Nota, M. H. C. | Search bioRxiv

bioRxiv2026

Subcortical recruitment dissociates isoflurane emergence from distinct wakeful states in mice

Emergence from general anesthesia, defined by a recovery of consciousness to the wakeful state, is a clinically consequential state transition that remains a passive process dependent on drug clearance. Despite the critical use of anesthesia, the neural circuitry underlying behavioral recovery remains poorly defined. Here, we map whole-brain neural activity during emergence from isoflurane anesthesia in mice using Fos immunolabeling, tissue clearing, and light-sheet microscopy. This approach enables unbiased quantification of neural activity at cellular resolution across the intact whole brain and supports subsequent network analysis. Rather than resembling wakefulness, emergence exhibits widespread cortical suppression alongside selective activation of discrete subcortical nuclei. This pattern of activity includes both previously implicated arousal-related regions and lesser-studied structures linked to respiratory, autonomic, interoceptive, and cerebellar function. By comparing emergence to two behaviorally distinct wakeful control states, we find that control state selection substantially shapes interpretation of whole-brain activity maps. This establishes dual-state comparisons as a broadly useful strategy for state-dependent circuit mapping. Functional network analysis further elucidates candidate central regions that strongly covary together during emergence, with the most integrated region being the ventral orbital cortex. This approach allows for targeted causal investigation, linking brain-wide circuit discovery with future hypothesis-driven mechanistic interrogation. Together, we find that emergence from isoflurane anesthesia reflects selective subcortical recruitment rather than broad global reactivation toward wakefulness. Significance StatementMillions of people undergo general anesthesia each year. While anesthetic unconsciousness is induced rapidly, emergence from altered consciousness is unpredictable. Neural mechanisms that underlie behavioral emergence remain poorly defined. Using whole-brain Fos mapping at cellular resolution, we found that emergence from isoflurane anesthesia is characterized by widespread cortical suppression alongside selective activation of discrete subcortical, autonomic, hindbrain, and cerebellar nuclei. This selective systems-level activity pattern identifies behavioral emergence as more than a simple global return toward wakefulness and highlights underappreciated neural circuitry involved in post-anesthetic recovery. Network analysis of the Fos maps further identifies candidate regions for targeted causal investigation of emergence-related regions.

neuroscience↗

bioRxiv2025

Synthetic modulation of brain-wide anesthesia-activated neural ensembles using a transgenic mouse system

BackgroundGeneral anesthesia is commonly used to produce unconsciousness across species, though the underlying neural substrates remain poorly understood. Here we test the hypothesis that isoflurane anesthesia produces unconsciousness by targeting discrete cell types and neural circuits distributed brain-wide, rather than by brain-wide non-specific binding or binding exclusively within single brain regions. MethodsWe take advantage of a transgenic mouse system that expresses chemogenetic designer receptors exclusively activated by a designer drug (DREADDs) in an inducible Cre-dependent manner driven by Fos immediate early gene expression. Since Fos peaks with metabolic activity, we use this system to insert DREADDs brain-wide into neurons that are active under isoflurane anesthesia. We then test the effects of chemogenetic manipulation of brain-wide anesthesia-activated neural ensembles on behavior, in the absence of isoflurane. ResultsUsing iDisco+ intact brain clearing and light sheet microscopy, we describe brain-wide expression of the captured neurons revealing sparse, heterogeneous and spatially distributed cells. We quantify dense labeling across mesolimbic pathways that include the amygdala, hypothalamus, thalamus, and hindbrain nuclei, implicating these regions as candidate mediators of the anesthetic state. Chemogenetic manipulation of the brain-wide activated neural ensembles reproduces key components of anesthesia, including immobility and thermal anti-nociception. We observe significantly increased isoflurane sensitivity, though not a complete loss of consciousness as measured by the righting reflex, suggesting alternative mechanisms contribute to unconsciousness that are not captured by specific neural signatures. ConclusionsWe provide causal evidence that isoflurane anesthesia engages discrete, distributed brain-wide circuitry, recapitulating dissociable components of general anesthesia. Significance StatementOver 300 million people worldwide undergo general anesthesia each year, yet the neural circuit mechanisms that produce unconsciousness remain unresolved. This fundamental gap limits the development of safer anesthetic strategies and hinders efforts to understand long-term cognitive consequences. Here we define the intact brain-wide neural signatures of isoflurane anesthesia-induced unconsciousness using a transgenic mouse system. We capture brain-wide neurons that are activated by isoflurane, manipulate those ensembles using chemogenetic tools and characterize their spatial representations at the cellular resolution using light sheet microscopy. Together, our data provides causal evidence that anesthesia engages discrete, distributed brain-wide circuitry, offering a systems-level framework for understanding how unconsciousness is generated.

neuroscience↗