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

The molecular differences between osteoarthritis (OA) and endemic OA (Kashin-Beck disease, KBD), have been investigated at bulk-level, inherently masking cellular heterogeneity and critical discriminative markers.We conducted single-cell RNA sequencing (scRNA-seq) on a total of 139,943 chondrocytes isolated from 17 human cartilage samples, including 3 healthy controls, 8 patients with OA, and 6 patients with KBD. Chondrocyte populations were identified and compared. Differentially expressed gene, functional enrichment, metabolic activity, and cell death signature analyses were performed, with validation by immunohistochemistry staining and quantitative real-time PCR. We found that the preHTC, FC, preInfC, and InfC populations were enriched in OA, whereas ProC and HomC populations predominated in KBD. The HTC population, located in the deep cartilage zone, showed no major differences between the two diseases. Although cell population–specific functions were largely conserved across 11 chondrocyte subtypes, disease-specific transcriptional signatures were evident. OA cartilage displayed upregulation of extracellular matrix (ECM) remodeling and immune activation pathways, particularly within preInfC and InfC populations. In contrast, KBD chondrocytes exhibited marked activation of endoplasmic reticulum (ER) stress and oxidative stress responses, especially in ProC-2, ProC-3, and HomC-2 populations. Ferroptosis activity was significantly higher in KBD cartilage compared with OA and controls, with the strongest enrichment observed in ProC and HomC populations. These findings deepen our understanding of chondrocyte heterogeneity and highlight the InfC population in OA, as well as ProC and HomC populations in KBD, as potential target cell populations for therapeutic intervention.