0061 Transcriptional Dynamics of Sleep Deprivation and Subsequent Recovery Sleep in the Male Mouse Cortex

Abstract Introduction Sleep is a critical physiological process governed by circadian and homeostatic mechanisms. The circadian clock controls sleep timing, while the sleep homeostat regulates sleep need (sleep pressure), which increases with wakefulness. Acute sleep deprivation (SD) raises sleep pressure, as measured by frontal cortex polysomnography. This pressure maximizes after 5-6 hours of SD and is largely alleviated with 2-3 hours of recovery sleep (RS). While sleep pressure dynamics are well understood, the molecular mechanisms underlying sleep homeostasis remain largely unexplored despite the established effects of SD on gene transcription. Methods Novel bulk RNA-sequencing data was combined with open-access cortex datasets (n = 3-5) of adult male C57BL/6J mice. Mice underwent SD (3 or 5-6 hours) followed by RS (2 or 6 hours). The remove unwanted variance method was used to normalize the data and correct for lab biases. The edgeR package was used to determine differentially expressed genes (DEGs) with a false discovery rate < 0.05. Functional annotation analysis occurred using the Database for Annotation, Visualization, and Integrated Discovery to understand the DEGs’ functional implications. Results We report that 5-6 hours of SD had the largest effect on gene expression, altering 7,493 genes. SD predominantly repressed gene expression. DEGs associated with circadian rhythm and DNA damage/repair uniquely showed changes at 3 and 5-6 hours of SD but returned to baseline by 2 hours of RS. DEGs that took longer to become uniquely expressed at 5-6 hours and normalized quickly within 2 hours of RS were associated with RNA-binding, chromatin regulation, oxidative phosphorylation, and glutathione metabolism. Conclusion Our findings reveal that gene expression patterns closely track sleep pressure dynamics, potentially illuminating the molecular underpinnings of sleep homeostasis. Most notably, we identified a substantial group of genes that mirror the build-up of sleep pressure during SD and rapidly normalize with RS. These genes regulate critical cellular processes, including DNA repair mechanisms, epigenetic modifications, and oxidative stress responses - pathways that may represent novel therapeutic targets for sleep disorders. Future investigations will focus on manipulating these pathways to understand better how they contribute to the cellular regulation of sleep. Support (if any) R35GM147020 awarded to LP and 3R35GM147020-03S1 to CO.