The Interaction with Nanotopographical Environment regulates nuclear mechanoresponse in mESCs via Histone Demethylase KDM3A

Abstract Cell identity is traditionally viewed as a product of biochemical signalling, yet cells are exposed to defined physical landscapes, whose role in fate control remains unclear. In particular, how pluripotent stem cells integrate nanoscale extracellular cues into gene regulatory programs remains poorly understood. Here, we show that biomimetic substrate nanotopography acts as a potent regulator of naïve pluripotency in mouse embryonic stem cells (mESCs). Using supersonic cluster beam deposition, we generate substrates with defined nanotopography that recapitulate native features of extracellular matrix. We demonstrate that nanotopography induces a mechanically relaxed cell state characterised by reduced adhesion, cellular and nuclear softening, and altered nuclear architecture. These mechanical changes are coupled with chromatin remodelling, including reduced H3K27me3 and H3K9me2, redistribution of H3K9me3, and increased H3K4me3. Transcriptomic analyses reveal suppression of adhesion- and cytoskeleton-associated programs together with the activation of a naïve pluripotency transcriptional signature, including upregulation of Nanog. Mechanistically, we identify the H3K9 demethylase KDM3A as a mechanosensitive epigenetic regulator required for nanotopography-induced Nanog expression. Together, our findings uncover a novel mechanotransductive pathway directly linking extracellular nanotopography to chromatin state and pluripotency control.