Mechanisms of immune-related differentially expressed genes in thyroid-associated ophthalmopathy based on the GEO database

Abstract

Background: We performed a differential analysis, enrichment analysis, and immune-infiltration analysis of the thyroid-associated ophthalmopathy (TAO) gene using data from the Gene Expression Omnibus (GEO) database to provide a theoretical basis for understanding the immune-related mechanisms of TAO.

Methods: We searched the GEO database for "Graves disease" and selected the genes expressed in the lacrimal gland of thyroid-related eye disease patients as the test group and the genes expressed in the lacrimal gland of normal subjects as the control group. Immune-related differentially expressed genes (irDEGs), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein-protein interaction, gene-gene interaction (GGI) network, pivotal gene identification, and immune-infiltration analyses were carried out, and finally, risk-prediction models were constructed.

Results: The GSE105149 and GSE58331 data sets contained 200 DEGs, of which 15 were immune-related. In relation to the GO biological processes (BPs), the main pathways included the interleukin (IL)-27-mediated signaling pathway, the IL-35-mediated signaling pathway, cytokine activity, T helper 17 cell differentiation, the phosphatidylinositol-3-kinase and protein kinase B signaling pathway, cytokine-cytokine receptor interaction, the Janus kinase and signal transducer and activator of transcription signaling pathway, and other KEGG pathways. Cluster of differentiation (CD)4⁺ T cells, monocytes, M0 macrophages, and Mast cells were significantly elevated in TAO, while M2 macrophages were significantly reduced. In the immune cell correlation analysis, CD4⁺ T cells and naïve B cells were significantly positively correlated with activated natural killer (NK) cells, and Mast cells were positively correlated with plasma cells and negatively correlated with M2 macrophages. Risk models for a total of 6 genes (i.e., Janus kinase 1, heat shock protein 90-α, phospholipase A 2 group IIA, fibroblast growth factor 3, glucose-6-phosphate isomerase, and protein disulfide isomerase family A, member 2), were constructed, and over 100 potential targeted therapeutic agents were obtained.

Conclusions: In TAO, various types of immune cells infiltrate to different degrees, and the immune response and inflammatory response are throughout the disease. Our constructed risk-prediction models provide a reference for predicting TAO.

Keywords: Gene Expression Omnibus database (GEO database); immune infiltration; thyroid-associated ophthalmopathy (TAO).

Figure 1

Differential expression analysis of the GEO data set. (A,B) Volcano plot and heat map of differential expression analysis of the GSE105149 data set. (C,D) Volcano plot and heat map of differential expression analysis of the GSE58331 data set. GEO, Gene Expression Omnibus; FC, fold change.

Figure 2

Functional analysis of irDEGs. (A) Wayne diagram of irDEGs for the GSE105149 and GSE58331 data sets. (B) GO analysis of irDEGs. (C) KEGG analysis of irDEGs. (D) PPI network of irDEGs. (E) GGI network of irDEGs. irDEGs, immune-related differentially expressed genes; GO, gene ontology; KEGG, Kyoto Gene and Genome Encyclopedia; PPI, protein-protein interaction; GGI, gene-gene interaction.

Figure 3

Prediction of irDEGs’ miRNAs. irDEGs, immune-related differentially expressed genes.

Figure 4

GSE58331 data set immune-infiltration analysis. (A) Histogram. (B) Heat map. (C) Immune cell correlation analysis. (D) Violin plot of immune cell infiltration levels in healthy individuals and TAO patients. TAO, thyroid-associated ophthalmopathy.

Figure 5

GSE105149 data set immune-infiltration analysis. (A) Bar graph. (B) Heat map. (C) Immune cell correlation analysis. (D) Violin plot of immune cell infiltration levels in healthy individuals and TAO patients. TAO, thyroid-associated ophthalmopathy.

Figure 6

Immune correlation analysis of irDEGs. (A) GSE58331 dataset. (B) GSE105149 dataset. irDEGs, immune-related differentially expressed genes; corr, correlation.

Figure 7

Drug sensitivity analysis. (A) Venn diagram of target genes. (B) Potential target drug analysis for a total of 6 genes (i.e., JAK1, HSP90AA1, PLA2G2A, FGF3, GPI, and PDIA2).

Figure 8

ROC analysis of core irDEGs. (A) GSE58331 data set. (B) GSE105149 data set. AUC, areas under the curve; ROC, receiver operator characteristic; irDEGs, immune-related differentially expressed genes.

Figure 9

Risk-prediction models. (A) GSE58331 data set. (B) GSE105149 data set.