| Literature DB >> 34867950 |
Liam J O'Neil1,2, Pingzhao Hu3,4, Qian Liu3,4, Md Mohaiminul Islam3,4, Victor Spicer2, Juergen Rech5, Axel Hueber5, Vidyanand Anaparti2, Irene Smolik1, Hani S El-Gabalawy1,2, Georg Schett5, John A Wilkins1,2.
Abstract
Objectives: Patients with Rheumatoid Arthritis (RA) are increasingly achieving stable disease remission, yet the mechanisms that govern ongoing clinical disease and subsequent risk of future flare are not well understood. We sought to identify serum proteomic alterations that dictate clinically important features of stable RA, and couple broad-based proteomics with machine learning to predict future flare.Entities:
Keywords: disease activity; outcomes research; proteomics; rheumatoid arthritis; treatment
Mesh:
Substances:
Year: 2021 PMID: 34867950 PMCID: PMC8636686 DOI: 10.3389/fimmu.2021.729681
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Baseline characteristics of the patients, split by proteomic cluster.
| Characteristics | Total (n = 130) | Cluster 1 (n = 34) | Cluster 2 (n = 12) | Cluster 3 (n = 46) | Cluster 4 (n = 38) |
|---|---|---|---|---|---|
| Age | 55.2 (13.1) | 52.7 (14.6) | 54.1 (13.7) | 54.7 (11.7) | 58.6 (13.1) |
| Females, % | 56.2% | 67.6% | 66.7% | 56.5% | 42.1% |
| Disease Duration (years) | 6.8 (7.0) | 7.9 (6.5) | 8.6 (9.3) | 6.9 (6.3) | 4.9 (7.3) |
| DAS-28 (ESR) | 1.7 (0.68) | 1.93 (0.60) | 1.73 (0.74) | 1.71 (0.65) | 1.51 (0.71) |
| ACR/EULAR remission, % | 76.6% | 67.7% | 66.6% | 88.9% | 72.9% |
| HAQ, units | 0.12 (0.32) | 0.11 (0.17) | 0.08 (0.12) | 0.16 (0.46) | 0.09 (0.26) |
| Positive RF, % | 56.2% | 73.5% | 50.0% | 52.2% | 47.3% |
| Positive ACPA, % | 57.7% | 67.6% | 66.7% | 55.6% | 50.0% |
| *Biological DMARD use, % (N) | 40.0% | 38.2% | 25.0% | 47.8% | 36.8% |
| Flare, % | 37.7% | 38.2% | 16.7% | 43.5% | 36.8% |
ACPA, anticitrullinated protein antibody; ACR, American College of Rheumatology; CRP, C-Reactive protein; DAS-28, disease activity score-28 (based on ESR); DMARDs, disease modifying antirheumatic drugs; ESR, erythrocyte sedimentation rate; EULAR, European League Against Rheumatism; HAQ, Health Assessment Questionnaire; RF, Rheumatoid Factor; VAS, Visual analogue scale.
*Tumor necrosis factor inhibitors and tocilizumab.
Figure 1Heatmap and hierarchical clustering of 200 serum proteins in stable RA. Protein expression is scaled and colored by relative expression. Each column is a protein and each row is a patient. Clustering is shown in both dimensions. Flare or remission is annotated in purple or grey to the left of the graph.
Figure 2XGboost machine learning to identify flare or remission in stable RA patients. (A) Box plots of EDAR, SPINT2, CX3CL1 and EPHB2 split by individuals who remained in Remission or Flare. (B) Receiver operator curves (ROC) of 2 machine learning models, XGboost and LASSO, trained on serum proteome to classify flare or remission. AUC is representative of test set cohort parameters. (C) Bar plot of model features that impact risk of flare or remission in the XGboost model with log2 expression and Uniprot ID annotated for each protein member. Feature importance is represented by relative size of bar. Values for different proteins represent their original values in the dataset for that particular sample. The base value means the average of the prediction scores, and 0.5 is the cutoff threshold to select a Flare status. (D) Gene concept plots derived from XGboost protein features. Each node represents a GO pathway with proteins connected by edges. EDAR, Ectodysplasin A receptor; SPINT2, Serine peptidase inhibitor; CX3CL1, Fractalkine; EPHB2, Ephrin type-B receptor 2. SNCA, Synuclein alpha; PLAUR, Plasminogen Activator; VEGFA, vascular endothelial growth factor A; MYC, Myc proto-oncogene protein; IL17F, Interleukin 17F; ROBO3, Roundabout homolog 3; CFB, complement factor B.
Figure 3Serum proteins are associated with DAS28 in stable RA. (A) Box plots of DAS28 disease scores in patients, split by cluster assignment (p = 0.03). (B) Correlation plots of DAS28 and serum protein expression of ITGA2B, BPI, CXCL2, C3, C4A, C1S. *p < 0.05.
Figure 4A serum proteomic signature is associated with DAS28 in stable RA. (A) Sliding window analysis of disease activity (Quintiles x-axis) and 34 proteins that vary with DAS score after controlling for Age and Sex. Heatmap is colored on coefficient relationship to DAS score (B) Box plots of disease activity protein score split by cluster assignment. (C) Gene concept plots derived from disease activity protein score. Each node represents a GO pathway with proteins connected by edges. ITGA2B, Integrin alpha 2B; BPI, Bactericidal permeability-increasing protein; CXCL2, Chemokine ligand 2; C3, Complement C3; C4A, Complement 4A; C1S, Complement 1S. ****p < 0.00001.