Multiple Processes May Involve in the IgG4-RD Pathogenesis: An Integrative Study via Proteomic and Transcriptomic Analysis

Abstract

Immunoglobulin G4-related disease (IgG4-RD) is a newly defined disease entity, while the exact pathogenesis is still not clear. Identifying the characters of IgG4-RD in proteomic and transcriptomic aspects will be critical to investigate the potential pathogenic mechanisms of IgG4-RD. We performed proteomic analysis realized with iTRAQ technique for serum samples from eight treatment-naive IgG4-RD patients and eight healthy volunteers, and tissue samples from two IgG4-RD patients and two non-IgG4-RD patients. Transcriptomic data (GSE40568 and GSE66465) was obtained from the GEO Dataset for validation. The weighted correlation network analysis (WGCNA) was applied to detect the gene modules correlated with IgG4-RD. KEGG pathway analysis was used to investigate pathways enriched in IgG4-RD samples. As a result, a total of 980 differentially expressed proteins (DEPs) in tissue and 94 DEPs in serum were identified between IgG4-RD and control groups. Three hundred fifty-four and two hundred forty-seven genes that most correlated with IgG4-RD were detected by WGCNA analysis in tissue and PBMC, respectively. We also found that DEPs in IgG4-RD samples were enriched in several immune-related activities including bacterial/viral infections and platelet activation as well as some immune related signaling pathways. In conclusion, we identified multiple processes/factors and several signaling pathways that may involve in the IgG4-RD pathogenesis, and found out some potential therapeutic targets for IgG4-RD.

Keywords: IgG4-RD pathogenesis; IgG4-related disease (IgG4-RD); WGCNA (Weighted Gene Co-expression Network Analyses); enrichment analysis; proteomic analysis.

Figure 1

Volcano plot of differentially expressed proteins between IgG4-RD patients and control. (A) 980 (542 up-regulated, 438 down-regulated) differentially expressed proteins were identified in tissue between IgG4-RD and control samples. (B) 94 (86 up-regulated, 8 down-regulated) proteins in serum were identified as differentially expressed between IgG4-RD and control samples. Proteins with mean ratio >1.2 and p < 0.05 were regarded as differentially expressed.

Figure 2

Functional enrichment of DEPs in tissue with proteomic data. (A) KEGG analysis and GO Biological process (GO BP) enrichment of up-regulated DEPs in tissue. (B) KEGG analysis and GO enrichment of down-regulated DEPs in tissue. X-axis: the number of DEPs of the proteomic data involved in the corresponding enriched terms.

Figure 3

KEGG analysis and GO Biological process (GO BP) enrichment of up-regulated DEPs in serum with proteomic data. X-axis: the number of DEPs of the proteomic data involved in the corresponding enriched terms. (A) GO BP enrichment analysis. (B) KEGG pathway analysis.

Figure 4

Heatmap of module-trait relationships revealed by WGCNA analysis. (A) 13 modules were detected by WGCNA in all samples from GSE40568. Among all these 13 modules, module “turquoise” showed strongest correlation with IgG4-RD phenotype. (B) 14 modules were detected by WGCNA in all samples from GSE66465, and module “yellow” showed strongest correlation with IgG4-RD (before treatment) phenotype.

Figure 5

Gene network of “Platelet activation” term derived from “turquoise” module in IgG4-RD tissue transcriptomic dataset, proteomic data from tissue, and serum.

Figure 6

Gene network of “Rap1 signaling pathway” term enriched in both IgG4-RD tissue proteomic data and LSG transcriptomic dataset.

Figure 7

Networks constructed by all proteins involved in the top 30 (A) KEGG and (B) GO Biological process (GO BP) terms enriched from all tissue DEPs. Circles (nodes) in the network represents proteins or KEGG/GO terms. Degree (number of connection) of each node was calculated, and nodes (except that represent KEGG/GO terms) with top 15 degree were regarded as hub nodes, and their corresponding proteins were identified as hub proteins. Hub nodes (proteins): red, large size; Term nodes: dark green, large size; other nodes (proteins): yellow, small size; Protein's involvement into biological process: line, dark gray.