Investigation of Novel Therapeutic Targets for Rheumatoid Arthritis Through Human Plasma Proteome
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Sources of Plasma Proteins and RA
2.2. Pro-MR Analysis
2.3. Colocalization Analysis
2.4. Transcriptome-Wide Summary-Data-Based MR (SMR)
2.5. Reliability Stratification of Prioritized Proteins
2.6. Protein–Protein Interaction and Enrichment Analyses
2.7. Pleiotropy Assessment
2.8. Genetically Engineered Mouse Models
2.9. Cell-Type-Specific Expression Analysis
2.10. Druggability Evaluation
2.11. Phenome-Wide MR (Phe-MR) Analysis
2.12. Mediation Analysis
3. Results
3.1. Pro-MR Prioritized 32 Plasma Proteins for RA
3.2. Colocalization Analysis Supported Causations Between 14 Prioritized Proteins and RA
3.3. SMR Validated 18 Prioritized Proteins of RA from Transcriptive Perspective
3.4. Four Reliability Tiers of Prioritized Proteins
3.5. PPI Network and Enriched Pathways of Prioritized Proteins
3.6. Four Trans-Associated Proteins Exhibited Vertical or Horizontal Pleiotropy
3.7. Genetically Engineered Mouse Models of Prioritized Protein-Coding Genes
3.8. Cell-Type-Specific Expression of Prioritized Proteins in Synovium
3.9. Druggable Evidence for Nine Prioritized Proteins
3.10. Phe-MR Identified Potential Side Effects of Nine Prioritized Proteins
3.11. Six Prioritized Proteins Partially Mediate the Effects of Modifiable Factors on RA
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
RA | rheumatoid arthritis |
DMARD | disease-modifying antirheumatic drug |
SNP | single nucleotide polymorphism |
GWAS | genome-wide association study |
pQTL | protein quantitative trait locus |
MR | Mendelian randomization |
IVs | instrumental variables |
Pro-MR | proteome-wide Mendelian randomization |
LD | linkage disequilibrium |
PPH4 | posterior probability for hypothesis 4 |
SMR | summary-data-based Mendelian randomization |
eQTL | expression quantitative trait locus |
HEIDI | Heterogeneity in Dependent Instruments |
PPI | protein–protein interaction |
STRING | Search Tool for Recurring Instances of Neighboring Genes |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
MGI | Mouse Genomics Informatics |
scRNA-seq | single-cell RNA sequencing |
TTD | Therapeutic Target Database |
Phe-MR | phenome-wide Mendelian randomization |
MVMR | multivariate Mendelian randomization |
NFKB | nuclear factor kappa-B |
ECM | extracellular matrix |
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Protein Short Name a | Uniprot ID | Full Name | MR Meta-Analysis | Colocalization | SMR | Tier | |
---|---|---|---|---|---|---|---|
OR | p Value | ||||||
NFKBIE | O00221 | NF-kappa-B inhibitor epsilon | 0.747 | 3.560 × 10−17 | + | − | 2 |
CCL21 | O00585 | C-C motif chemokine 21 | 0.654 | 9.605 × 10−6 | − | − | 3 |
ICOSLG | O75144 | ICOS ligand | 1.095 | 1.286 × 10−5 | + | + | 1 |
ERBB2 | P04626 | Receptor tyrosine-protein kinase erbB-2 | 1.320 | 5.989 × 10−2 | − | + | 3 |
ALDH2 | P05091 | Aldehyde dehydrogenase, mitochondrial | 1.804 | 3.840 × 10−6 | + | + | 1 |
FCGR3A | P08637 | Low-affinity immunoglobulin gamma Fc region receptor III-A | 1.052 | 7.118 × 10−10 | − | + | 2 |
IL6R | P08887 | Interleukin-6 receptor subunit alpha | 0.958 | 2.113 × 10−8 | + | − | 2 |
CD28 | P10747 | T cell-specific surface glycoprotein CD28 | 0.795 | 5.446 × 10−6 | − | − | 3 |
FCGR2A | P12318 | Low-affinity immunoglobulin gamma Fc region receptor II-a | 0.955 | 2.933 × 10−9 | + | + | 1 |
PAM | P19021 | Peptidyl-glycine alpha-amidating monooxygenase | 1.054 | 4.011 × 10−1 | − | + | 3 |
TNFAIP3 | P21580 | Tumor necrosis factor alpha-induced protein 3 | 1.275 | 2.751 × 10−10 | − | + | 2 |
CD40 | P25942 | Tumor necrosis factor receptor superfamily member 5 | 1.174 (cis-pQTL) 1.191 (all pQTLs) | 7.047 × 10−4 (cis-pQTL) 1.007 × 10−12 (all pQTLs) | + | + | 1 |
FLT3 | P36888 | Receptor-type tyrosine-protein kinase FLT3 | 0.602 | 8.046 × 10−2 | − | + | 3 |
IFNGR2 | P38484 | Interferon gamma receptor 2 | 0.943 | 9.349 × 10−4 | + | + | 1 |
MFAP2 | P55001 | Microfibrillar-associated protein 2 | 1.172 | 2.050 × 10−9 | − | + | 2 |
BCL2L15 | Q5TBC7 | Bcl-2-like protein 15 | 1.290 | 1.829 × 10−1 | − | + | 3 |
SPRED2 | Q7Z698 | Sprouty-related, EVH1 domain-containing protein 2 | 0.474 | 7.533 × 10−3 | − | − | 3 |
HAPLN4 | Q86UW8 | Hyaluronan and proteoglycan link protein 4 | 1.478 | 4.386 × 10−2 | + | + | 1 |
SUGP1 | Q8IWZ8 | SURP and G-patch domain-containing protein 1 | 1.252 | 7.287 × 10−2 | + | + | 2 |
FCRL3 | Q96P31 | Fc receptor-like protein 3 | 1.055 | 1.256 × 10−8 | + | + | 1 |
CCL19 | Q99731 | C-C motif chemokine 19 | 0.618 | 3.105 × 10−6 | − | − | 3 |
OLFML3 | Q9NRN5 | Olfactomedin-like protein 3 | 1.230 | 3.293 × 10−1 | − | + | 3 |
PADI4 | Q9UM07 | Protein-arginine deiminase type-4 | 1.298 | 2.813 × 10−4 | + | + | 1 |
WASL | O00401 | Actin nucleation-promoting factor WASL | 4.424 | 2.875 × 10−4 | + | − | 2 |
CELF2 | O95319 | CUGBP Elav-like family member 2 | 0.565 | 2.405 × 10−1 | − | − | 4 |
H2AZ1 | P0C0S5 | Histone H2A.Z | 0.491 | 1.975 × 10−1 | − | − | 4 |
POLR2F | P61218 | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | 4.250 | 1.693 × 10−13 | + | − | 2 |
H2BC21 | Q16778 | Histone H2B type 2-E | 0.635 | 3.379 × 10−8 | − | − | 3 |
IGSF11 | Q5DX21 | Immunoglobulin superfamily member 11 | 2.812 | 1.081 × 10−7 | − | + | 2 |
H2AC25 | Q7L7L0 | Histone H2A type 3 | 0.646 | 1.039 × 10−1 | − | − | 4 |
H2BC26 | Q8N257 | Histone H2B type 3-B | 0.654 | 3.602 × 10−6 | − | − | 3 |
ADPGK | Q9BRR6 | ADP-dependent glucokinase | 4.840 | 3.853 × 10−14 | + | − | 2 |
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Wang, H.; Huang, C.; Huang, K.; Wu, T.; Liu, H. Investigation of Novel Therapeutic Targets for Rheumatoid Arthritis Through Human Plasma Proteome. Biomedicines 2025, 13, 1841. https://doi.org/10.3390/biomedicines13081841
Wang H, Huang C, Huang K, Wu T, Liu H. Investigation of Novel Therapeutic Targets for Rheumatoid Arthritis Through Human Plasma Proteome. Biomedicines. 2025; 13(8):1841. https://doi.org/10.3390/biomedicines13081841
Chicago/Turabian StyleWang, Hong, Chengyi Huang, Kangkang Huang, Tingkui Wu, and Hao Liu. 2025. "Investigation of Novel Therapeutic Targets for Rheumatoid Arthritis Through Human Plasma Proteome" Biomedicines 13, no. 8: 1841. https://doi.org/10.3390/biomedicines13081841
APA StyleWang, H., Huang, C., Huang, K., Wu, T., & Liu, H. (2025). Investigation of Novel Therapeutic Targets for Rheumatoid Arthritis Through Human Plasma Proteome. Biomedicines, 13(8), 1841. https://doi.org/10.3390/biomedicines13081841