In this study, we performed the first PWAS by integrating the largest up-to-date RA GWAS and human plasma pQTL data to identify candidate proteins associated with RA pathogenesis and find potential therapeutic targets for RA treatment. Collectively, 21 genes were identified whose genetically regulated protein abundances were significantly associated with RA risk. After causal effect inference, 10 out of 21 genes were potentially causal and prioritized as candidate RA genes. Of note, among the 10 causal genes, six (OLFML3, PAM, ICOSLG, FCRL3, ERAP2, IL6R) also show evidence of association with RA at transcriptional level, reflecting consistent findings at the mRNA and protein levels. The rest four causal genes, FCGR3B, CCL21, FCGR3A, FCGR2A, as the well-known risk genes and drug targets for RA, were only identified by the PWAS alone, highlighting the importance and necessity of integrating proteomes with GWAS. These high-confidence risk genes may serve as promising targets for further mechanistic investigations and drug development.
Of note, among the 10 causal PWAS genes, three genes (ICOSLG, ERAP2, FCRL3) were not nominated by the original GWAS, thus were regarded as novel candidate genes for RA, underscoring the effectiveness of PWAS in identifying risk genes for RA. The gene FCRL3 encodes the one of several Fc receptor-like glycoproteins, a member of the immunoglobulin receptor superfamily, which possesses tyrosine-based immunoregulatory function. According to our results of TWAS and single-cell transcriptome, FCRL3 were significant in lymphocytes, especially high expressed in FOXP3+ Tregs cell of synovium from RA patients. Studies have showed that regulatory T-cells expressing FCRL3 exhibited a memory phenotype and high levels of PD-1, thus reducing capacity to suppress the proliferation of effector T cells, which contribute to the progression of autoimmunity[41, 42]. In addition, FCRL3 has been proved to enhances activation of NF-kappa-B and MAPK signaling pathways in TLR9 stimulated B-cells, ultimately promoting proliferation, activation, and survival of B cells[43]. Gene ICOSLG encodes ligand for the T-cell-specific cell surface receptor ICOS, which has been proved to not only co-stimulate the T cells proliferation and cytokine secretion, but also induce B cells proliferation and differentiation into plasma cells[44]. Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a key enzyme that generate antigenic epitopes, which bind to major histocompatibility complex class I (MHC-I)[45]. A recent study has indicated that ERAP2 inhibits the Hedgehog signaling pathway and upregulates the expression of NLRP3, cleaved Caspase-1, and Gasdermin D to promote pyroptosis in CD4+ T cells[46]. These findings provided the genetic and biological evidences that these novel PWAS genes are more likely functional associated with RA pathogenesis, which also emphasized the significance of linking genetic factors to RA etiology via specific proteins.
Exploring potential therapeutic targets is particularly vital for RA treatment, since some individuals do not respond adequately to currently pharmacologic therapies[2]. The druggability exploration analysis observed 120 drug-gene interactions involving in 7 genes, including several drugs have been commonly used as first-line treatment for rheumatoid arthritis, such as methotrexate (targeting FCGR3B), tocilizumab (targeting IL6R), and indomethacin (targeting FCGR3A), demonstrating the effectiveness of PWAS genes in exploration of novel drugs for RA. Notably, AMG-557, a human antibody against T cell co-stimulator ligand, were found closely interacted with novel PWAS gene ICOSLG. In a randomized, double-blind, placebo-controlled study, AMG-557 has showed safety and potential efficacy in subjects with SLE accompanied by arthritis[47], which supports further studies of AMG 557 as a potential therapeutic for autoimmune diseases. Furthermore, six drugs or compounds were identified to interacted with PWAS novel gene ERAP2, including scopoletin, tosedostat, and esculetin. Scopoletin and tosedostat is a coumarin synthesized by diverse medicinal and edible plants, which possesses promising medicinal properties, including anti-bacterial, anti-oxidative, anti-inflammatory, and anti-neoplastic activity. Resent study has identified scopoletin as major anti-rheumatic components that may bind and inhibit tyrosine kinases on fibroblast-like synoviocytes to block NF-κB signaling, and thus combat the progression of rheumatoid arthritis[48]. Analogously, esculetin treatment could suppress NF-κB and MPAK pathway activation, and inflammatory cytokine production, which are the main causes of joint deterioration in RA[49]. Further pharmacological experiments and clinical trials are required to confirm the clinical safety and efficacy of these drugs in RA treatment.
Our study possesses several strengths. Primarily, we performed the first PWAS for RA using the largest and most comprehensive reference human proteomes integrated with the latest GWAS summary statistics of RA. After causal effect inference using MR and COLOC, 10 genes were prioritized as candidate causal genes whose proteomic abundance was associated with RA, which reduced the false-positive of our study. Furthermore, we spotlighted three potential novel candidate genes for RA, presenting prospective avenues for further mechanistic investigations and drug development of RA. Additionally, targeting PWAS genes, we identified several drugs that possesses superior anti-inflammatory and anti-rheumatic activity in autoimmune diseases, which could be serve as the potential therapeutics for RA.
Admittedly, the results of this study should be carefully interpreted in conjunction with its limitations. First, though over 4,000 proteins or protein complexes were examined in the present study, it does not provide coverage for the entire plasma proteome. More comprehensive and larger proteomic datasets will be required in the future to estimate the genetic effects on protein abundance of the rest proteins. Second, owing to the absence of proteomes in other tissues, the present PWAS were only conducted using plasma proteome as reference. Assessing the role of genetically regulated protein in other tissues, especially in synovium, will provide more insight into RA pathogenesis. Third, the present findings were restricted to European participants to avoid population stratification confounding, which limits the generalizability of our results. Further expansion of the scale and diversity of PWAS studies can help with more precise estimates and enable its broader applications. Despite these limitations, PWAS genes are key to understand disease etiology, facilitate biological interpretation of GWAS results, and prioritize follow-up functional studies.
In summary, using PWAS, we identified ten causal genes whose genetically regulated protein abundances were significantly associated with RA risk, including three novel genes (ICOSLG, FCRL3, ERAP2). Our results illuminated the causal pathways and potential drug of these PWAS genes, which highlight promising targets for future mechanistic and therapeutic studies to find effective treatments for RA.