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Sen S, Mukhopadhyay D. A Holistic Analysis of Alzheimer's Disease-Associated lncRNA Communities Reveals Enhanced lncRNA-miRNA-RBP Regulatory Triad Formation Within Functionally Segregated Clusters. J Mol Neurosci 2024; 74:77. [PMID: 39143264 PMCID: PMC11324768 DOI: 10.1007/s12031-024-02244-0] [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: 05/13/2024] [Accepted: 07/04/2024] [Indexed: 08/16/2024]
Abstract
Recent studies on the regulatory networks implicated in Alzheimer's disease (AD) evince long non-coding RNAs (lncRNAs) as crucial regulatory players, albeit a poor understanding of the mechanism. Analyzing differential gene expression in the RNA-seq data from the post-mortem AD brain hippocampus, we categorized a list of AD-dysregulated lncRNA transcripts into functionally similar communities based on their k-mer profiles. Using machine-learning-based algorithms, their subcellular localizations were mapped. We further explored the functional relevance of each community through AD-dysregulated miRNA, RNA-binding protein (RBP) interactors, and pathway enrichment analyses. Further investigation of the miRNA-lncRNA and RBP-lncRNA networks from each community revealed the top RBPs, miRNAs, and lncRNAs for each cluster. The experimental validation community yielded ELAVL4 and miR-16-5p as the predominant RBP and miRNA, respectively. Five lncRNAs emerged as the top-ranking candidates from the RBP/miRNA-lncRNA networks. Further analyses of these networks revealed the presence of multiple regulatory triads where the RBP-lncRNA interactions could be augmented by the enhanced miRNA-lncRNA interactions. Our results advance the understanding of the mechanism of lncRNA-mediated AD regulation through their interacting partners and demonstrate how these functionally segregated but overlapping regulatory networks can modulate the disease holistically.
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Affiliation(s)
- Somenath Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, Kolkata, 700 064, India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, Kolkata, 700 064, India.
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2
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Filomena E, Picardi E, Tullo A, Pesole G, D’Erchia AM. Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets. Front Aging Neurosci 2024; 16:1437278. [PMID: 39086756 PMCID: PMC11288953 DOI: 10.3389/fnagi.2024.1437278] [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: 05/23/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction The deregulation of lncRNAs expression has been associated with neuronal damage in Alzheimer's disease (AD), but how or whether they can influence its onset is still unknown. We investigated 2 RNA-seq datasets consisting, respectively, of the hippocampal and fusiform gyrus transcriptomic profile of AD patients, matched with non-demented controls. Methods We performed a differential expression analysis, a gene correlation network analysis (WGCNA) and a pathway enrichment analysis of two RNA-seq datasets. Results We found deregulated lncRNAs in common between hippocampus and fusiform gyrus and deregulated gene groups associated to functional pathways related to neurotransmission and memory consolidation. lncRNAs, co-expressed with known AD-related coding genes, were identified from the prioritized modules of both brain regions. Discussion We found common deregulated lncRNAs in the AD hippocampus and fusiform gyrus, that could be considered common signatures of AD pathogenesis, providing an important source of information for understanding the molecular changes of AD.
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Affiliation(s)
- Ermes Filomena
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Apollonia Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Anna Maria D’Erchia
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
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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. 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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4
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Huo Y, Jing R, Li P, Chen P, Si J, Liu G, Liu Y. Delineating the Heterogeneity of Alzheimer's Disease and Mild Cognitive Impairment Using Normative Models of Dynamic Brain Functional Networks. Biol Psychiatry 2024:S0006-3223(24)01365-9. [PMID: 38857821 DOI: 10.1016/j.biopsych.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Alzheimer's disease (AD), which has been identified as the most common type of dementia, presents considerable heterogeneity in its clinical manifestations. Early intervention at the stage of mild cognitive impairment (MCI) holds potential in AD prevention. However, characterizing the heterogeneity of neurobiological abnormalities and identifying MCI subtypes pose significant challenges. METHODS We constructed sex-specific normative age models of dynamic brain functional networks and mapped the deviations of the brain characteristics for individuals from multiple datasets, including 295 patients with AD, 441 patients with MCI, and 1160 normal control participants. Then, based on these individual deviation patterns, subtypes for both AD and MCI were identified using the clustering method, and their similarities and differences were comprehensively assessed. RESULTS Individuals with AD and MCI were clustered into 2 subtypes, and these subtypes exhibited significant differences in their intrinsic brain functional phenotypes and spatial atrophy patterns, as well as in disease progression and cognitive decline trajectories. The subtypes with positive deviations in AD and MCI shared similar deviation patterns, as did those with negative deviations. There was a potential transformation of MCI with negative deviation patterns into AD, and participants with MCI had a more severe cognitive decline rate. CONCLUSIONS In this study, we quantified neurophysiological heterogeneity by analyzing deviation patterns from the dynamic functional connectome normative model and identified disease subtypes of AD and MCI using a comprehensive resting-state functional magnetic resonance imaging multicenter dataset. The findings provide new insights for developing early prevention and personalized treatment strategies for AD.
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Affiliation(s)
- Yanxi Huo
- School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, China
| | - Rixing Jing
- School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, China.
| | - Peng Li
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Chinese Academy of Medical Sciences Research Unit, Peking University, Beijing, China
| | - Pindong Chen
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Juanning Si
- School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, China
| | - Guozhong Liu
- School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, China
| | - Yong Liu
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China.
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5
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Lian P, Cai X, Yang X, Ma Z, Wang C, Liu K, Wu Y, Cao X, Xu Y. Analysis and experimental validation of necroptosis-related molecular classification, immune signature and feature genes in Alzheimer's disease. Apoptosis 2024; 29:726-742. [PMID: 38478169 PMCID: PMC11055779 DOI: 10.1007/s10495-024-01943-8] [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] [Accepted: 02/04/2024] [Indexed: 04/28/2024]
Abstract
Necroptosis, a programmed cell death pathway, has been demonstrated to be activated in Alzheimer's disease (AD). However, the precise role of necroptosis and its correlation with immune cell infiltration in AD remains unclear. In this study, we conducted non-negative matrix factorization clustering analysis to identify three subtypes of AD based on necroptosis-relevant genes. Notably, these subtypes exhibited varying necroptosis scores, clinical characteristics and immune infiltration signatures. Cluster B, characterized by high necroptosis scores, showed higher immune cell infiltration and was associated with a more severe pathology, potentially representing a high-risk subgroup. To identify potential biomarkers for AD within cluster B, we employed two machine learning algorithms: the least absolute shrinkage and selection operator regression and Random Forest. Subsequently, we identified eight feature genes (CARTPT, KLHL35, NRN1, NT5DC3, PCYOX1L, RHOQ, SLC6A12, and SLC38A2) that were utilized to develop a diagnosis model with remarkable predictive capacity for AD. Moreover, we conducted validation using bulk RNA-seq, single-nucleus RNA-seq, and in vivo experiments to confirm the expression of these feature genes. In summary, our study identified a novel necroptosis-related subtype of AD and eight diagnostic biomarkers, explored the roles of necroptosis in AD progression and shed new light for the clinical diagnosis and treatment of this disease.
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Affiliation(s)
- Piaopiao Lian
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Cai
- Department of Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoman Yang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhuoran Ma
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cailin Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Wu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuebing Cao
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Xu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Karimani F, Asgari Taei A, Abolghasemi-Dehaghani MR, Safari MS, Dargahi L. Impairment of entorhinal cortex network activity in Alzheimer's disease. Front Aging Neurosci 2024; 16:1402573. [PMID: 38882526 PMCID: PMC11176617 DOI: 10.3389/fnagi.2024.1402573] [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: 03/17/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
The entorhinal cortex (EC) stands out as a critical brain region affected in the early phases of Alzheimer's disease (AD), with some of the disease's pathological processes originating from this area, making it one of the most crucial brain regions in AD. Recent research highlights disruptions in the brain's network activity, characterized by heightened excitability and irregular oscillations, may contribute to cognitive impairment. These disruptions are proposed not only as potential therapeutic targets but also as early biomarkers for AD. In this paper, we will begin with a review of the anatomy and function of EC, highlighting its selective vulnerability in AD. Subsequently, we will discuss the disruption of EC network activity, exploring changes in excitability and neuronal oscillations in this region during AD and hypothesize that, considering the advancements in neuromodulation techniques, addressing the disturbances in the network activity of the EC could offer fresh insights for both the diagnosis and treatment of AD.
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Affiliation(s)
- Farnaz Karimani
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Asgari Taei
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mir-Shahram Safari
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Dargahi
- Neurobiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Prasanth MI, Sivamaruthi BS, Cheong CSY, Verma K, Tencomnao T, Brimson JM, Prasansuklab A. Role of Epigenetic Modulation in Neurodegenerative Diseases: Implications of Phytochemical Interventions. Antioxidants (Basel) 2024; 13:606. [PMID: 38790711 PMCID: PMC11118909 DOI: 10.3390/antiox13050606] [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: 04/07/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Epigenetics defines changes in cell function without involving alterations in DNA sequence. Neuroepigenetics bridges neuroscience and epigenetics by regulating gene expression in the nervous system and its impact on brain function. With the increase in research in recent years, it was observed that alterations in the gene expression did not always originate from changes in the genetic sequence, which has led to understanding the role of epigenetics in neurodegenerative diseases (NDDs) including Alzheimer's disease (AD) and Parkinson's disease (PD). Epigenetic alterations contribute to the aberrant expression of genes involved in neuroinflammation, protein aggregation, and neuronal death. Natural phytochemicals have shown promise as potential therapeutic agents against NDDs because of their antioxidant, anti-inflammatory, and neuroprotective effects in cellular and animal models. For instance, resveratrol (grapes), curcumin (turmeric), and epigallocatechin gallate (EGCG; green tea) exhibit neuroprotective effects through their influence on DNA methylation patterns, histone acetylation, and non-coding RNA expression profiles. Phytochemicals also aid in slowing disease progression, preserving neuronal function, and enhancing cognitive and motor abilities. The present review focuses on various epigenetic modifications involved in the pathology of NDDs, including AD and PD, gene expression regulation related to epigenetic alterations, and the role of specific polyphenols in influencing epigenetic modifications in AD and PD.
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Affiliation(s)
- Mani Iyer Prasanth
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bhagavathi Sundaram Sivamaruthi
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand;
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Clerance Su Yee Cheong
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanika Verma
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - James Michael Brimson
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- Research, Innovation and International Affairs, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Anchalee Prasansuklab
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand; (M.I.P.); (C.S.Y.C.); (K.V.); (T.T.); (J.M.B.)
- College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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8
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Long Y, Zhao Z, Xie W, Shi J, Yang F, Zhu D, Jiang P, Tang Q, Ti Z, Jiang B, Yang X, Gao G, Qi W. Kallistatin leads to cognition impairment via downregulating glutamine synthetase. Pharmacol Res 2024; 202:107145. [PMID: 38492829 DOI: 10.1016/j.phrs.2024.107145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
In many neurodegenerative disorders, such as Alzheimer's disease (AD), glutamate-mediated neuronal excitotoxicity is considered the basis for cognitive impairment. The mRNA and protein expression of SERPINA4(Kallistatin) are higher in patients with AD. However, whether Kallistatin plays a regulatory role in glutamate-glutamine cycle homeostasis remains unclear. In this study, we identified impaired cognitive function in Kallistatin transgenic (KAL-TG) mice. Baseline glutamate levels were elevated and miniature excitatory postsynaptic current (mEPSC) frequency was increased in the hippocampus, suggesting the impairment of glutamate homeostasis in KAL-TG mice. Mechanistically, we demonstrated that Kallistatin promoted lysine acetylation and ubiquitination of glutamine synthetase (GS) and facilitated its degradation via the proteasome pathway, thereby downregulating GS. Fenofibrate improved cognitive memory in KAL-TG mice by downregulating serum Kallistatin. Collectively, our study findings provide insights the mechanism by which Kallistatin regulates cognitive impairment, and suggest the potential of fenofibrate to prevente and treat of AD patients with high levels of Kallistatin.
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Affiliation(s)
- Yanlan Long
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhen Zhao
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wanting Xie
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinhui Shi
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fengyu Yang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Dan Zhu
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Jiang
- Department of Clinical Medical Laboratory, Guangzhou First People Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qilong Tang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhou Ti
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bin Jiang
- Guangdong Province Key Laboratory of Brain Function and Disease, School of Medicine, Sun Yat-sen University, Shenzhen, China.
| | - Xia Yang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Guoquan Gao
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; China Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China; Guangdong Provincial Key Laboratory of Diabetology, Guangzhou, Guangdong, China.
| | - Weiwei Qi
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Guangdong Engineering & Technology Research Center for Gene Manipulation and Biomacromolecular Products (Sun Yat-sen University), Guangzhou, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, China.
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9
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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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10
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Dai Z, Liang L, Wang W, Zuo P, Yu S, Liu Y, Zhao X, Lu Y, Jin Y, Zhang F, Ding D, Deng W, Yin Y. Structural insights into the ubiquitylation strategy of the oligomeric CRL2 FEM1B E3 ubiquitin ligase. EMBO J 2024; 43:1089-1109. [PMID: 38360992 PMCID: PMC10943247 DOI: 10.1038/s44318-024-00047-y] [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: 08/22/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer's disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.
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Affiliation(s)
- Zonglin Dai
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ling Liang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weize Wang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shang Yu
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yaqi Liu
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Jin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Fangting Zhang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Dian Ding
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weiwei Deng
- Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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11
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Paudel B, Jeong SY, Martinez CP, Rickman A, Haluck-Kangas A, Bartom ET, Fredriksen K, Affaneh A, Kessler JA, Mazzulli JR, Murmann AE, Rogalski E, Geula C, Ferreira A, Heckmann BL, Green DR, Sadleir KR, Vassar R, Peter ME. Death Induced by Survival gene Elimination (DISE) correlates with neurotoxicity in Alzheimer's disease and aging. Nat Commun 2024; 15:264. [PMID: 38238311 PMCID: PMC10796375 DOI: 10.1038/s41467-023-44465-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive neurodegeneration, but the specific events that cause cell death remain poorly understood. Death Induced by Survival gene Elimination (DISE) is a cell death mechanism mediated by short (s) RNAs acting through the RNA-induced silencing complex (RISC). DISE is thus a form of RNA interference, in which G-rich 6mer seed sequences in the sRNAs (position 2-7) target hundreds of C-rich 6mer seed matches in genes essential for cell survival, resulting in the activation of cell death pathways. Here, using Argonaute precipitation and RNAseq (Ago-RP-Seq), we analyze RISC-bound sRNAs to quantify 6mer seed toxicity in several model systems. In mouse AD models and aging brain, in induced pluripotent stem cell-derived neurons from AD patients, and in cells exposed to Aβ42 oligomers, RISC-bound sRNAs show a shift to more toxic 6mer seeds compared to controls. In contrast, in brains of "SuperAgers", humans over age 80 who have superior memory performance, RISC-bound sRNAs are shifted to more nontoxic 6mer seeds. Cells depleted of nontoxic sRNAs are sensitized to Aβ42-induced cell death, and reintroducing nontoxic RNAs is protective. Altogether, the correlation between DISE and Aβ42 toxicity suggests that increasing the levels of nontoxic miRNAs in the brain or blocking the activity of toxic RISC-bound sRNAs could ameliorate neurodegeneration.
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Affiliation(s)
- Bidur Paudel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Si-Yeon Jeong
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Ministry of Food and Drug Safety, Pharmaceutical Safety Bureau, Pharmaceutical Policy Division 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Carolina Pena Martinez
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Alexis Rickman
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Ashley Haluck-Kangas
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kristina Fredriksen
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Amira Affaneh
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John A Kessler
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Joseph R Mazzulli
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea E Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily Rogalski
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Healthy Aging & Alzheimer's Research Care (HAARC) Center, Department of Neurology, The University of Chicago, Chicago, IL, 60637, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Adriana Ferreira
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Bradlee L Heckmann
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine R Sadleir
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Robert Vassar
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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12
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Boon BDC, Labuzan SA, Peng Z, Matchett BJ, Kouri N, Hinkle KM, Lachner C, Ross OA, Ertekin-Taner N, Carter RE, Ferman TJ, Duara R, Dickson DW, Graff-Radford NR, Murray ME. Retrospective Evaluation of Neuropathologic Proxies of the Minimal Atrophy Subtype Compared With Corticolimbic Alzheimer Disease Subtypes. Neurology 2023; 101:e1412-e1423. [PMID: 37580158 PMCID: PMC10573142 DOI: 10.1212/wnl.0000000000207685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/07/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Alzheimer disease (AD) is neuropathologically classified into 3 corticolimbic subtypes based on the neurofibrillary tangle distribution throughout the hippocampus and association cortices: limbic predominant, typical, and hippocampal sparing. In vivo, a fourth subtype, dubbed "minimal atrophy," was identified using structural MRI. The objective of this study was to identify a neuropathologic proxy for the neuroimaging-defined minimal atrophy subtype. METHODS We applied 2 strategies in the Florida Autopsied Multi-Ethnic (FLAME) cohort to evaluate a neuropathologic proxy for the minimal atrophy subtype. In the first strategy, we selected AD cases with a Braak tangle stage IV (Braak IV) because of the relative paucity of neocortical tangle involvement compared with Braak >IV. Braak IV cases were compared with the 3 AD subtypes. In the alternative strategy, typical AD was stratified by brain weight and cases having a relatively high brain weight (>75th percentile) were defined as minimal atrophy. RESULTS Braak IV cases (n = 37) differed from AD subtypes (limbic predominant [n = 174], typical [n = 986], and hippocampal sparing [n = 187] AD) in having the least years of education (median 12 years, group-wise p < 0.001) and the highest brain weight (median 1,140 g, p = 0.002). Braak IV cases most resembled the limbic predominant cases owing to their high proportion of APOE ε4 carriers (75%, p < 0.001), an amnestic syndrome (100%, p < 0.001), as well as older age of cognitive symptom onset and death (median 79 and 85 years, respectively, p < 0.001). Only 5% of Braak IV cases had amygdala-predominant Lewy bodies (the lowest frequency observed, p = 0.017), whereas 32% had coexisting pathology of Lewy body disease, which was greater than the other subtypes (p = 0.005). Nearly half (47%) of the Braak IV samples had coexisting limbic predominant age-related TAR DNA-binding protein 43 encephalopathy neuropathologic change. Cases with a high brain weight (n = 201) were less likely to have amygdala-predominant Lewy bodies (14%, p = 0.006) and most likely to have Lewy body disease (31%, p = 0.042) compared with those with middle (n = 455) and low (n = 203) brain weight. DISCUSSION The frequency of Lewy body disease was increased in both neuropathologic proxies of the minimal atrophy subtype. We hypothesize that Lewy body disease may underlie cognitive decline observed in minimal atrophy cases.
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Affiliation(s)
- Baayla D C Boon
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Sydney A Labuzan
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Zhongwei Peng
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Billie J Matchett
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Naomi Kouri
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Kelly M Hinkle
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Christian Lachner
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Owen A Ross
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Nilufer Ertekin-Taner
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Rickey E Carter
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Tanis J Ferman
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Ranjan Duara
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Dennis W Dickson
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Neill R Graff-Radford
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL
| | - Melissa E Murray
- From the Department of Neuroscience (B.D.C.B., S.A.L., B.J.M., N.K., K.M.H., O.A.R., N.E.-T., D.W.D., M.E.M.), Department of Quantitative Health Sciences (Z.P., R.E.C.), Department of Neurology (C.L., N.E.-T., N.R.G.-R.), and Department of Psychiatry & Psychology (C.L., T.J.F.), Mayo Clinic, Jacksonville; and Wien Center for Alzheimer's Disease and Memory Disorders (R.D.), Mount Sinai Medical Center, Miami Beach, FL.
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13
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Cheng Y, Zhou X, Zou T, Zhang L, Li L, Yang C, Ma L. Plasma long non-coding RNAs ASMTL-AS1, AP001363.1, AC005730.3 and AL133415.1 as a potential biomarker for Alzheimer's disease. Neurol Res 2023; 45:804-817. [PMID: 37486018 DOI: 10.1080/01616412.2023.2203616] [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: 11/01/2022] [Accepted: 04/12/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical role in the pathogenesis of neurodegenerative diseases. Human plasma contains lncRNAs that are present in the blood, and their disease-specific profile has been considered a potential biomarker in some diseases. METHODS This study reports screening of the plasma levels of lncRNAs between Alzheimer disease(AD) (n = 45) and matched healthy controls (n = 45). The plasma samples of 5 AD patients and 5 matched healthy controls were randomly selected for expression levels of lncRNAs using the TruSeq RNA Sample Prep Kit (Illumina). The receiver operating characteristic (ROC) curve and area under the curve (AUC) were used to study the potential of lncRNAs as biomarkers. RESULTS The differential expression profiles of plasma showed that 514 lncRNAs were upregulated, whereas 499 lncRNAs were downregulated.We found that the lncRNAs AL133415.1, AC020916.1, ENST00000654948, ASMTL-AS, AC005730.3, and AP001363.1 levels in the plasma of the AD patients were significantly lower compared to the control group (p1 = 0.0006, p2 < 0.001, p3 < 0.001, p4 = 0.039, p5 = 0.006, p6 < 0.001, respectively). ROC curve analysis revealed that the AUC of AL133415.1 was 0.635 (95% CI]: 0.507-0.763, p = 0.036), the AUC of ASMTL-AS1 was 0.658 (95% CI: 0.513-0.785, p = 0.015), the AUC of AC005730.3 was 0.627 (95%CI: 0.498-0.756, p = 0.049), and the AUC of AP001363.1 was 0.708 (95%CI: 0.595-0.822, p = 0.001). CONCLUSION This study indicated that the plasma levels of the lncRNAs ASMTL-AS1, AP001363.1, AC005730.3, and AL133415.1 might be considered potential biomarkers for AD in the Chinese Population.
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Affiliation(s)
- Yi Cheng
- Department of Public Health, Xinjiang Medical University, Xinjiang, China
- Drug Clinical Institutions, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Xiaohui Zhou
- Department of Geriatrics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Ting Zou
- Department of Geriatrics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Lei Zhang
- Department of Geriatrics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Lihua Li
- Pharmacy, Maternal and Child Health Hospital of Urumqi, Urumqi, China
| | - Chang Yang
- Department of Geriatrics, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Long Ma
- Department of Public Health, Xinjiang Medical University, Xinjiang, China
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14
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Li M, Larsen PA. Single-cell sequencing of entorhinal cortex reveals widespread disruption of neuropeptide networks in Alzheimer's disease. Alzheimers Dement 2023; 19:3575-3592. [PMID: 36825405 DOI: 10.1002/alz.12979] [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: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 02/25/2023]
Abstract
INTRODUCTION Abnormalities of neuropeptides (NPs) that play important roles in modulating neuronal activities are commonly observed in Alzheimer's disease (AD). We hypothesize that NP network disruption is widespread in AD brains. METHODS Single-cell transcriptomic data from the entorhinal cortex (EC) were used to investigate the NP network disruption in AD. Bulk RNA-sequencing data generated from the temporal cortex by independent groups and machine learning were employed to identify key NPs involved in AD. The relationship between aging and AD-associated NP (ADNP) expression was studied using GTEx data. RESULTS The proportion of cells expressing NPs but not their receptors decreased significantly in AD. Neurons expressing higher level and greater diversity of NPs were disproportionately absent in AD. Increased age coincides with decreased ADNP expression in the hippocampus. DISCUSSION NP network disruption is widespread in AD EC. Neurons expressing more NPs may be selectively vulnerable to AD. Decreased expression of NPs participates in early AD pathogenesis. We predict that the NP network can be harnessed for treatment and/or early diagnosis of AD.
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Affiliation(s)
- Manci Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
- Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA
- Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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15
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Matchett BJ, Lincoln SJ, Baker M, Tamvaka N, Labuzan SA, Hicks Sirmans TN, Moloney CM, Helminger J, Hinkle KM, Cabrera-Rodriguez J, Wickland DP, Johnson PW, Heckman MG, Reddy JS, Younkin SG, Carrasquillo MM, Duara R, Graff-Radford NR, Pottier C, Ertekin-Taner N, Ross OA, Rademakers R, Dickson DW, Murray ME. The SERPINA5 coding variant E228Q does not contribute to clinicopathologic characteristics in Alzheimer's disease: A cross-sectional study. Medicine (Baltimore) 2023; 102:e34017. [PMID: 37327267 PMCID: PMC10270469 DOI: 10.1097/md.0000000000034017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 05/24/2023] [Indexed: 06/18/2023] Open
Abstract
We previously demonstrated that increased expression of the SERPINA5 gene is associated with hippocampal vulnerability in Alzheimer's disease (AD) brains. SERPINA5 was further demonstrated to be a novel tau-binding partner that colocalizes within neurofibrillary tangles. Our goal was to determine whether genetic variants in the SERPINA5 gene contributed to clinicopathologic phenotypes in AD. To screen for SERPINA5 variants, we sequenced 103 autopsy-confirmed young-onset AD cases with a positive family history of cognitive decline. To further assess the frequency of a rare missense variant, SERPINA5 p.E228Q, we screened an additional 1114 neuropathologically diagnosed AD cases. To provide neuropathologic context in AD, we immunohistochemically evaluated SERPINA5 and tau in a SERPINA5 p.E228Q variant carrier and a matched noncarrier. In the initial SERPINA5 screen, we observed 1 individual with a rare missense variant (rs140138746) that resulted in an amino acid change (p.E228Q). In our AD validation cohort, we identified an additional 5 carriers of this variant, resulting in an allelic frequency of 0.0021. There was no significant difference between SERPINA5 p.E228Q carriers and noncarriers in terms of demographic or clinicopathologic characteristics. Although not significant, on average SERPINA5 p.E228Q carriers were 5 years younger at age of disease onset than noncarriers (median: 66 [60-73] vs 71 [63-77] years, P = .351). In addition, SERPINA5 p.E228Q carriers exhibited a longer disease duration than noncarriers that approached significance (median: 12 [10-15]) vs 9 [6-12] years, P = .079). More severe neuronal loss was observed in the locus coeruleus, hippocampus, and amygdala of the SERPINA5 p.E228Q carrier compared to noncarrier, although no significant difference in SERPINA5-immunopositive lesions was observed. Throughout the AD brain in either carrier or noncarrier, areas with early pretangle pathology or burnt-out ghost tangle accumulation did not reveal SERPINA5-immunopositive neurons. Mature tangles and newly formed ghost tangles appeared to correspond well with SERPINA5-immunopositive tangle-bearing neurons. SERPINA5 gene expression was previously associated with disease phenotype; however, our findings suggest that SERPINA5 genetic variants may not be a contributing factor to clinicopathologic differences in AD. SERPINA5-immunopositive neurons appear to undergo a pathologic process that corresponded with specific levels of tangle maturity.
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Affiliation(s)
| | | | - Matt Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | | | | | | | | | - Jacqueline Helminger
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
- Paracelsus Medical University, Salzburg, Austria
| | | | | | - Daniel P. Wickland
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - Patrick W. Johnson
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - Michael G. Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - Joseph S. Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | | | | | - Ranjan Duara
- Wien Center for Alzheimer’s Disease and Memory Disorders, Mount Sinai Medical Center, Miami Beach, FL
| | | | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
- Department of Neurology, Mayo Clinic, Jacksonville, FL
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL
- Applied and Translational Neurogenomics, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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16
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Bunner W, Wang J, Cohen S, Bashtovyy D, Perry R, Shookster D, Landry T, Harris EM, Stackman R, Tran TD, Yasuda R, Szatmari EM. Behavioral and Transcriptome Profiling of Heterozygous Rab10 Knock-Out Mice. eNeuro 2023; 10:ENEURO.0459-22.2023. [PMID: 37156612 PMCID: PMC10208283 DOI: 10.1523/eneuro.0459-22.2023] [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: 11/10/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
A central question in the field of aging research is to identify the cellular and molecular basis of neuroresilience. One potential candidate is the small GTPase, Rab10. Here, we used Rab10+/- mice to investigate the molecular mechanisms underlying Rab10-mediated neuroresilience. Brain expression analysis of 880 genes involved in neurodegeneration showed that Rab10+/- mice have increased activation of pathways associated with neuronal metabolism, structural integrity, neurotransmission, and neuroplasticity compared with their Rab10+/+ littermates. Lower activation was observed for pathways involved in neuroinflammation and aging. We identified and validated several differentially expressed genes (DEGs), including Stx2, Stx1b, Vegfa, and Lrrc25 (downregulated) and Prkaa2, Syt4, and Grin2d (upregulated). Behavioral testing showed that Rab10+/- mice perform better in a hippocampal-dependent spatial task (object in place test), while their performance in a classical conditioning task (trace eyeblink classical conditioning, TECC) was significantly impaired. Therefore, our findings indicate that Rab10 differentially controls the brain circuitry of hippocampal-dependent spatial memory and higher-order behavior that requires intact cortex-hippocampal circuitry. Transcriptome and biochemical characterization of these mice suggest that glutamate ionotropic receptor NMDA type subunit 2D (GRIN2D or GluN2D) is affected by Rab10 signaling. Further work is needed to evaluate whether GRIN2D mediates the behavioral phenotypes of the Rab10+/- mice. We conclude that Rab10+/- mice described here can be a valuable tool to study the mechanisms of resilience in Alzheimer's disease (AD) model mice and to identify novel therapeutical targets to prevent cognitive decline associated with normal and pathologic aging.
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Affiliation(s)
- Wyatt Bunner
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834
| | - Jie Wang
- Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458
| | - Sarah Cohen
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458
| | - Denys Bashtovyy
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834
| | - Rachel Perry
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834
| | | | - Taylor Landry
- Department of Kinesiology, East Carolina University, NC 27858
| | - Elizabeth M Harris
- Department of Psychology, East Carolina University, Greenville, NC 27858
| | - Robert Stackman
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458
| | - Tuan D Tran
- Department of Psychology, East Carolina University, Greenville, NC 27858
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458
| | - Erzsebet M Szatmari
- Department of Physical Therapy, East Carolina University, Greenville, NC 27834
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17
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Saura CA, Deprada A, Capilla-López MD, Parra-Damas A. Revealing cell vulnerability in Alzheimer's disease by single-cell transcriptomics. Semin Cell Dev Biol 2023; 139:73-83. [PMID: 35623983 DOI: 10.1016/j.semcdb.2022.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that by affecting specific brain cell types and regions cause severe pathological and functional changes in memory neural circuits. A comprehensive knowledge of the pathogenic mechanisms underlying AD requires a deeper understanding of the cell-specific pathological responses through integrative molecular analyses. Recent application of high-throughput single-cell transcriptomics to postmortem tissue has proved powerful to unravel cell susceptibility and biological networks responding to amyloid and tau pathologies. Here, we review single-cell transcriptomic studies successfully applied to decipher cell-specific gene expression programs and pathways in the brain of AD patients. Transcriptional information reveals both specific and common gene signatures affecting the major cerebral cell types, including astrocytes, endothelial cells, microglia, neurons, and oligodendrocytes. Cell type-specific transcriptomes associated with AD pathology and clinical symptoms are related to common biological networks affecting, among others pathways, synaptic function, inflammation, proteostasis, cell death, oxidative stress, and myelination. The general picture that emerges from systems-level single-cell transcriptomics is a spatiotemporal pattern of cell diversity and biological pathways, and novel cell subpopulations affected in AD brain. We argue that broader implementation of cell transcriptomics in larger AD human cohorts using standardized protocols is fundamental for reliable assessment of temporal and regional cell-type gene profiling. The possibility of applying this methodology for personalized medicine in clinics is still challenging but opens new roads for future diagnosis and treatment in dementia.
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Affiliation(s)
- Carlos A Saura
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain.
| | - Angel Deprada
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Maria Dolores Capilla-López
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Arnaldo Parra-Damas
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona 08193, Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Spain
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18
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Chehimi SN, Crist RC, Reiner BC. Unraveling Psychiatric Disorders through Neural Single-Cell Transcriptomics Approaches. Genes (Basel) 2023; 14:genes14030771. [PMID: 36981041 PMCID: PMC10047992 DOI: 10.3390/genes14030771] [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: 02/18/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The development of single-cell and single-nucleus transcriptome technologies is enabling the unraveling of the molecular and cellular heterogeneity of psychiatric disorders. The complexity of the brain and the relationships between different brain regions can be better understood through the classification of individual cell populations based on their molecular markers and transcriptomic features. Analysis of these unique cell types can explain their involvement in the pathology of psychiatric disorders. Recent studies in both human and animal models have emphasized the importance of transcriptome analysis of neuronal cells in psychiatric disorders but also revealed critical roles for non-neuronal cells, such as oligodendrocytes and microglia. In this review, we update current findings on the brain transcriptome and explore molecular studies addressing transcriptomic alterations identified in human and animal models in depression and stress, neurodegenerative disorders (Parkinson's and Alzheimer's disease), schizophrenia, opioid use disorder, and alcohol and psychostimulant abuse. We also comment on potential future directions in single-cell and single-nucleus studies.
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Affiliation(s)
- Samar N Chehimi
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard C Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin C Reiner
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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19
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McDew-White M, Lee E, Premadasa LS, Alvarez X, Okeoma CM, Mohan M. Cannabinoids modulate the microbiota-gut-brain axis in HIV/SIV infection by reducing neuroinflammation and dysbiosis while concurrently elevating endocannabinoid and indole-3-propionate levels. J Neuroinflammation 2023; 20:62. [PMID: 36890518 PMCID: PMC9993397 DOI: 10.1186/s12974-023-02729-6] [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: 10/31/2022] [Accepted: 02/13/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Although the advent of combination anti-retroviral therapy (cART) has transformed HIV into a manageable chronic disease, an estimated 30-50% of people living with HIV (PLWH) exhibit cognitive and motor deficits collectively known as HIV-associated neurocognitive disorders (HAND). A key driver of HAND neuropathology is chronic neuroinflammation, where proinflammatory mediators produced by activated microglia and macrophages are thought to inflict neuronal injury and loss. Moreover, the dysregulation of the microbiota-gut-brain axis (MGBA) in PLWH, consequent to gastrointestinal dysfunction and dysbiosis, can lead to neuroinflammation and persistent cognitive impairment, which underscores the need for new interventions. METHODS We performed RNA-seq and microRNA profiling in basal ganglia (BG), metabolomics (plasma) and shotgun metagenomic sequencing (colon contents) in uninfected and SIV-infected rhesus macaques (RMs) administered vehicle (VEH/SIV) or delta-9-tetrahydrocannabinol (THC) (THC/SIV). RESULTS Long-term, low-dose THC reduced neuroinflammation and dysbiosis and significantly increased plasma endocannabinoid, endocannabinoid-like, glycerophospholipid and indole-3-propionate levels in chronically SIV-infected RMs. Chronic THC potently blocked the upregulation of genes associated with type-I interferon responses (NLRC5, CCL2, CXCL10, IRF1, IRF7, STAT2, BST2), excitotoxicity (SLC7A11), and enhanced protein expression of WFS1 (endoplasmic reticulum stress) and CRYM (oxidative stress) in BG. Additionally, THC successfully countered miR-142-3p-mediated suppression of WFS1 protein expression via a cannabinoid receptor-1-mediated mechanism in HCN2 neuronal cells. Most importantly, THC significantly increased the relative abundance of Firmicutes and Clostridia including indole-3-propionate (C. botulinum, C. paraputrificum, and C. cadaveris) and butyrate (C. butyricum, Faecalibacterium prausnitzii and Butyricicoccus pullicaecorum) producers in colonic contents. CONCLUSION This study demonstrates the potential of long-term, low-dose THC to positively modulate the MGBA by reducing neuroinflammation, enhancing endocannabinoid levels and promoting the growth of gut bacterial species that produce neuroprotective metabolites, like indole-3-propionate. The findings from this study may benefit not only PLWH on cART, but also those with no access to cART and more importantly, those who fail to suppress the virus under cART.
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Affiliation(s)
- Marina McDew-White
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227-5302, USA
| | - Eunhee Lee
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227-5302, USA
| | - Lakmini S Premadasa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227-5302, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227-5302, USA
| | - Chioma M Okeoma
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, 10595-1524, USA
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227-5302, USA.
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20
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Crawford K, Leonenko G, Baker E, Grozeva D, Lan-Leung B, Holmans P, Williams J, O'Donovan MC, Escott-Price V, Ivanov DK. Golgi apparatus, endoplasmic reticulum and mitochondrial function implicated in Alzheimer's disease through polygenic risk and RNA sequencing. Mol Psychiatry 2023; 28:1327-1336. [PMID: 36577842 PMCID: PMC10005937 DOI: 10.1038/s41380-022-01926-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022]
Abstract
Polygenic risk scores (PRS) have been widely adopted as a tool for measuring common variant liability and they have been shown to predict lifetime risk of Alzheimer's disease (AD) development. However, the relationship between PRS and AD pathogenesis is largely unknown. To this end, we performed a differential gene-expression and associated disrupted biological pathway analyses of AD PRS vs. case/controls in human brain-derived cohort sample (cerebellum/temporal cortex; MayoRNAseq). The results highlighted already implicated mechanisms: immune and stress response, lipids, fatty acids and cholesterol metabolisms, endosome and cellular/neuronal death, being disrupted biological pathways in both case/controls and PRS, as well as previously less well characterised processes such as cellular structures, mitochondrial respiration and secretion. Despite heterogeneity in terms of differentially expressed genes in case/controls vs. PRS, there was a consensus of commonly disrupted biological mechanisms. Glia and microglia-related terms were also significantly disrupted, albeit not being the top disrupted Gene Ontology terms. GWAS implicated genes were significantly and in their majority, up-regulated in response to different PRS among the temporal cortex samples, suggesting potential common regulatory mechanisms. Tissue specificity in terms of disrupted biological pathways in temporal cortex vs. cerebellum was observed in relation to PRS, but limited tissue specificity when the datasets were analysed as case/controls. The largely common biological mechanisms between a case/control classification and in association with PRS suggests that PRS stratification can be used for studies where suitable case/control samples are not available or the selection of individuals with high and low PRS in clinical trials.
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Affiliation(s)
- Karen Crawford
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, School of Medicine, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Ganna Leonenko
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Emily Baker
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Detelina Grozeva
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
- Centre for Trials Research, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Benoit Lan-Leung
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, School of Medicine, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Julie Williams
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, School of Medicine, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, School of Medicine, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK
| | - Dobril K Ivanov
- UK Dementia Research Institute (UKDRI) at Cardiff University, College of Biomedical and Life Sciences, Hadyn Ellis Building, Cardiff, CF24 4HQ, UK.
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21
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Moloney CM, Labuzan SA, Crook JE, Siddiqui H, Castanedes-Casey M, Lachner C, Petersen RC, Duara R, Graff-Radford NR, Dickson DW, Mielke MM, Murray ME. Phosphorylated tau sites that are elevated in Alzheimer's disease fluid biomarkers are visualized in early neurofibrillary tangle maturity levels in the post mortem brain. Alzheimers Dement 2023; 19:1029-1040. [PMID: 35920592 PMCID: PMC9895127 DOI: 10.1002/alz.12749] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) biomarkers are increasingly more reliable in predicting neuropathology. To facilitate interpretation of phosphorylated tau sites as an early fluid biomarker, we sought to characterize which neurofibrillary tangle maturity levels (pretangle, intermediary 1, mature tangle, intermediary 2, and ghost tangle) are recognized. METHODS We queried the Florida Autopsied Multi-Ethnic (FLAME) cohort for cases ranging from Braak stages I through VI, excluding non-AD neuropathologies and tauopathies. Thioflavin-S staining was compared to immunohistochemical measures of phosphorylated threonine (pT) 181, pT205, pT217, and pT231 in two hippocampal subsectors across n = 24 cases. RESULTS Each phosphorylated tau site immunohistochemically labeled early neurofibrillary tangle maturity levels compared to advanced levels recognized by thioflavin-S. Hippocampal burden generally increased with each Braak stage. DISCUSSION These results provide neurobiologic evidence that these phosphorylated tau fluid biomarker sites are present during early neurofibrillary tangle maturity levels and may explain why these fluid biomarker measures are observed before symptom onset. HIGHLIGHTS Immunohistochemical evaluation of four phosphorylated tau fluid biomarker sites. Earlier neurofibrillary tangle maturity levels recognized by phosphorylated tau in proline-rich region. Advanced tangle pathology is elevated in the subiculum compared to the cornu ammonis 1 of the hippocampus. Novel semi-quantitative frequency to calculate tangle maturity frequency.
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Affiliation(s)
| | | | - Julia E. Crook
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Habeeba Siddiqui
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Christian Lachner
- Division of Psychiatry, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Ranjan Duara
- Wien Center for Alzheimer’s Disease and Memory Disorders, Mount Sinai Medical Center, Miami Beach, FL, USA
| | | | | | - Michelle M. Mielke
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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22
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Pan D, Zeng A, Yang B, Lai G, Hu B, Song X, Jiang T. Deep Learning for Brain MRI Confirms Patterned Pathological Progression in Alzheimer's Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204717. [PMID: 36575159 PMCID: PMC9951348 DOI: 10.1002/advs.202204717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Deep learning (DL) on brain magnetic resonance imaging (MRI) data has shown excellent performance in differentiating individuals with Alzheimer's disease (AD). However, the value of DL in detecting progressive structural MRI (sMRI) abnormalities linked to AD pathology has yet to be established. In this study, an interpretable DL algorithm named the Ensemble of 3-dimensional convolutional neural network (Ensemble 3DCNN) with enhanced parsing techniques is proposed to investigate the longitudinal trajectories of whole-brain sMRI changes denoting AD onset and progression. A set of 2369 T1-weighted images from the multi-centre Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies cohorts are applied to model derivation, validation, testing, and pattern analysis. An Ensemble-3DCNN-based P-score is generated, based on which multiple brain regions, including amygdala, insular, parahippocampal, and temporal gyrus, exhibit early and connected progressive neurodegeneration. Complex individual variability in the sMRI is also observed. This study combining non-invasive sMRI and interpretable DL in detecting patterned sMRI changes confirmed AD pathological progression, shedding new light on predicting AD progression using whole-brain sMRI.
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Affiliation(s)
- Dan Pan
- School of Electronics and InformationGuangdong Polytechnic Normal UniversityGuangzhou510665China
| | - An Zeng
- Faculty of Computers, Guangdong University of TechnologyGuangzhou510006China
| | - Baoyao Yang
- Faculty of Computers, Guangdong University of TechnologyGuangzhou510006China
| | - Gangyong Lai
- Faculty of Computers, Guangdong University of TechnologyGuangzhou510006China
| | - Bing Hu
- Department of RadiologyThe Third Affiliated Hospital of SUN Yat‐sen UniversityGuangzhou510630China
| | - Xiaowei Song
- Clinical Research CentreSurrey Memorial HospitalFraser HealthSurreyBritish ColumbiaV3V 1Z2Canada
| | - Tianzi Jiang
- Brainnetome Center & National Laboratory of Pattern RecognitionInstitute of AutomationChinese Academy of SciencesBeijing100190China
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23
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Han K, Ji L, Wang C, Shao Y, Chen C, Liu L, Feng M, Yang F, Wu X, Li X, Xie Q, He L, Shi Y, He G, Dong Z, Yu T. The host genetics affects gut microbiome diversity in Chinese depressed patients. Front Genet 2023; 13:976814. [PMID: 36699448 PMCID: PMC9868868 DOI: 10.3389/fgene.2022.976814] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
The gut microbiome and host genetics are both associated with major depressive disorder (MDD); however, the molecular mechanisms among the associations are poorly understood, especially in the Asian, Chinese group. Our study applied linear discriminant analysis (LDA) effect size (LEfSe) and genome-wide association analysis in the cohort with both gut sequencing data and genomics data. We reported the different gut microbiota characteristics between MDD and control groups in the Chinese group and further constructed the association between host genetics and the gut microbiome. Actinobacteria and Pseudomonades were found more in the MDD group. We found significant differences in the ACE and Chao indexes of alpha diversity while no discrepancy in beta diversity. We found three associations between host genetics with microbiome features: beta diversity and rs6108 (p = 8.65 × 10-9), Actinobacteria and rs77379751 (p = 8.56 × 10-9), and PWY-5913 and rs1775633082 (p = 4.54 × 10-8). A species of the Romboutsia genus was co-associated with the species of Ruminococcus gnavus in an internetwork through four genes: METTL8, ITGB2, OTULIN, and PROSER3, with a strict threshold (p < 5 × 10-4). Furthermore, our findings suggested that the gut microbiome diversity might affect microRNA expression in the brain and influenced SERPINA5 and other spatially close genes afterward. These findings suggest new linkages between depression and gut microbiome in Asian, Chinese people, which might be mediated by genes and microRNA regulation in space distance.
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Affiliation(s)
- Ke Han
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Ji
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Chenliu Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Shao
- Asbios (Tianjin) Biotechnology Co., Ltd., Tianjin, China
| | - Changfeng Chen
- School of Mental Health, Jining Medical University, Jining, China
| | - Liangjie Liu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Yang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Qinglian Xie
- Out-patient Department of West China Hospital, Sichuan University, Chengdu, China
| | - Lin He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Guang He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
| | - Zaiquan Dong
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
| | - Tao Yu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Center for Women and Children’s Health, Shanghai, China,*Correspondence: Guang He, ; Zaiquan Dong, ; Tao Yu,
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24
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The Emerging Roles of Extracellular Chaperones in Complement Regulation. Cells 2022; 11:cells11233907. [PMID: 36497163 PMCID: PMC9738919 DOI: 10.3390/cells11233907] [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: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022] Open
Abstract
The immune system is essential to protect organisms from internal and external threats. The rapidly acting, non-specific innate immune system includes complement, which initiates an inflammatory cascade and can form pores in the membranes of target cells to induce cell lysis. Regulation of protein homeostasis (proteostasis) is essential for normal cellular and organismal function, and has been implicated in processes controlling immunity and infection. Chaperones are key players in maintaining proteostasis in both the intra- and extracellular environments. Whilst intracellular proteostasis is well-characterised, the role of constitutively secreted extracellular chaperones (ECs) is less well understood. ECs may interact with invading pathogens, and elements of the subsequent immune response, including the complement pathway. Both ECs and complement can influence the progression of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease and amyotrophic lateral sclerosis, as well as other diseases including kidney diseases and diabetes. This review will examine known and recently discovered ECs, and their roles in immunity, with a specific focus on the complement pathway.
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25
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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Li H, Tan Y, Cheng X, Zhang Z, Huang J, Hui S, Zhu L, Liu Y, Zhao D, Liu Z, Peng W. Untargeted metabolomics analysis of the hippocampus and cerebral cortex identified the neuroprotective mechanisms of Bushen Tiansui formula in an aβ25-35-induced rat model of Alzheimer’s disease. Front Pharmacol 2022; 13:990307. [PMID: 36339577 PMCID: PMC9630565 DOI: 10.3389/fphar.2022.990307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Bushen Tiansui Formula (BSTSF) is a traditional formulation of Chinese medicine that has been used to treat Alzheimer’s disease (AD) for decades; however, the underlying mechanisms by which this formula achieves such therapeutic effects have yet to be elucidated. Prupose: To investigate the neuroprotective mechanisms of BSTSF against AD by analyzing metabolite profiles in the hippocampus and cortex of AD rats. Methods: The rat models of AD were established by the injection of Aβ25–35. The Morris water maze (MWM) test was performed to evaluate the effect of BSTSF treatment on cognitive dysfunction. Hematoxylin and eosin (HE) staining was used to assess the effect of BSTSF on typical AD pathologies. Underlying mechanisms were investigated using LC-MS/MS-based untargeted metabolomics analysis of the cerebral cortex and hippocampus. Results: BSTSF significantly improved memory deficits and the typical histopathological changes of AD rats. Untargeted metabolomics analysis showed that 145 and 184 endogenous metabolites in the cerebral cortex and hippocampus, respectively, were significantly different in the BSTSF group when compared with the AD group. The differential metabolites in the cerebral cortex were primarily involved in cysteine and methionine metabolism, while those in the hippocampus were mainly involved in d-Glutamine and d-glutamate metabolism. Conclusion: In the present study, we confirmed the neuroprotective effects of BSTSF treatment against AD using a rat model. Our findings indicate that the BSTSF-mediated protective effects were associated with amelioration of metabolic disorders in the hippocampus and cerebral cortex.
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Affiliation(s)
- Hongli Li
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Mental Disorder, Changsha, China
| | - Yejun Tan
- School of mathematics, University of Minnesota twin Cities, St. Paul, MS, United States
| | - Xin Cheng
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Mental Disorder, Changsha, China
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Mental Disorder, Changsha, China
| | | | - Shan Hui
- Department of Geratology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Yuqing Liu
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Di Zhao
- Hunan Academy of Chinese Medicine, Changsha, China
| | - Zhao Liu
- Hunan Academy of Chinese Medicine, Changsha, China
| | - Weijun Peng
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Mental Disorder, Changsha, China
- *Correspondence: Weijun Peng,
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An Integrative Analysis of Identified Schizophrenia-Associated Brain Cell Types and Gene Expression Changes. Int J Mol Sci 2022; 23:ijms231911581. [PMID: 36232882 PMCID: PMC9569514 DOI: 10.3390/ijms231911581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Schizophrenia (SCZ) is a severe mental disorder that may result in hallucinations, delusions, and extremely disordered thinking. How each cell type in the brain contributes to SCZ occurrence is still unclear. Here, we leveraged the human dorsolateral prefrontal cortex bulk RNA-seq data, then used the RNA-seq deconvolution algorithm CIBERSORTx to generate SCZ brain single-cell RNA-seq data for a comprehensive analysis to understand SCZ-associated brain cell types and gene expression changes. Firstly, we observed that the proportions of brain cell types in SCZ differed from normal samples. Among these cell types, astrocyte, pericyte, and PAX6 cells were found to have a higher proportion in SCZ patients (astrocyte: SCZ = 0.163, control = 0.145, P.adj = 4.9 × 10-4, effect size = 0.478; pericyte: SCZ = 0.057, control = 0.066, P.adj = 1.1 × 10-4, effect size = 0.519; PAX6: SCZ = 0.014, control = 0.011, P.adj = 0.014, effect size = 0.377), while the L5/6_IT_CAR3 cells and LAMP5 cells are the exact opposite (L5/6_IT_Car3: SCZ = 0.102, control = 0.108, P.adj = 0.016, effect size = 0.369; LAMP5: SCZ = 0.057, control = 0.066, P.adj = 2.2 × 10-6, effect size = 0.617). Next, we investigated gene expression in cell types and functional pathways in SCZ. We observed chemical synaptic transmission dysregulation in two types of GABAergic neurons (PVALB and LAMP5), and immune reaction involvement in GABAergic neurons (SST) and non-neuronal cell types (endothelial and oligodendrocyte). Furthermore, we observed that some differential expression genes from bulk RNA-seq displayed cell-type-specific abnormalities in the expression of molecules in SCZ. Finally, the cell types with the SCZ-related transcriptomic changes could be considered to belong to the same module since we observed two major similar coordinated transcriptomic changes across these cell types. Together, our results offer novel insights into cellular heterogeneity and the molecular mechanisms underlying SCZ.
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Luo W, Pryzbyl KJ, Bigio EH, Weintraub S, Mesulam MM, Redei EE. Reduced Hippocampal and Anterior Cingulate Expression of Antioxidant Enzymes and Membrane Progesterone Receptors in Alzheimer's Disease with Depression. J Alzheimers Dis 2022; 89:309-321. [PMID: 35871353 PMCID: PMC10041688 DOI: 10.3233/jad-220574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a risk factor for dementia including that caused by Alzheimer's disease (AD). Both MDD and AD have a higher prevalence in women than men, and estrogen-related processes have been implicated in this sex difference. OBJECTIVE To identify if enhanced oxidative stress and decreased expression of the memory enhancer insulin-like growth factor 2 (IGF2), each implicated separately in MDD and AD, are exaggerated in individuals with both AD and MDD compared to those with AD. METHODS Expression of target genes are determined by qPCR in postmortem hippocampus (Hip) and anterior cingulate cortex (ACC) of individuals with dementia and autopsy confirmed AD and those of AD+MDD. RESULTS Transcript levels of the antioxidant enzymes catalase (CAT) and superoxide dismutase 1 (SOD1), as well as IGF2 and its receptor (IGF2R) were significantly lower in the Hip and ACC of individuals with both AD and MDD compared to those with AD and no MDD. Expressions of Progestin and AdipoQ Receptor Family Member 7 (PAQR7, alias progesterone receptor alpha, mPRa) and PAQR8 (mPRβ), receptors that bind neurosteroids, were also lower in the Hip and ACC of AD+MDD samples compared to those of AD without MDD. Correlations among these transcripts revealed that estrogen receptor 2 (ESR2) and mPR β are direct or indirect regulators of the expression of the antioxidant enzymes and IGF2R. CONCLUSION Reduced levels of antioxidant enzymes, decreased IGF2 expression, and diminished estrogen or membrane progesterone receptor-dependent processes might be more pronounced in the subpopulation of individuals with AD and MDD than without MDD.
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Affiliation(s)
- Wendy Luo
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Katherine J Pryzbyl
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eileen H Bigio
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sandra Weintraub
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - M-Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eva E Redei
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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29
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Maffioli E, Murtas G, Rabattoni V, Badone B, Tripodi F, Iannuzzi F, Licastro D, Nonnis S, Rinaldi AM, Motta Z, Sacchi S, Canu N, Tedeschi G, Coccetti P, Pollegioni L. Insulin and serine metabolism as sex-specific hallmarks of Alzheimer's disease in the human hippocampus. Cell Rep 2022; 40:111271. [PMID: 36070700 DOI: 10.1016/j.celrep.2022.111271] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 07/01/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Healthy aging is an ambitious aspiration for humans, but neurodegenerative disorders, such as Alzheimer's disease (AD), strongly affect quality of life. Using an integrated omics approach, we investigate alterations in the molecular composition of postmortem hippocampus samples of healthy persons and individuals with AD. Profound differences are apparent between control and AD male and female cohorts in terms of up- and downregulated metabolic pathways. A decrease in the insulin response is evident in AD when comparing the female with the male group. The serine metabolism (linked to the glycolytic pathway and generating the N-methyl-D-aspartate [NMDA] receptor coagonist D-serine) is also significantly modulated: the D-Ser/total serine ratio represents a way to counteract age-related cognitive decline in healthy men and during AD onset in women. These results show how AD changes and, in certain respects, almost reverses sex-specific proteomic and metabolomic profiles, highlighting how different pathophysiological mechanisms are active in men and women.
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Affiliation(s)
- Elisa Maffioli
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Beatrice Badone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Filomena Iannuzzi
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy
| | | | - Simona Nonnis
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy
| | - Anna Maria Rinaldi
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Nadia Canu
- Department of System Medicine, University of Rome "Tor Vergata," 00133 Rome, Italy; Istituto di Biochimica e Biologia Cellulare (IBBC) CNR, 00015 Monterotondo Scalo, Italy.
| | - Gabriella Tedeschi
- DIVAS, Department of Veterinary Medicine and Animal Science, University of Milano, 20121 Milano, Italy; CIMAINA, University of Milano, 20121 Milano, Italy.
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy.
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy.
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30
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Khodayi M, Khalaj-Kondori M, Hoseinpour Feizi MA, Jabarpour Bonyadi M, Talebi M. Plasma lncRNA profiling identified BC200 and NEAT1 lncRNAs as potential blood-based biomarkers for late-onset Alzheimer's disease. EXCLI JOURNAL 2022; 21:772-785. [PMID: 35949493 PMCID: PMC9360476 DOI: 10.17179/excli2022-4764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/28/2022] [Indexed: 12/22/2022]
Abstract
Long non-coding RNAs (lncRNA) play critical roles in pathogenesis of neurodegenerative diseases. Human plasma carries lncRNAs that are stable in the blood, and their disease-specific profile have made them valuable biomarkers for some diseases. This study reports screening of the plasma levels of 90 lncRNAs in patients with Alzheimer disease (AD) to find out plasma-based AD biomarkers. Total RNA was isolated from plasma samples of 50 AD and 50 matched healthy controls. The plasma samples of 10 advanced AD patients and 10 matched healthy controls were screened for expression levels of 90 lncRNAs using Human LncRNA Profiler qPCR Array Kit (SBI). Based on the profiling results, lncRNAs BC200, NDM29, NEAT1, FAS-AS1 and GAS5-AS1 were selected for further analysis in all samples and their biomarker potency was evaluated by ROC curve analysis. We further surveyed RNAseq data by in silico analysis. We found that the NEAT1 and BC200 levels in the plasma of the AD patients were significantly higher compared with the control group (P=0.0021, p= 0.02, respectively). ROC curve analysis showed that the plasma level of NEAT1 and BC200 discriminated AD patients from healthy controls with sensitivity of 72 % and 60 %, and specificity of 84 % and 91 % respectively. Moreover, NEAT1 discriminated MCI (60 % sensitivity and 91 % specificity) and advanced-AD patients from healthy controls (73 % sensitivity and 71 % specificity). Besides, plasma level of BC200 discriminated the pre-clinical subjects from healthy controls with 83 % sensitivity and 66 % specificity. A positive correlation was also observed between plasma levels of BC200 with the age patients (r = 0.34, p=0.02). In silico RNAseq data analysis showed that a total of 33 lncRNAs were up-regulated but 13 lncRNAs were down-regulated significantly in AD patients compared with the healthy controls. In conclusion, this study elucidated that the plasma levels of lncRNAs NEAT1 and BC200 might be considered as potential blood-based biomarkers for AD development and progression.
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Affiliation(s)
- Majid Khodayi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Khalaj-Kondori
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | | | - Mahnaz Talebi
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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31
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Ramos-Campoy O, Lladó A, Bosch B, Ferrer M, Pérez-Millan A, Vergara M, Molina-Porcel L, Fort-Aznar L, Gonzalo R, Moreno-Izco F, Fernandez-Villullas G, Balasa M, Sánchez-Valle R, Antonell A. Differential Gene Expression in Sporadic and Genetic Forms of Alzheimer's Disease and Frontotemporal Dementia in Brain Tissue and Lymphoblastoid Cell Lines. Mol Neurobiol 2022; 59:6411-6428. [PMID: 35962298 DOI: 10.1007/s12035-022-02969-2] [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: 03/03/2022] [Accepted: 07/21/2022] [Indexed: 10/15/2022]
Abstract
Sporadic early-onset Alzheimer's disease (EOAD) and autosomal dominant Alzheimer's disease (ADAD) provide the opportunity to investigate the physiopathological mechanisms in the absence of aging, present in late-onset forms. Frontotemporal dementia (FTD) causes early-onset dementia associated to tau or TDP43 protein deposits. A 15% of FTD cases are caused by mutations in C9orf72, GRN, or MAPT genes. Lymphoblastoid cell lines (LCLs) have been proposed as an alternative to brain tissue for studying earlier phases of neurodegenerative diseases. The aim of this study is to investigate the expression profile in EOAD, ADAD, and sporadic and genetic FTD (sFTD and gFTD, respectively), using brain tissue and LCLs. Sixty subjects of the following groups were included: EOAD, ADAD, sFTD, gFTD, and controls. Gene expression was analyzed with Clariom D microarray (Affymetrix). Brain tissue pairwise comparisons revealed six common differentially expressed genes (DEG) for all the patients' groups compared with controls: RGS20, WIF1, HSPB1, EMP3, S100A11 and GFAP. Common up-regulated biological pathways were identified both in brain and LCLs (including inflammation and glial cell differentiation), while down-regulated pathways were detected mainly in brain tissue (including synaptic signaling, metabolism and mitochondrial dysfunction). CD163, ADAMTS9 and LIN7A gene expression disruption was validated by qPCR in brain tissue and NrCAM in LCLs in their respective group comparisons. In conclusion, our study highlights neuroinflammation, metabolism and synaptic signaling disturbances as common altered pathways in different AD and FTD forms. The use of LCLs might be appropriate for studying early immune system and inflammation, and some neural features in neurodegenerative dementias.
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Affiliation(s)
- Oscar Ramos-Campoy
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Beatriz Bosch
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Mireia Ferrer
- Statistics and Bioinformatics Unit, Vall d'Hebrón Institut de Recerca, Passeig Vall d'Hebrón, Barcelona, Spain
| | - Agnès Pérez-Millan
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Institute of Neurosciences, Department of Biomedicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Miguel Vergara
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.,Neurological Tissue Bank, Biobank-Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laura Fort-Aznar
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Ricardo Gonzalo
- Statistics and Bioinformatics Unit, Vall d'Hebrón Institut de Recerca, Passeig Vall d'Hebrón, Barcelona, Spain
| | - Fermín Moreno-Izco
- Cognitive Disorders Unit, Department of Neurology, Hospital Universitario Donostia, 20014, Donostia-San Sebastián, Spain.,Biodonostia, Neurosciences Area, Group of Neurodegenerative Diseases, 20014, San Sebastián, Spain
| | - Guadalupe Fernandez-Villullas
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Mircea Balasa
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
| | - Anna Antonell
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, IDIBAPS, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
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32
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Zhang L, Liu Y, Wang X, Wang D, Wu H, Chen H, Chen J, Liu Y. Treadmill exercise improve recognition memory by TREM2 pathway to inhibit hippocampal microglial activation and neuroinflammation in Alzheimer's disease model. Physiol Behav 2022; 251:113820. [PMID: 35452628 DOI: 10.1016/j.physbeh.2022.113820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/30/2022] [Accepted: 04/16/2022] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease-related cognition impairment is correlated with increased neuroinflammation. Studies show that physical exercises improve cognitive function and regulate neuroinflammation. However, no sufficient studies have been performed to directly observe the mechanism of exercise-related effects on microglia and neuroinflammation, in association with memory function under Alzheimer's disease. This study aims to explore the relationship of TREM2, microglia activation and neuroinflammation in the development of Alzheimer's disease, followed by investigating why physical exercises improve cognition in the Alzheimer's disease model by means of the adeno-associated virus (AAV) injection. We found that: 1) Recognition memory impairment in Aβ-induced Alzheimer's disease model was associated with the reduction in TREM2 which induced microglial activation and neuroinflammation; 2) Exercise activated the TREM2 pathway, which was necessary for inhibiting microglial activation and neuroinflammation, leading to improved recognition memory in the Alzheimer's disease model. Together, the improvement of AD-associated recognition memory by exercises is associated with up-regulation of the TREM2 pathway which promotes the phenotypic conversion of microglia and decreases the level of neuroinflammation.
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Affiliation(s)
- Linlin Zhang
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China; Comprehensive Key Laboratory of Sports Ability Evaluation and Research of the General Administration of Sport of China, Beijing Key Laboratory of Sports Function Assessment and Technical Analysis, Capital University of Physical Education and Sports, Beijing, 100191, China.
| | - Yanzhong Liu
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Xin Wang
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Dan Wang
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Hao Wu
- Comprehensive Key Laboratory of Sports Ability Evaluation and Research of the General Administration of Sport of China, Beijing Key Laboratory of Sports Function Assessment and Technical Analysis, Capital University of Physical Education and Sports, Beijing, 100191, China
| | - Haichun Chen
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Jiaxin Chen
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yiping Liu
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, 350007, China.
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33
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Khodayi-Shahrak M, Khalaj-Kondori M, Hosseinpour Feizi MA, Talebi M. Insights into the mechanisms of non-coding RNAs' implication in the pathogenesis of Alzheimer's disease. EXCLI JOURNAL 2022; 21:921-940. [PMID: 36110561 PMCID: PMC9441681 DOI: 10.17179/excli2022-5006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 11/06/2022]
Abstract
Non-coding RNAs including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are implicated in the regulation of gene expression at transcriptional, posttranscriptional, and epigenetic levels. Several studies in cell lines, animal models, and humans, have revealed that non-coding RNAs play crucial roles in the pathogenesis of Alzheimer's disease (AD). Detailed knowledge on their mechanism of implication in the AD pathogenesis can help to develop novel therapeutic and disease management strategies. The two main pathological hallmarks of AD are amyloid plaques resulting from the β-amyloid accumulation, and neurofibrillary tangles (NFT) due to the phosphorylated tau accumulation. Several lncRNAs and miRNAs play crucial roles in both these hallmarks of the AD pathogenesis and other AD-related pathological procedures such as neuronal and synaptic plasticity, neuroinflammation, neuronal differentiation and neuronal apoptosis. In this review, we outlined the non-coding RNAs and further discussed how they are implicated in these AD-related pathological procedures.
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Affiliation(s)
- Majid Khodayi-Shahrak
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Khalaj-Kondori
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran,*To whom correspondence should be addressed: Mohammad Khalaj-Kondori, Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran, E-mail:
| | | | - Mahnaz Talebi
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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34
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Chen P, Yao H, Tijms BM, Wang P, Wang D, Song C, Yang H, Zhang Z, Zhao K, Qu Y, Kang X, Du K, Fan L, Han T, Yu C, Zhang X, Jiang T, Zhou Y, Lu J, Han Y, Liu B, Zhou B, Liu Y. Four Distinct Subtypes of Alzheimer's Disease Based on Resting-State Connectivity Biomarkers. Biol Psychiatry 2022; 93:759-769. [PMID: 36137824 DOI: 10.1016/j.biopsych.2022.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disorder with significant heterogeneity. Different AD phenotypes may be associated with specific brain network changes. Uncovering disease heterogeneity by using functional networks could provide insights into precise diagnoses. METHODS We investigated the subtypes of AD using nonnegative matrix factorization clustering on the previously identified 216 resting-state functional connectivities that differed between AD and normal control subjects. We conducted the analysis using a discovery dataset (n = 809) and a validated dataset (n = 291). Next, we grouped individuals with mild cognitive impairment according to the model obtained in the AD groups. Finally, the clinical measures and brain structural characteristics were compared among the subtypes to assess their relationship with differences in the functional network. RESULTS Individuals with AD were clustered into 4 subtypes reproducibly, which included those with 1) diffuse and mild functional connectivity disruption (subtype 1), 2) predominantly decreased connectivity in the default mode network accompanied by an increase in the prefrontal circuit (subtype 2), 3) predominantly decreased connectivity in the anterior cingulate cortex accompanied by an increase in prefrontal cortex connectivity (subtype 3), and 4) predominantly decreased connectivity in the basal ganglia accompanied by an increase in prefrontal cortex connectivity (subtype 4). In addition to these differences in functional connectivity, differences between the AD subtypes were found in cognition, structural measures, and cognitive decline patterns. CONCLUSIONS These comprehensive results offer new insights that may advance precision medicine for AD and facilitate strategies for future clinical trials.
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Affiliation(s)
- Pindong Chen
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Yao
- Department of Radiology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC - Location VUmc, The Netherlands
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin University, Tianjin, China
| | - Dawei Wang
- Department of Radiology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Chengyuan Song
- Department of Neurology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Hongwei Yang
- Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | | | - Kun Zhao
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science & Medical Engineering, Beihang University, Beijing, China
| | - Yida Qu
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaopeng Kang
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Du
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Lingzhong Fan
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Tong Han
- Department of Radiology, Tianjin Huanhu Hospital, Tianjin University, Tianjin, China
| | - Chunshui Yu
- Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xi Zhang
- Department of Neurology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Tianzi Jiang
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Yuying Zhou
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin University, Tianjin, China
| | - Jie Lu
- Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China; Beijing Institute of Geriatrics, Beijing, China; National Clinical Research Center for Geriatric Disorders, Beijing, China
| | - Bing Liu
- State Key Laboratory of Cognition Neuroscience & Learning, Beijing Normal University, Beijing, China
| | - Bo Zhou
- Department of Neurology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
| | - Yong Liu
- Brainnetome Center & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China.
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Abdul Aziz M, Md Ashraf G, Safiqul Islam M. Link of BIN1, CLU and IDE gene polymorphisms with the susceptibility of Alzheimer's disease: evidence from a meta-analysis. Curr Alzheimer Res 2022; 19:302-316. [PMID: 35546756 DOI: 10.2174/1567205019666220511140955] [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: 12/29/2021] [Revised: 02/15/2022] [Accepted: 03/06/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common form of neurodegenerative disorder. The association of BIN1, CLU and IDE genetic polymorphisms with AD risk have been evaluated overtimes that produced conflicting outcomes. OBJECTIVE We performed this meta-analysis to investigate the contribution of BIN1 (rs744373 and rs7561528), CLU (rs11136000 and rs9331888), and IDE (rs1887922) polymorphisms to AD risk. METHODS From a systemic literature search up to July 15, 2021, we included 25 studies with rs744373, 16 studies with rs7561528, 37 studies with rs11136000, 16 studies with rs9331888, and 4 studies with rs1887922. To analyze the correlation, we constructed seven genetic models that used odds ratio and 95% confidence intervals. We used RevMan 5.4 for meta-analysis. RESULTS Our study suggests that BIN1 rs744373 is associated with a significantly increased risk of AD in five genetic models (OR>1). Again, CLU rs11136000 showed reduced association in all genetic models (OR<1). CLU rs9331888 revealed an increased association in two models (OR>1). The IDE rs1887922 showed significantly increased risk in four models (OR>1). From subgroup analysis, a significantly increased risk of AD was observed in Caucasians and Asians for BIN1 rs744373. Again, BIN1 rs7561528 showed a significantly enhanced risk of AD only in Caucasians. CLU rs11136000 showed significantly reduced risk in Caucasians but rs9331888 showed increased risk in the same ethnicity. CONCLUSION Our meta-analysis confirms the association of BIN1 rs744373, CLU rs9331888 and IDE rs1887922 polymorphisms with an increased risk of AD, especially in Caucasians. Again, CLU rs11136000 is associated with reduced AD risk in the overall population and Caucasians.
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Affiliation(s)
- Md Abdul Aziz
- Department of Pharmacy, Faculty of Pharmacy and Health Sciences, State University of Bangladesh, Dhaka-1205, Bangladesh
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Safiqul Islam
- Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
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Fixemer S, Ameli C, Hammer G, Salamanca L, Uriarte Huarte O, Schwartz C, Gérardy JJ, Mechawar N, Skupin A, Mittelbronn M, Bouvier DS. Microglia phenotypes are associated with subregional patterns of concomitant tau, amyloid-β and α-synuclein pathologies in the hippocampus of patients with Alzheimer's disease and dementia with Lewy bodies. Acta Neuropathol Commun 2022; 10:36. [PMID: 35296366 PMCID: PMC8925098 DOI: 10.1186/s40478-022-01342-7] [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: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022] Open
Abstract
The cellular alterations of the hippocampus lead to memory decline, a shared symptom between Alzheimer’s disease (AD) and dementia with Lewy Bodies (DLB) patients. However, the subregional deterioration pattern of the hippocampus differs between AD and DLB with the CA1 subfield being more severely affected in AD. The activation of microglia, the brain immune cells, could play a role in its selective volume loss. How subregional microglia populations vary within AD or DLB and across these conditions remains poorly understood. Furthermore, how the nature of the hippocampal local pathological imprint is associated with microglia responses needs to be elucidated. To this purpose, we employed an automated pipeline for analysis of 3D confocal microscopy images to assess CA1, CA3 and DG/CA4 subfields microglia responses in post-mortem hippocampal samples from late-onset AD (n = 10), DLB (n = 8) and age-matched control (CTL) (n = 11) individuals. In parallel, we performed volumetric analyses of hyperphosphorylated tau (pTau), amyloid-β (Aβ) and phosphorylated α-synuclein (pSyn) loads. For each of the 32,447 extracted microglia, 16 morphological features were measured to classify them into seven distinct morphological clusters. Our results show similar alterations of microglial morphological features and clusters in AD and DLB, but with more prominent changes in AD. We identified two distinct microglia clusters enriched in disease conditions and particularly increased in CA1 and DG/CA4 of AD and CA3 of DLB. Our study confirms frequent concomitance of pTau, Aβ and pSyn loads across AD and DLB but reveals a specific subregional pattern for each type of pathology, along with a generally increased severity in AD. Furthermore, pTau and pSyn loads were highly correlated across subregions and conditions. We uncovered tight associations between microglial changes and the subfield pathological imprint. Our findings suggest that combinations and severity of subregional pTau, Aβ and pSyn pathologies transform local microglia phenotypic composition in the hippocampus. The high burdens of pTau and pSyn associated with increased microglial alterations could be a factor in CA1 vulnerability in AD.
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Highet B, Parker R, Faull RLM, Curtis MA, Ryan B. RNA Quality in Post-mortem Human Brain Tissue Is Affected by Alzheimer's Disease. Front Mol Neurosci 2022; 14:780352. [PMID: 34992523 PMCID: PMC8724529 DOI: 10.3389/fnmol.2021.780352] [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: 09/20/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Gene expression studies of human post-mortem brain tissue are useful for understanding the pathogenesis of neurodegenerative disease. These studies rely on the assumption that RNA quality is consistent between disease and neurologically normal cases; however, previous studies have suggested that RNA quality may be affected by neurodegenerative disease. Here, we compared RNA quality in human post-mortem brain tissue between neurologically normal cases (n = 14) and neurodegenerative disease cases (Alzheimer’s disease n = 10; Parkinson’s disease n = 11; and Huntington’s disease n = 9) in regions affected by pathology and regions that are relatively devoid of pathology. We identified a statistically significant decrease in RNA integrity number (RIN) in Alzheimer’s disease tissue relative to neurologically normal tissue (mixed effects model, p = 0.04). There were no statistically significant differences between neurologically normal cases and Parkinson’s disease or Huntington’s disease cases. Next, we investigated whether total RNA quality affected mRNA quantification, by correlating RIN with qPCR threshold cycle (CT). CT values for all six genes investigated were strongly correlated with RIN (p < 0.05, Pearson correlation); this effect was only partially mitigated by normalization to RPL30. Our results indicate that RNA quality is decreased in Alzheimer’s disease tissue. We recommend that RIN should be considered when this tissue is used in gene expression analyses.
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Affiliation(s)
- Blake Highet
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Remai Parker
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Brigid Ryan
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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Cha HJ, Shen J, Kang J. Regulation of gene expression by the APP family in the adult cerebral cortex. Sci Rep 2022; 12:66. [PMID: 34997052 PMCID: PMC8741778 DOI: 10.1038/s41598-021-04027-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
Amyloid precursor protein (APP) is associated with both familial and sporadic forms of Alzheimer's disease. APP has two homologs, amyloid precursor-like protein 1 and 2 (APLP1 and APLP2), and they have functional redundancy. APP intracellular c-terminal domain (AICD), produced by sequential α- or β- and γ-secretase cleavages, is thought to control gene expression, similarly as the ICD of Notch. To investigate the role of APP family in transcriptional regulation, we examined gene expression changes in the cerebral cortex of APP/APLP1/APLP2 conditional triple knockout (cTKO) mice, in which APP family members are selectively inactivated in excitatory neurons of the postnatal forebrain. Of the 12 previously reported AICD target genes, only Nep and Npas4 mRNA levels were significantly reduced in the cerebral cortex of cTKO mice, compared to littermate controls. We further examined global transcriptional changes by RNA-seq and identified 189 and 274 differentially expressed genes in the neocortex and hippocampus, respectively, of cTKO mice relative to controls. Gene Ontology analysis indicated that these genes are involved in a variety of cellular functions, including extracellular organization, learning and memory, and ion channels. Thus, inactivation of APP family alters transcriptional profiles of the cerebral cortex and affects wide-ranging molecular pathways.
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Affiliation(s)
- Hye Ji Cha
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Shen
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Jongkyun Kang
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Abstract
The key pathological hallmarks-extracellular plaques and intracellular neurofibrillary tangles (NFT)-described by Alois Alzheimer in his seminal 1907 article are still central to the postmortem diagnosis of Alzheimer's disease (AD), but major advances in our understanding of the underlying pathophysiology as well as significant progress in clinical diagnosis and therapy have changed the perspective and importance of neuropathologic evaluation of the brain. The notion that the pathological processes underlying AD already start decades before symptoms are apparent in patients has brought a major change reflected in the current neuropathological classification of AD neuropathological changes (ADNC). The predictable progression of beta-amyloid (Aβ) plaque pathology from neocortex, over limbic structures, diencephalon, and basal ganglia, to brainstem and cerebellum is captured in phases described by Thal and colleagues. The progression of NFT pathology from the transentorhinal region to the limbic system and ultimately the neocortex is described in stages proposed by Braak and colleagues. The density of neuritic plaque pathology is determined by criteria defined by the Consortium to establish a registry for Alzheimer's diseases (CERAD). While these changes neuropathologically define AD, it becomes more and more apparent that the majority of patients present with a multitude of additional pathological changes which are possible contributing factors to the clinical presentation and disease progression. The impact of co-existing Lewy body pathology has been well studied, but the importance of more recently described pathologies including limbic-predominant age-related TDP-43 encephalopathy (LATE), chronic traumatic encephalopathy (CTE), and aging-related tau astrogliopathy (ARTAG) still needs to be evaluated in large cohort studies. In addition, it is apparent that vascular pathology plays an important role in the AD patient population, but a lack of standardized reporting criteria has hampered progress in elucidating the importance of these changes for clinical presentation and disease progression. More recently a key role was ascribed to the immune response to pathological protein aggregates, and it will be important to analyze these changes systematically to better understand the temporal and spatial distribution of the immune response in AD and elucidate their importance for the disease process. Advances in digital pathology and technologies such as single cell sequencing and digital spatial profiling have opened novel avenues for improvement of neuropathological diagnosis and advancing our understanding of underlying molecular processes. Finally, major strides in biomarker-based diagnosis of AD and recent advances in targeted therapeutic approaches may have shifted the perspective but also highlight the continuous importance of postmortem analysis of the brain in neurodegenerative diseases.
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Affiliation(s)
- Jorge A Trejo-Lopez
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anthony T Yachnis
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Stefan Prokop
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA.
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
- Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, 32610, USA.
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Identifying new molecular players in extracellular proteostasis. Biochem Soc Trans 2021; 50:321-334. [PMID: 34940856 DOI: 10.1042/bst20210369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 02/02/2023]
Abstract
Proteostasis refers to a delicately tuned balance between the processes of protein synthesis, folding, localization, and the degradation of proteins found inside and outside cells. Our understanding of extracellular proteostasis is rather limited and largely restricted to knowledge of 11 currently established extracellular chaperones (ECs). This review will briefly outline what is known of the established ECs, before moving on to discuss experimental strategies used to identify new members of this growing family, and an examination of a group of putative new ECs identified using one of these approaches. An observation that emerges from an analysis of the expanding number of ECs is that all of these proteins are multifunctional. Strikingly, the armory of activities each possess uniquely suit them as a group to act together at sites of tissue damage, infection, and inflammation to restore homeostasis. Lastly, we highlight outstanding questions to guide future research in this field.
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Heterotypic amyloid interactions: Clues to polymorphic bias and selective cellular vulnerability? Curr Opin Struct Biol 2021; 72:176-186. [PMID: 34942566 DOI: 10.1016/j.sbi.2021.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/18/2022]
Abstract
The number of atomic-resolution structures of disease-associated amyloids has greatly increased in recent years. These structures have confirmed not only the polymorphic nature of amyloids but also the association of specific polymorphs to particular proteinopathies. These observations are strengthening the view that amyloid polymorphism is a marker for specific pathological subtypes (e.g. in tauopathies or synucleinopathies). The nature of this association and how it relates to the selective cellular vulnerability of amyloid nucleation, propagation and toxicity are still unclear. Here, we provide an overview of the mechanistic insights provided by recent patient-derived amyloid structures. We discuss the framework organisation of amyloid polymorphism and how heterotypic amyloid interactions with the physiological environment could modify the solubility and assembly of amyloidogenic proteins. We conclude by hypothesising how such interactions could contribute to selective cellular vulnerability.
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