RA) is a chronic inflammatory autoimmune disease, which can result in irreversible cartilage and bone damage and disability. The activation of synovial fibroblasts and the overproduction of several cytokines and chemokines are key players in the pathogenesis and progression of RA[16, 17]. However, the exact origin and pathogenesis of RA still incompletely understood. An improved understanding of the molecular mechanisms underlying RA will lead us to discover more effective therapeutic strategies for RA patients.
In this study, we sought to identify the target genes which were related to synovitis by comparing synovial tissue gene expression profiles between RA patients and healthy control groups. Through bioinformatics analysis, a total of 385 overlapping genes were identified, including 366 upregulated and 19 downregulated genes. Subsequently, GO and KEGG enrichment analyses of overlapping genes were carried out. With respect to GO analysis, the DEGs was mainly enriched in various immune and inflammatory response-related functions and pathways. These results were consistent with previous works demonstrated that immune and inflammation response played an important role in pathogenic process underlying RA[18, 19]. KEGG pathway analysis showed that the DEGs of our results were primarily enriched in cytokine-cytokine receptor interaction, tuberculosis and chemokine signaling pathway. The cytokine-cytokine receptor interaction and chemokine signaling pathway has been regarded as
to be relevant to multiple autoimmune diseases[20, 21]. Consistent with our results, these pathway was also found to be of great significance in other related RA studies. Furthermore, it’s widely accepted that RA may be manifested with an increased risk of tuberculosis. Previous studies by Loreto et al. also demonstrated that the risk of subsequent tuberculosis infections increased approximately four fold in RA patients. Therefore, prevention of tuberculosis should be considered during the routine management and treatment of patients with RA.
Based on PPI network construction and hub gene screening, ten candidate hub genes were obtained. Additionally, the top 10 candidate hub genes have been validated through area of the ROC curve based on the GSE12021 dataset. Eight of these 10 genes had favourable diagnostic effect and were accredited as hub genes. They are HLA-DRA, HLA-DRB1, LCK, VAV1, HLA-DPA1, HLA-DPB1, C3AR1 and CD3D. Functional enrichment analysis revealed that all of these hub genes were important immune-related genes. The HLA-DRA, HLA-DRB1, HLA-DPA1 and HLA-DPB1 belong to MHC class II molecules. MHC class II molecules are heterodimeric glycoproteins on the cell surface which are mapped on human chromosome 6 and are encoded by MHC gene locus.
Moreover, the MHC class II molecules play an essential role in various immune response[25, 26]. Research has shown that HLA-DRA expression can accurately reflect immune status of patients and were associated with abnormal T cell differentiation. Moreover, HLA-DRA was reported as a DEG and its level was upregulated in primary Sjögren's syndrome. HLA-DRA was also shown to be one of the hub genes associated gene module in peripheral blood mononuclear cells of RA . In the present study HLA-DRA was screened out as one of hub genes in RA synovial tissue. Accumulating studies have revealed that HLA-DRB1 is closely associated with RA. A previous study from Biljana et al. demonstrated the presence of HLA-DRB1 gene-specific variation possibly contribute to the increased risk of RA. Jamil et al. had similar results in their study of RA patients. In addition, one study also showed that HLA-DRB1 may be associated with drug resistance and drug efficacy in RA patients treated with adalimumab. HLA-DP was also reported to be strongly associated with several autoimmune diseases, including ankylosing spondylitis and systemic lupus erythematosus[33, 34]. It was also demonstrated that HLA-DPB1 might be an related factor of susceptibility to RA and there were association between HLA-DPB1 and serum anti-CCP antibodies levels . Moreover, there were also other studies suggesting that the polymorphisms of HLA-DPB1 may be as a protective factor for RA. The present study identified HLA-DPA1 as a key gene correlated with RA, which are similar to the findings of Li et al. However, another study showed that HLA-DPB1 or HLA-DPA1 had no correlation with the disease severity or susceptibility in RA patients. Therefore, additional studies will be needed to clarify the role of HLA-DPB1 and HLA-DPA1 in RA and the underlying mechanisms. The lymphocyte-specific protein tyrosine kinase (LCK) is a member of the Src family, which was shown to participated in the pathogenesis of multiple autoimmune diseases through TCR signaling pathway. It has been reported that LCK-deficient mice appeared severe deficiency of T cell development in the thymus. Remarkably, LCK play a critical role in T lymphocytes hyporesponsiveness present in the synovial fluid of RA patients. VAV1 is a GDP/GTP nucleotide exchange factor (GEF) specific to the hematopoietic system, the function of which was regulated by tyrosine phosphorylation after the end of T cell antigen receptor (TCR) stimulation. And some scholars showed that VAV1 gene Polymorphisms were directly linked with RA, especially in anti-CCP negative rheumatoid arthritis. As a member of G-protein coupled receptor family, the complement component 3a receptor 1 (C3aR1) was confirmed to be involved in the regulation of both innate and adaptive immune responses. Previous study has shown that C3aR-knock out MRL/lpr lupus mice suffered faster renal injury, suggesting a protective role of C3aR in lupus nephritis. In contrast, other studies showed that C3aR expression strongly associated with disease activity in patients with lupus nephritis. CD3D mainly functions by forming T cell receptor (TCR) -CD3 complex, which could affect the outcome of T cell response. It was reported that CD3D was mainly involved in immune activation, particularly being strongly linked with CD8+T cell activation in colon cancer . However, there are few studies about the role of C3aR1 and CD3D in RA. Thus, these will be studied in our future works.
However, there are some limitations in our study. Firstly, our results are required to further validate by more studies with larger sample size. Additionally, to better comprehend the roles of DEGs reported by us in RA pathogenesis, molecular experiments are imperative. In all, integrated bioinformatics analysis of multiple gene expression datasets obtained from GEO database identified a total number of eight hub genes which might be associated with the pathogenesis of RA. Our results also revealed that the eight hub genes may be applied in the diagnosis of RA. Furthermore, our findings may contribute to increase the understanding of the underlying mechanisms of RA.