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

Sixteen mitochondria-associated genes were dysregulated in MSC aging, identified through transcriptomic profiling intersected with MitoCarta3.0.

• The methodology combined transcriptomic profiling of rat MSCs from GEO datasets with intersection against MitoCarta3.0 to identify mitochondria-associated aging genes.
• A multi-algorithm machine learning strategy was used to screen hub genes from among these 16 dysregulated mitochondria-associated genes.
• The bioinformatic pipeline analyzed transcriptomes of rat MSCs obtained from publicly available GEO datasets.

RPIA was consistently identified by machine learning as the critical hub gene among mitochondria-associated aging genes in MSCs.

• Multiple machine learning algorithms were applied, and RPIA (ribose-5-phosphate isomerase A) was consistently selected as the top hub gene across algorithms.
• RPIA is a key enzyme of the pentose phosphate pathway.
• RPIA was found to be up-regulated in aged MSCs.
• The study describes RPIA as 'a metabolic switch driving mitochondrial dysfunction in senescent MSCs.'

RPIA upregulation in aged MSCs predicted senescence with high accuracy in both discovery and validation datasets.

• In the primary dataset, RPIA predicted MSC senescence with an area under the ROC curve (AUROC) of 0.909.
• Validation in an independent dataset confirmed RPIA upregulation with comparable predictive accuracy (AUROC = 0.917).
• The consistent performance across datasets supports the reliability of RPIA as a biomarker of MSC senescence.

Clinical tissue samples from patients aged 20 to 80 years confirmed the importance and upregulation of RPIA in skeletal aging.

• Discarded bone tissue samples were obtained from patients aged 20 to 80 years who had undergone osteotomy.
• Samples were examined histologically to validate computational findings.
• Analysis of clinical tissue samples confirmed the importance and effectiveness of RPIA as identified in the bioinformatic analysis.

High RPIA levels significantly suppressed the osteogenic potential of bone marrow mesenchymal stromal cells.

• Under high RPIA expression conditions, osteogenic potential of bone marrow mesenchymal stromal cells was significantly suppressed (P < 0.01).
• This finding links elevated RPIA to the skewed lineage commitment of MSCs away from osteogenesis towards adipogenesis observed in age-related osteoporosis.
• This represents the first study to implicate RPIA in the pathobiology of skeletal aging.

Age-related osteoporosis is characterized by skewed MSC lineage commitment away from osteogenesis towards adipogenesis, closely linked to mitochondrial dysregulation.

• The functional decline of MSCs in aging is described as 'hallmarked by the skewed lineage commitment of mesenchymal stem cells away from osteogenesis towards adipogenesis.'
• This functional decline is stated to be 'closely linked to mitochondrial dysregulation.'
• Prior to this study, the upstream metabolic regulators orchestrating this cell-fate switch at the interface of mitochondrial function and cellular senescence were described as 'largely unknown.'