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AIM To evaluate the safety and efficacy of autologous periodontal ligament-derived mesenchymal stem cells (PDL-MSCs) embedded in a xenogeneic bone substitute (XBS) for the regenerative treatment of intra-bony periodontal defects. MATERIAL AND METHODS This quasi-randomized controlled pilot phase II clinical trial included patients requiring a tooth extraction and presence of one intra-bony lesion (1-2 walls). Patients were allocated to either the experimental (XBS + 10x106 PDL-MSCs/100mg) or the control group (XBS). Clinical and radiographical parameters were recorded at baseline, 6, 9 and 12 months. The presence of adverse events was also evaluated. Chi-square, Student`s t-test, U-Mann Whitney, repeated-measures ANOVA and regression models were used. RESULTS Twenty patients were included. No serious adverse events were reported. Patients in the experimental group (n=9) showed greater clinical attachment level (CAL) gain [1.44, standard deviation (SD)=1.87] and probing pocket depth (PPD) reduction (2.33, SD=1.32) than the control group (n=10; CAL gain=0.88, SD=1.68, and PPD reduction=2.10, SD=2.46), without statistically significant differences. CONCLUSION The application of PDL-MSCs to XBS for the treatment of one-two wall intra-bony lesions was safe and resulted in low postoperative morbidity and appropriate healing, although its additional benefit, when compared with the XBS alone, was not demonstrated.