RA is a chronic autoimmune disease that primarily affects the joints and is characterized by progressive, symmetrical inflammation of the joints, ultimately leading to destruction of articular cartilage, bone erosion, and disability (Smolen et al., 2016). The histological manifestations of RA are mainly three stages: cell proliferation, fibrin exudation, and inflammatory infiltration (Aigner and McKenna, 2002). The disease is primarily caused by the transport of hyperplastic synovial tissue fibroblasts, T and B lymphocytes, neutrophils and monocytes into the synovial tissue (Muller-Ladner et al., 2005).

PVNS, also known as tenosynovial giant cell tumor, is a rare joint disease. The annual incidence of PVNS is 1.8 per million and is increasing each year as awareness of the disease grows (Xie et al., 2015). It is characterized by inflammatory synovitis, synovial cell hyperplasia, and massive monocyte-derived osteoclast accumulation in joint synovial tissue (Rubin, 2007). It is a classic single-joint disease that frequently affects the knee, followed by the hip, ankle, shoulder, and elbow (Myers and Masi, 1980; Abdul-Karim et al., 1992; Chebib et al., 2018). The histological features of PVNS are fibrous matrix hyperplasia, macrophage infiltration, and hemosiderin deposition (Dorwart et al., 1984).

Both RA and PVNS are joint diseases, and their common feature is synovial hyperplasia due to excessive proliferation of synovial cells. Both RA and PVNS have an inflammatory environment (Berger et al., 2005). A study comparing the pathological features of RA and PVNS found hyperplasia of macrophages and fibroblasts in the lesioned synovial tissue (Berger et al., 2005). On arthroscopy and pathological examination, the villous nodular tissue exhibited more typical features of PVNS. Intra-articular injection of TNF-α inhibitors showed significant therapeutic effects in both RA and PVNS (Fiocco and Punzi, 2011). The lack of attention to PVNS has led to an increasing incidence of coexisting PVNS and RA, and the ability to correctly identify PVNS and RA will have a direct impact on patient outcome, so there is an urgent need to develop new biomarkers to identify these two diseases.

In this study, we extracted 18 RA samples and 11 PVNS samples. After normalization of the GSE3698 dataset, 107 differentially expressed genes (60 up-regulated and 47 down-regulated) were identified. In this way, the genes that are differentially expressed in RA and PVNS were analyzed, and the common target for diagnosing RA and PVNS was developed.

Innate immune system cells, such as monocytes, macrophages, and dendritic cells (DCs), play an important role in the occurrence and development of RA disease through their functions of phagocytosis, antigen presentation, and cytokine production (McInnes et al., 2016; Narasimhan et al., 2019; Saferding and Bluml, 2020), eventually leading to the destruction of bone and cartilage (Elshabrawy et al., 2015). In particular, macrophages play a central role in the initiation and drive of RA (Udalova et al., 2016; Ardura et al., 2019; Siouti and Andreakos, 2019). The number of synovial tissue macrophages is clinically the most reliable indicator for assessing the severity of RA and response to treatment (Tak and Bresnihan, 2000; Van Raemdonck et al., 2020). In inflamed RA synovial tissue, the majority of antigen-presenting cells (APCs) are fully differentiated dendritic cells (Iwasaki and Medzhitov, 2015; Yu and Langridge, 2017), and a decrease in the number of circulating DC cells in RA patients is associated with increased inflammation (Eisenbarth, 2019). Furthermore, in RA pathology, ROS production by neutrophils at sites of inflammation leads to endothelial dysfunction and tissue damage (Cedergren et al., 2007; Cecchi et al., 2018). In the inflamed RA synovium, NK cells aggregate and lead to bone destruction (Dalbeth et al., 2004). Other studies have shown that the number of granzyme-positive NK cells is increased in early RA synovial fluid compared with osteoarthritis (Tak et al., 1994). High serum granzyme levels have been shown to be an independent predictor of early erosion in RF-positive individuals (Goldbach-Mansky et al., 2005). Under the stimulation of APC, naive CD4⁺ T cells can differentiate into different types of cells, which in turn triggers the overactivation of autoantigen T cells and B cells, which eventually leads to persistent synovitis and joint destruction (Derksen et al., 2017; Rao et al., 2017; Sparks, 2019; Lee et al., 2020; Wu et al., 2020). Th17 cells are able to produce various pro-inflammatory cytokines to promote synovitis, while Treg cells suppress inflammation and maintain immune tolerance (Bilate and Lafaille, 2012; Noack and Miossec, 2014; Shi and Chi, 2019).

PVNS may be caused by the disturbance of the CSF-1 gene at 1p13 and the COL6A3 gene at 2q35 (West et al., 2006; Cupp et al., 2007). Studies have shown that IL-1β, IL-6, TNF-α and MMP-9 are highly expressed in PVNS tissues. TNF-α stimulates the production of MMPs, which can lead to cartilage and bone destruction in PVNS (O’Keefe et al., 1998). In PVNS, the presence of macrophage, histiocyte, and plasma cell infiltration stimulates an inflammatory response (Bhatnagar et al., 2017).

The differential expression of 28 immune infiltrating cells in the GSE3698 dataset was assessed by immune infiltration analysis. We found that macrophages, plasma cells, dendritic cells, monocytes, etc. were positively correlated with PVNS. Natural killer cells, neutrophils, macrophages, etc. were significantly associated with RA. Both RA and PVNS are associated with immune infiltration, but they are also influenced by other metabolic pathways. In damaged joint tissue, MAPKs not only govern the synthesis of pro-inflammatory cytokines but also play a crucial role in the signaling cascade downstream of interleukin (IL)-1, IL-17, and tumor necrosis factor (TNF)-α receptors (McGeachy et al., 2019). PI3K/AKT interacts with the mammalian target of rapamycin (mTOR) protein, inhibits fibroblastic synoviocyte (FLS) autophagy, promotes sustained synoviocyte growth, and aggravates RA (Miryala et al., 2019). O Osteoclasts migrate, damage bones and articular cartilage via the PI3K/AKT signaling pathway, and eventually cause joint abnormalities and exacerbate the progression of RA) (Xin et al., 2020). The absence of Cadherin-11 inhibited PVNS and FLS migration and invasion. Moreover, the expression of cadherin-11 was upregulated by inflammatory stimuli, which in turn activated the NF-κB and MAPK signaling pathways and facilitated cartilage destruction. Cadherin-11 inhibition prevented IL-1β- and TNF-α-induced activation of the aforementioned pathways, migration and invasion of PVNS FLS, and chondrocyte injury (Cao et al., 2020).

Studies have shown that the cytological features of RA are very similar to the proliferating mononuclear synoviocytes in PVNS, and synovial cell proliferation appears to be a common feature in the pathogenesis of RA and PVNS (O’Keefe et al., 1998; Sarkissian and Lafyatis, 1999; Nanki et al., 2001), proliferating synovial cells can stimulate the expression of the macrophage marker CD68 (Aigner et al., 1998; Sarkissian and Lafyatis, 1999). Comparing the immunophenotype of proliferating synovial cells in RA and PVNS found that the same cell population was involved in the proliferative process. In localized and diffuse PVNS, macrophage-like and fibroblast-like cells proliferated, while cells expressing markers of macrophage and fibroblast-like cells hyperproliferated. In localized PVNS, a significant increase in the number of fibroblast-like synovial cells was found compared with diffuse PVNS (Flandry et al., 1994; Kobayashi et al., 1994). M1 and M2 macrophages also play a role in PVNS and RA, the detection of macrophage marker (CD68/CD163) expression showed that macrophage-positive synoviocytes were found in both RA and PVNS, In RA, CD68/CD163⁺ synoviocytes were most often found in the synovial lining layer, but in PVNS, they were more spread out (Sehgal et al., 2021). CD14⁺ cells from RA synovial fluid express low levels of M2 anti-inflammatory markers, accordingly with a high-level production of pro-inflammatory genes (Sierra-Filardi et al., 2014). Non-classical Ly6C monocytes undergo polarization into inflammatory macrophages (M1), increase disease pathogenesis, and exhibit plasticity during the resolution phase. What’s more, these cells differentiate into anti-inflammatory M2 macrophages that address the combustion environment (Misharin et al., 2014). Another study revealed that Notch signaling has a strong relationship with M1 macrophage polarization, and that inhibiting Notch signaling lowers joint tissue inflammation by inducing a switch from M1 to M2 macrophages (Sun et al., 2017). Likewise, two M2 markers remain high and stable during RA disease (Arg1 and Ym1) and M1 markers were strongly upregulated (IL-1, IL-6, and CD86) (Hofkens et al., 2013). In PVNS, a major component of the cells is composed of bystander macrophages responding to CSF1, which stimulates increased numbers of macrophages through CSF1 and also promotes monocyte infiltration, damage cell clearance, and repair (Sehgal et al., 2021).

When building a generalized linear model, the lasso machine learning algorithm can include one dimensional continuous dependent variable, multidimensional continuous dependent variables, non-negative count dependent variables, binary discrete dependent variables, and multivariate discrete dependent variables. Lasso can handle both continuous and discrete dependent variables, and in general, the data requirement (quantity) of lasso is extremely low, so the application degree is wide. This solves the problem of screening for accurate results with a small sample. Random forest is not sensitive to multivariate common linearity, and the results are relatively robust for missing data and non-equilibrium data. It can well predict the effects of up to thousands of explanatory variables (Breiman, 2001) and is known as one of the best algorithms at present (Iverson et al., 2008). This solves the problem of more robust and better prediction of data results under the same algorithm. Hence, we screened hub genes among 36 common genes using LASSO and RF analysis. By overlapping the genes selected by LASSO and RF, PLIN, PPAP2A and TYROBP were identified as central genes in PVNS and RA.

Our study found that PLIN mainly affects the intestinal immune network of allograft rejection, ether lipid metabolism, and IgA production. Existing studies have also found that PLIN1 is up-regulated in steatohepatitis caused by non-alcoholic fatty liver disease (NAFLD), but PLIN1 protein is generally not expressed in normal hepatocytes (Straub et al., 2008; Fujii et al., 2009). PLIN2 is overexpressed in patients with alcoholic steatohepatitis (Mak et al., 2008; Straub et al., 2008; Carr et al., 2014). PLIN3 upregulation has been observed in human steatotic livers (Straub et al., 2008; Pawella et al., 2014). Hypoxia-inducible protein 2 (HIG2), a target of hypoxia-inducible factor 1 (HIF1), co-localizes with PLIN2 and PLIN3 and may be a marker of hepatic hypoxia (Gimm et al., 2010). However, relatively few studies have been conducted on PLIN4 or PLIN5 in human liver, and PLIN5 may play a role in lipolysis and oxidative disposal of stored lipids (Wang et al., 2011).

The most functionally important member of the PPAP family is PPAP2A, which reduces LPA activity by dephosphorylation (Blackburn and Mansell, 2012). High levels of LPA can be detected around larger microvessels expressing autotaxin (ATX). In osteoblasts remote from microvessels, ATX was least expressed and LPA was lowest due to high PPAP2A activity (Yanai et al., 2000). Interestingly, our study also found that PPAP2A strongly affects protein export, pentose and glucuronic acid interconversion, and allograft rejection.

TYROBP is a gene located on chromosome 19. TYROBP affects allograft rejection and graft-versus-host disease by mediating cytotoxicity of natural killer cells, activation of immune cells (T cells, B cells, and macrophages) (Lanier et al., 1998; Ono et al., 2018; Zheng et al., 2020). In addition, it was found that the low expression of TYROBP can participate in the regulation of OS immune environment by participating in the activation of macrophages (Gomez-Brouchet et al., 2017; Withers et al., 2019; Wolf-Dennen et al., 2020).

At the same time, we also found a positive correlation between PLIN and PPAP2A. PLIN was negatively correlated with TYROBP, the expression level of TYROBP in PVNS samples was significantly higher than that in RA samples, while the expression levels of PPAP2A and PLIN in PVNS samples were significantly lower than those in RA samples.

In a word, our findings suggest that PLIN, PPAP2A and TYROBP are associated with the occurrence and development of PVNS and RA. They are expected to become new targets and research directions for the diagnosis and treatment of PVNS and RA, thus providing new opportunities and references for improving the diagnosis and treatment level and clinical prognosis of PVNS and RA patients in the future.