Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis
BackgroundAlzheimer’s disease (AD) is a common, refractory, progressive neurodegenerative disorder in which cognitive and memory deficits are highly correlated with abnormalities in hippocampal brain regions. There is still a lack of hippocampus-related markers for AD diagnosis and prevention.Method...
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnins.2024.1359631/full |
| _version_ | 1797271415374741504 |
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| author | Yang Chen Zhaoxiang Li Xin Ge Huandi Lv Zuojun Geng |
| author_facet | Yang Chen Zhaoxiang Li Xin Ge Huandi Lv Zuojun Geng |
| author_sort | Yang Chen |
| collection | DOAJ |
| description | BackgroundAlzheimer’s disease (AD) is a common, refractory, progressive neurodegenerative disorder in which cognitive and memory deficits are highly correlated with abnormalities in hippocampal brain regions. There is still a lack of hippocampus-related markers for AD diagnosis and prevention.MethodsDifferently expressed genes were identified in the gene expression profile GSE293789 in the hippocampal brain region. Enrichment analyses GO, KEGG, and GSEA were used to identify biological pathways involved in the DEGs and AD-related group. WGCNA was used to identify the gene modules that are highly associated with AD in the samples. The intersecting genes of the genes in DEGs and modules were extracted and the top ten ranked hub genes were identified. Finally GES48350 was used as a validation cohort to predict the diagnostic efficacy of hub genes.ResultsFrom GSE293789, 225 DEGs were identified, which were mainly associated with calcium response, glutamatergic synapses, and calcium-dependent phospholipid-binding response. WGCNA analysis yielded dark green and bright yellow modular genes as the most relevant to AD. From these two modules, 176 genes were extracted, which were taken to be intersected with DEGs, yielding 51 intersecting genes. Then 10 hub genes were identified in them: HSPA1B, HSPB1, HSPA1A, DNAJB1, HSPB8, ANXA2, ANXA1, SOX9, YAP1, and AHNAK. Validation of these genes was found to have excellent diagnostic performance.ConclusionTen AD-related hub genes in the hippocampus were identified, contributing to further understanding of AD development in the hippocampus and development of targets for therapeutic prevention. |
| first_indexed | 2024-03-07T14:03:24Z |
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| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-03-07T14:03:24Z |
| publishDate | 2024-03-01 |
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| series | Frontiers in Neuroscience |
| spelling | doaj.art-c54ef44a449a40fc9d752a88de7fdddb2024-03-07T04:53:50ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2024-03-011810.3389/fnins.2024.13596311359631Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysisYang Chen0Zhaoxiang Li1Xin Ge2Huandi Lv3Zuojun Geng4Graduate School, Hebei Medical University, Shijiazhuang, ChinaDepartment of Immunology and Pathogenic Biology, Yanbian University Medical College, Yanji, ChinaScience and Education Section, Baoding First Central Hospital, Baoding, ChinaDepartment of Medical Imaging, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Medical Imaging, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaBackgroundAlzheimer’s disease (AD) is a common, refractory, progressive neurodegenerative disorder in which cognitive and memory deficits are highly correlated with abnormalities in hippocampal brain regions. There is still a lack of hippocampus-related markers for AD diagnosis and prevention.MethodsDifferently expressed genes were identified in the gene expression profile GSE293789 in the hippocampal brain region. Enrichment analyses GO, KEGG, and GSEA were used to identify biological pathways involved in the DEGs and AD-related group. WGCNA was used to identify the gene modules that are highly associated with AD in the samples. The intersecting genes of the genes in DEGs and modules were extracted and the top ten ranked hub genes were identified. Finally GES48350 was used as a validation cohort to predict the diagnostic efficacy of hub genes.ResultsFrom GSE293789, 225 DEGs were identified, which were mainly associated with calcium response, glutamatergic synapses, and calcium-dependent phospholipid-binding response. WGCNA analysis yielded dark green and bright yellow modular genes as the most relevant to AD. From these two modules, 176 genes were extracted, which were taken to be intersected with DEGs, yielding 51 intersecting genes. Then 10 hub genes were identified in them: HSPA1B, HSPB1, HSPA1A, DNAJB1, HSPB8, ANXA2, ANXA1, SOX9, YAP1, and AHNAK. Validation of these genes was found to have excellent diagnostic performance.ConclusionTen AD-related hub genes in the hippocampus were identified, contributing to further understanding of AD development in the hippocampus and development of targets for therapeutic prevention.https://www.frontiersin.org/articles/10.3389/fnins.2024.1359631/fullAlzheimer’s diseasecomprehensive analysisWGCNAhippocampibiomarker differentially expressed gene (DEG) selection |
| spellingShingle | Yang Chen Zhaoxiang Li Xin Ge Huandi Lv Zuojun Geng Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis Frontiers in Neuroscience Alzheimer’s disease comprehensive analysis WGCNA hippocampi biomarker differentially expressed gene (DEG) selection |
| title | Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis |
| title_full | Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis |
| title_fullStr | Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis |
| title_full_unstemmed | Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis |
| title_short | Identification of novel hub genes for Alzheimer’s disease associated with the hippocampus using WGCNA and differential gene analysis |
| title_sort | identification of novel hub genes for alzheimer s disease associated with the hippocampus using wgcna and differential gene analysis |
| topic | Alzheimer’s disease comprehensive analysis WGCNA hippocampi biomarker differentially expressed gene (DEG) selection |
| url | https://www.frontiersin.org/articles/10.3389/fnins.2024.1359631/full |
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