: Two-dimensional (2D) models fail to mimic a three-dimensional (3D) environment in studying mechanosensing of stem cells. Here, we present a 3D culture model to investigate how 3D matrix stiffness influences YAP activation and osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) and evaluate the osteogenic potential of hydrogels in vivo. In this study, a 3D culture model with an adjustable matrix stiffness was established. In the in vitro study, first the osteogenic differentiation of hPDLSCs by the expression of OCN, ALP, COL-1, and RUNX-2 was assessed using qRT-PCR, accompanied by ALP staining, and then YAP expression was evaluated by immunofluorescence. In the in vivo study, hPDLSCs, together with gelatin methacrylate (GelMA) hydrogels of different stiffnesses, were implanted into a rat alveolar bone defect model. As matrix stiffness increased, hPDLSCs showed reduced spreading and significantly decreased expression of OCN, ALP, COL-1, RUNX-2, and YAP activation. Specifically, COL-1 expression in the low-stiffness group was 4.3-fold higher than that in the high-stiffness group, and the YAP nuclear/cytoplasmic ratio under low stiffness was 5.5-fold greater than that under high stiffness at day 7. In vivo, the soft-matrix-cell-laden group exhibited more new bone (86.04%) and collagen formation (74.43%) in the defect area than other groups at week 6. Reduced matrix stiffness likely promotes hPDLSC proliferation, spreading, and osteogenic differentiati
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