The epigenetic mechanisms of nanotopography-guided osteogenic differentiation of mesenchymal stem cells via high-throughput transcriptome sequencing

BACKGROUND: Nanotopography directs stem cell fate; however, the underlying mechanisms, especially those at the epigenetic level, remain vague. The TiO(2)-nanotube array, a classical example of nanotopography, is a good model to investigate topography–cell interactions because of its good controllability and easy manufacturing process. Previously, we found that a TiO(2)-nanotube array with an optimal diameter promoted osteogenic differentiation of human adipose-tissue-derived stem cells (hASCs). METHODS: We used RNA sequencing and bioinformatics to reveal the overall gene expression profile of hASCs on TiO(2)-nanotube arrays. RESULTS: Bioinformatics analyses revealed that the epigenetic regulatory network plays an important role in TiO(2)-nanotube-guided osteogenic differentiation. Changes in cell adhesion and cytoskeletal reorganization are linked to epigenetic alterations, including upregulation of KDM4E and downregulation of histone deacetylases. Meanwhile, microRNAs, including miR-24-1-5p, miR-24–3 p, miR-154–3 p, miR-154–5 p, miR-433–5 p, miR-589–3 p, and miR-589–5 p were downregulated, whereas miR-186–5 p and miR-770–5 p were upregulated. Long non-coding RNAs, including LINC00941, LINC01279, and ZFAS1, were downregulated in this process. CONCLUSION: Using next-generation sequencing, we illustrated the overall picture of the regulatory mechanisms of TiO(2) nanotubes, thus providing a basis for future clinical applications of nanotopography in the field of bone tissue engineering. Our results offer insights into material-based nanomedicine and epigenetic therapy.