Optogenetic modeling of wake-like transcriptional progression in human SH-SY5Y neuronal cells

Sleep deprivation induces widespread transcriptional remodeling in the brain, but the extent to which this response arises from sustained neuronal excitation rather than systemic confounders remains unclear. Here we establish a reductionist human neuronal model to isolate the cell-autonomous effects of prolonged depolarization. Optogenetic stimulation of SH-SY5Y cells produced controlled calcium influx and robust induction of activity-dependent genes, enabling precise manipulation of excitation history.

Time-resolved RNA sequencing revealed that sustained excitation partitions transcriptional responses into discrete temporal modules, including early-, mid-, and late-peaking, sustained, biphasic, and suppressed patterns, each with distinct functional signatures. At the pathway level, these modules combine into sequential transcriptional states that evolve directionally across stimulation and recovery. Transitions were asymmetric, indicating excitation-history-dependent reorganization rather than simple reversal.

Cross-dataset comparisons revealed selective concordance between defined temporal modules and in vivo sleep deprivation signatures. Together, these findings demonstrate that sustained neuronal excitation alone can drive staged, wake-like transcriptional progression, linking gene-level temporal dynamics to higher-order regulatory states. A.B.R. was funded by the Perelman School of Medicine, University of Pennsylvania, the EMBO Young Investigators Programme, and the Lister Institute of Preventative Medicine.

This work was supported also by NIH R35GM161590 (to A.B.R.). Present address: National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, 500 032, Telangana, India These authors contributed equally: Shintaro Yamazaki and William Gee.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA Shintaro Yamazaki, Utham K. Reddy Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA Chronobiology and Sleep Institute (CSI), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge Metabolic Research Laboratories, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK The authors declare no competing interests. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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