Journal List > J Rheum Dis > v.18(2) > 1063891

Ji, Kim, Lee, Choi, Lee, and Song: Study of the Gene Expressions in Rheumatoid Arthritis Synovial Macrophages Using Network Analysis

Abstract

Objective

We wanted to investigate the mechanisms that could account for the pathogenesis of rheumatoid arthritis, so we examined the different expressions of the genes in rheumatoid arthritis (RA) synovial fluid macrophages as compared with that of normal peripheral blood (PB) mon-ocyte-derived macrophages using microarray and bioinformatic analysis.

Methods

We examined the expression of genes by using a gene expression oligonucleotide microarray. The differences of the gene expressions between the RA synovial macrophages and the normal PB monocytes-derived macrophages were analyzed using bioinformatic tools, including cytoscape and its plugin.

Results

In this study, we found that 899 genes (464 genes upregulated and 435 genes down-regulated) were differentially expressed between the two groups. Among the 899 genes, 552 genes were included for gene ontology analysis and network analysis. Based on biological process ontology, they were categorised mainly into immune response processes, responses to stimulus and signaling and regulation of biological processes. In addition to the genes related with STAT1 and AP-1 signaling, we found that the genes involved in the antigen processing and the cell cycle are abundantly expressed in RA synovial macrophages, sug-gesting that these genes may play an important role in the pathogenesis of RA.

Conclusion

Our study suggest that this approach using integration of the gene expression profile with the protein interaction data may help to find several important pathogenic mechanisms in RA.

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Figure 1.
Overview of the bioinformatic analysis using cytoscape.
jrd-18-101f1.tif
Figure 2.
The array data for the gene expressions was validated by performing quantitative real-time PCR in the healthy volunteer PB monocyte-derive macrophages and the RA synovial macrophages ∗p<0.05 versus the healthy volunteer PB monocyte-derive macrophages.
jrd-18-101f2.tif
Figure 3.
(A) Map of the biological processes associated with RA synovial macrophages. Darker nodes mean the more significant ontology terms. The size is proportional to the number of genes included in that ontology term. (B) Network of the genes included in the immune system processes (GO. 2376). A blue node means down-regulation of genes and a red node means upregulation of genes in the RA synovial macrophages.
jrd-18-101f3.tif
Figure 4.
Different expressions of the STAT1-related genes in the RA synovial macrophages. A blue node means down-regulation of genes and a red node means upregulation of genes in the RA synovial macrophages.
jrd-18-101f4.tif
Figure 5.
(A) Detection of densely connected regions in the network of genes differentially expressed in the RA synovial macrophages and the PB monocyte-derived macrophages from healthy volunteer using MCODE. A square node is a seed node. (B) Identification of the functional modules as highly connected regions with similar responses using jActiveModules. A blue node means down-regulation of genes and a red node means upregulation of genes in the RA synovial macrophages.
jrd-18-101f5.tif
Table 1.
The gene ontology analysis (biological process) of the differentially expressed genes in RA synovial macrophages using the BiNGO plugin (The top ten GO terms were statistically significant)
Biological process GO No. Array data frequency n/501 (%) Expected frequency n/14,306 (%) p-value
Immune system processes 2376 96/501 (19.1) 948/14,306 (6.6) 2.41E-18
  Regulation of immune system processes 2682 47/501 (9.3) 424/14,306 (2.9) 2.35E-09
  Immune responses 6955 54/501 (10.7) 619/14,306 (4.3) 1.80E-07
    Regulation of immune responses 50776 30/501 (5.9) 235/14,306 (1.6) 2.72E-07
Response to stimulus 50896 197/501 (39.3) 3,633/14,306 (25.3) 2.35E-09
  Response to stress 6950 115/501 (22.9) 1,773/14,306 (12.3) 1.40E-08
    Defense responses 6952 55/501 (10.9) 620/14,306 (4.3) 7.40E-08
Signaling 23052 172/501 (34.3) 3,131/14,306 (21.8) 2.78E-08
Regulation of biological processes
  Positive regulation of biological processes 48518 133/501 (26.5) 2,208/14306 (15.4) 2.78E-08
  Regulation of responses to stimulus 48583 50/501 (9.9) 524/14306 (3.6) 4.78E-08
Table 2.
The gene ontology analysis (molecular function) of the differentially expressed genes in RA synovial macrophages using the BiNGO plugin (The top ten GO terms were statistically significant)
Molecular function GO No. Array data frequency n/501 (%) Expected frequency n/14,306 (%) p-value
Binding 5488 474/501 (89.9) 12,368/14,306 (80.0) 1.17E-07
 Protein binding 5515 381/501 (72.2) 8,123/14,306 (52.5) 3.70E-18
  Protein dimerization activity 46983 52/501 (9.8) 578/14,306 (3.7) 7.02E-08
   Protein homodimerization activity 42803 30/501 (5.6) 377/14,306 (2.4) 2.83E-03
  Cytoskeletal protein binding        
   Actin binding        
    Actin filament binding 51015 9/501 (1.7) 47/14,306 (0.3) 3.07E-03
 Ion binding        
  Cation binding        
   Metal ion binding        
    Magnesium ion binding 287 18/501 (3.4) 159/14,306 (1.0) 1.86E-03
 Antigen binding 3823 10/501 (1.8) 59/14,306 (0.3) 3.07E-03
 Lipid binding 8289 31/501 (5.8) 411/14,306 (2.6) 3.22E-03
Catalytic activity        
 Lyase activity        
  Carbon-carbon lyase activity        
   Aldehyde-lyase activity 16832 4/501 (0.7) 6/14,306 (0.0) 2.85E-03
 Transferase activity        
  Transferase activity, transferring phosphorus-containing groups        
   Kinase activity 16301 46/501 (8.7) 741/14,306 (4.7) 5.78E-03
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