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Cruchaga C, Ali M, Shen Y, Do A, Wang L, Western D, Liu M, Beric A, Budde J, Gentsch J, Schindler S, Morris J, Holtzman D, Fernández M, Ruiz A, Alvarez I, Aguilar M, Pastor P, Rutledge J, Oh H, Wilson E, Le Guen Y, Khalid R, Robins C, Pulford D, Ibanez L, Wyss-Coray T, Ju Sung Y. Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-3631708. [PMID: 38410465 PMCID: PMC10896368 DOI: 10.21203/rs.3.rs-3631708/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Changes in Amyloid-β (A), hyperphosphorylated Tau (T) in brain and cerebrospinal fluid (CSF) precedes AD symptoms, making CSF proteome a potential avenue to understand the pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 proteins dysregulated in AD, that were further validated in a third totally independent cohort. Machine learning was implemented to create and validate highly accurate and replicable (AUC>0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD and those AD cases with faster progression. The associated proteins cluster in four different protein pseudo-trajectories groups spanning the AD continuum and were enrichment in specific pathways including neuronal death, apoptosis and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfuncton(mid-stages), brain plasticity and longevity (mid-stages) and late microglia-neuron crosstalk (late stages).
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Affiliation(s)
| | | | | | - Anh Do
- Washington University School of Medicine
| | - Lihua Wang
- Washington University School of Medicine
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca MútuaTerrassa, Terrassa, Barcelona, Spain
| | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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Lai Y, Lin P, Lin F, Chen M, Lin C, Lin X, Wu L, Zheng M, Chen J. Identification of immune microenvironment subtypes and signature genes for Alzheimer's disease diagnosis and risk prediction based on explainable machine learning. Front Immunol 2022; 13:1046410. [PMID: 36569892 PMCID: PMC9773397 DOI: 10.3389/fimmu.2022.1046410] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Background Using interpretable machine learning, we sought to define the immune microenvironment subtypes and distinctive genes in AD. Methods ssGSEA, LASSO regression, and WGCNA algorithms were used to evaluate immune state in AD patients. To predict the fate of AD and identify distinctive genes, six machine learning algorithms were developed. The output of machine learning models was interpreted using the SHAP and LIME algorithms. For external validation, four separate GEO databases were used. We estimated the subgroups of the immunological microenvironment using unsupervised clustering. Further research was done on the variations in immunological microenvironment, enhanced functions and pathways, and therapeutic medicines between these subtypes. Finally, the expression of characteristic genes was verified using the AlzData and pan-cancer databases and RT-PCR analysis. Results It was determined that AD is connected to changes in the immunological microenvironment. WGCNA revealed 31 potential immune genes, of which the greenyellow and blue modules were shown to be most associated with infiltrated immune cells. In the testing set, the XGBoost algorithm had the best performance with an AUC of 0.86 and a P-R value of 0.83. Following the screening of the testing set by machine learning algorithms and the verification of independent datasets, five genes (CXCR4, PPP3R1, HSP90AB1, CXCL10, and S100A12) that were closely associated with AD pathological biomarkers and allowed for the accurate prediction of AD progression were found to be immune microenvironment-related genes. The feature gene-based nomogram may provide clinical advantages to patients. Two immune microenvironment subgroups for AD patients were identified, subtype2 was linked to a metabolic phenotype, subtype1 belonged to the immune-active kind. MK-866 and arachidonyltrifluoromethane were identified as the top treatment agents for subtypes 1 and 2, respectively. These five distinguishing genes were found to be intimately linked to the development of the disease, according to the Alzdata database, pan-cancer research, and RT-PCR analysis. Conclusion The hub genes associated with the immune microenvironment that are most strongly associated with the progression of pathology in AD are CXCR4, PPP3R1, HSP90AB1, CXCL10, and S100A12. The hypothesized molecular subgroups might offer novel perceptions for individualized AD treatment.
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Affiliation(s)
- Yongxing Lai
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Peiqiang Lin
- Department of Neurology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Fan Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Manli Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Chunjin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Xing Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lijuan Wu
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Mouwei Zheng
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China,*Correspondence: Jianhao Chen, ; Mouwei Zheng,
| | - Jianhao Chen
- Department of Rehabilitation Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China,*Correspondence: Jianhao Chen, ; Mouwei Zheng,
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Zhou Z, Bai J, Zhong S, Zhang R, Kang K, Zhang X, Xu Y, Zhao C, Zhao M. Downregulation of PIK3CB Involved in Alzheimer's Disease via Apoptosis, Axon Guidance, and FoxO Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1260161. [PMID: 35096262 PMCID: PMC8794666 DOI: 10.1155/2022/1260161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/08/2022] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To investigate the molecular function of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta (PIK3CB) underlying Alzheimer's disease (AD). METHODS RNA sequencing data were used to filtrate differentially expressed genes (DEGs) in AD/nondementia control and PIK3CB-low/high groups. An unbiased coexpression network was established to evaluate module-trait relationships by using weight gene correlation network analysis (WGCNA). Global regulatory network was constructed to predict the protein-protein interaction. Further cross-talking pathways of PIK3CB were identified by functional enrichment analysis. RESULTS The mean expression of PIK3CB in AD patients was significantly lower than those in nondementia controls. We identified 2,385 DEGs from 16,790 background genes in AD/control and PIK3CB-low/high groups. Five coexpression modules were established using WGCNA, which participated in apoptosis, axon guidance, long-term potentiation (LTP), regulation of actin cytoskeleton, synaptic vesicle cycle, FoxO, mitogen-activated protein kinase (MAPK), and vascular endothelial growth factor (VEGF) signaling pathways. DEGs with strong relation to AD and low PIK3CB expression were extracted to construct a global regulatory network, in which cross-talking pathways of PIK3CB were identified, such as apoptosis, axon guidance, and FoxO signaling pathway. The occurrence of AD could be accurately predicted by low PIK3CB based on the area under the curve of 71.7%. CONCLUSIONS These findings highlight downregulated PIK3CB as a potential causative factor of AD, possibly mediated via apoptosis, axon guidance, and FoxO signaling pathway.
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Affiliation(s)
- Zhike Zhou
- Department of Geriatrics, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Jun Bai
- Cancer Systems Biology Center, The China-Japan Union Hospital, Jilin University, Changchun, 130033 Jilin, China
| | - Shanshan Zhong
- Department of Neurology, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Rongwei Zhang
- Department of Geriatrics, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Kexin Kang
- Department of Geriatrics, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Xiaoqian Zhang
- Department of Neurology, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Ying Xu
- Cancer Systems Biology Center, The China-Japan Union Hospital, Jilin University, Changchun, 130033 Jilin, China
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, USA
| | - Chuansheng Zhao
- Department of Neurology, The First Affiliated Hospital, China Medical University, Shenyang, 110001 Liaoning, China
| | - Mei Zhao
- Department of Cardiology, The Shengjing Affiliated Hospital, China Medical University, Shenyang, 110004 Liaoning, China
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