlying causal genes and epigenetic mechanisms remain unclear. This study aimed to systematically identify glycolysis-related genes and their methylation-regulated expression that may causally influence RA susceptibility. We conducted a multi-omics Mendelian randomization (MR) analysis integrating genome-wide association study (GWAS) summary statistics for RA (FinnGen, UK Biobank, GCST90129453) with quantitative trait loci (QTLs) for blood-derived methylation (mQTL), expression (eQTL), and protein abundance (pQTL). Summary-data-based Mendelian randomization (SMR) and colocalization analyses were used to identify causal molecular signatures linking DNA methylation, gene expression, and protein abundance with RA risk. Replication was conducted in independent RA cohorts. Our SMR analysis identified 129 CpG sites (75 genes), 28 transcripts, and 9 proteins significantly associated with RA risk. Among these, seven glycolytic genes—PKD1, SLC2A4, ALAS1, ALDH7A1, LRFN3, PFKFB2, and PYGB—exhibited consistent causal associations across methylation, expression, and GWAS datasets. Notably, hypomethylation at cg07036112 (PKD1; OR=0.68, 95% CI: 0.59 – 0.78) and cg06891043 (SLC2A4; OR=0.92, 95% CI: 0.89 – 0.96) significantly increased respective gene expression and RA susceptibility. Colocalization analyses confirmed shared causal variants at these loci (PP.H4>0.5). Additional signals included cg13241645 (ALAS1; OR=0.72, 95% CI: 0.65–0.80) and cg01380361 (PFKFB2; OR=1.33, 95% CI: 1.17–1.51), reinforcing epigenetic control of RA-related glycolysis. In an independent whole-blood cohort (30 RA patients and 30 healthy controls), qPCR confirmed increased PKD1 and SLC2A4 mRNA expression in RA. Our integrated multi-omics analysis identified PKD1 and SLC2A4 as robust causal candidate genes for RA, regulated by epigenetic modifications at cg07036112 and cg06891043, respectively. These findings highlight methylation-mediated gene expression changes supporting a role for methylation-linked transcriptional changes in glycolysis-related pathways implicated in RA, offering novel insights into disease mechanisms and identifying promising biomarkers and therapeutic targets.