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Integrated transcriptomic identification and validation reveal key autophagy-associated biomarkers in sleep deprivation

bioinformatics
genomics
neurology
statistics

Abstract

Background. Sleep deprivation (SD) is harmful to individuals, but its pathogenesis is not clarified.

Objective. This study seeks to identify SD-linked autophagy genes via integrated transcriptomic and experimental validation approaches.

Methods. The SD dataset was from the GEO database, and differentially expressed genes (DEGs) were identified. Combined with the autophagy-related genes of GeneCards, autophagy-related DEGs screening and functional enrichment analysis were carried out. The hub genes were obtained by Machine Learning(ML) algorithms. The expression of hub genes was validated utilizing both internal and external datasets. In parallel, an SD rat model was established by subjecting male Sprague-Dawley rats to continuous SD for seven consecutive days. Brain tissues from the prefrontal cortex and hippocampus were subsequently analyzed via real-time quantitative polymerase chain reaction (RT-qPCR) to validate the expression of hub genes. The hub genes were verified by nomogram analysis and ROC curve evaluation. The immune landscape of SD was explored through ssGSEA analysis. The cellular localization and biological functions of the hub genes were determined through single-cell RNA sequencing and gene set enrichment analysis. A ceRNA network centered on the hub genes was constructed, and potential drug targets linked to these hub genes were predicted.

Results. We identified three significantly expressed Hub genes: CDKN1A, HSPA5, and NR4A1, with the diagnostic model exhibiting high predictive power. Analysis of immune cell infiltration results demonstrated a close correlation between the three hub genes associated with SD and interactions with immune cells. Single-cell RNA sequencing analysis determined that monocytes may play a crucial role under SD conditions.

Conclusion. CDKN1A, HSPA5, and NR4A1 can be utilized as potential molecular biomarkers following SD.

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