THE molecular mechanisms underlying synovial fibroblast differentiation in knee osteoarthritis revealed by single-cell transcriptome sequencing

This study aims to conduct an in-depth analysis of single-cell transcriptome data from synovial fibroblast differentiation in knee osteoarthritis (KOA), identify key target genes and underlying molecular mechanisms, and provide molecular-level theoretical support for clinical targeted therapy of KOA. The dataset (GSE176308), containing 3 KOA samples, was downloaded from the gene expression omnibus database. The R language was used to analyze key marker genes in synovial fibroblast differentiation. A series of analyses including quality control, data filtering, principal component analysis, t-distributed stochastic neighbor embedding analysis, cell trajectory mapping, gene ontology, and Kyoto encyclopedia of genes and genomes pathway analyses were performed to reveal the differentiation mechanisms of synovial fibroblasts. This dataset included 10,512 genes, 20 principal components, 8 synovial fibroblast subpopulations, 2991 marker genes, and 7 differentiation trajectories. Synovial fibroblasts were identified as early differentiated cells within the synovium. Gene ontology enrichment analysis indicated involvement in vascular regulation, ossification, wound healing, and extracellular matrix (ECM)-related functions, whereas Kyoto encyclopedia of genes and genomes analysis highlighted pathways related to ECM-receptor interaction, focal adhesion, cytoskeletal regulation, immune-related processes, and cellular metabolism. Single-cell ribonucleic acid sequencing revealed pronounced heterogeneity of synovial fibroblasts in KOA, identifying 7 differentiation trajectories and key marker genes including SPP1, TYROBP, CD74, CCL4, CCL3, APOE, and HLA-DRA. These genes and pathways are mainly involved in immune–inflammatory regulation, ECM remodeling, and cell-matrix interactions, which are central to KOA progression. Our findings provide a refined molecular framework for synovial fibroblast differentiation and suggest potential biomarkers and therapeutic targets for synovium-focused precision diagnosis and targeted intervention in KOA.