A magnetogenetic atlas of cytoskeleton-resolved gene regulation in mesenchymal stem cells

Mechanical force is a universal language of cells, yet which transcripts report tension on individual cytoskeletal polymers has remained unknown. Existing stretchers and drugs distort every filament simultaneously, blurring the signal. Here we apply a magnetogenetic approach, using antibody-guided 10 nm Fe₃O₄ nanoparticles to exert ∼0.5 pN force on β-actin, α-tubulin, or vimentin in human mesenchymal stem cells, and record the 20-h transcriptional response by bulk RNA-seq. Tension on microtubules amplifies Wnt, focal-adhesion, and extracellular-matrix modules; vimentin loading activates Hippo signalling, DNA-replication, and cell-cycle engines; actin loading elicits a TGF-β-centred oxidative-stress and ferroptosis programme, revealing a striking division of labour among the three polymers. Only four genes: KLHL24, RGS4, FMN2, and PDE4DIP are shared across the 384-405 differentially expressed transcripts per condition, exposing an orthogonal "filament code" for mechanosensation. The data overturn the view that the cytoskeleton transmits force through common pathways and identify a minimal, four-gene set that reports intracellular tension regardless of where it is applied. Because magnetic fields penetrate tissue centimetres deep and can be shaped in space and time, this platform offers a non-invasive route to steer stem-cell migration (via tubulin), proliferation (via vimentin), or cytoprotection (via actin), informing the design of mechano-responsive biomaterials and remotely controllable cell therapies. STATEMENT OF SIGNIFICANCE: Cells sense mechanical forces, but standard stretch devices and drugs activate the whole cytoskeleton at once, making it hard to isolate each filament's role. We used antibody-guided 10 nm Fe₃O₄ nanoparticles to apply ∼0.5 pN tension specifically to actin, microtubules, or vimentin in mesenchymal stem cells, then read out the 20 h response by RNA sequencing. Each filament triggers a largely distinct gene program, with only four shared genes, revealing a simple filament code for force signaling. This resolves a long-standing assignment problem and provides testable markers of intracellular tension. Because magnetic fields penetrate tissue and are easily shaped, our strategy suggests non-invasive ways to guide migration, proliferation, or cytoprotection, informing mechano-responsive biomaterials and remotely controllable cell therapies.