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Bioinformatics identification and experimental validation of hub genes associated with narcolepsy type 1

Published online by Cambridge University Press:  02 January 2026

Di Wang
Affiliation:
Department of Neurology, First Hospital of Tsinghua University , Beijing, China
Yangyue Cao
Affiliation:
Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
Haiyan Gou
Affiliation:
Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
Yu Zhang
Affiliation:
Department of Neurology, First Hospital of Tsinghua University , Beijing, China
Juan Li
Affiliation:
Department of Neurology, First Hospital of Tsinghua University , Beijing, China
Yulan Zhu
Affiliation:
Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
Yujuan Jiao*
Affiliation:
Department of Neurology, First Hospital of Tsinghua University , Beijing, China
*
Corresponding author: Y. Jiao; Email: yjj271776@gmail.com
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Abstract

Introduction:

Narcolepsy type 1 (NT1) is a chronic neurological disorder with a genetic predisposition, yet its precise molecular pathogenesis remains unclear. Despite increasing recognition of its clinical and genetic basis, the precise molecular mechanisms remain unclear. This study aimed to identify NT1-associated hub genes and investigate their biological functions and interactions through comprehensive bioinformatics analysis, followed by experimental validation.

Methods:

NT1-related microarray data (GSE21592) were retrieved from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using integrated analysis with R software and the GEO2R platform. Functional enrichment analyses for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were conducted using Database for Annotation, Visualization, and Integrated Discovery online tool. Protein–protein interaction (PPI) networks were constructed using STRING database and visualized with Cytoscape. Quantitative real-time PCR (qRT-PCR) was used to experimentally validate the expression of identified hub genes in NT1 patients.

Results:

A total of 148 DEGs were identified. GO analysis revealed involvement primarily in biosynthesis, humoral immune response, viral gene expression, oxidoreductase activity, cytoplasmic translation, etc. KEGG analysis showed enrichment in oxidative phosphorylation, ribosomal pathways, thermogenesis, and glutathione metabolism pathways. Five hub genes – CREB1, PIK3R1, MED1, GATA3, and KDM5A – were identified from the PPI network. qRT-PCR validation confirmed significantly reduced expression of these genes in NT1 patients compared to healthy controls.

Conclusions:

Our study identified and experimentally validated five critical hub genes associated with NT1, providing new insights into its molecular mechanisms and highlighting potential therapeutic targets for future research and clinical intervention strategies.

Information

Type
Research Article
Creative Commons
Creative Common License - CCCreative Common License - BYCreative Common License - NC
This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial licence (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original article is properly cited. The written permission of Cambridge University Press or the rights holder(s) must be obtained prior to any commercial use.
Copyright
© The Author(s), 2026. Published by Cambridge University Press on behalf of Association for Clinical and Translational Science
Figure 0

Figure 1. Differential expression analysis of NT1. Heatmap illustrating DEGs in GSE21592 dataset between NT1 and healthy control groups. DEGs, differentially expressed genes; NT1, narcolepsy type 1.

Figure 1

Table 1. Upregulated differentially expressed genes [16]

Figure 2

Table 2. Top 10 downregulated DEGs identified in patients with NT1 compared with controls. (The full list of downregulated DEGs is provided in Supplementary Table S2)

Figure 3

Figure 2. Functional enrichment analysis based on screened DEGs. GO (cellular component, biological process, and molecular function) enrichment analyses of genes commonly upregulated and downregulated in NT1 group.

Figure 4

Figure 3. Machine learning in screening candidate diagnostic biomarkers. The top functional pathways associated with genes in KEGG enrichment analysis of common DEGs from GSE21592.

Figure 5

Figure 4. Protein–protein interaction (PPI) networks of DEGs. (a) PPI network constructed with the DEGs without further processing. (b) The top-scoring module was identified from the PPI network using the MCODE method.

Figure 6

Table 3. Central hub genes identified in PPI network

Figure 7

Figure 5. Validation of hub genes in peripheral blood from the HC and NT1 groups. a. Boxplots with jittered individual data points show relative mRNA expression for CREB1, PIK3R1, MED1, GATA3, and KDM5A in peripheral blood from healthy controls (HC, n = 10) and narcolepsy type 1 (NT1, n = 10). Each dot represents one participant. Boxes indicate the median and interquartile range (IQR); whiskers extend to 1.5×IQR. b–f. ROC curve analysis of CREB1 (b), PIK3R1 (c), MED1 (d), GATA3 (e), and KDM5A (f) based on expression levels in NT1 patients. AUC: area under the ROC curve; CI: confidence interval; ROC: receiver operating characteristic; HC: healthy control; NT1: narcolepsy type 1.

Figure 8

Table 4. Demographic and clinical characteristics of narcolepsy type 1 (NT1) patients and healthy controls (HC)

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