Effects of trichostatin A and phenamil methanesulfonate treatment on gene expression during osteogenic differentiation of senescent rMSCs

Cell fate transitions are governed by coordinated programs involving epigenetic regulators and lineage-specific transcription factors. RNA sequencing was performed to profile transcriptomic responses of senescent rat mesenchymal stem cells (rMSCs) subjected to a sequential small-molecule treatment paradigm designed to enhance osteogenic competence. TSA treatment increased expression of the epigenetic regulator KDM1B and was associated with activation of early epigenetic/lineage priming programs. Subsequent phenamil treatment increased BMP2 expression and enrichment of BMP-responsive signaling, consistent with activation of downstream osteogenic gene networks. Collectively, this dataset provides a molecular framework for how epigenetic modulation followed by pro-osteogenic signaling can cooperate to restore osteogenic differentiation capacity in senescent rMSCs. Overall design: Senescent rat mesenchymal stem cells (rMSCs) were allocated to experimental groups cultured in osteogenic induction medium, with or without addition of the indicated extracts (TSA and benzyl ether). After 24 hours of treatment to capture early transcriptional responses, total RNA was isolated, sequencing libraries were prepared using standard RNA-seq workflows, and samples were sequenced to generate gene-level expression profiles. Each condition was represented by a single sample (no biological replicates).