Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation

Yann Vanrobaeys, Zeru J. Peterson, Emily. N. Walsh, Snehajyoti Chatterjee, Li-Chun Lin, Lisa C. Lyons, Thomas Nickl-Jockschat () and Ted Abel ()
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Yann Vanrobaeys: University of Iowa
Zeru J. Peterson: University of Iowa
Emily. N. Walsh: University of Iowa
Snehajyoti Chatterjee: University of Iowa
Li-Chun Lin: University of Iowa
Lisa C. Lyons: Florida State University
Thomas Nickl-Jockschat: University of Iowa
Ted Abel: University of Iowa

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain in male mice. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.

Date: 2023
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DOI: 10.1038/s41467-023-42751-z

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