1
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Juvenal G, Meinerz C, Ayupe AC, Campos HC, Reis EM, Longo BM, Pillat MM, Ulrich H. Bradykinin promotes immune responses in differentiated embryonic neurospheres carrying APP swe and PS1 dE9 mutations. Cell Biosci 2024; 14:82. [PMID: 38890712 PMCID: PMC11184896 DOI: 10.1186/s13578-024-01251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Neural progenitor cells (NPCs) can be cultivated from developing brains, reproducing many of the processes that occur during neural development. They can be isolated from a variety of animal models, such as transgenic mice carrying mutations in amyloid precursor protein (APP) and presenilin 1 and 2 (PSEN 1 and 2), characteristic of familial Alzheimer's disease (fAD). Modulating the development of these cells with inflammation-related peptides, such as bradykinin (BK) and its antagonist HOE-140, enables the understanding of the impact of such molecules in a relevant AD model. RESULTS We performed a global gene expression analysis on transgenic neurospheres treated with BK and HOE-140. To validate the microarray data, quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR) was performed on 8 important genes related to the immune response in AD such as CCL12, CCL5, CCL3, C3, CX3CR1, TLR2 and TNF alpha and Iba-1. Furthermore, comparative analysis of the transcriptional profiles was performed between treatments, including gene ontology and reactome enrichment, construction and analysis of protein-protein interaction networks and, finally, comparison of our data with human dataset from AD patients. The treatments affected the expression levels of genes mainly related to microglia-mediated neuroinflammatory responses, with BK promoting an increase in the expression of genes that enrich processes, biological pathways, and cellular components related to immune dysfunction, neurodegeneration and cell cycle. B2 receptor inhibition by HOE-140 resulted in the reduction of AD-related anomalies caused in this system. CONCLUSIONS BK is an important immunomodulatory agent and enhances the immunological changes identified in transgenic neurospheres carrying the genetic load of AD. Bradykinin treatments modulate the expression rates of genes related to microglia-mediated neuroinflammation. Inhibiting bradykinin activity in Alzheimer's disease may slow disease progression.
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Affiliation(s)
- Guilherme Juvenal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | - Carine Meinerz
- Department of Microbiology and Parasitology, Health Sciences Center, Federal University of Santa Maria, Santa Maria-RS, Brazil
| | - Ana Carolina Ayupe
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | | | - Eduardo Moraes Reis
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | | | - Micheli Mainardi Pillat
- Department of Microbiology and Parasitology, Health Sciences Center, Federal University of Santa Maria, Santa Maria-RS, Brazil.
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil.
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2
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Han Y, Chen K, Yu H, Cui C, Li H, Hu Y, Zhang B, Li G. Maf1 loss regulates spinogenesis and attenuates cognitive impairment in Alzheimer's disease. Brain 2024; 147:2128-2143. [PMID: 38226680 PMCID: PMC11146433 DOI: 10.1093/brain/awae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Alzheimer's disease is neurodegenerative and characterized by progressive cognitive impairment. Synaptic dysfunction appears in the early stage of Alzheimer's disease and is significantly correlated with cognitive impairment. However, the specific regulatory mechanism remains unclear. Here, we found the transcription factor Maf1 to be upregulated in Alzheimer's disease and determined that conditional knockout of Maf1 in a transgenic mouse model of Alzheimer's disease restored learning and memory function; the downregulation of Maf1 reduced the intraneuronal calcium concentration and restored neuronal synaptic morphology. We also demonstrated that Maf1 regulated the expression of NMDAR1 by binding to the promoter region of Grin1, further regulating calcium homeostasis and synaptic remodelling in neurons. Our results clarify the important role and mechanism of the Maf1-NMDAR1 signalling pathway in stabilizing synaptic structure, neuronal function and behaviour during Alzheimer's disease pathogenesis. This therefore serves as a potential diagnostic and therapeutic target for the early stage of Alzheimer's disease.
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Affiliation(s)
- Yingying Han
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Kui Chen
- Department of Neurosurgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Hongxiang Yu
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Can Cui
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Hongxia Li
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yongbo Hu
- Department of Neurology, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), the Second Military Medical University, Shanghai 200092, China
| | - Bei Zhang
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Gang Li
- Department of Neurology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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3
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Gaur P, Bryois J, Calini D, Foo L, Hoozemans JJM, Malhotra D, Menon V. Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590816. [PMID: 38712204 PMCID: PMC11071354 DOI: 10.1101/2024.04.23.590816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.
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Affiliation(s)
- Pallavi Gaur
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
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4
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Dohm-Hansen S, English JA, Lavelle A, Fitzsimons CP, Lucassen PJ, Nolan YM. The 'middle-aging' brain. Trends Neurosci 2024; 47:259-272. [PMID: 38508906 DOI: 10.1016/j.tins.2024.02.001] [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: 10/16/2023] [Revised: 01/09/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
Middle age has historically been an understudied period of life compared to older age, when cognitive and brain health decline are most pronounced, but the scope for intervention may be limited. However, recent research suggests that middle age could mark a shift in brain aging. We review emerging evidence on multiple levels of analysis indicating that midlife is a period defined by unique central and peripheral processes that shape future cognitive trajectories and brain health. Informed by recent developments in aging research and lifespan studies in humans and animal models, we highlight the utility of modeling non-linear changes in study samples with wide subject age ranges to distinguish life stage-specific processes from those acting linearly throughout the lifespan.
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Affiliation(s)
- Sebastian Dohm-Hansen
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; INFANT Research Centre, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jane A English
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; INFANT Research Centre, University College Cork, Cork, Ireland
| | - Aonghus Lavelle
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Carlos P Fitzsimons
- Swammerdam Institute for Life Sciences, Brain Plasticity Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul J Lucassen
- Swammerdam Institute for Life Sciences, Brain Plasticity Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Yvonne M Nolan
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
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5
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Ceylan B, Düz E, Çakir T. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer's Disease. Mol Neurobiol 2024; 61:2120-2135. [PMID: 37855983 DOI: 10.1007/s12035-023-03690-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
Alzheimer's disease (AD) is a highly heterogenous neurodegenerative disease, and several omic-based datasets were generated in the last decade from the patients with the disease. However, the vast majority of studies evaluate these datasets in bulk by considering all the patients as a single group, which obscures the molecular differences resulting from the heterogeneous nature of the disease. In this study, we adopted a personalized approach and analyzed the transcriptome data from 403 patients individually by mapping the data on a human protein-protein interaction network. Patient-specific subnetworks were discovered and analyzed in terms of the genes in the subnetworks, enriched functional terms, and known AD genes. We identified several affected pathways that could not be captured by the bulk comparison. We also showed that our personalized findings point to patterns of alterations consistent with the recently suggested AD subtypes.
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Affiliation(s)
- Betül Ceylan
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Elif Düz
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakir
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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6
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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7
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Ainslie AP, Klaver M, Voshart DC, Gerrits E, den Dunnen WFA, Eggen BJL, Bergink S, Barazzuol L. Glioblastoma and its treatment are associated with extensive accelerated brain aging. Aging Cell 2024; 23:e14066. [PMID: 38234228 PMCID: PMC10928584 DOI: 10.1111/acel.14066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
Progressive neurocognitive dysfunction is the leading cause of a reduced quality of life in patients with primary brain tumors. Understanding how the human brain responds to cancer and its treatment is essential to improve the associated cognitive sequelae. In this study, we performed integrated transcriptomic and tissue analysis on postmortem normal-appearing non-tumor brain tissue from glioblastoma (GBM) patients that had received cancer treatments, region-matched brain tissue from unaffected control individuals and Alzheimer's disease (AD) patients. We show that normal-appearing non-tumor brain regions of patients with GBM display hallmarks of accelerated aging, in particular mitochondrial dysfunction, inflammation, and proteostasis deregulation. The extent and spatial pattern of this response decreased with distance from the tumor. Gene set enrichment analyses and a direct comparative analysis with an independent cohort of brain tissue samples from AD patients revealed a significant overlap in differentially expressed genes and a similar biological aging trajectory. Additionally, these responses were validated at the protein level showing the presence of increased lysosomal lipofuscin, phosphorylated microtubule-associated protein Tau, and oxidative DNA damage in normal-appearing brain areas of GBM patients. Overall, our data show that the brain of GBM patients undergoes accelerated aging and shared AD-like features, providing the basis for novel or repurposed therapeutic targets for managing brain tumor-related side effects.
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Affiliation(s)
- Anna P. Ainslie
- Department of Radiation OncologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- European Research Institute for the Biology of AgeingUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Myrthe Klaver
- Department of Radiation OncologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- European Research Institute for the Biology of AgeingUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Daniëlle C. Voshart
- Department of Radiation OncologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Emma Gerrits
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Wilfred F. A. den Dunnen
- Department of Pathology and Medical BiologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Bart J. L. Eggen
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- University College Groningen, University of GroningenGroningenThe Netherlands
| | - Lara Barazzuol
- Department of Radiation OncologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
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8
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Li W, Chang C, Kundu S, Long Q. Accounting for network noise in graph-guided Bayesian modeling of structured high-dimensional data. Biometrics 2024; 80:ujae012. [PMID: 38483282 PMCID: PMC10938547 DOI: 10.1093/biomtc/ujae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/31/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
There is a growing body of literature on knowledge-guided statistical learning methods for analysis of structured high-dimensional data (such as genomic and transcriptomic data) that can incorporate knowledge of underlying networks derived from functional genomics and functional proteomics. These methods have been shown to improve variable selection and prediction accuracy and yield more interpretable results. However, these methods typically use graphs extracted from existing databases or rely on subject matter expertise, which are known to be incomplete and may contain false edges. To address this gap, we propose a graph-guided Bayesian modeling framework to account for network noise in regression models involving structured high-dimensional predictors. Specifically, we use 2 sources of network information, including the noisy graph extracted from existing databases and the estimated graph from observed predictors in the dataset at hand, to inform the model for the true underlying network via a latent scale modeling framework. This model is coupled with the Bayesian regression model with structured high-dimensional predictors involving an adaptive structured shrinkage prior. We develop an efficient Markov chain Monte Carlo algorithm for posterior sampling. We demonstrate the advantages of our method over existing methods in simulations, and through analyses of a genomics dataset and another proteomics dataset for Alzheimer's disease.
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Affiliation(s)
- Wenrui Li
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, PA 19104, United States
| | - Changgee Chang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Suprateek Kundu
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, PA 19104, United States
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9
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Zhang J, Guo S, Tao R, Wang F, Xie Y, Wang H, Ding L, Shen Y, Zhou X, Feng J, Shen Q. Neuroprotective effect of plasmalogens on AlCl 3-induced Alzheimer's disease zebrafish via acting on the regulatory network of ferroptosis, apoptosis and synaptic neurotransmission release with oxidative stress as the center. Neurosci Lett 2024; 818:137560. [PMID: 37979715 DOI: 10.1016/j.neulet.2023.137560] [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: 09/16/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
Plasmalogens (Pls) are considered to play a potential role in the treatment of neurodegenerative diseases. In the present study, an Alzheimer's disease (AD) model of zebrafish induced by AlCl3 was established to investigate whether the marine-derived Pls could alleviate cognitive impairments of AD zebrafish. Behavioral tests were carried out to assess the athletic ability. The transcriptional profiles of zebrafish in the control, AD model and AD_PLS group were compared and analyzed to determine the potential mechanisms of dietary Pls on AD. The study found that Pls could reverse athletic impairment in the AD zebrafish model, and the expression levels of genes related to ferroptosis, synaptic dysfunction and apoptosis were significantly altered between experimental groups. Further analysis showed that all of these genes were associated with oxidative stress (OS). These data suggest that healthy protective role of marine-derived Pls on AD zebrafish may result from inhibition of ferroptosis and neuronal apoptosis, restoring synaptic neurotransmission release, and reducing neuroinflammation. Among them, Oxidative stress is acted as the center to connect different regulation pathways. This study provides evidence to support the essential roles of OS in pathogenesis of AD, and the application of Pls in relieving AD.
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Affiliation(s)
- Jian Zhang
- Collaborative Innovation Center of Seafood Deep Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Shunyuan Guo
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Rong Tao
- Collaborative Innovation Center of Seafood Deep Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Fan Wang
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Yihong Xie
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Huizi Wang
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Lan Ding
- Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Yuejian Shen
- Hangzhou Linping District Maternal & Child Health Care Hospital, Hangzhou, Zhejiang 311113, China
| | - Xiaoli Zhou
- Hangzhou Linping District Maternal & Child Health Care Hospital, Hangzhou, Zhejiang 311113, China
| | - Junli Feng
- Collaborative Innovation Center of Seafood Deep Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China; Zhejiang Province Joint Key Laboratory of Aquatic Products Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China.
| | - Qing Shen
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China; Zhejiang Province Joint Key Laboratory of Aquatic Products Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China.
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10
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Cao Q, Kumar M, Frazier A, Williams JB, Zhao S, Yan Z. Longitudinal characterization of behavioral, morphological and transcriptomic changes in a tauopathy mouse model. Aging (Albany NY) 2023; 15:11697-11719. [PMID: 37925173 PMCID: PMC10683589 DOI: 10.18632/aging.205057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/02/2023] [Indexed: 11/06/2023]
Abstract
Neurodegenerative disorders, such as Alzheimer's disease (AD), have the gradual onset of neurobiological changes preceding clinical diagnosis by decades. To elucidate how brain dysfunction proceeds in neurodegenerative disorders, we performed longitudinal characterization of behavioral, morphological, and transcriptomic changes in a tauopathy mouse model, P301S transgenic mice. P301S mice exhibited cognitive deficits as early as 3 months old, and deficits in social preference and social cognition at 5-6 months. They had a significant decrease of arborization in basal dendrites of hippocampal pyramidal neurons from 3 months and apical dendrites of PFC pyramidal neurons at 9 months. Transcriptomic analysis of genome-wide changes revealed the enrichment of synaptic gene upregulation at 3 months of age, while most of these synaptic genes were downregulated in PFC and hippocampus of P301S mice at 9 months. These time-dependent changes in gene expression may lead to progressive alterations of neuronal structure and function, resulting in the manifestation of behavioral symptoms in tauopathies.
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Affiliation(s)
- Qing Cao
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Manasa Kumar
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Allea Frazier
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Jamal B. Williams
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Shengkai Zhao
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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Krokidis MG, Vrahatis AG, Lazaros K, Skolariki K, Exarchos TP, Vlamos P. Machine Learning Analysis of Alzheimer's Disease Single-Cell RNA-Sequencing Data across Cortex and Hippocampus Regions. Curr Issues Mol Biol 2023; 45:8652-8669. [PMID: 37998721 PMCID: PMC10670182 DOI: 10.3390/cimb45110544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Advancements in molecular biology have revolutionized our understanding of complex diseases, with Alzheimer's disease being a prime example. Single-cell sequencing, currently the most suitable technology, facilitates profoundly detailed disease analysis at the cellular level. Prior research has established that the pathology of Alzheimer's disease varies across different brain regions and cell types. In parallel, only machine learning has the capacity to address the myriad challenges presented by such studies, where the integration of large-scale data and numerous experiments is required to extract meaningful knowledge. Our methodology utilizes single-cell RNA sequencing data from healthy and Alzheimer's disease (AD) samples, focused on the cortex and hippocampus regions in mice. We designed three distinct case studies and implemented an ensemble feature selection approach through machine learning, also performing an analysis of distinct age-related datasets to unravel age-specific effects, showing differential gene expression patterns within each condition. Important evidence was reported, such as enrichment in central nervous system development and regulation of oligodendrocyte differentiation between the hippocampus and cortex of 6-month-old AD mice as well as regulation of epinephrine secretion and dendritic spine morphogenesis in 15-month-old AD mice. Our outcomes from all three of our case studies illustrate the capacity of machine learning strategies when applied to single-cell data, revealing critical insights into Alzheimer's disease.
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Affiliation(s)
- Marios G. Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece; (A.G.V.); (K.L.); (K.S.); (T.P.E.); (P.V.)
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12
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Stein-O’Brien GL, Palaganas R, Meyer EM, Redding-Ochoa J, Pletnikova O, Guo H, Bell WR, Troncoso JC, Huganir RL, Morris M. Transcriptional Signatures of Hippocampal Tau Pathology in Primary Age-Related Tauopathy and Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295440. [PMID: 37745408 PMCID: PMC10516095 DOI: 10.1101/2023.09.12.23295440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Tau pathology is common in age-related neurodegenerative diseases. Tau pathology in primary age-related tauopathy (PART) and in Alzheimer's disease (AD) has a similar biochemical structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, the molecular changes associated with intraneuronal tau pathology in PART and AD, and whether these changes are similar in the two diseases, is largely unexplored. Methods Using GeoMx spatial transcriptomics, mRNA was quantified in CA1 pyramidal neurons with tau pathology and adjacent neurons without tau pathology in 6 cases of PART and 6 cases of AD, and compared to 4 control cases without pathology. Transcriptional changes were analyzed for differential gene expression and for coordinated patterns of gene expression associated with both disease state and intraneuronal tau pathology. Results Synaptic gene changes and two novel gene expression signatures associated with intraneuronal tau were identified in PART and AD. Overall, gene expression changes associated with intraneuronal tau pathology were similar in PART and AD. Synaptic gene expression was decreased overall in neurons in AD and PART compared to control cases. However, this decrease was largely driven by neurons lacking tau pathology. Synaptic gene expression was increased in tau-positive neurons compared to tau-negative neurons in disease. Two novel gene expression signatures associated with intraneuronal tau were identified by examining coordinated patterns of gene expression. Genes in the up-regulated expression pattern were enriched in calcium regulation and synaptic function pathways, specifically in synaptic exocytosis. These synaptic gene changes and intraneuronal tau expression signatures were confirmed in a published transcriptional dataset of cortical neurons with tau pathology in AD. Conclusions PART and AD show similar transcriptional changes associated with intraneuronal tau pathology in CA1 pyramidal neurons, raising the possibility of a mechanistic relationship between the tau pathology in the two diseases. Intraneuronal tau pathology was also associated with increased expression of genes associated with synaptic function and calcium regulation compared to tau-negative disease neurons. The findings highlight the power of molecular analysis stratified by pathology in neurodegenerative disease and provide novel insight into common molecular pathways associated with intraneuronal tau in PART and AD.
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Affiliation(s)
- Genevieve L Stein-O’Brien
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Single Cell Training and Analysis Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Ryan Palaganas
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ernest M. Meyer
- UPMC Hillman Cancer Center Cytometry Facility, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY
| | - Haidan Guo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William R Bell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Baltimore, MD
| | - Meaghan Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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13
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Patel PJ, Ren Y, Yan Z. Epigenomic analysis of Alzheimer's disease brains reveals diminished CTCF binding on genes involved in synaptic organization. Neurobiol Dis 2023; 184:106192. [PMID: 37302762 PMCID: PMC10519202 DOI: 10.1016/j.nbd.2023.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023] Open
Abstract
Epigenetic aberrations are suggested to play an important role in transcriptional alterations in Alzheimer's disease (AD). One of the key mechanisms of epigenetic regulation of gene expression is through the dynamic organization of chromatin structure via the master genome architecture protein, CCCTC-binding factor (CTCF). By forming chromatin loops, CTCF can influence gene transcription in a complex manner. To find out whether genome-wide DNA binding sites for CTCF are altered in AD, we compared CTCF chromatin immunoprecipitation sequencing (ChIP-Seq) data from frontal cortex of human AD patients and normal controls (n = 9 pairs, all females). We have revealed that CTCF-binding affinity on many genes is significantly reduced in AD patients, and these genes are enriched in synaptic organization, cell adhesion, and actin cytoskeleton, including synaptic scaffolding molecules and receptors, such as SHANK2, HOMER1, NRXN1, CNTNAP2 and GRIN2A, and protocadherin (PCDH) and cadherin (CDH) family members. By comparing transcriptomic data from AD patients, we have discovered that many of the synaptic and adhesion genes with reduced CTCF binding in AD are significantly reduced in their mRNA expression. Moreover, a significant overlap of genes with the diminished CTCF binding and the reduced H3K27ac is identified in AD, with the common genes enriched in synaptic organization. These data suggest that the CTCF-controlled 3D chromatin organization is perturbed in AD, which may be linked to the diminished expression of target genes, probably through changes in histone modification.
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Affiliation(s)
- Prachetas J Patel
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yong Ren
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA.
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14
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Tang X, Tena J, Di Lucente J, Maezawa I, Harvey DJ, Jin LW, Lebrilla CB, Zivkovic AM. Transcriptomic and glycomic analyses highlight pathway-specific glycosylation alterations unique to Alzheimer's disease. Sci Rep 2023; 13:7816. [PMID: 37188790 PMCID: PMC10185676 DOI: 10.1038/s41598-023-34787-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023] Open
Abstract
Glycosylation has been found to be altered in the brains of individuals with Alzheimer's disease (AD). However, it is unknown which specific glycosylation-related pathways are altered in AD dementia. Using publicly available RNA-seq datasets covering seven brain regions and including 1724 samples, we identified glycosylation-related genes ubiquitously changed in individuals with AD. Several differentially expressed glycosyltransferases found by RNA-seq were confirmed by qPCR in a different set of human medial temporal cortex (MTC) samples (n = 20 AD vs. 20 controls). N-glycan-related changes predicted by expression changes in these glycosyltransferases were confirmed by mass spectrometry (MS)-based N-glycan analysis in the MTC (n = 9 AD vs. 6 controls). About 80% of glycosylation-related genes were differentially expressed in at least one brain region of AD participants (adjusted p-values < 0.05). Upregulation of MGAT1 and B4GALT1 involved in complex N-linked glycan formation and galactosylation, respectively, were reflected by increased concentrations of corresponding N-glycans. Isozyme-specific changes were observed in expression of the polypeptide N-acetylgalactosaminyltransferase (GALNT) family and the alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (ST6GALNAC) family of enzymes. Several glycolipid-specific genes (UGT8, PIGM) were upregulated. The critical transcription factors regulating the expression of N-glycosylation and elongation genes were predicted and found to include STAT1 and HSF5. The miRNA predicted to be involved in regulating N-glycosylation and elongation glycosyltransferases were has-miR-1-3p and has-miR-16-5p, respectively. Our findings provide an overview of glycosylation pathways affected by AD and potential regulators of glycosyltransferase expression that deserve further validation and suggest that glycosylation changes occurring in the brains of AD dementia individuals are highly pathway-specific and unique to AD.
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Affiliation(s)
- Xinyu Tang
- Department of Nutrition, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Jennyfer Tena
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Jacopo Di Lucente
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Izumi Maezawa
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Danielle J Harvey
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
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15
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Jin B, Fei G, Sang S, Zhong C. Identification of biomarkers differentiating Alzheimer's disease from other neurodegenerative diseases by integrated bioinformatic analysis and machine-learning strategies. Front Mol Neurosci 2023; 16:1152279. [PMID: 37234685 PMCID: PMC10205980 DOI: 10.3389/fnmol.2023.1152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Background Alzheimer's disease (AD) is the most common neurodegenerative disease, imposing huge mental and economic burdens on patients and society. The specific molecular pathway(s) and biomarker(s) that distinguish AD from other neurodegenerative diseases and reflect the disease progression are still not well studied. Methods Four frontal cortical datasets of AD were integrated to conduct differentially expressed genes (DEGs) and functional gene enrichment analyses. The transcriptional changes after the integrated frontal cortical datasets subtracting the cerebellar dataset of AD were further compared with frontal cortical datasets of frontotemporal dementia and Huntingdon's disease to identify AD-frontal-associated gene expression. Integrated bioinformatic analysis and machine-learning strategies were applied for screening and determining diagnostic biomarkers, which were further validated in another two frontal cortical datasets of AD by receiver operating characteristic (ROC) curves. Results Six hundred and twenty-six DEGs were identified as AD frontal associated, including 580 downregulated genes and 46 upregulated genes. The functional enrichment analysis revealed that immune response and oxidative stress were enriched in AD patients. Decorin (DCN) and regulator of G protein signaling 1 (RGS1) were screened as diagnostic biomarkers in distinguishing AD from frontotemporal dementia and Huntingdon's disease of AD. The diagnostic effects of DCN and RGS1 for AD were further validated in another two datasets of AD: the areas under the curve (AUCs) reached 0.8148 and 0.8262 in GSE33000, and 0.8595 and 0.8675 in GSE44770. There was a better value for AD diagnosis when combining performances of DCN and RGS1 with the AUCs of 0.863 and 0.869. Further, DCN mRNA level was correlated to CDR (Clinical Dementia Rating scale) score (r = 0.5066, p = 0.0058) and Braak staging (r = 0.3348, p = 0.0549). Conclusion DCN and RGS1 associated with the immune response may be useful biomarkers for diagnosing AD and distinguishing the disease from frontotemporal dementia and Huntingdon's disease. DCN mRNA level reflects the development of the disease.
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Affiliation(s)
- Boru Jin
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Guoqiang Fei
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Shaoming Sang
- Shanghai Raising Pharmaceutical Technology Co., Ltd., Shanghai, China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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16
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Kim S, Fuselier J, Latoff A, Manges J, Jazwinski SM, Zsombok A. Upregulation of extracellular proteins in a mouse model of Alzheimer's disease. Sci Rep 2023; 13:6998. [PMID: 37117484 PMCID: PMC10147640 DOI: 10.1038/s41598-023-33677-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
Various risk factors of Alzheimer's disease (AD) are known, such as advanced age, possession of certain genetic variants, accumulation of toxic amyloid-β (Aβ) peptides, and unhealthy lifestyle. An estimate of heritability of AD ranges from 0.13 to 0.25, indicating that its phenotypic variation is accounted for mostly by non-genetic factors. DNA methylation is regarded as an epigenetic mechanism that interfaces the genome with non-genetic factors. The Tg2576 mouse model has been insightful in AD research. These transgenic mice express a mutant form of human amyloid precursor protein linked to familial AD. At 9-13 months of age, these mice show elevated levels of Aβ peptides and cognitive impairment. The current literature lacks integrative multiomics of the animal model. We applied transcriptomics and DNA methylomics to the same brain samples from ~ 11-month-old transgenic mice. We found that genes involved in extracellular matrix structures and functions are transcriptionally upregulated, and genes involved in extracellular protein secretion and localization are differentially methylated in the transgenic mice. Integrative analysis found enrichment of GO terms related to memory and synaptic functionability. Our results indicate a possibility of transcriptional modulation by DNA methylation underlying AD neuropathology.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Deming Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA.
- Deming Department of Medicine, Tulane University Health Sciences Center, 1430 Tulane Ave., MBC 8513, New Orleans, LA, 70112, USA.
| | - Jessica Fuselier
- Tulane Center for Aging and Deming Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
- Data Science Department, Catalytic Data Science, Charleston, SC, USA
| | - Anna Latoff
- Tulane Center for Aging and Deming Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Justin Manges
- Tulane Center for Aging and Deming Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Deming Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Andrea Zsombok
- Tulane Center for Aging and Department of Physiology, Tulane University Health Sciences Center, New Orleans, LA, USA
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17
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Ho PWL, Li L, Liu HF, Choi ZYK, Chang EES, Pang SYY, Malki Y, Leung CT, Kung MHW, Ramsden DB, Ho SL. In vivo overexpression of synaptogyrin-3 promotes striatal synaptic dopamine uptake in LRRK2 R1441G mutant mouse model of Parkinson's disease. Brain Behav 2023; 13:e2886. [PMID: 36624932 PMCID: PMC9927849 DOI: 10.1002/brb3.2886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/17/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Leucine-rich repeat kinase 2 (LRRK2) mutation is a common genetic risk factor of Parkinson's disease (PD). Presynaptic dysfunction is an early pathogenic event associated with dopamine (DA) dysregulation in striatum of the brain. DA uptake activity of DA uptake transporter (DAT) affects synaptic plasticity and motor and non-motor behavior. Synaptogyrin-3 (SYNGR3) is part of the synaptogyrin family, especially abundant in brain. Previous in vitro studies demonstrated interaction between SYNGR3 and DAT. Reduced SYNGR3 expression was observed in human PD brains with unclear reasons. METHODS Here, we further explored whether inducing SYNGR3 expression can influence (i) cellular DA uptake using differentiated human SH-SY5Y neuronal cells, (ii) striatal synaptosomal DA uptake in a mutant LRRK2R1441G knockin mouse model of PD, and (iii) innate rodent behavior using the marble burying test. RESULTS Young LRRK2 mutant mice exhibited significantly lower SYNGR3 levels in striatum compared to age-matched wild-type (WT) controls, resembling level in aged WT mice. SYNGR3 is spatially co-localized with DAT at striatal presynaptic terminals, visualized by immuno-gold transmission electron microscopy and immunohistochemistry. Their protein-protein interaction was confirmed by co-immunoprecipitation. Transient overexpression of SYNGR3 in differentiated SH-SY5Y cells increased cellular DA uptake activity without affecting total DAT levels. Inducing SYNGR3 overexpression by adeno-associated virus-7 (AAV7) injection in vivo into striatum increased ex vivo synaptosomal DA uptake in LRRK2 mutant mice and improved their innate marble burying behavior. CONCLUSION Brain SYNGR3 expression may be an important determinant to striatal DA homeostasis and synaptic function. Our preliminary behavioral test showed improved innate behavior after SYNGR3 overexpression in LRRK2 mutant mice, advocating further studies to determine the influence of SYNGR3 in the pathophysiology of DA neurons in PD.
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Affiliation(s)
- Philip Wing-Lok Ho
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Lingfei Li
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Hui-Fang Liu
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Zoe Yuen-Kiu Choi
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Eunice Eun Seo Chang
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Yasine Malki
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Chi-Ting Leung
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Michelle Hiu-Wai Kung
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - David Boyer Ramsden
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
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Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model. Nat Commun 2023; 14:91. [PMID: 36609445 PMCID: PMC9822922 DOI: 10.1038/s41467-022-35749-6] [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: 12/22/2021] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
Pleiotropic mechanisms have been implicated in Alzheimer's disease (AD), including transcriptional dysregulation, protein misprocessing and synaptic dysfunction, but how they are mechanistically linked to induce cognitive deficits in AD is unclear. Here we find that the histone methyltransferase Smyd3, which catalyzes histone H3 lysine 4 trimethylation (H3K4me3) to activate gene transcription, is significantly elevated in prefrontal cortex (PFC) of AD patients and P301S Tau mice, a model of tauopathies. A short treatment with the Smyd3 inhibitor, BCI-121, rescues cognitive behavioral deficits, and restores synaptic NMDAR function and expression in PFC pyramidal neurons of P301S Tau mice. Fbxo2, which encodes an E3 ubiquitin ligase controlling the degradation of NMDAR subunits, is identified as a downstream target of Smyd3. Smyd3-induced upregulation of Fbxo2 in P301S Tau mice is linked to the increased NR1 ubiquitination. Fbxo2 knockdown in PFC leads to the recovery of NMDAR function and cognitive behaviors in P301S Tau mice. These data suggest an integrated mechanism and potential therapeutic strategy for AD.
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Wang X, Zhou X, Lee J, Furdui CM, Ma T. In-Depth Proteomic Analysis of De Novo Proteome in a Mouse Model of Alzheimer's Disease. J Alzheimers Dis 2023; 91:1471-1482. [PMID: 36641677 PMCID: PMC10016629 DOI: 10.3233/jad-221044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common dementia syndrome in the elderly characterized by synaptic failure and unique brain pathology. De novo protein synthesis is required for the maintenance of memory and synaptic plasticity. Mounting evidence links impaired neuronal protein synthesis capacity and overall protein synthesis deficits to AD pathogenesis. Meanwhile, identities of AD-associated dysregulation of "newly synthesized proteome" remain elusive. OBJECTIVE To investigate de novo proteome alterations in the hippocampus of aged Tg19959 AD model mice. METHODS In this study, we combined the bioorthogonal noncanonical amino acid tagging (BONCAT) method with the unbiased large-scale proteomic analysis in acute living brain slices (we name it "BONSPEC") to investigate de novo proteome alterations in the hippocampus of Tg19959 AD model mice. We further applied multiple bioinformatics methods to analyze in-depth the proteomics data. RESULTS In total, 1,742 proteins were detected across the 10 samples with the BONSPEC method. After exclusion of those only detected in less than half of the samples in both groups, 1,362 proteins were kept for further analysis. 37 proteins were differentially expressed (based on statistical analysis) between the WT and Tg19959 groups. Among them, 19 proteins were significantly decreased while 18 proteins were significantly increased in the hippocampi of Tg19959 mice compared to WT mice. The results suggest that proteins involved in synaptic function were enriched in de novo proteome of AD mice. CONCLUSION Our study could provide insights into the future investigation into the molecular signaling mechanisms underlying AD and related dementias (ADRDs).
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Affiliation(s)
- Xin Wang
- Department of Internal Medicine, Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Xueyan Zhou
- Department of Internal Medicine, Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jingyun Lee
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Cristina M Furdui
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Tao Ma
- Department of Internal Medicine, Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Winston-Salem, NC, USA
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20
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Mu L, Xia D, Cai J, Gu B, Liu X, Friedman V, Liu QS, Zhao L. Treadmill Exercise Reduces Neuroinflammation, Glial Cell Activation and Improves Synaptic Transmission in the Prefrontal Cortex in 3 × Tg-AD Mice. Int J Mol Sci 2022; 23:12655. [PMID: 36293516 PMCID: PMC9604030 DOI: 10.3390/ijms232012655] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Physical exercise improves memory and cognition in physiological aging and Alzheimer's disease (AD), but the mechanisms remain poorly understood. Here, we test the hypothesis that Aβ oligomer accumulation, neuroinflammation, and glial cell activation may lead to disruption of synaptic transmission in the prefrontal cortex of 3 × Tg-AD Mice, resulting in impairment of learning and memory. On the other hand, treadmill exercise could prevent the pathogenesis and exert neuroprotective effects. Here, we used immunohistochemistry, western blotting, enzyme-linked immunosorbent assay, and slice electrophysiology to analyze the levels of GSK3β, Aβ oligomers (Aβ dimers and trimers), pro-inflammatory cytokines (IL-1β, IL-6, and TNFα), the phosphorylation of CRMP2 at Thr514, and synaptic currents in pyramidal neurons in the prefrontal cortex. We show that 12-week treadmill exercise beginning in three-month-old mice led to the inhibition of GSK3β kinase activity, decreases in the levels of Aβ oligomers, pro-inflammatory cytokines (IL-1β, IL-6, and TNFα), and the phosphorylation of CRMP2 at Thr514, reduction of microglial and astrocyte activation, and improvement of excitatory and inhibitory synaptic transmission of pyramidal neurons in the prefrontal cortex of 3 × Tg-AD Mice. Thus, treadmill exercise reduces neuroinflammation, glial cell activation and improves synaptic transmission in the prefrontal cortex in 3 × Tg-AD mice, possibly related to the inhibition of GSK3β kinase activity.
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Affiliation(s)
- Lianwei Mu
- Department of Exercise Physiology, Guangzhou Sport University, Guangzhou 510500, China
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education, Beijing Sport University, Beijing 100084, China
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Dongdong Xia
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education, Beijing Sport University, Beijing 100084, China
| | - Jiajia Cai
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education, Beijing Sport University, Beijing 100084, China
| | - Boya Gu
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education, Beijing Sport University, Beijing 100084, China
| | - Xiaojie Liu
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Vladislav Friedman
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Qing-Song Liu
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Li Zhao
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education, Beijing Sport University, Beijing 100084, China
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21
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Wahl D, Moreno JA, Santangelo KS, Zhang Q, Afzali MF, Walsh MA, Musci RV, Cavalier AN, Hamilton KL, LaRocca TJ. Nontransgenic Guinea Pig Strains Exhibit Hallmarks of Human Brain Aging and Alzheimer's Disease. J Gerontol A Biol Sci Med Sci 2022; 77:1766-1774. [PMID: 35323931 PMCID: PMC9434446 DOI: 10.1093/gerona/glac073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Indexed: 11/14/2022] Open
Abstract
Older age is the primary risk factor for most chronic diseases, including Alzheimer's disease (AD). Current preclinical models to study brain aging and AD are mainly transgenic and harbor mutations intended to mirror brain pathologies associated with human brain aging/AD (eg, by increasing production of the amyloid precursor protein, amyloid beta [Aβ], and/or phosphorylated tau, all of which are key pathological mediators of AD). Although these models may provide insight on pathophysiological processes in AD, none completely recapitulate the disease and its strong age-dependence, and there has been limited success in translating preclinical results and treatments to humans. Here, we describe 2 nontransgenic guinea pig (GP) models, a standard PigmEnTed (PET) strain, and lesser-studied Dunkin-Hartley (DH) strain, that may naturally mimic key features of brain aging and AD in humans. We show that brain aging in PET GP is transcriptomically similar to human brain aging, whereas older DH brains are transcriptomically more similar to human AD. Both strains/models also exhibit increased neurofilament light chain (NFL, a marker of neuronal damage) with aging, and DH animals display greater S100 calcium-binding protein B (S100β), ionized calcium-binding adapter molecule 1 (Iba1), and Aβ and phosphorylated tau-which are all important markers of neuroinflammation-associated AD. Collectively, our results suggest that both the PET and DH GP may be useful, nontransgenic models to study brain aging and AD, respectively.
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Affiliation(s)
- Devin Wahl
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
- Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, USA
| | - Julie A Moreno
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Kelly S Santangelo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Qian Zhang
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maryam F Afzali
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Maureen A Walsh
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Robert V Musci
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Alyssa N Cavalier
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Karyn L Hamilton
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
- Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, USA
| | - Thomas J LaRocca
- Address correspondence to: Thomas J. LaRocca, PhD, Department of Health and Exercise Science, Center for Healthy Aging, Colorado State University, 1582 Campus Delivery, Fort Collins, CO 80523-1582, USA. E-mail:
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22
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Integrated Excitatory/Inhibitory Imbalance and Transcriptomic Analysis Reveals the Association between Dysregulated Synaptic Genes and Anesthetic-Induced Cognitive Dysfunction. Cells 2022; 11:cells11162497. [PMID: 36010580 PMCID: PMC9406780 DOI: 10.3390/cells11162497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Emerging evidence from human epidemiologic and animal studies has demonstrated that developmental anesthesia neurotoxicity could cause long-term cognitive deficits and behavioral problems. However, the underlying mechanisms remain largely unknown. We conducted an electrophysiological analysis of synapse activity and a transcriptomic assay of 24,881 mRNA expression on hippocampal tissues from postnatal day 60 (P60) mice receiving propofol exposure at postnatal day 7 (P7). We found that developmentally propofol-exposed P60 mouse hippocampal neurons displayed an E/I imbalance, compared with control mice as evidenced by the decreased excitation and increased inhibition. We found that propofol exposure at P7 led to the abnormal expression of 317 mRNAs in the hippocampus of P60 mice, including 23 synapse-related genes. Various bioinformatic analyses revealed that these abnormally expressed synaptic genes were associated with the function and development of synapse activity and plasticity, E/I balance, behavior, and cognitive impairment. Our findings suggest that the altered E/I balance may constitute a mechanism for propofol-induced long-term impaired learning and memory in mice. The transcriptomic and bioinformatic analysis of these dysregulated genes related to synaptic function paves the way for development of therapeutic strategies against anesthetic neurodegeneration through the restoration of E/I balance and the modification of synaptic gene expression.
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23
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Webberley TS, Masetti G, Bevan RJ, Kerry-Smith J, Jack AA, Michael DR, Thomas S, Glymenaki M, Li J, McDonald JAK, John D, Morgan JE, Marchesi JR, Good MA, Plummer SF, Hughes TR. The Impact of Probiotic Supplementation on Cognitive, Pathological and Metabolic Markers in a Transgenic Mouse Model of Alzheimer's Disease. Front Neurosci 2022; 16:843105. [PMID: 35685773 PMCID: PMC9172594 DOI: 10.3389/fnins.2022.843105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
Brain degenerative disorders such as Alzheimer’s disease (AD) can be exacerbated by aberrant metabolism. Supplementation with probiotic bacteria is emerging as a promising preventative strategy for both neurodegeneration and metabolic syndrome. In this study, we assess the impact of the Lab4b probiotic consortium on (i) cognitive and pathological markers of AD progression and (ii) metabolic status in 3xTg-AD mice subjected to metabolic challenge with a high fat diet. The group receiving the probiotic performed better in the novel object recognition test and displayed higher hippocampal neuronal spine density than the control group at the end of the 12 weeks intervention period. These changes were accompanied by differences in localised (brain) and systemic anti-inflammatory responses that favoured the Probiotic group together with the prevention of diet induced weight gain and hypercholesterolaemia and the modulation of liver function. Compositional differences between the faecal microbiotas of the study groups included a lower Firmicutes:Bacteroidetes ratio and less numbers of viable yeast in the Probiotic group compared to the Control. The results illustrate the potential of the Lab4b probiotic as a neuroprotective agent and encourage further studies with human participants.
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Affiliation(s)
- Thomas S Webberley
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.,Cultech Ltd., Port Talbot, United Kingdom
| | | | - Ryan J Bevan
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom.,School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | - Maria Glymenaki
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jia Li
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Julie A K McDonald
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - James E Morgan
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mark A Good
- School of Psychology, Cardiff University, Cardiff, United Kingdom
| | | | - Timothy R Hughes
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.,UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
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24
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Cao Q, Wang W, Yan Z. Epigenetics-based treatment strategies for Alzheimer's disease. Aging (Albany NY) 2022; 14:4193-4194. [PMID: 35604397 PMCID: PMC9186760 DOI: 10.18632/aging.204096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 12/03/2022]
Affiliation(s)
- Qing Cao
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Wei Wang
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
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25
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Li L, Ho PWL, Liu H, Pang SYY, Chang EES, Choi ZYK, Malki Y, Kung MHW, Ramsden DB, Ho SL. Transcriptional Regulation of the Synaptic Vesicle Protein Synaptogyrin-3 (SYNGR3) Gene: The Effects of NURR1 on Its Expression. Int J Mol Sci 2022; 23:ijms23073646. [PMID: 35409005 PMCID: PMC8998927 DOI: 10.3390/ijms23073646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Synaptogyrin-3 (SYNGR3) is a synaptic vesicular membrane protein. Amongst four homologues (SYNGR1 to 4), SYNGR1 and 3 are especially abundant in the brain. SYNGR3 interacts with the dopamine transporter (DAT) to facilitate dopamine (DA) uptake and synaptic DA turnover in dopaminergic transmission. Perturbed SYNGR3 expression is observed in Parkinson’s disease (PD). The regulatory elements which affect SYNGR3 expression are unknown. Nuclear-receptor-related-1 protein (NURR1) can regulate dopaminergic neuronal differentiation and maintenance via binding to NGFI-B response elements (NBRE). We explored whether NURR1 can regulate SYNGR3 expression using an in silico analysis of the 5′-flanking region of the human SYNGR3 gene, reporter gene activity and an electrophoretic mobility shift assay (EMSA) of potential cis-acting sites. In silico analysis of two genomic DNA segments (1870 bp 5′-flanking region and 1870 + 159 bp of first exon) revealed one X Core Promoter Element 1 (XCPE1), two SP1, and three potential non-canonical NBRE response elements (ncNBRE) but no CAAT or TATA box. The longer segment exhibited gene promoter activity in luciferase reporter assays. Site-directed mutagenesis of XCPE1 decreased promoter activity in human neuroblastoma SH-SY5Y (↓43.2%) and human embryonic kidney HEK293 cells (↓39.7%). EMSA demonstrated NURR1 binding to these three ncNBRE. Site-directed mutagenesis of these ncNBRE reduced promoter activity by 11–17% in SH-SY5Y (neuronal) but not in HEK293 (non-neuronal) cells. C-DIM12 (Nurr1 activator) increased SYNGR3 protein expression in SH-SY5Y cells and its promoter activity using a real-time luciferase assay. As perturbed vesicular function is a feature of major neurodegenerative diseases, inducing SYNGR3 expression by NURR1 activators may be a potential therapeutic target to attenuate synaptic dysfunction in PD.
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Affiliation(s)
- Lingfei Li
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Philip Wing-Lok Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Huifang Liu
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Eunice Eun-Seo Chang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Zoe Yuen-Kiu Choi
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Yasine Malki
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Michelle Hiu-Wai Kung
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - David Boyer Ramsden
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
- Correspondence: (D.B.R.); (S.-L.H.)
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
- Correspondence: (D.B.R.); (S.-L.H.)
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26
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Paasila PJ, Aramideh JA, Sutherland GT, Graeber MB. Synapses, Microglia, and Lipids in Alzheimer's Disease. Front Neurosci 2022; 15:778822. [PMID: 35095394 PMCID: PMC8789683 DOI: 10.3389/fnins.2021.778822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is characterised by synaptic dysfunction accompanied by the microscopically visible accumulation of pathological protein deposits and cellular dystrophy involving both neurons and glia. Late-stage AD shows pronounced loss of synapses and neurons across several differentially affected brain regions. Recent studies of advanced AD using post-mortem brain samples have demonstrated the direct involvement of microglia in synaptic changes. Variants of the Apolipoprotein E and Triggering Receptors Expressed on Myeloid Cells gene represent important determinants of microglial activity but also of lipid metabolism in cells of the central nervous system. Here we review evidence that may help to explain how abnormal lipid metabolism, microglial activation, and synaptic pathophysiology are inter-related in AD.
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Affiliation(s)
- Patrick J. Paasila
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Jason A. Aramideh
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Greg T. Sutherland
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Manuel B. Graeber
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
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