Investigating the efficacy and toxicity of partial in vivo reprogramming as a rejuvenation intervention

Partial reprogramming by cyclic expression of Yamanaka factors has been proposed as a rejuvenation strategy, yet evaluating tissue-specific responses and potential risks remains challenging. Here, we reanalyzed RNA-seq data from the liver, kidney, and spleen of aged mice subjected to seven months of partial reprogramming. We used the Adverse Outcome Pathway (AOP) framework to estimate adverse and beneficial signatures, assessed functional changes via gene set enrichment analysis and deconvoluted bulk RNA-seq data to estimate differences in cell type proportion. In the liver and kidney, partial reprogramming suppressed age-activated immune and inflammatory processes, while activating age-suppressed metabolic and catabolic pathways. In the spleen, cell cycle, DNA replication, and DNA damage response programs were prominent, indicative of increased proliferative activity, and cell type deconvolution showed increased proportions of megakaryocyte-erythroid progenitor cells and decreased proportions of natural killer cells, while AOPs flagged a potential risk of sustained genomic and proliferative stress. Based on the existing AOP framework, we did not find any enriched Key Events in the kidney (reprogrammed vs. old). In the liver, AOP analysis identified pathways regulated in opposition to liver steatosis, indicated by activation of nuclear receptor signaling (Ppara, Pparg) and restoration of fatty-acid oxidation and metabolism. Our findings highlight tissue-specific responses to partial reprogramming and emphasize the need for larger, controlled studies to clarify physiological outcomes and safety.