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bioRxiv · 10.1101/2025.04.21.648791

Short Report: A Meta-Analysis of the Effects of Sleep Deprivation on the Cortical Transcriptome in Animal Models

Rhoads, C. A.·Hagenauer, M. H.·Xiong, J.·Hernandez, E.·Nguyen, D. M.·Saffron, A.·Flandreau, E. I.·Watson, S.·Akil, H.
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Abstract

Sleep deprivation (SD) causes large disturbances in mood and cognition. The molecular basis for these effects can be explored using transcriptional profiling to quantify brain gene expression. In this report, we used a meta-analysis of public transcriptional profiling data to discover SD effects on gene expression that are consistent across studies and paradigms. To conduct the meta-analysis, we used pre-specified search terms related to rodent SD paradigms to identify relevant studies within Gemma, a database containing >19,000 re-analyzed microarray and RNA-Seq datasets. Eight studies met our systematic inclusion/exclusion criteria. These studies characterized the effect of 18 SD interventions on gene expression in the mouse cerebral cortex (collective n=293). For each gene with sufficient data (n=16,290), we fit a random effects meta-analysis model to the SD effect sizes (log(2) fold changes). Our meta-analysis revealed 182 differentially expressed genes in response to SD (false discovery rate: FDR<0.05), most of which (115/182) showed similar effects (FDR<0.05) in an independent large dataset (GSE114845: n=86 RNA-Seq samples from n=222 mice). Gene-set enrichment analysis revealed down-regulation in pathways related to stress response (e.g., glucocorticoid receptor Nr3c1), vasculature, growth and development, and upregulation related to stress, inflammation, and neuropeptide signalling. Exploratory analyses suggested that recovery sleep (included in six contrasts: range: 1-18 hrs), could reverse the impact of SD on gene expression. Our meta-analysis provides a useful reference database illustrating the diverse molecular impact of SD on the rodent cerebral cortex. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/648791v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@52984dorg.highwire.dtl.DTLVardef@8d1174org.highwire.dtl.DTLVardef@174ed85org.highwire.dtl.DTLVardef@195e8bf_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

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Rhoads, C. A., Hagenauer, M. H., Xiong, J., Hernandez, E., Nguyen, D. M., Saffron, A., Flandreau, E. I., Watson, S., Akil, H.. 2025-04-23. Short Report: A Meta-Analysis of the Effects of Sleep Deprivation on the Cortical Transcriptome in Animal Models. https://doi.org/10.1101/2025.04.21.648791

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