| Literature DB >> 35514972 |
Peng Han1, Chao Hou2, Xi Zheng1,3, Lulu Cao1, Xiaomeng Shi4, Xiaohui Zhang4, Hua Ye1, Hudan Pan5, Liang Liu5, Tingting Li2, Fanlei Hu1,4,6, Zhanguo Li1,3,4.
Abstract
Objective: The study aimed to investigate the serum antigenomic profiling in rheumatoid arthritis (RA) and determine potential diagnostic biomarkers using label-free proteomic technology implemented with machine-learning algorithm. Method: Serum antigens were captured from a cohort consisting of 60 RA patients (45 ACPA-positive RA patients and 15 ACPA-negative RA patients), together with sex- and age-matched 30 osteoarthritis (OA) patients and 30 healthy controls. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was then performed. The significantly upregulated and downregulated proteins with fold change > 1.5 (p < 0.05) were selected. Based on these differentially expressed proteins (DEPs), a machine learning model was trained and validated to classify RA, ACPA-positive RA, and ACPA-negative RA.Entities:
Keywords: antigenome; biomarkers; mass spectrometry; random forest; rheumatoid arthritis
Mesh:
Substances:
Year: 2022 PMID: 35514972 PMCID: PMC9065411 DOI: 10.3389/fimmu.2022.884462
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 8.786
Clinical and laboratory characteristics of RA patients and controls in the study.
| Characteristics | RA ( | OA ( | HC ( |
|---|---|---|---|
| Age, mean (range), years | 61.77 (44–78) | 64.27 (46–81) | 62.37 (52–69) |
| Gender, no. male/female | 11/49 | 7/23 | 8/22 |
| Duration, mean (range), years | 12.37 (1–42) | – | – |
| ESR, mean (range), mm/h | 39.28 (5–106) | – | – |
| CRP, median (range), mg/L | 23.85 (0.22–172) | – | - |
| RF, median (range), IU/ml | 327.4 (2–3750) | – | – |
| Anti-CCP, median (range), U/ml | 147.4 (1.93–296.9) | – | – |
| WBC, median (range), 109/L | 5.793 (2.6–12.3) | – | - |
| TJC, median (range) | 7 (0–22) | – | - |
| SJC, median (range) | 5 (0–21) | – | - |
| DAS28, median (range) | 4.258 (1.15–6.93) | – | - |
| Medication, no (%) | |||
| Steroids | 25 (41.67%) | – | – |
| NSAIDs | 13 (21.67%) | – | – |
| DMARDs | 59 (98.3%) | – | – |
| Biologics | 31 (51.67%) | – | – |
HC, healthy controls; ESR, erythrocyte sedimentation rate; CRP, C-reactive protein; RF, rheumatoid factor; Anti-CCP, anti-cyclic citrullinated peptide antibody; WBC, white blood cell; TJC, tender joint count; SJC, swollen joint count; DAS28, disease activity score 28; NSAIDs, nonsteroidal anti-inflammatory drugs; DMARDs, disease-modifying anti-rheumatic drugs.
Figure 1Study overview and antigenome characterization. Overview of the study cohort and schematic workflow. RA, rheumatoid arthritis; OA, osteoarthritis; ACPA, anti-citrullinated protein antibody; HC, healthy control; MS, mass spectrometry; DEP, differentially expressed protein.
Figure 2Protein quantification through LC-MS/MS. (A) Venn diagram of the identified proteins among RA patients and controls. (B) Clustering analysis of differentially expressed proteins on PCA analysis. ACPA+, ACPA-positive RA; ACPA-, ACPA-negative RA; PCA, principal component analysis.
Figure 3Analysis of differential expressed proteins. Volcano plots compare RA (A), ACPA-positive RA (B), ACPA-negative RA (C), and controls. Heatmap analysis of proteins that differ significantly (p < 0.05, fold change > 1.5) in abundance in RA (A), ACPA-positive RA (B), and ACPA-negative RA (C).
Figure 4Functional analysis of DEPS. Pathway analysis of DEPs in patients with RA (A), ACPA-positive RA (B), and ACPA-negative RA (C). GO, gene ontology.
Figure 5PPI network construction of DEPs. Interaction network analysis of DEPs in RA (A), ACPA-positive RA (B), and ACPA-negative RA (C) by STRING and Cytoscape. Cytohubba plug-in was applied to identify the hub proteins in the network by protein degrees. Red indicated DEPs were at the center of the network and possessing 5–10 edges. Orange indicated DEPs possessing 3–5 edges. Yellow indicated DEPs possessing 1 to 2 edges. PPI, protein–protein interaction.
Figure 6Identification of potential biomarkers based on machine learning. Classification of RA (A), ACPA-positive RA (B), and ACPA-negative RA (C). Top 15 proteins prioritized by random forest analysis (left). ROC of the random forest model in the test cohort (right). AUC, area under curve.