GP4d - Cross-Tissue Transcriptomics Reveals Opposing Immune Dysregulation in TMJOA Saliva and Synovium

Abstract: Temporomandibular joint osteoarthritis (TMJOA) is a chronic inflammatory joint disorder characterized by progressive tissue degradation. Synovium and saliva are two primary tissue compartments used to investigate disease-associated molecular changes in TMJOA, and previous clinical studies have reported elevated inflammatory and metabolic biomarkers in both tissues. However, these studies have largely been limited to a small number of candidate proteins or cytokines, and the broader relationship between synovial and salivary transcriptomic signatures remains poorly understood. To address this gap, we performed an integrative transcriptomic analysis of salivary and synovial tissues to characterize differentially expressed genes and identify shared pathways between both compartments. Bulk RNA sequencing data from salivary and synovial tissue samples of TMJOA patients and healthy controls were obtained from the Gene Expression Omnibus (GEO) database. Salivary transcriptomic data were retrieved from the dataset GSE289871, which included 7 TMJOA patients and 7 healthy controls. Synovial transcriptomic data were retrieved from the dataset GSE205389, comprising synovial samples from 5 TMJOA patients and 5 control patients diagnosed with disc displacement without reduction and without bony changes. All bioinformatic analyses were performed in R. Principal component analysis (PCA) and unsupervised hierarchical clustering were conducted to assess sample heterogeneity and identify potential molecular subtypes. Differential gene expression (DEG) analysis was performed using DESeq2/Limma with a threshold of adjusted P-value < .05 and |log2 fold change| > 1. Gene set enrichment analysis (GSEA) and pathway enrichment analysis were conducted using the clusterProfiler package against the KEGG/GO gene set collections. Immune cell infiltration was estimated using xCell deconvolution analysis. Cross-tissue analysis was performed by intersecting salivary and synovial DEG lists to identify shared molecular pathways and genes altered, thereby characterizing coordinated regulation across tissue compartments. Unsupervised clustering of salivary transcriptomic profiles revealed a molecularly distinct TMJOA subtype with 2 patients, characterized by coordinated downregulation of core immune activation pathways, including interferon alpha/gamma response, TNF signaling, IL6-JAK-STAT3 signaling, and inflammatory response. This immunosuppressive phenotype was further supported at the protein level by published LC-MS/MS proteomics data.¹ Notably, upregulated pathways in the immunosuppressive salivary subtype included glycolysis, oxidative phosphorylation, cholesterol homeostasis, xenobiotic metabolism, and estrogen response. Interestingly, several of these pathways are known to be positively associated with cortisol activity. This is consistent with previous clinical studies reporting elevated salivary cortisol levels in TMD patients.² Given that cortisol is a well-established immunosuppressive hormone, its potential elevation in this salivary subtype may offer a plausible explanation for the observed downregulation of core immune activation pathways. In contrast, the synovial tissue of TMJOA patients showed expected upregulation of immune activation pathways, consistent with active synovial inflammation. Cross-tissue analysis revealed a set of shared DEGs between salivary and synovial tissues, with the majority upregulated in synovium and downregulated in saliva. Pathway enrichment of these shared DEGs converged exclusively on immune response pathways, suggesting that the immune suppression observed in saliva and the immune activation in synovium may represent coordinated but compartment-specific immune dysregulation in TMJOA. This study provides the first high-throughput transcriptomic evidence of a molecularly distinct immunosuppressive salivary subtype in TMJOA and reveals divergent cross-tissue immune signatures, suggesting coordinated immune compartmentalization between salivary and synovial tissues. These findings suggest that TMJOA pathology extends beyond synovial inflammation alone and that salivary transcriptomics may offer a non-invasive approach for identifying disease subtypes.


References:

1. Talian, I., Laputková, G. & Schwartzová, V. Identification of crucial salivary proteins/genes and pathways involved in pathogenesis of temporomandibular disorders. Open Chemistry 20, 1378-1401 (2022).

2. Soares, J. M., Carneiro, B. D. & Pozza, D. H. The Role of Biomarkers in Temporomandibular Disorders: A Systematic Review. IJMS 26, 5971 (2025).