Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor

The study investigates whether evolutionarily conserved metabolic programs underpin regenerative capacity across species and whether such metabolic drivers can be leveraged to enhance tissue repair. Regeneration varies widely across species, being robust in organisms like the axolotl and deer antler and comparatively limited in humans, particularly with aging. Stem cells are central to regeneration in diverse organisms, with axolotl limb regeneration involving blastema stem cells and deer antler regeneration arising from deer antler stem cells (dASCs). Human mesenchymal stem cells (hMSCs) display more limited regenerative abilities that decline with age. Because metabolites are structurally conserved across species, comparative metabolomics offers a promising route to discover conserved metabolic features of regeneration. The authors thus apply cross-species transcriptomic and metabolomic profiling to identify metabolic signatures linked to enhanced regenerative capacity and to uncover metabolites that promote regeneration, identifying fatty acid oxidation pathways and uridine as key features.

Background literature highlights: axolotl as a vertebrate model with high regenerative capacity; deer antler as the only mammalian organ capable of complete annual regeneration; and the decline of regenerative potential with age in most mammals. Prior knowledge establishes that stem cells drive tissue repair across species, with axolotl blastema formation and dASCs expressing mesenchymal stem cell markers. The limited regenerative capacity of human stem cells, which diminishes with age and in progeroid conditions, motivates comparative analysis. Metabolites, being conserved structurally, are posited as ideal read-outs to compare conserved biology across species.

The authors used a comparative multi-omic approach across species and age groups with differential regenerative capacities. Models included: (i) whole-organ regeneration models (axolotl limb blastema at day 0 and day 11 post amputation [DPA 0 and DPA 11], capturing peak axolotl blastema stem cells at DPA 11; and deer antler stem cells from the amputation surface), (ii) human stem cell models (young wild-type hMSCs versus prematurely aged WRN-depleted hMSCs mimicking Werner syndrome), and (iii) non-human primate (NHP) tissues representing young and old states across multiple organs (liver, skeletal muscle, skin, kidney, brain, heart, white adipose tissue) and blood plasma. Transcriptomic profiling was performed via genome-wide RNA sequencing to identify differentially expressed genes (DEGs) and enriched Gene Ontology (GO) terms and pathways associated with regeneration. Metabolomic profiling employed ultrahigh-performance liquid chromatography–mass spectrometry (UPLC-MS/MS) for untargeted metabolomics, with stringent quality control and normalization. Across samples, 400–759 metabolites spanning multiple classes (including lipids) were identified. Comparative analyses focused on convergence of metabolic pathways and genes across models with higher regenerative capacity, with emphasis on mitochondrial organization, energy generation, nucleotide metabolism, and fatty acid oxidation (FAO).

• Cross-species convergence: RNA-seq revealed extensive overlap of DEGs between axolotl and young NHP tissues, with upregulation of regeneration-related GO terms such as response to growth factor and tissue morphogenesis in axolotl DPA 11 blastema and young tissues.
• Metabolism-centric signature: Upregulated DEGs were enriched in metabolic terms including mitochondrial organization, energy generation, and nucleotide metabolic processes.
• FAO gene upregulation: Convergent upregulation of mitochondrial and metabolic pathways included FAO enzymes ACADVL, ACADS, ECH1, and ECI1; ACADVL (catalyzing the first step of mitochondrial FAO) was upregulated in most young tissues. The mitochondrial biogenesis regulator noted as PARG1C4 was also highlighted.
• Metabolomics breadth: Untargeted UPLC-MS/MS metabolomics identified approximately 400–759 metabolites across models after stringent QC and normalization.
• Pathway correlates of regeneration: Active pyrimidine metabolism and fatty acid metabolism correlated with higher regenerative capacity across species and age groups.
• Pro-regenerative metabolite: Uridine, a pyrimidine nucleoside, was identified as a potent regeneration-related metabolite promoting stem cell responses and associated with enhanced regenerative potential.

The comparative profiling supports the hypothesis that conserved metabolic programs underlie regenerative capability. Convergent upregulation of mitochondrial function and fatty acid oxidation genes, alongside enrichment of nucleotide metabolism, indicates that robust energy production and biosynthetic readiness are hallmarks of tissues and models with higher regenerative capacity. The identification of active pyrimidine metabolism and the metabolite uridine links nucleotide metabolism to regenerative responses, suggesting a mechanistic role for pyrimidine availability in supporting stem cell function and tissue repair. These findings underscore metabolism, particularly FAO and pyrimidine pathways, as key regulatory axes for regeneration and point to metabolite-based strategies to enhance repair in less regenerative species.

This study establishes a cross-species metabolic signature of regeneration, highlighting conserved upregulation of mitochondrial and fatty acid oxidation pathways and identifying uridine as a pro-regenerative metabolite. By integrating transcriptomic and metabolomic data from axolotl blastema, deer antler stem cells, human MSCs, and primate tissues across ages, the work provides a foundation for metabolic interventions to enhance tissue repair. Future research should mechanistically dissect how uridine and FAO pathways modulate stem cell function and test translational strategies to harness these pathways for regenerative medicine.