Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma

Abstract

Glaucoma is characterized as a visual field defect, which is the second most common cause of blindness. The present study performed an integrated analysis of microarray studies of glaucoma derived from Gene Expression Omnibus (GEO). Following the identification of the differentially expressed genes (DEGs) in glaucoma compared with normal control (NC) tissues, the functional annotation, glaucoma‑specific protein‑protein interaction (PPI) network and transcriptional regulatory network constructions were performed. The acute intraocular pressure (IOP) elevation rat models were established and reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed for DEGs expression confirmation. Three datasets were downloaded from GEO. A total of 97 DEGs, 82 upregulated and 15 downregulated were identified in glaucoma compared with NC groups with false discovery rate <0.05. Response to virus and immune response were two significantly enriched GO terms in glaucoma. Valine, leucine and isoleucine degradation was a significantly enriched pathway of DEGs in glaucoma. According to the PPI network, HDAC1, HBN, UBR4 and PDK1 were hub proteins in glaucoma. FOXD3, HNF‑4 and AP‑1 were the three transcription factors (TFs) derived from top 10 TFs which covered the majority of downstream DEGs in glaucoma. Based on the RT‑qPCR results, the expression levels of 3 DEGs, raftlin, lipid raft linker 1 (RFTN1), PBX homeobox 1 (PBX1), HDAC1 were significantly upregulated and the expression of GEM was significantly downregulated in acute IOP elevation rat model at the first and fifth day. These four DEGs had the same expression pattern with our integrated analysis. Therefore, the current study concluded that 6 DEGs, including HEPH, SELENBP1, RFTN1, ID1, HDAC‑1 and PBX1 and three TFs, including FOXD3, HNF‑4 and AP‑1 may be involved with the pathogenesis of glaucoma. The findings of the current study may improve diagnosis and drug design for glaucoma.

Figure 1.

Heatmap of differentially expressed genes in glaucoma samples compared with normal control.

Figure 2.

Top 20 significantly enriched Gene Ontology terms of differentially expressed genes in glaucoma compared to normal control.

Figure 3.

Top 20 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways of differentially expressed genes in glaucoma compared to normal control. BP, biological processes; MF, molecular function, CC, cellular components; FDR, false discovery rate.

Figure 4.

Glaucoma-specific protein-protein interaction network of top 20 upregulated DEGs. The red ellipses indicate the proteins encoded by upregulated DEGs and the purple ellipses indicate other proteins. DEGs, differentially expressed genes.

Figure 5.

Glaucoma-specific protein-protein interaction network of top 20 downregulated DEGs. The green ellipses indicate the proteins encoded by downregulated DEGs and the purple ellipses indicate the other proteins. DEGs, differentially expressed genes.

Figure 6.

Transcriptional regulatory network of top 20 upregulated DEGs in glaucoma. The red ellipses indicate the upregulated DEGs and the blue rhombus indicate the TFs. The lines represent the TF-DEG pairs. DEGs, differentially expressed genes; TF, transcription factor.

Figure 7.

Transcriptional regulatory network of downregulated DEGs in glaucoma. The green ellipses represented the downregulated DEGs and the blue rhombus indicated the TFs. The lines represent the TF-DEG pairs. DEGs, differentially expressed genes; TF, transcription factor.

Figure 8.

Reverse transcription-quantitative polymerase chain reaction results of the top 20 differentially expressed genes in acute intraocular pressure elevation rat models. *P<0.05 and **P<0.01 vs. control group.