Screening for key genes and transcription factors in ankylosing spondylitis by RNA-Seq

Abstract

Ankylosing spondylitis (AS) is a chronic inflammatory arthritis and autoimmune disease, the etiology and pathogenesis of which remain largely unknown. In the present study, blood samples were harvested from patients with AS and from healthy volunteers as a normal control (NC) for RNA-sequencing. Differentially expressed genes (DEGs) in the AS group compared with the NC group were identified, and gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were subsequently performed. Protein-protein interaction (PPI) network and AS-specific transcriptional regulatory network construction was performed for the DEGs. A total of 503 DEGs, including 338 upregulated and 165 downregulated DEGs, were identified in patients with AS compared with the NC group. Three upregulated DEGs identified, interferon-induced protein with tetratricopeptide repeats (IFIT)1, IFIT3 and radical S-adenosyl methionine domain containing (RSAD)2, are interferon (IFN)-stimulated genes that serve a role in the IFN signaling pathway. The most significantly enriched GO term was response to other organisms. Osteoclast differentiation was a significantly enriched pathway for eight DEGs [High affinity immunoglobulin gamma Fc receptor (FCGR)1A, FCGR2B, four and a half LIM domains 2, integrin β3, signal transducer and activator of transcription 2 (STAT2), suppressor of cytokine signaling 3 (SOCS3), leukocyte immunoglobulin like receptor (LILR)A4 and LILRA6]. The six hub genes in the PPI network constructed were interferon-stimulated gene 15, heat shock protein β1, microtubule-associated proteins 1A/1B light chain 3A, IFIT1, IFIT3 and SOCS3. POU domain class 2 transcription factor 1 (1-Oct) and ecotropic virus integration site-1 (Evi-1) were identified as two important transcription factors (TFs) in AS according to the AS-specific transcriptional regulatory network constructed. In addition, IFIT1 and IFIT3 were identified as targets of 1-Oct. The results of the present study indicate that osteoclast differentiation, the IFN signaling pathway and genes associated with these two signaling pathways, particularly FCGR2B, STAT2, SOCS3, IFIT1 and IFIT3, may serve a role in AS. In addition, Evi-1 and 1-Oct may be two important TFs associated with AS. These results may provide a basis for elucidating the underlying mechanisms of and developing novel treatments for AS.

Keywords: RNA-sequencing; ankylosing spondylitis; differentially expressed genes; protein-protein interaction networks; transcription factors.

Figure 1.

Heatmap of the 50 most upregulated and downregulated differentially expressed genes in patients with ankylosing spondylitis compared with the normal controls.

Figure 2.

Top 20 most enriched gene ontology terms for the differentially expressed genes identified in patients with ankylosing spondylitis.

Figure 3.

Enriched Kyoto Encyclopedia of Genes and Genomes signaling pathways for the differentially expressed genes identified in patients with ankylosing spondylitis.

Figure 4.

Osteoclast differentiation signaling pathway. The DEGs identified in patients with ankylosing spondylitis were significantly enriched in the osteoclast differentiation signaling pathway. Red rectangles represent downregulated DEGs. DEG, differentially expressed gene.

Figure 5.

AS-specific protein-protein interaction network. Nodes (circles) represent the proteins encoded by DEGs. The radius of the circle indicates the significance of enrichment, a red color indicates that the DEG is upregulated and a green color indicates that the DEG is downregulated. DEG, differentially expressed gene.

Figure 6.

Ankylosing spondylitis-specific transcriptional regulatory network. Blue rhombuses represent downregulated DEGs, and red rhombuses represent upregulated DEGs. Rectangles represent TFs. The lines indicate TF-DEG pairs. DEG, differentially expressed gene; TF, transcription factor,.