Integrated analysis of transcriptome and proteome reveals a core set of genes involved in osteoblast under oxidative stress

Osteoblasts dysfunction, induced by oxidative stress (OS), is a significant contributor to the pathogenesis of osteoporosis. However, the genes implicated in regulating osteoblast dysfunction remain unclear. Here, we employed the hydrogen peroxide (H₂O₂)-induced osteoblast dysfunction model to assess its impact on osteoblast phenotype and to conduct transcriptome and proteome analyses in osteoblasts under OS. We identified 164 genes and 186 proteins with altered expression (differentially expressed genes (DEGs) and differentially expressed proteins (DEPs), respectively). Functional analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed enrichment in pathways associated with apoptosis and osteoblast differentiation. We constructed a protein-protein interaction (PPI) network of DEPs, which comprised 175 DEPs as nodes. Furthermore, seven key DEGs and DEPs with positive correlation (cor-DEGs-DEPs genes) were characterized based on the integrated analysis of mRNA-protein expression. Among these seven genes, Ho-1, Fosl1, and Fosl2 were shown to be upregulated, associated with OS-induced cell differentiation impairment and apoptosis. Conversely, Ccnd2, Col1α1, Col12α1, and Fgfr2 were shown to be downregulated, linked to OS-induced cell cycle delay, apoptosis, impaired mineralization, and differentiation. PPI analysis revealed interactions between these key genes. Lastly, we validated these genes at both mRNA and protein levels using qRT-PCR and Western blot experiments. This study identified seven candidate genes potentially involved in the detrimental effects of OS on MC3T3-E1 apoptosis and dysfunction. These findings offer new insights into how OS disrupts bone formation and may contribute to the development of osteoporosis.