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Adeoye T, Shah SI, Ullah G. Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer's Disease. Aging Dis 2024:AD.2024.0429. [PMID: 38913039 DOI: 10.14336/ad.2024.0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024] Open
Abstract
Alzheimer's disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions-middle temporal gyrus, superior frontal gyrus, and entorhinal cortex-we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type-specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, suggesting that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, suggesting that DEGs exert more impact on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we observe an overall downregulation of astrocyte and microglia modules across all brain regions in AD, indicating a prevailing trend of functional repression in glial cells across these regions. Notable genes from the CALM and HSP90 families emerged as hub genes across neuronal modules in all brain regions, suggesting conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems-oriented approach combining pathway and network analysis to comprehensively understand the cell-type-specific roles of genes in AD-related biological processes.
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2
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Risby-Jones G, Lee JD, Woodruff TM, Fung JN. Sex differences in Huntington's disease from a neuroinflammation perspective. Front Neurol 2024; 15:1384480. [PMID: 38915800 PMCID: PMC11194371 DOI: 10.3389/fneur.2024.1384480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024] Open
Abstract
Huntington's disease (HD) is a debilitating neurodegenerative condition characterized by motor, cognitive and psychiatric abnormalities. Immune dysregulation, prominently featuring increased immune activity, plays a significant role in HD pathogenesis. In addition to the central nervous system (CNS), systemic innate immune activation and inflammation are observed in HD patients, exacerbating the effects of the Huntingtin (HTT) gene mutation. Recent attention to sex differences in HD symptom severity underscores the need to consider gender as a biological variable in neurodegenerative disease research. Understanding sex-specific immune responses holds promise for elucidating HD pathophysiology and informing targeted treatment strategies to mitigate cognitive and functional decline. This perspective will highlight the importance of investigating gender influence in HD, particularly focusing on sex-specific immune responses predisposing individuals to disease.
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Affiliation(s)
- Grace Risby-Jones
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - John D. Lee
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Trent M. Woodruff
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Jenny N. Fung
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
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3
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Adeoye T, Shah SI, Ullah G. Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585267. [PMID: 38559218 PMCID: PMC10980062 DOI: 10.1101/2024.03.15.585267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions-middle temporal gyrus, superior frontal gyrus, and entorhinal cortex-we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type-specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, indicating that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, highlighting the differential impact of DEGs on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we note an overall downregulation of both astrocyte and microglia modules in AD across all brain regions, suggesting a prevailing trend of functional repression in glial cells across these regions. Notable genes, including those of the CALM and HSP90 family genes emerged as hub genes across neuronal modules in all brain regions, indicating conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems-oriented approach combining pathway and network analysis for a comprehensive understanding of the cell-type-specific roles of genes in AD-related biological processes.
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Affiliation(s)
- Temitope Adeoye
- Department of Physics, University of South Florida, Tampa, FL 33620
| | - Syed I Shah
- Department of Physics, University of South Florida, Tampa, FL 33620
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620
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4
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Delphin N, Aust C, Griffiths L, Fernandez F. Epigenetic Regulation in Schizophrenia: Focus on Methylation and Histone Modifications in Human Studies. Genes (Basel) 2024; 15:272. [PMID: 38540331 PMCID: PMC10970389 DOI: 10.3390/genes15030272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Despite extensive research over the last few decades, the etiology of schizophrenia (SZ) remains unclear. SZ is a pathological disorder that is highly debilitating and deeply affects the lifestyle and minds of those affected. Several factors (one or in combination) have been reported as contributors to SZ pathogenesis, including neurodevelopmental, environmental, genetic and epigenetic factors. Deoxyribonucleic acid (DNA) methylation and post-translational modification (PTM) of histone proteins are potentially contributing epigenetic processes involved in transcriptional activity, chromatin folding, cell division and apoptotic processes, and DNA damage and repair. After establishing a summary of epigenetic processes in the context of schizophrenia, this review aims to highlight the current understanding of the role of DNA methylation and histone PTMs in this disorder and their potential roles in schizophrenia pathophysiology and pathogenesis.
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Affiliation(s)
- Natasha Delphin
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Caitlin Aust
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Lyn Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
| | - Francesca Fernandez
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
- Healthy Brain and Mind Research Centre, Australian Catholic University, Melbourne, VIC 3000, Australia
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5
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Xie YH, Jiang L, Zhang Y, Deng YH, Yang H, He Q, Zhou YN, Zhou CN, Luo YM, Liang X, Wang J, Huang DJ, Zhu L, Tang Y, Chao FL. Antagonizing LINGO-1 reduces activated microglia and alleviates dendritic spine loss in the hippocampus of APP/PS1 transgenic mice. Neurosci Lett 2024; 820:137612. [PMID: 38142924 DOI: 10.1016/j.neulet.2023.137612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/25/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
In Alzheimer's disease (AD), microglia are involved in synaptic pruning and mediate synapse loss. LINGO-1 is a negative regulator of nerve growth, and whether antagonizing LINGO-1 can attenuate synaptic pruning by microglia and rescue dendritic spines in the hippocampus in AD is still unclear. On this basis, the anti-LINGO-1 antibody, which binds to LINGO-1 protein and antagonizes the effects of LINGO-1, was administered to 10-month-old APP/PS1 transgenic mice for 2 months. The Morris water maze test, immunohistochemical and stereological methods, immunofluorescence and 3D reconstruction were used. Compared to wild-type mice, APP/PS1 transgenic mice had worse performance on behavioral tests, fewer dendritic spines but more microglia in the hippocampus. Meanwhile, the microglia in APP/PS1 transgenic mice had more branches of medium length (4-6 µm) and a cell body area with greater variability. Moreover, APP/PS1 transgenic mice had more postsynaptic termini colocalized with microglia in the hippocampus than wild-type mice. The anti-LINGO-1 antibody significantly reversed these changes in AD, indicating that the anti-LINGO-1 antibody can improve hippocampus-dependent learning and memory abilities and effectively rescue dendritic spines in the hippocampus of AD mice and that microglia might participate in this progression in AD. These results provide a scientific basis for further studying the mechanism of the anti-LINGO-1 antibody in AD and help to elucidate the role of LINGO-1 in the treatment of AD.
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Affiliation(s)
- Yu-Han Xie
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Jiang
- Lab Teaching & Management Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Yu-Hui Deng
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Hao Yang
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Qi He
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yu-Ning Zhou
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Chun-Ni Zhou
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan-Min Luo
- Department of Physiology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Xin Liang
- Department of Pathology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Jin Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Du-Juan Huang
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Zhu
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yong Tang
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
| | - Feng-Lei Chao
- Department of Histology and Embryology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
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6
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Zhou YN, Jiang L, Zhang Y, Zhou CN, Yang H, He Q, Wang YY, Xiao Q, Huang DJ, Luo YM, Tang Y, Chao FL. Anti-LINGO-1 antibody protects neurons and synapses in the medial prefrontal cortex of APP/PS1 transgenic mice. Neurosci Res 2023:S0168-0102(23)00039-1. [PMID: 36804877 DOI: 10.1016/j.neures.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
The medial prefrontal cortex (mPFC), one of the most vulnerable brain regions in Alzheimer's disease (AD), plays a critical role in cognition. Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein-1 (LINGO-1) negatively affects nerve growth in the central nervous system; however, its role in the pathological damage to the mPFC remains to be studied in AD. In this study, an anti-LINGO-1 antibody was administered to 10-month-old APP/PS1 mice, and behavioral tests, stereological methods, immunohistochemistry and immunofluorescence were used to answer this question. Our results revealed that LINGO-1 was highly expressed in the neurons of the mPFC of AD mice, and the anti-LINGO-1 antibody improved prefrontal cortex-related function and reduced the protein level of LINGO-1, atrophy of the volume, Aβ deposition and massive losses of synapses and neurons in the mPFC of AD mice. Antagonizing LINGO-1 could effectively alleviate the pathological damage in the mPFC of AD mice, which might be an important structural basis for improving prefrontal cortex-related function. Abnormal expression of LINGO-1 in the mPFC may be one of the key targets of AD, and the effect initiated by the anti-LINGO-1 antibody may provide an important basis in the search for drugs for the prevention and treatment of AD.
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Affiliation(s)
- Yu-Ning Zhou
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Jiang
- Experimental Teaching Management Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Chun-Ni Zhou
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Hao Yang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Qi He
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi-Ying Wang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Qian Xiao
- Department of Radioactive Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Du-Juan Huang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan-Min Luo
- Department of Physiology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yong Tang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
| | - Feng-Lei Chao
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
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7
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Yang H, Jiang L, Zhang Y, Liang X, Tang J, He Q, Luo YM, Zhou CN, Zhu L, Zhang SS, Xiao K, Zhu PL, Wang J, Li Y, Chao FL, Tang Y. Anti-LINGO-1 antibody treatment alleviates cognitive deficits and promotes maturation of oligodendrocytes in the hippocampus of APP/PS1 mice. J Comp Neurol 2022; 530:1606-1621. [PMID: 35014704 DOI: 10.1002/cne.25299] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 01/18/2023]
Abstract
Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1 (LINGO-1), a negative regulator of oligodendrocyte differentiation and myelination, is associated with cognitive function, and its expression is highly upregulated in Alzheimer's disease (AD) patients. Anti-LINGO-1 antibody treatment can effectively antagonize the negative regulatory effect of LINGO-1. In this study, we aim to assess the effect of anti-LINGO-1 antibody treatment on cognition and hippocampal oligodendrocytes in an AD transgenic animal model. First, 10-month-old male APP/PS1 mice were administered anti-LINGO-1 antibody for 8 weeks. Then, learning and memory abilities were assessed with the Morris water maze (MWM) and Y-maze tests, and amyloid-beta (Aβ) deposition and hippocampal oligodendrocytes were investigated by immunohistochemistry, immunofluorescence, and stereology. We found that anti-LINGO-1 antibody alleviated the deficits in spatial learning and memory abilities and working and reference memory abilities, decreased the density of LINGO-1 positive cells, decreased Aβ deposition, significantly increased the number of mature oligodendrocytes and the density of myelin, reversed the abnormal increases in the number of oligodendrocyte lineage cells and the densities of oligodendrocytes precursor cells in APP/PS1 mice. Our results provide evidence that LINGO-1 might be involved in the process of oligodendrocyte dysmaturity in the hippocampus of AD mice and that antagonizing LINGO-1 can alleviate cognitive deficits in APP/PS1 mice and decrease Aβ deposition and promote oligodendrocyte differentiation and maturation in the hippocampus of these mice. Our findings suggest that changes in LINGO-1 and oligodendrocytes in the hippocampus play important roles in the pathogenesis of AD and that antagonizing LINGO-1 might be a potential therapeutic strategy for AD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hao Yang
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China.,Department of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. R. China
| | - Lin Jiang
- Experimental Teaching Management Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yi Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Xin Liang
- Department of Pathophysiology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jing Tang
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Qi He
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Yan-Min Luo
- Department of Physiology, Chongqing Medical University, Chongqing, 400016, PR China
| | - Chun-Ni Zhou
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Lin Zhu
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Shan-Shan Zhang
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Kai Xiao
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Pei-Lin Zhu
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Jin Wang
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Yue Li
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Feng-Lei Chao
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
| | - Yong Tang
- Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, P. R. China.,Laboratory of Stem Cell and Tissue Engineering, College of Basic Medicine, Chongqing Medical University, P. R. China
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8
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Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Mol Neurobiol 2021; 59:276-293. [PMID: 34669146 PMCID: PMC8786804 DOI: 10.1007/s12035-021-02591-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can inform new therapeutic approaches for both sexes. Previous bulk human brain RNA sequencing studies have revealed sex differences in dysregulated molecular pathways related to energy production, neuronal function, and immune response; however, the sex differences in disease mechanisms are yet to be examined comprehensively on a single-cell level. We leveraged nearly 74,000 cells from human prefrontal and entorhinal cortex samples from the first two publicly available single-cell RNA sequencing AD datasets to perform a case versus control sex-stratified differential gene expression analysis and pathway network enrichment in a cell type-specific manner for each brain region. Our examination at the single-cell level revealed sex differences in AD prominently in glial cells of the prefrontal cortex. In the entorhinal cortex, we observed the same genes and networks to be perturbed in opposing directions between sexes in AD relative to healthy state. Our findings contribute to growing evidence of sex differences in AD-related transcriptomic changes, which can fuel the development of therapies that may prove more effective at reversing AD pathophysiology.
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Affiliation(s)
- Stella A Belonwu
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Bunis
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Caroline Warly Solsberg
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Alice Tang
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Bioengineering Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA, USA
| | - Dena B Dubal
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.,Neurosciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA. .,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
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Wang XL, Li L. Cell type-specific potential pathogenic genes and functional pathways in Alzheimer's Disease. BMC Neurol 2021; 21:381. [PMID: 34600516 PMCID: PMC8487122 DOI: 10.1186/s12883-021-02407-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a pervasive age-related and highly heritable neurodegenerative disorder but has no effective therapy. The complex cellular microenvironment in the AD brain impedes our understanding of pathogenesis. Thus, a comprehensive investigation of cell type-specific responses in AD is crucial to provide precise molecular and cellular targets for therapeutic development. METHODS Here, we integrated analyzed 4,441 differentially expressed genes (DEGs) that were identified from 263,370 single-cells in cortex samples by single-nucleus RNA sequencing (snRNA-seq) between 42 AD-pathology subjects and 39 normal controls within 3 studies. DEGs were analyzed in microglia, astrocytes, oligodendrocytes, excitatory neurons, inhibitory neurons, and endothelial cells, respectively. In each cell type, we identified both common DEGs which were observed in all 3 studies, and overlapping DEGs which have been seen in at least 2 studies. Firstly, we showed the common DEGs expression and explained the biological functions by comparing with existing literature or multil-omics signaling pathways knowledgebase. We then determined the significant modules and hub genes, and explored the biological processes using the overlapping DEGs. Finally, we identified the common and distinct dysregulated pathways using overall DEGs and overlapping DEGs in a cell type-specific manner. RESULTS Up-regulated LINGO1 has been seen in both oligodendrocytes and excitatory neurons across 3 studies. Interestingly, genes enriched in the mitochondrial module were up-regulated across all cell types, which indicates mitochondrial dysfunction in the AD brain. The estrogen signaling pathway seems to be the most common pathway that is disrupted in AD. CONCLUSION Together, these analyses provide detailed information of cell type-specific and overall transcriptional changes and pathways underlying the human AD-pathology. These findings may provide important insights for drug development to tackle this disease.
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Affiliation(s)
- Xiao-Lan Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Université de Strasbourg, Strasbourg, France
| | - Lianjian Li
- Department of Surgery, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061 China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430076 China
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Rangsinth P, Duangjan C, Sillapachaiyaporn C, Isidoro C, Prasansuklab A, Tencomnao T. Caesalpinia mimosoides Leaf Extract Promotes Neurite Outgrowth and Inhibits BACE1 Activity in Mutant APP-Overexpressing Neuronal Neuro2a Cells. Pharmaceuticals (Basel) 2021; 14:ph14090901. [PMID: 34577601 PMCID: PMC8469274 DOI: 10.3390/ph14090901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023] Open
Abstract
Alzheimer’s disease (AD) is implicated in the imbalance of several proteins, including Amyloid-β (Aβ), amyloid precursor protein (APP), and BACE1. APP overexpression interferes with neurite outgrowth, while BACE1 plays a role in Aβ generation. Medicinal herbs with effects on neurite outgrowth stimulation and BACE1 inhibition may benefit AD. This study aimed to investigate the neurite outgrowth stimulatory effect, along with BACE1 inhibition of Caesalpinia mimosoides (CM), using wild-type (Neuro2a) and APP (Swedish mutant)-overexpressing (Neuro2a/APPSwe) neurons. The methanol extract of CM leaves stimulated neurite outgrowth in wild-type and APP-overexpressing cells. After exposure to the extract, the mRNA expression of the neurite outgrowth activation genes growth-associated protein-43 (GAP-43) and teneurin-4 (Ten-4) was increased in both Neuro2a and Neuro2a/APPSwe cells, while the mRNA expression of neurite outgrowth negative regulators Nogo receptor (NgR) and Lingo-1 was reduced. Additionally, the extract suppressed BACE1 activity in the APP-overexpressing neurons. Virtual screening demonstrated that quercetin-3′-glucuronide, quercetin-3-O-glucoside, clausarinol, and theogallin were possible inhibitors of BACE1. ADMET was analyzed to predict drug-likeness properties of CM-constituents. These results suggest that CM extract promotes neurite outgrowth and inhibits BACE1 activity in APP-overexpressing neurons. Thus, CM may serve as a source of drugs for AD treatment. Additional studies for full identification of bioactive constituents and to confirm the neuritogenesis in vivo are needed for translation into clinic of the present findings.
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Affiliation(s)
- Panthakarn Rangsinth
- Graduate Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (P.R.); (C.D.); (C.S.)
| | - Chatrawee Duangjan
- Graduate Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (P.R.); (C.D.); (C.S.)
| | - Chanin Sillapachaiyaporn
- Graduate Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (P.R.); (C.D.); (C.S.)
| | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale “A. Avogadro”, Via Solaroli 17, 28100 Novara, Italy;
| | - Anchalee Prasansuklab
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
- College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (A.P.); (T.T.); Tel.: +66-2218-8048 (A.P.); +66-2218-1533 (T.T.)
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (A.P.); (T.T.); Tel.: +66-2218-8048 (A.P.); +66-2218-1533 (T.T.)
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Lewcock JW, Schlepckow K, Di Paolo G, Tahirovic S, Monroe KM, Haass C. Emerging Microglia Biology Defines Novel Therapeutic Approaches for Alzheimer’s Disease. Neuron 2020; 108:801-821. [DOI: 10.1016/j.neuron.2020.09.029] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 02/01/2023]
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Wu Y, Zhan Z, Quan Y, Yang Y, Chen X, Liu L, Wu K, Yu M. SP1-mediated upregulation of LINGO-1 promotes degeneration of retinal ganglion cells in optic nerve injury. CNS Neurosci Ther 2020; 26:1010-1020. [PMID: 32562344 PMCID: PMC7539844 DOI: 10.1111/cns.13426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/27/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUNDS Insults to the axons in the optic nerve head are the primary cause of loss of retinal ganglion cells (RGCs) in traumatic, ischemic nerve injury or degenerative ocular diseases. The central nervous system-specific leucine-rich repeat protein, LINGO-1, negatively regulates axon regeneration and neuronal survival after injury. However, the upstream molecular mechanisms that regulate LINGO-1 signaling and contribute to LINGO-1-mediated death of RGCs are unclear. METHODS The expression of SP1 was profiled in optic nerve crush (ONC)-injured RGCs. LINGO-1 level was examined after SP1 overexpression by qRT-PCR. Luciferase assay was used to examine the binding of SP1 to the promoter regions of LINGO-1. Primary RGCs from rat retina were isolated by immunopanning and RGCs apoptosis were determined by Tunnel. SP1 and LINGO-1 expression was investigated using immunohistochemistry and Western bolting. Neuroprotection was assessed by RGC counts, RNFL thickness, and VEP tests after inhibition of SP1 shRNA. RESULTS We demonstrate that SP1 was upregulated in ONC-injured RGCs. SP1 was bound to the LINGO-1 promoter, which led to increased expression of LINGO-1. Treatment with recombinant Nogo-66 or LINGO-1 promoted apoptosis of RGCs cultured under serum-deprivation conditions, while silencing of SP1 promoted the survival of RGCs. SP1 and LINGO-1 colocalized and were upregulated in ONC-injured retinas. Silencing of SP1 in vivo reduced LINGO-1 expression and protected the structure of RGCs from ONC-induced injury, but there was no sign of recovery in VEP. CONCLUSIONS Our findings imply that SP1 regulates LINGO-1 expression in RGCs in the injured retina and provide insight into mechanisms underlying LINGO-1-mediated RGC death in optic nerve injury.
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Affiliation(s)
- Yali Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zongyi Zhan
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yadan Quan
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yangfan Yang
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Xiaotao Chen
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Liling Liu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Kaili Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Minbin Yu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
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Single-cell transcriptomic analysis of Alzheimer's disease. Nature 2019; 570:332-337. [PMID: 31042697 DOI: 10.1038/s41586-019-1195-2] [Citation(s) in RCA: 1259] [Impact Index Per Article: 251.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 04/24/2019] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease is a pervasive neurodegenerative disorder, the molecular complexity of which remains poorly understood. Here, we analysed 80,660 single-nucleus transcriptomes from the prefrontal cortex of 48 individuals with varying degrees of Alzheimer's disease pathology. Across six major brain cell types, we identified transcriptionally distinct subpopulations, including those associated with pathology and characterized by regulators of myelination, inflammation, and neuron survival. The strongest disease-associated changes appeared early in pathological progression and were highly cell-type specific, whereas genes upregulated at late stages were common across cell types and primarily involved in the global stress response. Notably, we found that female cells were overrepresented in disease-associated subpopulations, and that transcriptional responses were substantially different between sexes in several cell types, including oligodendrocytes. Overall, myelination-related processes were recurrently perturbed in multiple cell types, suggesting that myelination has a key role in Alzheimer's disease pathophysiology. Our single-cell transcriptomic resource provides a blueprint for interrogating the molecular and cellular basis of Alzheimer's disease.
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Yang T, Guo Q, Shi X, Wu S, Li Y, Sun Y, Zhao Y, Chai L, Gao Y, Lou L, Dong B, Zhu L. Panax notoginseng saponins promotes cerebral recovery from ischemic injury by downregulating LINGO-1 and activating the EGFR/PI3K/AKT signaling pathways in vivo. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2018. [DOI: 10.1016/j.jtcms.2018.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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