Decoding transcriptional, metabolic, and cell death signatures in osteoarthritis and endemic osteoarthritis at single-cell resolution

Aims This study aims to investigate the molecular differences of cellular heterogeneity, metabolic, and cell death signatures between osteoarthritis (OA) and Kashin-Beck disease (KBD) at single-cell resolution. Methods Single-cell RNA sequencing was performed on 139,943 chondrocytes isolated from 17 human cartilage samples, comparising three healthy controls, eight patients with OA, and six patients with KBD. Chondrocyte populations were identified using the Louvain algorithm and systematically compared across the three groups. Differentially expressed genes, functional enrichment, metabolic activity, and cell death-related signatures were analyzed. Key findings were further validated using immunohistochemistry staining and quantitative real-time polymerase chain reaction (PCR). Results We found that pre-hypertrophic chondrocytes (preHTC), fibrocartilage chondrocytes (FC), pre-inflammatory chondrocytes (preInfC), and inflammatory chondrocytes (InfC) populations were enriched in OA, whereas proliferation chondrocytes (ProC) and homeostasis chondrocytes (HomC) predominated in KBD. In OA cartilage, OA-associated genes displayed upregulation of extracellular matrix (ECM) remodelling and immune activation pathways in preInfC and InfC populations. In contrast, KBD-associated genes exhibited marked activation of endoplasmic reticulum stress and oxidative stress responses in ProC-2, ProC-3, and HomC-2 subpopulations. OA was characterized by metabolic reprogramming with enhanced ECM remodelling and inflammation-related pathways, whereas KBD exhibited a globally suppressed metabolic profile. Additionally, ferroptosis activity was significantly higher in KBD cartilage compared with OA and control cartilage, with the strongest enrichment observed in ProC and HomC populations. Conclusion Although OA and KBD chondrocytes were broadly conserved across 11 identified populations, they exhibited distinct disease-specific transcriptional profiles, metabolic activities, and cell death signatures. These findings enhance our understanding of chondrocyte heterogeneity and identify the InfC population in OA, as well as the ProC and HomC populations in KBD, as potential targets for therapeutic intervention. Cite this article: Bone Joint Res 2026;15(11):1327–1340.