Transcriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3

To investigate the transcriptional regulation associated with spheroid formation and biomimetic factor-mediated functional modulation, RNA sequencing was performed on human DPSCs cultured under 2D and 3D conditions with or without spermidine (SPD) and transforming growth factor-β3 (TGF-β3) treatment.

Four experimental groups, including 2D cultured DPSCs (DPSC_2D), ST-GH-treated 2D cultured DPSCs (DPSC_2ST), 3D DPSC spheroids (DPSC_3D), and ST-GH-treated 3D DPSC spheroids (DPSC_3ST), were analyzed. Transcriptomic profiling identified differentially expressed genes associated with extracellular matrix (ECM) organization, cell adhesion, angiogenesis, inflammatory regulation, and tissue regeneration. Comparative analyses revealed that 3D spheroid formation enhanced regenerative-associated transcriptional signatures, while SPD/TGF-β3 treatment further promoted ECM remodeling, angiogenic signaling, and suppression of inflammation-related pathways.