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Therapy with mesenchymal stem cells (MSCs) has been reported to provide beneficial effects in the treatment of different disorders. To visualize cells in repair tissue and indicate of their role the superparamagnetic iron oxide nanoparticles (SPIONs) can be used. SPIONs can effectively and quickly label most cells in in vitro, and evidence to date suggests such labeling does not compromise the proliferation or differentiation of cells. However how can the inclusion of SPIONs influences on the functional activity of cells it is unknown. In this study, we have analyzed whether there is any negative influence of SPIONs on cell function in particular on the synthesis of the extracellular matrix (ECM) proteins and their reorganization by matrix metalloproteinases (MMPs) under 3D cell culture conditions. MATERIALS AND METHODS: Human MSCs were incubated with SPIONs (at a Fe concentration of 150 μg/mL) for one day in a CO2-incubator. 3D-sсaffold based on poly (ε-caprolactone) was used for cultivation of cells. The cultivation of MSCs without SPIONs under 2D conditions we used as control. Cells viability and proliferation were assessed by Trypan blue exclusion and MTT assay. The evaluation of the synthesis of the ECM proteins and their reorganization by MMPs by the methods of protein electrophoresis, immunoblotting and zimography was performed on the various terms of cultivation. The samples of medium and scaffolds were analyzed separately. RESULTS AND CONCLUSION: We did not observe any influence of the SPIONs on the viability and proliferative activity of cells. Essential distinctions of the synthesis of the ECM proteins and the MMPs for cells which were containing and not containing SPIONs have been shown. The cells with SPIONs synthesized much more ECM proteins (collagen I and III types, fibronectin etc) and demonstrated more activity of MMPs then control cells. Thus there was not any negative influence of SPIONs on cells function. Opposite the SPIONs increased the synthesis of the ECM proteins and their reorganization by MMPs. The work was supported by a grant from the Russian Science Foundation № 14-50-00068.