Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit

Park, H.; Kim, G.; Shin, J.; Kim, S.-H.; Hwang, E.-b.; Kim, M.; Hwang, T.; Lim, A.; Yoon, G.; Park, J.; Jeon, Y.-w.; Kim, N.-S.; Park, Y.; Yoon, K.-J.

doi:10.64898/2026.04.23.720508

bioRxiv · 10.64898/2026.04.23.720508

Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit

Park, H.·Kim, G.·Shin, J.·Kim, S.-H.·Hwang, E.-b.·Kim, M.·Hwang, T.·Lim, A.·Yoon, G.·Park, J.·Jeon, Y.-w.·Kim, N.-S.·Park, Y.·Yoon, K.-J.

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Abstract

Real-time assessment of human pluripotent stem cell (hPSC) quality is critical for reproducibility and safety in regenerative medicine, yet current methods are invasive, labor-intensive, or highly operator-dependent. We present DeepHOPE (Deep-learning-guided Holotomography for Pluripotency Evaluation), a non-invasive, automatizable, and statistics-driven platform that integrates three-dimensional (3D) refractive index imaging with deep learning to assess pluripotency. DeepHOPE performs robustly across diverse contexts, including germ-layer differentiation, retinoic acid-induced differentiation, and mid-reprogramming cultures, enabling streamlined cell production workflows and improving the efficiency of midbrain dopaminergic neuron differentiation through informed colony selection. Mechanistically, DeepHOPE detects minute colony-scale topological changes that precede molecular loss of pluripotency. These early changes are associated with rapid F-actin remodeling, including apical-to-basal redistribution during early differentiation. Consistent with a functional role for cytoskeletal regulation in state transitions, sustained reduction of actomyosin tension decreases pluripotency, identifying cytoskeletal dynamics as an upstream determinant of early pluripotency exit. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/720508v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1d73508org.highwire.dtl.DTLVardef@1dab29aorg.highwire.dtl.DTLVardef@1039f76org.highwire.dtl.DTLVardef@da29a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Park, H., Kim, G., Shin, J., Kim, S.-H., Hwang, E.-b., Kim, M., Hwang, T., Lim, A., Yoon, G., Park, J., Jeon, Y.-w., Kim, N.-S., Park, Y., Yoon, K.-J.. 2026-04-27. Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit. https://doi.org/10.64898/2026.04.23.720508

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