Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes

• Published in: Frontiers in immunology Vol. 15; p. 1381765
• Main Authors: Lin, Junhan, Liu, Changyuan, Hu, Ende
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 2024
• Subjects: Animals; Computational Biology - methods; Databases, Genetic; diagnostic model; Disease Models, Animal; drugs; functional gene sets; Gene Expression Profiling; Gene Regulatory Networks; hub genes; Humans; Mice; Mice, Inbred C57BL; MicroRNAs - genetics; Protein Interaction Maps - genetics; sleep disorders; Sleep Wake Disorders - genetics; Sleep Wake Disorders - immunology; Transcriptome; sleep disorders; diagnostic model; hub genes; drugs; functional gene sets
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2024.1381765

Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood.
The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses.
The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis.
In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.