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Background Recent studies showed that bone marrow-derived mesenchymal stem cells (BMSCs) had risk of ectopic bone formation.In this study,we aimed to investigate the effect of growth and differentiation factor 6 (GDF-6) on the tenogenic differentiation of BMSCs in vitro,and then combined with small intestine submucous (SIS) to promote tendon regeneration in vivo.Methods The BMSCs were isolated from the green fluorescent protein (GFP) rats,and were characterized by multi-differentiation assays following our previous study protocol.BMSCs cultured with different concentrations of GDF-6,without growth factors served as control.After 2 weeks,mRNA expression and protein expression of tendon specific markers were examined by qRT-PCR and West blotting to define an optimal concentration of GDF-6.Mann-Whitney U-test was used to compare the difference in relative mRNA expression among all groups; P ≤0.05 was regarded as statistically significant.The GDF-6 treated BMSCs combined with SIS were implanted in nude mice and SD rat acute patellar tendon injury model,the BMSCs combined with SIS served as control.After 12 and 4 weeks in nude mice and tendon injury model,the samples were collected for histology.Results After the BMSCs were treated with different concentration of GDF-6 for 2 weeks,the fold changes of the specific markers (Tenomodulin and Scleraxis) mRNA expression were significantly higher in GDF-6 (20 ng/ml) group (P ≤0.05),which was also confirmed by West blotting result.The BMSCs became parallel in orientation after GDF-6 (20 ng/ml) treatment,but the BMSCs in control group were randomly oriented.The GDF-6 (20 ng/ml) treated BMSCs were combined with SIS,and were implanted in nude mice for 12 weeks,the histology showed neo-tendon formation.In the SD rat patellar tendon window injury model,the histology also indicated the GDF-6 (20 ng/ml) treated BMSCs combined with SIS could promote tendon regeneration.Conclusions GDF-6 has tenogenic effect on the tenogenic differentiation of BMSCs,and GDF-6 (20 ng/ml) has better tenogenic effect compared to other concentrations.The GDF-6 (20 ng/ml) treated BMSCs combined with SIS can form neo-tendons and promote tendon regeneration.