Transcriptomic profiling and experimental validation of myeloid-cell-differentiation-related key genes in...

This study aims to leverage publicly available databases to systematically investigate the pathogenic mechanisms of osteoarthritis (OA), with particular focus on the role of myeloid cell differentiation (MCD)-related genes. Comprehensive multidimensional analyses were performed to elucidate the potential mechanisms through which these genes contribute to the pathophysiological processes of OA. The findings of this study are expected to provide a theoretical foundation for targeting MCD-related abnormalities in OA.

We systematically integrated data acquisition, differential expression analysis, intersection with MCD-associated gene sets, machine learning-based feature selection, and multidimensional bioinformatics analysis-including functional enrichment, immune infiltration profiling (using the CIBERSORT algorithm), and structure-guided molecular docking to elucidate the molecular links between MCD and OA pathogenesis. We subsequently performed a comprehensive suite of functionally complementary downstream analyses, including nomogram construction for clinical risk prediction, receiver operating characteristic (ROC) curve analysis to assess diagnostic performance, decision curve analysis (DCA) to evaluate clinical utility, and structure-based molecular docking to probe potential ligand-target interactions.

We identified eight key genes (GRP183, MFAP2, NDP, TF, TFRC, TYROBP, VEGFA, and ZBTB16) through systematic screening. Following expression level validation, VEGFA, ZBTB16, and TYROBP were found to exhibit consistent expression trends and statistically significant differences across two independent datasets. Using the immunological atlas (the CIBERSORT algorithm), we estimated the infiltration levels of 22 immune cell subtypes and found that immune cell infiltration was significantly associated with OA progression and molecular subtype. Furthermore, molecular docking simulations were performed between the three key genes and two candidate therapeutic compounds, which provided preliminary insights and potential clues for future clinical drug development targeting these molecular interactions. To investigate the mRNA expression levels of the key genes, we performed real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis.

We integrated transcriptomic data with bioinformatics approaches and machine-learning techniques in this study to identify potential biomarkers associated with OA. We identified VEGFA, ZBTB16, and TYROBP as three key MCD-associated genes in OA; we further explored their biological functions and underlying regulatory mechanisms, which were supported by the experimental validation of the expression of the key genes.