Here, we used large scale data integration method to characterize the molecular signatures of OA, which extended our understanding of the disease mechanisms. We also identified several essential regulators of OA, such as JUN, IL-6, and SOCS3, which might provide a scientific rationale for the development of novel pharmacological therapies. Of note, we found JUN, a crucial dysregulated transcription factor, plays a central role in regulating the aberrant gene expression pattern in OA. Moreover, we used a computational drug repurposing method to identify potential FDA-approved drugs that can be repurposed to improve the treatment of OA.
In this study, we integrated and analyzed multiple published datasets, which confirms some findings from previous studies using genome-wide gene expression analyses. Common findings of these studies are the differential expression of genes involved in matrix-degrading enzymes (MMPs, ADAMTS), collagen organization, and inflammation[7, 44]. In our analysis, we also found increased expression of genes associated with carbohydrate metabolism (BPGM, CHST2, GNPDA1, GUSB, HYAL1), integrin mediated signaling (FUT8, ITGA5, ITGB5), and ossification (COL5A2, COL6A1, CTGF, EXT2) in patients with OA, which is suggestive of active remodeling of cartilage homeostasis during OA pathogenesis. During the early stages of OA, the molecular composition and organization of the extracellular matrix are altered first. The articular chondrocytes exhibit increased cell proliferation and matrix synthesis for the purpose of initiating repairing for pathological injury[45, 46]. Changes in the composition and structure of the articular cartilage further stimulate chondrocytes to produce more catabolic factors involved in cartilage degradation. Thus, the expression of genes involved in the carbohydrate metabolism and extracellular matrix components were up-regulated. Moreover, chronic low-grade inflammation has also been found contributing to the development and progression of OA. During OA progression, the entire synovial joints were involved in the inflammation process. Pro-inflammatory factors, such as IL-1β and TNF-α, as well as chemokines, were reported to contribute to the systemic inflammation that led to the activation of NF-κB signaling in both synovial cells and chondrocytes. Based on these studies, multiple novel pharmacological strategies have emerged, including anti-inflammatory mediators (anti-IL-1, anti-TNF-α, and anti-IL-6) and inhibition of catabolic pathways (Wnt, ADAMTS, and cathepsin K). Apart from these findings, we were able to find some essential regulators that might associate with the pathogenesis of OA. The hub genes we identified, such as IL-6, VAMP8, and SOCS3, could serve as important diagnostic and/or therapeutic targets for OA.
Our study also identified JUN, a transcription factor, as a key regulator of these DEGs. JUN is one of the members of the Activator protein 1 (AP-1) family proteins. AP-1 family proteins are basic leucine zipper (bZIP) transcription factors that consist of Jun (c-Jun, JunB, and JunD), Fos (c-Fos, FosB, Fra-1, and Fra-2), Jun dimerization partners (JDP1 and JDP2) and the closely related activating transcription factors (ATF2, LRF1/ ATF3, and B-ATF) subfamilies. AP-1 family proteins are implicated in the regulation of a variety of cellular processes, including proliferation and survival, differentiation, apoptosis, cell migration, and transformation. JUN has been reported to play a crucial role in regulating cell proliferation and apoptosis. Ventura et al. reported that the c-Jun NH2-terminal kinase JNK signaling pathway contributes to the regulation of TGF-β-mediated biological responses. TGF-β is crucial for cartilage maintenance, and lack of TGF-β results in OA-like changes. Thus, JUN might regulate the development of OA by coordinating with TGF-β signaling.
In our analysis, we found two subgroups of OA patients. Patients in subgroup 1 had increased expression levels of genes related with inflammatory response, such as IL1B, TNF, TLR1, TLR7. Currently, countering inflammation is the mainstay of osteoarthritis therapy today. However, only a minority of patients respond to such therapy, suggesting the necessity to select appropriate patient subgroups. Patients with high expression of genes involved in inflammatory response might show a better response to anti-inflammatory drugs, such as anti-TNF and anti-IL1B. Patients in subgroup 2 had a higher expression level of extracellular matrix organization-related genes, such as MMP2, MMP28, ADAMTS5. Matrix metallopeptidases (MMPs), capable of degrading all kinds of extracellular matrix proteins, are therapeutic targets that showed efficacy in preventing joint destruction in some preclinical evaluations. However, many MMPs inhibitors failed phase I or phase II clinical trials due to the limited efficacy or drug toxicity. We hypothesized that patients in subgroup 2 who had a higher expression level of extracellular matrix proteins might better respond to MMPs inhibitors. Our analysis provided new possibilities for different treatment strategies according to the gene expression pattern of different OA subgroups.
Using a computational drug repurposing method, we found cardiac glycosides might be repurposed in the treatment of OA. Cardiac glycosides are drugs that inhibit the Na+/K+-ATPases and applied to treat heart failure and certain irregular heartbeats. However, recent studies reported that cardiac glycosides as a novel class of broad-spectrum senolytics for therapeutic applications in many age-related disorders, including osteoarthritis. Cardiac glycosides were capable of reducing the number of senescent cells, diminishing the level of local inflammation, and improved some metabolic and physical fitness parameters that decline with aging in some animal models[61, 62]. Although the effectiveness of cardiac glycosides in treating OA needs more systemic and detailed validation, our analysis offers a novel and valuable option for patients with OA.
There are several limitations of our studies. First, osteoarthritis is typically described as a heterogeneous disease with complex pathogenesis. Different patients might have different mechanistic pathways, such that the mechanisms of OA in the elderly might be different from those after a joint injury in a younger adult or in obese individuals. Further detailed analyses that take these co-variants (age, obesity and/or injury) into consideration may help better identify OA subgroups, which might explain the heterogeneity of OA patients and the different response to the treatment. Second, although we have discovered some molecular signatures of OA by transcriptome data analysis, multi-omics investigations, such as the integrated analysis of epigenetic (DNA methylation, histone post-translational modification, and/or noncoding RNA), transcriptomic (via RNA-seq or microarray), and proteomic (by LC-MS) changes are needed to better elucidate the changes during the pathogenesis of OA. Such detailed and systematic analyses offer important mechanistic and potentially therapeutic insights into OA. Finally, we have highlighted several essential regulators and uncovered that cardiac glycosides might benefit the patients with OA by countering the inflammation. However, further experimental studies are needed to validate their clinical implications.
Our study integrated multiple public transcriptome data sets together, which provides more comprehensive and reliable insights into the genetic risk associated with the disease phenotype. Moreover, we used a computational drug repurposing method to identify potent drug candidates to improve the treatment of OA.