Identification of hub genes correlated with sleep deprivation using co-expression analysis

Molecular basis identification and hypnotic drug interactions for cognitive impairment related to sleep deprivation

Chronic sleep deprivation can lead to cognitive impairment which makes it difficult to think, focus, and make comprehensive decisions. This in turn leads to the progression and increased risk of several diseases. This study aimed to explore potential drug targets and biomarkers underlying the increased disease risk due to sleep deprivation, including stress responses, immune dysfunction, and metabolic dysregulation. Four datasets namely GSE40562, GSE98566, GSE98582 for sleep deprivation, and GSE26576 normal brain cells were utilized to understand the molecular basis and potential drug targets associated with sleep deprivation. The GEO2R tool, Robust rank aggregations, and Venny were used to retrieve the common DEGs. Functional gene and pathway analyses were carried out via GO and the KEGG analyses. The STRING and CytoHuba plugins were utilized to identify the protein-protein interactions (PPIs) as well as the hub genes in the main PPI subnetworks following the drug interaction of the hub genes and GEPIA-based survival analysis of the DEGs. A total of 160 common DEGs were retrieved from all four datasets. Among them, 65 were down-regulated and 95 were up-regulated. TOP2A, AURKB, NEFL, CDC42, ASPM, GAP43, PVALB, NUF2, CALM1, TPR, KIF5B, KIF15, TROAP, NDC80, PBK, MKI67, SST, AHSP, ALAS2, and NEFH were retrieved as hub genes. While based on drug interaction, survival analysis and gene expression profile eight hub gene named TOP2A, AURKB, PVALB, CALM1, KIF5B, PBK, MKI67, and SST were found to be potential drug candidates and significantly correlated with infiltration levels of CD8 + T cells, B cells, macrophages, CD4 + T cells, neutrophils, and dendritic cells. These genes might play a role in sleep disorders via various pathways associated with neurodegeneration and diseases, potentially serving as biomarkers to support treatment and diagnosis.

Altered hippocampal transcriptome dynamics following sleep deprivation

Widespread sleep deprivation is a continuing public health problem in the United States and worldwide affecting adolescents and adults. Acute sleep deprivation results in decrements in spatial memory and cognitive impairments. The hippocampus is vulnerable to acute sleep deprivation with changes in gene expression, cell signaling, and protein synthesis. Sleep deprivation also has long lasting effects on memory and performance that persist after recovery sleep, as seen in behavioral studies from invertebrates to humans. Although previous research has shown that acute sleep deprivation impacts gene expression, the extent to which sleep deprivation affects gene regulation remains unknown. Using an unbiased deep RNA sequencing approach, we investigated the effects of acute sleep deprivation on gene expression in the hippocampus. We identified 1,146 genes that were significantly dysregulated following sleep deprivation with 507 genes upregulated and 639 genes downregulated, including protein coding genes and long non-coding RNAs not previously identified as impacted by sleep deprivation. Notably, genes significantly upregulated after sleep deprivation were associated with RNA splicing and the nucleus. In contrast, downregulated genes were associated with cell adhesion, dendritic localization, the synapse, and postsynaptic membrane. Furthermore, we found through independent experiments analyzing a subset of genes that three hours of recovery sleep following acute sleep deprivation was sufficient to normalize mRNA abundance for most genes, although exceptions occurred for some genes that may affect RNA splicing or transcription. These results clearly demonstrate that sleep deprivation differentially regulates gene expression on multiple transcriptomic levels to impact hippocampal function.