The characteristics of RA is synovitis, systemic inflammation, and the arrival of autoantibodies [2]. As a result, synovial membrane break down body’s immune system, causing chronic inflammation, destruction of cartilage and bone, and dysfunction to other essential organs [1012]. It is reported that 50% of the risk for occurrence and development of RA is related to genetic factors. At the same time, smoking is an environmental risk factor for RA. The early onset of RA is not easy to identify, and in the meantime, cartilage and bone disintegration are frequently found in the end stages of this disease. RA occurrence and development can occur at any age, gender, and nationality for complex biological processes, and the positive rate of serum examination is low as well as non-specific. Consequently, it is miles critical to observe and study the mechanisms and development of RA at molecular level. On the basis of this, differentially expressed genes (DEGs) have been efficaciously used to predict the response of therapeutic approaches for RA patients. As an example, the capability of certain genes (type I interferon-responsive) to predict nonresponders of rituximab [13] and anti-tumor necrosis factor[14].
In this study, we integrated gene expression profile datasets from four specific groups (GSE55235, GSE55457, GSE55584 and GSE77298) and used R (version 3.6.1) to analyze these datasets. A total of 828 DEGs were identified using the limma package, consisting of 758 up-regulated genes and 70 down-regulated genes. The pinnacle 20 most significantly up-regulated genes were ADAMDEC1, IGHM, IGJ, IGKC, IGLL3, IGLV1-44, IGLC1, TNFRSF17, IGLL5, CRTAM, CXCL9, IGLJ3, TRAT1, SDC1, TPD52, IGK, CD27, CXCL10, IL21R and IGHG1. The pinnacle 20 most significantly down-regulated genes were SLC19A2, PLIN1, KLF9, ADCY2, PPAP2B, EBF2, ADH1B, KLF4, PPARGC1A, GABARAPL1, TRHDE, PHKA1, FBXW12, TCEAL2, PCK1, PCDH9, MAFF, LEP, RERGL and SGCA. Constructing a PPI network (minimum required interaction score = 0.990) of DEG-encoding proteins from STRING database and screening the 30 most significant related genes. The enriched GO of DEGs in RA were analyzed by R software, and correlation analysis confirmed that the up-regulated genes have been specifically involved in cytokine receptor activity, G protein-coupled chemoattractant receptor activity, chemokine receptor activity, MHC protein complex binding, chemokine binding, chemokine receptor binding and cytokine activity, and that the down-regulated DEGs were mainly involved in peroxidase activity and oxidoreductase activity, acting on peroxide as acceptor. This finding is consistent with the knowledge that cytokine, chemokine and peroxidase activity play crucial roles in the RA occurrence and progression.
The detection of auto-antibodies (including RA, A-CCP, CRP) in RA patients is identification that distinguishes the disease from other inflammatory arthritis, such as psoriatic arthritis, reactive arthritis and osteoarthritis. In addition to the clinical symptoms and signs arising from arthritis processes in the joints, muscles weakness around joints are also commonly reported by RA patients[1517]. Takashi Yamada et al.[17] discovered that altered Ca2 + and free radical signaling (such as reactive oxygen and reactive nitrogen species) can result to RA-based muscle weakness. In a general way, RA with CCP + RF + subjects had excessively high citrulline-specific IgG binding, and CCP + RF‐ and CCP‐RF + subjects had modest binding to array peptides[18]. As a systemic autoimmune disease, RA is characterized by inflammation and angiogenesis in synovium. Many cytokines and inflammatory medium are observed in synovial tissues and synovial fluids, whose function is to display angiogenic properties. Inhibitor of DNA binding 1, one of transcription factors, is a marker of cellular self-renewal. This factor within the bone marrow causes the significant reduction of endothelial progenitor cell association with tumor-related vasculogenesis [19, 20]. Amélie Simon et al [21] observed that microscopic polyangiitis is vasculitides typical of necrotizing inflammation for small-sized vessels and is usually connected with serum positivity for those anti-neutrophil cytoplasmic antibodies. In most conditions, anti-neutrophil cytoplasmic antibodies are directed against two constituents of neutrophil primary granules as well as monocyte lysosomes: myeloperoxydase or proteinase 3.
Furthermore, the up-regulated enriched Kyoto Encyclopedia of Genes and (KEGG) pathways of DEGs included the chemokine signaling pathway, hematopoietic cell lineage, cytokin-cytokin receptor interaction, viral protein interaction with cytokine and cytokine receptor, primary immunodeficiency, leishmaniasis, osteoclast differentiation, rheumatoid arthritis, cell adhesion molecules (CAMs). The down-regulated enriched KEGG pathways of DEGs included PPAR signaling pathway, regulation of lipolysis in adipocytes, adipocytokine signaling pathway, glucagon signaling pathway, AMPK signaling pathway, calcium signaling pathway, thyroid hormone synthesis, apelin signaling, cGMP-PKG signaling pathway. Relative studies have demonstrated that fibroblast-like synoviocytes play a crucial role by producing cytokines in all stages of RA. Once fibroblast-like synoviocytes are activated during the course of RA, a series of inflammatory factors and proteases will be produced involved in the inflammatory response, causing progressive destruction of bone and cartilage[22].
RA is associated with an increase in mortality. Previous research displayed that the occurrence rate of the malignancies in RA patients has been reported to be high [7]. A review of scientific studies compiled in Romania demonstrated findings that anaemia and other chronic disease manifestations are relatively common in approximately 6–10% RA patients, and are all related to worse outcomes in particular functional impairment and mortality[23, 24]. The adaptive immune system is closely connected with the generation of anti-tumor immune response. For that reason, RA patients with gastrointestinal cancer history must be carefully monitored while receiving the treatment of disease-modifying antirheumatic drugs[25]. However in many factors, tumor necrosis factor-α (TNF-α) is recognized as performing biological functions association with the pathogenesis of RA [26]. Its capabilities include: chemokine amplification, endothelial cell activation, leukocyte accumulation[27], experiencing cardiovascular comorbidity[28], acceleration destruction of osteoclast and chondrocyte, and demonstrating metabolic syndrome[29]. Related studies have reported that PPAR-γ may additionally induce activation Wnt/β-catenin signaling [30]. Numerous studies have indicated that decreased expression of adipocyte genes such as nuclear receptors PPARg in the RA synovial tissue [31, 32], and PPARg mediates mesenchymal stem cells as well as fibroblast-like synovial cells differentiation into adipocytes[33]. As for the gene expression of AMPK in those newly diagnosed RA patients, a master regulator of metabolic process was decreased in the peripheral blood leukocytes and elevated levels of TGF-β1 in plasma accounts for the occurrence of RA pathogenesis[34]. Recent data evidence suggests that S100A8/A9 is member of the Ca2 + binding S100 protein family and has become a hot topic as a critical alarmin modulating the inflammatory response. Using small molecule inhibitors that block off S100A8/A9 activity can exhibits beneficial functions on disease relative activities in animal models of autoimmune diseases such as RA [35, 36].
We constructed a PPI network of protein encoded by DEGs and identified the subsequent top 10 closely related genes: CDK1, KIF11, CDC20, CCNB1, CCNB2, MAD2L1, BUB1B, NDC80, AURKA and CCNA2. These genes are key nodes for construction a PPI network and play a distinct role in the pathogenesis of RA. In accordance with the proinflammatory CDK signaling, p16INK4A protein as a Cyclin-Dependent Kinases inhibitor in synovial fibroblasts also demonstrates an inhibitory action in the development of RA[37]. Ectopic expression of p16INK4A protein can also suppress LPS-induced IL-6 expression in macrophages[38], and simultaneously enhance the observations that CDK inhibitory proteins relative features to counteract inflammation[39]. Interleukin-6 (IL-6) signaling is a critical target in inflammatory pathways[40]. In patients with RA, the high level of IL-6 and IL-6R are found in both serum and synovial fluid of related joints effected by the disease. IL-6 is a cytokine serving several biological and biochemical functions that affect the immune and vasculature system. Generally speaking, conventional IL-6 signaling is in charge of the anti-inflammatory capabilities of IL-6, conversely, trans-signaling is in charge of the pro-inflammatory properties of IL-6. Consequently, disorders of the IL-6 axis can result in the onset or progression of disease states, especially in autoimmune and inflammatory dysregulation [41]. Activation of epidermal growth factor receptor (EGFR) signaling leads to propagation and metabolism of synovial fibroblast in RA. Beyond that, in addition to its function in propagation and metabolism, EGFR can generate cytokine in synovial tissues during the pathogenesis of RA. Some animal experiments have yielded potentially prospective results aiming at target EGFR involving RA. As a result, pharmacologic modulations or its ligands targeting EGFR may reveal undiscovered methods for the treatment of RA[42]. EGF receptor is a tyrosine kinase. At present, only NEK6 and CDK1 kinases can phosphorylate KIF11 at Ser1033 and Thr926 respectively, causing the combination of microtubules and KIF11 in the process of mitotic spindle assembly[4345]. Some inflammatory cytokines are controlled by the expression of the c-Fos. Both IL-1β and c-Fos are interacted with each other, including its gene expression and activities, and causing cross-link effect that is vital mechanism to arthritic joint destruction. As a result, the blockade of IL-1β, c-Fos or link between both can be an effective therapeutically as a treatment method for RA patients joint destruction[46]. Researchers at the University of Chicago, found through mice experiments that the inhibition of c-Myc or c-Raf-1 can significantly decreased the invasiveness of RA synovial fibroblasts. Besides, dominant-negative mutants c-Raf-1 reduced the expression of phosphorylated c-Jun in vivo as well as the expression of disease-relevant MMPs[47].