Dissecting the effect of a 3D micro-scaffold on the transcriptome of Neural Stem Cells with computational genomics

3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds there is the Nichoid: an engineered 3D micro-scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular response simply by subjecting the cells to mechanical stimuli. This kind of influence results in different cellular morphology and organization, but the molecular bases of these changes remain largely unknown. Here, we show that the main cellular response to the Nichoid is an alteration of the mechanotransduction, which in turn affects the global cellular activity. Through RNA-seq approach on murine Neural Precursors Stem Cells (NPCs) expanded inside the Nichoid, we investigated the deregulated genes and pathways showing that the Nichoid causes alteration in genes strongly connected to mechanical properties. We found 1934 deregulated RNAs, 81% of which were coding genes. Moreover, we fully dissected this mechanism highlighting how the changes start at a membrane level, with subsequent alterations in the cytoskeleton, signalling pathways, and metabolism, all leading to a final alteration in gene expression. The results shown here demonstrate that the 3D scaffold Nichoid influences the biological and genetic response of stem cells thorough specific alterations of cellular signaling. 3 Neural Precursor Stem Cells (NPCs) grown in standard floating condition (CTRL) and 3 NPCs grown inside the Nichoid (NIC)