A high-throughput all-optical platform for mapping gene perturbations to electrophysiology

Zhang, J.; Gong, D.; Barrios, A. M.; Itkis, D. G.; Sahni, K.; Fandl, H.; Uenaka, T.; Walton, R. T.; Plutkis, S. E.; Lavis, L.; Blainey, P. C.; Wernig, M.; Nehme, R.; Lee, R. T.; Fraenkel, E.; Farhi, S. L.; Cohen, A. E.

doi:10.64898/2026.11.09.765233

bioRxiv · 10.64898/2026.11.09.765233

A high-throughput all-optical platform for mapping gene perturbations to electrophysiology

Zhang, J.·Gong, D.·Barrios, A. M.·Itkis, D. G.·Sahni, K.·Fandl, H.·Uenaka, T.·Walton, R. T.·Plutkis, S. E.·Lavis, L.·Blainey, P. C.·Wernig, M.·Nehme, R.·Lee, R. T.·Fraenkel, E.·Farhi, S. L.·Cohen, A. E.

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Abstract

Electrical phenotyping remains a bottleneck in linking genes to cellular function. We developed a high-throughput all-optical electrophysiology platform combining an engineered human induced pluripotent stem cell (hiPSC) line, wide-field voltage imaging, and automated analysis. The hiPSC line integrates inducible NGN2, CRISPR interference, and degron-gated expression of Voltron2 and CheRiff, enabling neuronal differentiation, targeted gene knockdown, and optical electrophysiology. The microscope records approximately 1,500 spiking glutamatergic neurons at 800 Hz across a 4x4 mm field, with larger fields supporting approximately 3,000 neurons at 660 Hz. Automated analysis extracts single-cell voltage traces and quantifies firing patterns, action-potential waveforms, and subthreshold dynamics. Arrayed knockdown of five sodium- and potassium-channel genes produced distinct electrophysiological phenotypes. The engineered hiPSC line also supported optical electrophysiology recordings from motor neurons, astrocytes, and cardiomyocytes. These results establish a scalable platform for high-throughput electrophysiological phenotyping and functional genomics in hiPSC-derived cells.

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Zhang, J., Gong, D., Barrios, A. M., Itkis, D. G., Sahni, K., Fandl, H., Uenaka, T., Walton, R. T., Plutkis, S. E., Lavis, L., Blainey, P. C., Wernig, M., Nehme, R., Lee, R. T., Fraenkel, E., Farhi, S. L., Cohen, A. E.. 2026-11-11. A high-throughput all-optical platform for mapping gene perturbations to electrophysiology. https://doi.org/10.64898/2026.11.09.765233

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