Identification of a Novel Mitochondrial-Related Gene Signature for BMSCs in Osteoporosis Combining Single-Cell and Bulk Transcriptome Data

Osteoporosis (OS) is a prevalent skeletal disorder characterized by reduced bone mass and increased fracture risk, often linked to compromised functions of bone mesenchymal stem cells (BMSCs). Mitochondrial dysfunction and aberrant mitophagy are implicated in OS pathogenesis. This study aimed to identify a novel mitochondrial-related gene signature in BMSCs from OS patients by integrating single-cell and bulk transcriptome data. We analyzed single-cell RNA sequencing data from GSE147287 and bulk transcriptome data from GSE35956 to identify differentially expressed mitochondrial-related genes (MRGs) in BMSCs between healthy individuals and OS patients. Key genes were identified using LASSO logistic regression and random forest algorithms, and their differential expression was validated by RT-qPCR, Western blot, and immunofluorescence. Functional assays, including osteogenic differentiation and β-galactosidase staining, were conducted following siRNA-mediated knockdown of DUT. We identified 28 differentially expressed MRGs, with four key genes (DUT, UQCR10, DNAJC4, and MRPL33) further confirmed. Electron microscopy scanning showed damage to BMSCs mitochondria and decreased osteogenic differentiation ability in OS. Silencing DUT significantly impairs the mitochondrial function and osteogenic differentiation ability of BMSCs, indicating its potential role in OS development. This study identifies a mitochondrial gene signature in BMSCs linked to osteoporosis, with DUT emerging as a key regulator. DUT silencing impairs mitochondrial function and osteogenic differentiation, suggesting it as a potential therapeutic target for OS.