Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics
ObjectiveDementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are collectively known as Lewy body dementia (LBD). Considering the heterogeneous nature of LBD and the different constellations of symptoms with which patients can present, the exact molecular mechanism underlying...
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Neurology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fneur.2023.1029370/full |
| _version_ | 1811157777114988544 |
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| author | Jing Xu Jia Li Ya-juan Sun Wei Quan Li Liu Qing-hui Zhang Yi-dan Qin Xiao-chen Pei Hang Su Jia-jun Chen |
| author_facet | Jing Xu Jia Li Ya-juan Sun Wei Quan Li Liu Qing-hui Zhang Yi-dan Qin Xiao-chen Pei Hang Su Jia-jun Chen |
| author_sort | Jing Xu |
| collection | DOAJ |
| description | ObjectiveDementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are collectively known as Lewy body dementia (LBD). Considering the heterogeneous nature of LBD and the different constellations of symptoms with which patients can present, the exact molecular mechanism underlying the differences between these two isoforms is still unknown. Therefore, this study aimed to explore the biomarkers and potential mechanisms that distinguish between PDD and DLB.MethodsThe mRNA expression profile dataset of GSE150696 was acquired from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between 12 DLB and 12 PDD were identified from Brodmann area 9 of human postmortem brains using GEO2R. A series of bioinformatics methods were applied to identify the potential signaling pathways involved, and a protein–protein interaction (PPI) network was constructed. Weighted gene co-expression network analysis (WGCNA) was used to further investigate the relationship between gene co-expression and different LBD subtypes. Hub genes that are strongly associated with PDD and DLB were obtained from the intersection of DEGs and selected modules by WGCNA.ResultsA total of 1,864 DEGs between PDD and DLB were filtered by the online analysis tool GEO2R. We found that the most significant GO- and KEGG-enriched terms are involved in the establishment of the vesicle localization and pathways of neurodegeneration-multiple diseases. Glycerolipid metabolism and viral myocarditis were enriched in the PDD group. A B-cell receptor signaling pathway and one carbon pool by folate correlated with DLB in the results obtained from the GSEA. We found several clusters of co-expressed genes which we designated by colors in our WGCNA analysis. Furthermore, we identified seven upregulated genes, namely, SNAP25, GRIN2A, GABRG2, GABRA1, GRIA1, SLC17A6, and SYN1, which are significantly correlated with PDD.ConclusionThe seven hub genes and the signaling pathways we identified may be involved in the heterogeneous pathogenesis of PDD and DLB. |
| first_indexed | 2024-04-10T05:13:04Z |
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| id | doaj.art-c9c1b0ae71b44042994f7d8e909df05f |
| institution | Directory Open Access Journal |
| issn | 1664-2295 |
| language | English |
| last_indexed | 2024-04-10T05:13:04Z |
| publishDate | 2023-03-01 |
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| series | Frontiers in Neurology |
| spelling | doaj.art-c9c1b0ae71b44042994f7d8e909df05f2023-03-09T06:31:27ZengFrontiers Media S.A.Frontiers in Neurology1664-22952023-03-011410.3389/fneur.2023.10293701029370Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformaticsJing XuJia LiYa-juan SunWei QuanLi LiuQing-hui ZhangYi-dan QinXiao-chen PeiHang SuJia-jun ChenObjectiveDementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are collectively known as Lewy body dementia (LBD). Considering the heterogeneous nature of LBD and the different constellations of symptoms with which patients can present, the exact molecular mechanism underlying the differences between these two isoforms is still unknown. Therefore, this study aimed to explore the biomarkers and potential mechanisms that distinguish between PDD and DLB.MethodsThe mRNA expression profile dataset of GSE150696 was acquired from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between 12 DLB and 12 PDD were identified from Brodmann area 9 of human postmortem brains using GEO2R. A series of bioinformatics methods were applied to identify the potential signaling pathways involved, and a protein–protein interaction (PPI) network was constructed. Weighted gene co-expression network analysis (WGCNA) was used to further investigate the relationship between gene co-expression and different LBD subtypes. Hub genes that are strongly associated with PDD and DLB were obtained from the intersection of DEGs and selected modules by WGCNA.ResultsA total of 1,864 DEGs between PDD and DLB were filtered by the online analysis tool GEO2R. We found that the most significant GO- and KEGG-enriched terms are involved in the establishment of the vesicle localization and pathways of neurodegeneration-multiple diseases. Glycerolipid metabolism and viral myocarditis were enriched in the PDD group. A B-cell receptor signaling pathway and one carbon pool by folate correlated with DLB in the results obtained from the GSEA. We found several clusters of co-expressed genes which we designated by colors in our WGCNA analysis. Furthermore, we identified seven upregulated genes, namely, SNAP25, GRIN2A, GABRG2, GABRA1, GRIA1, SLC17A6, and SYN1, which are significantly correlated with PDD.ConclusionThe seven hub genes and the signaling pathways we identified may be involved in the heterogeneous pathogenesis of PDD and DLB.https://www.frontiersin.org/articles/10.3389/fneur.2023.1029370/fullLewy body dementiasdementia with Lewy bodiesParkinson's disease dementiaweighted gene co-expression network analysishub genebiomarker |
| spellingShingle | Jing Xu Jia Li Ya-juan Sun Wei Quan Li Liu Qing-hui Zhang Yi-dan Qin Xiao-chen Pei Hang Su Jia-jun Chen Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics Frontiers in Neurology Lewy body dementias dementia with Lewy bodies Parkinson's disease dementia weighted gene co-expression network analysis hub gene biomarker |
| title | Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics |
| title_full | Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics |
| title_fullStr | Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics |
| title_full_unstemmed | Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics |
| title_short | Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics |
| title_sort | identification of key genes and signaling pathways associated with dementia with lewy bodies and parkinson s disease dementia using bioinformatics |
| topic | Lewy body dementias dementia with Lewy bodies Parkinson's disease dementia weighted gene co-expression network analysis hub gene biomarker |
| url | https://www.frontiersin.org/articles/10.3389/fneur.2023.1029370/full |
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