Age-dependent regulation of the replicative senescence molecular program in mesenchymal stem cells: a comparative transcriptomics meta-analysis with methylomics validation

Mesenchymal stem cells (MSCs) hold promises for regenerative medicine, but replicative senescence limits their proliferative capacity and therapeutic utility. Although donor age influences the senescence state of MSC populations, whether it shapes the molecular phenotype of replicative senescence remains unclear. Here, we performed an integrative multi-omics analysis comprising transcriptomics meta-analysis (Lipták's method) and methylomics validation on human MSCs spanning five donor age groups: pluripotent-derived (pMSC), juvenile (jMSC), young adult (yaMSC), middle-aged adult (maMSC), and older adult (oaMSC). Our analysis revealed 28 common genes across all groups, with only CDKN2A (upregulated) and FKBP4 (downregulated) showing consistent directional changes, while 26 genes exhibited donor age-specific patterns. Among these, six genes showed strong age-correlated expression: DPYSL2, TPP1, and ETV6 positively; DBF4, ERH, and HAPLN1 negatively. Functional enrichment revealed universal cell cycle suppression but donor age-specific regulation of G1/S transition, nuclear division, endocytosis, and differentiation. Notably, jMSC uniquely activated DNA damage response and chromatin remodeling pathways. Transcription factor analysis identified 8 consistently regulated TFs (NFKB1, JUN activated; CEBPA, STAT1 repressed) and 46 age-specific TFs, including TP53, GATA6, and RUNX2. Methylomics validation identified 45 (yaMSC), 12 (oaMSC), 16 (maMSC), and 61 (jMSC) concordant multi-omics genes. Our findings demonstrate that MSC replicative senescence is governed by both universal and donor age-specific molecular programs, highlighting the importance of considering donor age in MSC-based therapies and underscoring the need for donor age-tailored approaches for cell rejuvenation and anti-aging strategies.