Classifying Integrated Signature Molecules in Macrophages of Rheumatoid Arthritis, Osteoarthritis, and Periodontal Disease: An Omics-Based Study

Abstract

Rheumatoid arthritis (RA), osteoarthritis (OA), and periodontal disease (PD) are chronic inflammatory diseases that are globally prevalent, and pose a public health concern. The search for a potential mechanism linking PD to RA and OA continues, as it could play a significant role in disease prevention and treatment. Recent studies have linked RA, OA, and PD to Porphyromonas gingivalis (PG), a periodontal bacterium, through a similar dysregulation in an inflammatory mechanism. This study aimed to identify potential gene signatures that could assist in early diagnosis as well as gain insight into the molecular mechanisms of these diseases. The expression data sets with the series IDs GSE97779, GSE123492, and GSE24897 for macrophages of RA, OA synovium, and PG stimulated macrophages (PG-SM), respectively, were retrieved and screened for differentially expressed genes (DEGs). The 72 common DEGs among RA, OA, and PG-SM were further subjected to gene-gene correlation analysis. A GeneMANIA interaction network of the 47 highly correlated DEGs comprises 53 nodes and 271 edges. Network centrality analysis identified 15 hub genes, 6 of which are DEGs (API5, ATE1, CCNG1, EHD1, RIN2, and STK39). Additionally, two significantly up-regulated non-hub genes (IER3 and RGS16) showed interactions with hub genes. Functional enrichment analysis of the genes showed that "apoptotic regulation" and "inflammasomes" were among the major pathways. These eight genes can serve as important signatures/targets, and provide new insights into the molecular mechanism of PG-induced RA, OA, and PD.

Keywords: Porphyromonas gingivalis (PG); gene expression analysis; network biology; osteoarthritis (OA); periodontitis; rheumatoid arthritis (RA).

Figure 1

Workflow of the present study. GEO = Gene Expression Omnibus, RA = rheumatoid arthritis, OA = osteoarthritis, PG = Porphyromonas gingivalis, DEGs = differentially expressed genes.

Figure 2

MA plots illustrating the distribution of differentially expressed genes (DEGs) in (a) rheumatoid arthritis (RA), (b) osteoarthritis (OA), and (c) Porphyromonas gingivalis (PG) macrophages based on the following statistical parameters: p-value ≤ 0.05 and log2-fold change (logFC) ≥ ±1. The red and blue dots indicate genes that have been considerably up- and down-regulated, respectively, whereas the black dots indicate genes with no significant difference between the diseased and control groups.

Figure 3

Venn diagram representing the intersection of differentially expressed genes (DEGs) in rheumatoid arthritis (RA), osteoarthritis (OA), and Porphyromonas gingivalis (PG) macrophages. All three data sets shared 72 DEGs.

Figure 4

A gene–gene correlation grid map illustrating the correlation between an expression similarity matrix across multiple samples in synovial macrophages in (a) rheumatoid arthritis (RA), (b) osteoarthritis (OA), and (c) Porphyromonas gingivalis (PG) stimulated macrophages individually using Cladist. A Pearson correlation coefficient (r) score of >0.7 was used to screen out significantly correlated gene–gene pairs. Pairs of genes that are co-expressed in similar patterns are labeled yellow; anti-correlated genes are designated blue, and those with no relationship are rendered black according to the correlation coefficient threshold.

Figure 5

Venn diagram depicting the intersection of significantly correlated differentially expressed genes (DEGs) in macrophages of rheumatoid (RA) synovium, osteoarthritis (OA) synovium, and macrophages stimulated with Porphyromonas gingivalis (PG), using a Pearson correlation coefficient (r) score of >0.7. Forty-seven highly correlated DEGs were identified. (why is the blue circle small?).

Figure 5

Venn diagram depicting the intersection of significantly correlated differentially expressed genes (DEGs) in macrophages of rheumatoid (RA) synovium, osteoarthritis (OA) synovium, and macrophages stimulated with Porphyromonas gingivalis (PG), using a Pearson correlation coefficient (r) score of >0.7. Forty-seven highly correlated DEGs were identified. (why is the blue circle small?).

Figure 6

The interaction network of highly correlated common differentially expressed genes (DEGs) as predicted using the GeneMANIA plugin of Cytoscape. The red and green nodes represent common DEGs and related genes, respectively. The red, green, purple, and grey edges represent physical interactions, genetic interactions, co-expression, and consolidated pathways, respectively.

Figure 7

Subnetwork of top 15 hub genes identified by cytoHubba. The intensity of the node’s color denotes the degree of interaction (red = high DC, orange = intermediate DC, and yellow = low DC), whereas the shapes of the nodes represent query/DEG (diamond) and result/related gene (circle).

Figure 8

The significantly enriched hub genes in GO-BP (gene ontology-biological process) terms identified using Enrichr.

Figure 9

The significantly enriched hub genes in GO-MF (gene ontology-molecular function) terms identified using Enrichr.

Figure 10

The significantly enriched hub genes in GO-CC (gene ontology-cellular component) terms identified using Enrichr.

Figure 11

Venn diagram depicting the overlapped KEGG pathways identified using Enrichr and DAVID.

Figure 12

Enrichr-Jensen DISEASES analysis of hub genes.