Integrated analysis identifies conserved transcription factors TCF12, E2F1, and TEAD4 with diagnostic and therapeutic value in osteoarthritis subchondral bone.

Osteoarthritis (OA) is a multifactorial joint disease involving both cartilage and subchondral bone. The molecular mechanism of subchondral bone in OA is still unclear. This study aimed to identify key molecular targets and transcription factors (TFs) in subchondral bone that drive OA progression, with a focus on their diagnostic and therapeutic potential. Differentially expressed genes (DEGs) from human OA patients and rat OA models were analyzed using RNA-seq data from GEO database. Then functional enrichment analysis, including GSEA, GO and KEGG revealed high conservation. The iRegulon analysis was applied to identify common TFs. Bingo analysis linked TF target genes to OA-relevant biological functions, and single-cell RNA sequencing (sc-RNA seq) identified the primary cell types expressing these TFs. Finally, the expression of identified TFs was validated in human OA and animal OA samples using immunofluorescence (IF) and qPCR. We identified 77 common DEGs in OA patients and rat models, including genes associated with bone development or remodeling. Functional enrichment analysis identified common biological processes, such as skeletal system development, and shared pathways, including calcium signaling, across both species. Moreover, iRegulon analysis identified three conserved TFs-Transcription Factor 12 (TCF12), E2F Transcription Factor 1 (E2F1), and TEA domain transcription factor 4 (TEAD4) in both humans and rats. Single-cell analysis revealed that TFs mainly originate from bone-related cell populations. Finally, experimental validation confirmed that TCF12 was up-regulated, while E2F1 and TEAD4 were down-regulated in human OA subchondral bone and mouse DMM model. This study highlights TCF12, E2F1, and TEAD4 as key regulators of subchondral bone remodeling in OA. Their conserved expression patterns across species and strong correlation with OA progression suggest their potential as novel diagnostic markers and therapeutic targets for OA intervention.