Data Sheet 3_Immune cells with senescence-related transcriptional signatures orchestrate the inflammatory continuum in osteoarthritis synovium: a single-cell and machine learning study.xls

BackgroundSynovitis is a key driver of osteoarthritis (OA), characterized by a chronic inflammatory microenvironment. However, the contribution of immune-cell senescence to synovial pathology and its therapeutic potential remains poorly understood. This study aims to map the senescent immune landscape and identify actionable targets for OA therapy.
MethodsSingle-cell RNA dataset (GSE152805) of OA synovium was used to identify immune subsets with senescence-related transcriptional signatures and subset-specific gene signatures. These gene signatures served as machine-learning features to train and validate diagnostic models in a combine dataset of 4 OA transcriptomic datasets (GSE55235, GSE55457, GSE82107, GSE169077) using Random Forest, Support Vector Machine, Gradient Boosting Machine, and eXtreme Gradient Boosting. Immunofluorescence staining and Western blotting of human synovial tissues validated macrophage-associated markers. Pseudotime trajectory and cell–cell communication analyses defined temporal dynamics and intercellular communication. Drug–gene interaction analysis and molecular docking were performed to assess therapeutic potential.
ResultsMacrophages, mast cells, and dendritic cells were identified as the immune populations with senescence-related transcriptional signatures. Pseudotime and communication analyses revealed a coordinated inflammatory continuum: macrophages initiated and sustained synovial inflammation, mast cells amplified intermediate inflammatory responses, and dendritic cells contributed to late-stage matrix remodeling. Machine-learning models identified hub biomarkers, with RHOB and PDK4 emerging as the macrophage-associated biomarkers with therapeutic potential. RHOB and PDK4 were markedly upregulated and colocalized with CD68+ macrophages in OA synovium. Drug prediction suggested CHEMBL1797159 as a potential ligand for RHOB and dichloroacetate as a repurposable modulator of PDK4.
ConclusionThis study characterizes the transcriptomic landscape of senescence-related features in the OA synovial microenvironment. We identify RHOB and PDK4 as key macrophage-associated therapeutic targets, providing novel insights for immunomodulatory strategies in OA treatment.