Computational discovery and prioritization of ribose-5-phosphate isomerase A as a mitochondrial target for reversing senescence in mesenchymal stem cells

Age-related osteoporosis is increasingly recognized as a disease of stem cell dysfunction, hallmarked by the skewed lineage commitment of mesenchymal stem cells (MSCs) away from osteogenesis towards adipogenesis. This functional decline is closely linked to mitochondrial dysregulation. However, the upstream metabolic regulators that orchestrate this detrimental cell-fate switch, particularly the key nodes at the interface of mitochondrial function and cellular senescence, remain largely unknown, hindering the development of targeted therapies. To address this challenge, we implemented a bioinformatic pipeline analyzing transcriptomes of rat MSCs from GEO. Methodology included transcriptomic profiling and MitoCarta3.0 intersection to identify mitochondria-associated aging genes. A multi-algorithm strategy screened hub genes. Sixteen mitochondria-associated genes were dysregulated in MSC aging. Machine learning consistently identified ribose-5-phosphate isomerase A (RPIA), a key enzyme of the pentose phosphate pathway, as the critical hub. RPIA was up-regulated in aged MSCs, predicting senescence (area under the curve [AUROC] = 0.909). Validation in an independent dataset confirmed RPIA's up-regulation with comparable accuracy (AUROC = 0.917). To further validate the reliability of the results, we selected discarded bone tissue samples from patients aged 20 to 80 years who had undergone osteotomy, which we then examined histologically. The importance and effectiveness of RPIA have been confirmed through analysis of clinical tissue samples. At the same time, under high RPIA levels, the osteogenic potential of bone marrow mesenchymal stromal cells was significantly suppressed (P < 0.01). This study is the first to implicate RPIA in the pathobiology of skeletal aging. We propose RPIA as a metabolic switch driving mitochondrial dysfunction in senescent MSCs. Consequently, RPIA emerges as a novel, high-priority potential therapeutic target for osteoporosis, providing a compelling data-driven foundation for subsequent experimental investigation.