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Zalon AJ, Quiriconi DJ, Pitcairn C, Mazzulli JR. α-Synuclein: Multiple pathogenic roles in trafficking and proteostasis pathways in Parkinson's disease. Neuroscientist 2024; 30:612-635. [PMID: 38420922 PMCID: PMC11358363 DOI: 10.1177/10738584241232963] [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] [Indexed: 03/02/2024]
Abstract
Parkinson's disease (PD) is a common age-related neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. A hallmark of both familial and sporadic PD is the presence of Lewy body inclusions composed mainly of aggregated α-synuclein (α-syn), a presynaptic protein encoded by the SNCA gene. The mechanisms driving the relationship between α-syn accumulation and neurodegeneration are not completely understood, although recent evidence indicates that multiple branches of the proteostasis pathway are simultaneously perturbed when α-syn aberrantly accumulates within neurons. Studies from patient-derived midbrain cultures that develop α-syn pathology through the endogenous expression of PD-causing mutations show that proteostasis disruption occurs at the level of synthesis/folding in the endoplasmic reticulum (ER), downstream ER-Golgi trafficking, and autophagic-lysosomal clearance. Here, we review the fundamentals of protein transport, highlighting the specific steps where α-syn accumulation may intervene and the downstream effects on proteostasis. Current therapeutic efforts are focused on targeting single pathways or proteins, but the multifaceted pathogenic role of α-syn throughout the proteostasis pathway suggests that manipulating several targets simultaneously will provide more effective disease-modifying therapies for PD and other synucleinopathies.
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Affiliation(s)
- Annie J Zalon
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Drew J Quiriconi
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Caleb Pitcairn
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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2
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Galgani A, Scotto M, Giorgi FS. The Neuroanatomy of Induced Pluripotent Stem Cells: In Vitro Models of Subcortical Nuclei in Neurodegenerative Disorders. Curr Issues Mol Biol 2024; 46:10180-10199. [PMID: 39329959 PMCID: PMC11430477 DOI: 10.3390/cimb46090607] [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: 08/08/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Neuromodulatory subcortical systems (NSSs) are monoaminergic and cholinergic neuronal groups that are markedly and precociously involved in the pathogenesis of many neurodegenerative disorders (NDDs), including Parkinson's and Alzheimer's diseases. In humans, although many tools have been developed to infer information on these nuclei, encompassing neuroimaging and neurophysiological methods, a detailed and specific direct evaluation of their cellular features in vivo has been difficult to obtain until recent years. The development of induced pluripotent stem cell (iPSC) models has allowed research to deeply delve into the cellular and molecular biology of NSS neurons. In fact, iPSCs can be produced easily and non-invasively from patients' fibroblasts or circulating blood monocytes, by de-differentiating those cells using specific protocols, and then be re-differentiated towards neural phenotypes, which may reproduce the specific features of the correspondent brain neurons (including NSS ones) from the same patient. In this review, we summarized findings obtained in the field of NDDs using iPSCs, with the aim to understand how reliably these might represent in vitro models of NSS. We found that most of the current literature in the field of iPSCs and NSSs in NDDs has focused on midbrain dopaminergic neurons in Parkinson's disease, providing interesting results on cellular pathophysiology and even leading to the first human autologous transplantation. Differentiation protocols for noradrenergic, cholinergic, and serotoninergic neurons have also been recently defined and published. Thus, it might be expected that in the near future, this approach could extend to other NSSs and other NDDs.
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Affiliation(s)
- Alessandro Galgani
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Marco Scotto
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Filippo S. Giorgi
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- IRCCS Stella Maris Foundation, 56128 Pisa, Italy
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3
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Ali A, Manzoor S, Ali T, Asim M, Muhammad G, Ahmad A, Jamaludin MI, Devaraj S, Munawar N. Innovative aspects and applications of single cell technology for different diseases. Am J Cancer Res 2024; 14:4028-4048. [PMID: 39267684 PMCID: PMC11387862 DOI: 10.62347/vufu1836] [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: 06/21/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Recent developments in single-cell technologies have provided valuable insights from cancer genomics to complex microbial communities. Single-cell technologies including the RNA-seq, next-generation sequencing (NGS), epigenomics, genomics, and transcriptomics can be used to uncover the single cell nature and molecular characterization of individual cells. These technologies also reveal the cellular transition states, evolutionary relationships between genes, the complex structure of single-cell populations, cell-to-cell interaction leading to biological discoveries and more reliable than traditional bulk technologies. These technologies are becoming the first choice for the early detection of inflammatory biomarkers affecting the proliferation and progression of tumor cells in the tumor microenvironment and improving the clinical efficacy of patients undergoing immunotherapy. These technologies also hold a central position in the detection of checkpoint inhibitors and thus determining the signaling pathways evoked by tumor invasion. This review addressed the emerging approaches of single cell-based technologies in cancer immunotherapies and different human diseases at cellular and molecular levels and the emerging role of sequencing technologies leading to drug discovery. Advancements in these technologies paved for discovering novel diagnostic markers for better understanding the pathological and biochemical mechanisms also for controlling the rate of different diseases.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College Shantou 515041, Guangdong, China
| | - Saba Manzoor
- Department of Zoology, University of Sialkot Sialkot 51310, Pakistan
| | - Tayyab Ali
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Asim
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Ghulam Muhammad
- Jinnah Burn and Reconstructive Surgery Centre, Jinnah Hospital, Allama Iqbal Medical College Lahore 54000, Pakistan
| | - Aftab Ahmad
- Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad 38040, Pakistan
| | - Mohamad Ikhwan Jamaludin
- BioInspired Device and Tissue Engineering Research Group (BioInspira), Department of Biomedical Engineering and Health Sciences, Faculty of Electrical Engineering, Universiti Teknologi Malaysia Johor Bahru 81310, Johor, Malaysia
| | - Sutha Devaraj
- Graduate School of Medicine, Perdana University Wisma Chase Perdana, Changkat Semantan, Damansara Heights, Kuala Lumpur 50490, Malaysia
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University Al-Ain 15551, United Arab Emirates
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4
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Huang M, Jin H, Anantharam V, Kanthasamy A, Kanthasamy AG. Mitochondrial stress-induced H4K12 hyperacetylation dysregulates transcription in Parkinson's disease. Front Cell Neurosci 2024; 18:1422362. [PMID: 39188570 PMCID: PMC11345260 DOI: 10.3389/fncel.2024.1422362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/08/2024] [Indexed: 08/28/2024] Open
Abstract
Aberrant epigenetic modification has been implicated in the pathogenesis of Parkinson's disease (PD), which is characterized by the irreversible loss of dopaminergic (DAergic) neurons. However, the mechanistic landscape of histone acetylation (ac) in PD has yet to be fully explored. Herein, we mapped the proteomic acetylation profiling changes at core histones H4 and thus identified H4K12ac as a key epigenomic mark in dopaminergic neuronal cells as well as in MitoPark animal model of PD. Notably, the significantly elevated H4K12ac deposition in post-mortem PD brains highlights its clinical relevance to human PD. Increased histone acetyltransferase (HAT) activity and decreased histone deacetylase 2 (HDAC2) and HDAC4 were found in experimental PD cell models, suggesting the HAT/HDAC imbalance associated with mitochondrial stress. Following our delineation of the proteasome dysfunction that possibly contributes to H4K12ac deposition, we characterized the altered transcriptional profile and disease-associated pathways in the MitoPark mouse model of PD. Our study uncovers the axis of mitochondrial impairment-H4K12ac deposition-altered transcription/disease pathways as a neuroepigenetic mechanism underlying PD pathogenesis. These findings provide mechanistic information for the development of potential pharmacoepigenomic translational strategies for PD.
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Affiliation(s)
- Minhong Huang
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Huajun Jin
- Isakson Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
| | - Vellareddy Anantharam
- Isakson Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
| | - Arthi Kanthasamy
- Isakson Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
| | - Anumantha G. Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
- Isakson Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of Georgia, Athens, GA, United States
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5
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Zhang X, Ruan L, Wang H, Zhu J, Li T, Sun G, Dong Y, Wang Y, Berreby G, Shay A, Chen R, Ramachandran S, Dawson VL, Dawson TM, Li R. Enhancing mitochondrial proteolysis alleviates alpha-synuclein-mediated cellular toxicity. NPJ Parkinsons Dis 2024; 10:120. [PMID: 38906862 PMCID: PMC11192938 DOI: 10.1038/s41531-024-00733-y] [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: 08/03/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease characterized by mitochondrial dysfunction and accumulation of alpha-synuclein (α-Syn)-containing protein aggregates known as Lewy bodies (LB). Here, we investigated the entry of α-Syn into mitochondria to cause mitochondrial dysfunction and loss of cellular fitness in vivo. We show that α-Syn expressed in yeast and human cells is constitutively imported into mitochondria. In a transgenic mouse model, the level of endogenous α-Syn accumulation in mitochondria of dopaminergic neurons and microglia increases with age. The imported α-Syn is degraded by conserved mitochondrial proteases, most notably NLN and PITRM1 (Prd1 and Cym1 in yeast, respectively). α-Syn in the mitochondrial matrix that is not degraded interacts with respiratory chain complexes, leading to loss of mitochondrial DNA (mtDNA), mitochondrial membrane potential and cellular fitness decline. Importantly, enhancing mitochondrial proteolysis by increasing levels of specific proteases alleviated these defects in yeast, human cells, and a PD model of mouse primary neurons. Together, our results provide a direct link between α-synuclein-mediated cellular toxicity and its import into mitochondria and reveal potential therapeutic targets for the treatment of α-synucleinopathies.
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Affiliation(s)
- Xi Zhang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Linhao Ruan
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jin Zhu
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21218, USA
| | - Gordon Sun
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yi Dong
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yuhao Wang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gil Berreby
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ashley Shay
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rong Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sreekumar Ramachandran
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Valina L Dawson
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ted M Dawson
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore.
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6
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Carraro C, Montgomery JV, Klimmt J, Paquet D, Schultze JL, Beyer MD. Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. Front Mol Neurosci 2024; 17:1414886. [PMID: 38952421 PMCID: PMC11215216 DOI: 10.3389/fnmol.2024.1414886] [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: 04/09/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024] Open
Abstract
Drug discovery is a generally inefficient and capital-intensive process. For neurodegenerative diseases (NDDs), the development of novel therapeutics is particularly urgent considering the long list of late-stage drug candidate failures. Although our knowledge on the pathogenic mechanisms driving neurodegeneration is growing, additional efforts are required to achieve a better and ultimately complete understanding of the pathophysiological underpinnings of NDDs. Beyond the etiology of NDDs being heterogeneous and multifactorial, this process is further complicated by the fact that current experimental models only partially recapitulate the major phenotypes observed in humans. In such a scenario, multi-omic approaches have the potential to accelerate the identification of new or repurposed drugs against a multitude of the underlying mechanisms driving NDDs. One major advantage for the implementation of multi-omic approaches in the drug discovery process is that these overarching tools are able to disentangle disease states and model perturbations through the comprehensive characterization of distinct molecular layers (i.e., genome, transcriptome, proteome) up to a single-cell resolution. Because of recent advances increasing their affordability and scalability, the use of omics technologies to drive drug discovery is nascent, but rapidly expanding in the neuroscience field. Combined with increasingly advanced in vitro models, which particularly benefited from the introduction of human iPSCs, multi-omics are shaping a new paradigm in drug discovery for NDDs, from disease characterization to therapeutics prediction and experimental screening. In this review, we discuss examples, main advantages and open challenges in the use of multi-omic approaches for the in vitro discovery of targets and therapies against NDDs.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jessica V. Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
| | - Julien Klimmt
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
- Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
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7
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Ding Y, Peng YY, Li S, Tang C, Gao J, Wang HY, Long ZY, Lu XM, Wang YT. Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases. Cell Biochem Biophys 2024; 82:329-342. [PMID: 38133792 DOI: 10.1007/s12013-023-01207-3] [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: 08/21/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The mammalian central nervous system consists of a large number of cells, which contain not only different types of neurons, but also a large number of glial cells, such as astrocytes, oligodendrocytes, and microglia. These cells are capable of performing highly refined electrophysiological activities and providing the brain with functions such as nutritional support, information transmission and pathogen defense. The diversity of cell types and individual differences between cells have brought inspiration to the study of the mechanism of central nervous system diseases. In order to explore the role of different cells, a new technology, single-cell sequencing technology has emerged to perform specific analysis of high-throughput cell populations, and has been continuously developed. Single-cell sequencing technology can accurately analyze single-cell expression in mixed-cell populations and collect cells from different spatial locations, time stages and types. By using single-cell sequencing technology to compare gene expression profiles of normal and diseased cells, it is possible to discover cell subsets associated with specific diseases and their associated genes. Therefore, scientists can understand the development process, related functions and disease state of the nervous system from an unprecedented depth. In conclusion, single-cell sequencing technology provides a powerful technology for the discovery of novel therapeutic targets for central nervous system diseases.
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Affiliation(s)
- Yang Ding
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yu-Yuan Peng
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Sen Li
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Can Tang
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jie Gao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Yong-Tang Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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8
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Franks SN, Heon-Roberts R, Ryan BJ. CRISPRi: a way to integrate iPSC-derived neuronal models. Biochem Soc Trans 2024; 52:539-551. [PMID: 38526223 PMCID: PMC11088925 DOI: 10.1042/bst20230190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
The genetic landscape of neurodegenerative diseases encompasses genes affecting multiple cellular pathways which exert effects in an array of neuronal and glial cell-types. Deconvolution of the roles of genes implicated in disease and the effects of disease-associated variants remains a vital step in the understanding of neurodegeneration and the development of therapeutics. Disease modelling using patient induced pluripotent stem cells (iPSCs) has enabled the generation of key cell-types associated with disease whilst maintaining the genomic variants that predispose to neurodegeneration. The use of CRISPR interference (CRISPRi), alongside other CRISPR-perturbations, allows the modelling of the effects of these disease-associated variants or identifying genes which modify disease phenotypes. This review summarises the current applications of CRISPRi in iPSC-derived neuronal models, such as fluorescence-activated cell sorting (FACS)-based screens, and discusses the future opportunities for disease modelling, identification of disease risk modifiers and target/drug discovery in neurodegeneration.
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Affiliation(s)
- Sarah N.J. Franks
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J. Ryan
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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9
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Do QB, Noor H, Marquez-Gomez R, Cramb KML, Ng B, Abbey A, Ibarra-Aizpurua N, Caiazza MC, Sharifi P, Lang C, Beccano-Kelly D, Baleriola J, Bengoa-Vergniory N, Wade-Martins R. Early deficits in an in vitro striatal microcircuit model carrying the Parkinson's GBA-N370S mutation. NPJ Parkinsons Dis 2024; 10:82. [PMID: 38609392 PMCID: PMC11014935 DOI: 10.1038/s41531-024-00694-2] [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: 03/11/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Understanding medium spiny neuron (MSN) physiology is essential to understand motor impairments in Parkinson's disease (PD) given the architecture of the basal ganglia. Here, we developed a custom three-chambered microfluidic platform and established a cortico-striato-nigral microcircuit partially recapitulating the striatal presynaptic landscape in vitro using induced pluripotent stem cell (iPSC)-derived neurons. We found that, cortical glutamatergic projections facilitated MSN synaptic activity, and dopaminergic transmission enhanced maturation of MSNs in vitro. Replacement of wild-type iPSC-derived dopamine neurons (iPSC-DaNs) in the striatal microcircuit with those carrying the PD-related GBA-N370S mutation led to a depolarisation of resting membrane potential and an increase in rheobase in iPSC-MSNs, as well as a reduction in both voltage-gated sodium and potassium currents. Such deficits were resolved in late microcircuit cultures, and could be reversed in younger cultures with antagonism of protein kinase A activity in iPSC-MSNs. Taken together, our results highlight the unique utility of modelling striatal neurons in a modular physiological circuit to reveal mechanistic insights into GBA1 mutations in PD.
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Affiliation(s)
- Quyen B Do
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Humaira Noor
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Nuffield Department of Medicine (NDM), University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road, Oxford, OX3 7BN, UK
| | - Ricardo Marquez-Gomez
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Kaitlyn M L Cramb
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Bryan Ng
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Ajantha Abbey
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Naroa Ibarra-Aizpurua
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Parnaz Sharifi
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Charmaine Lang
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Dayne Beccano-Kelly
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
| | - Jimena Baleriola
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Ikerbasque-Basque Foundation for Science, Bilbao, Spain
| | - Nora Bengoa-Vergniory
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Achucarro Basque Center for Neuroscience, Leioa, Spain.
- Ikerbasque-Basque Foundation for Science, Bilbao, Spain.
- University of the Basque Country (UPV/EHU), Department of Neuroscience, Leioa, Spain.
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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10
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Yang B, Hu S, Jiang Y, Xu L, Shu S, Zhang H. Advancements in Single-Cell RNA Sequencing Research for Neurological Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04126-3. [PMID: 38564138 DOI: 10.1007/s12035-024-04126-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Neurological diseases are a major cause of the global burden of disease. Although the mechanisms of the occurrence and development of neurological diseases are not fully clear, most of them are associated with cells mediating neuroinflammation. Yet medications and other therapeutic options to improve treatment are still very limited. Single-cell RNA sequencing (scRNA-seq), as a delightfully potent breakthrough technology, not only identifies various cell types and response states but also uncovers cell-specific gene expression changes, gene regulatory networks, intercellular communication, and cellular movement trajectories, among others, in different cell types. In this review, we describe the technology of scRNA-seq in detail and discuss and summarize the application of scRNA-seq in exploring neurological diseases, elaborating the corresponding specific mechanisms of the diseases as well as providing a reliable basis for new therapeutic approaches. Finally, we affirm that scRNA-seq promotes the development of the neuroscience field and enables us to have a deeper cellular understanding of neurological diseases in the future, which provides strong support for the treatment of neurological diseases and the improvement of patients' prognosis.
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Affiliation(s)
- Bingjie Yang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuqi Hu
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiru Jiang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lei Xu
- Department of Neurology, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang, China
| | - Song Shu
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China.
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11
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Basavarajappa BS, Subbanna S. Unlocking the epigenetic symphony: histone acetylation's impact on neurobehavioral change in neurodegenerative disorders. Epigenomics 2024; 16:331-358. [PMID: 38321930 PMCID: PMC10910622 DOI: 10.2217/epi-2023-0428] [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: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Recent genomics and epigenetic advances have empowered the exploration of DNA/RNA methylation and histone modifications crucial for gene expression in response to stress, aging and disease. Interest in understanding neuronal plasticity's epigenetic mechanisms, influencing brain rewiring amid development, aging and neurodegenerative disorders, continues to grow. Histone acetylation dysregulation, a commonality in diverse brain disorders, has become a therapeutic focus. Histone acetyltransferases and histone deacetylases have emerged as promising targets for neurodegenerative disorder treatment. This review delves into histone acetylation regulation, potential therapies and future perspectives for disorders like Alzheimer's, Parkinson's and Huntington's. Exploring genetic-environmental interplay through models and studies reveals molecular changes, behavioral insights and early intervention possibilities targeting the epigenome in at-risk individuals.
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Affiliation(s)
- Balapal S Basavarajappa
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, NY 10032, USA
- Department of Psychiatry, Columbia University Irving Medical Center, NY 10032, USA
- Department of Psychiatry, New York University Langone Medical Center, NY 10016, USA
| | - Shivakumar Subbanna
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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12
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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13
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Martirosyan A, Ansari R, Pestana F, Hebestreit K, Gasparyan H, Aleksanyan R, Hnatova S, Poovathingal S, Marneffe C, Thal DR, Kottick A, Hanson-Smith VJ, Guelfi S, Plumbly W, Belgard TG, Metzakopian E, Holt MG. Unravelling cell type-specific responses to Parkinson's Disease at single cell resolution. Mol Neurodegener 2024; 19:7. [PMID: 38245794 PMCID: PMC10799528 DOI: 10.1186/s13024-023-00699-0] [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: 05/16/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024] Open
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disorder. The pathological hallmark of PD is loss of dopaminergic neurons and the presence of aggregated α-synuclein, primarily in the substantia nigra pars compacta (SNpc) of the midbrain. However, the molecular mechanisms that underlie the pathology in different cell types is not currently understood. Here, we present a single nucleus transcriptome analysis of human post-mortem SNpc obtained from 15 sporadic Parkinson's Disease (PD) cases and 14 Controls. Our dataset comprises ∼84K nuclei, representing all major cell types of the brain, allowing us to obtain a transcriptome-level characterization of these cell types. Importantly, we identify multiple subpopulations for each cell type and describe specific gene sets that provide insights into the differing roles of these subpopulations. Our findings reveal a significant decrease in neuronal cells in PD samples, accompanied by an increase in glial cells and T cells. Subpopulation analyses demonstrate a significant depletion of tyrosine hydroxylase (TH) enriched astrocyte, microglia and oligodendrocyte populations in PD samples, as well as TH enriched neurons, which are also depleted. Moreover, marker gene analysis of the depleted subpopulations identified 28 overlapping genes, including those associated with dopamine metabolism (e.g., ALDH1A1, SLC6A3 & SLC18A2). Overall, our study provides a valuable resource for understanding the molecular mechanisms involved in dopaminergic neuron degeneration and glial responses in PD, highlighting the existence of novel subpopulations and cell type-specific gene sets.
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Affiliation(s)
| | - Rizwan Ansari
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | | | | | - Hayk Gasparyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Department of Mathematics and Mechanics, Yerevan State University, Yerevan, Armenia
| | - Razmik Aleksanyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Department of Mathematics and Mechanics, Yerevan State University, Yerevan, Armenia
| | - Silvia Hnatova
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | | | | | - Dietmar R Thal
- Laboratory for Neuropathology, Department of Imaging and Pathology and Leuven Brain Institute, KU Leuven, and Department of Pathology, UZ Leuven, Leuven, Belgium
| | | | | | | | - William Plumbly
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | | | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK.
- bit.bio, The Dorothy Hodgkin Building, Babraham Research Institute, Cambridge, CB22 3FH, UK.
| | - Matthew G Holt
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, Belgium.
- Laboratory of Synapse Biology, i3S, Porto, Portugal.
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14
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Jeuken GS, Käll L. Pathway analysis through mutual information. Bioinformatics 2024; 40:btad776. [PMID: 38195928 PMCID: PMC10783954 DOI: 10.1093/bioinformatics/btad776] [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: 03/14/2023] [Revised: 12/09/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
MOTIVATION In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an upstream differential expression analysis, and many model the relations between the abundances of the analytes in a pathway as linear relationships. RESULTS Here, we propose a new method for pathway analysis, MIPath, that relies on information theoretical principles and, therefore, does not model the association between pathway activity and phenotype, resulting in relatively few assumptions. For this, we construct a graph of the data points for each pathway using a nearest-neighbor approach and score the association between the structure of this graph and the phenotype of these same samples using Mutual Information while adjusting for the effects of random chance in each score. The initial nearest neighbor approach evades individual gene-level comparisons, hence making the method scalable and less vulnerable to missing values. These properties make our method particularly useful for single-cell data. We benchmarked our method on several single-cell datasets, comparing it to established and new methods, and found that it produces robust, reproducible, and meaningful scores. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/statisticalbiotechnology/mipath, or through Python Package Index as "mipathway."
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Affiliation(s)
- Gustavo S Jeuken
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
- Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Lukas Käll
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
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15
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Wang W, Li T, Wang Z, Yin Y, Zhang S, Wang C, Hu X, Lu S. Bibliometric analysis of research on neurodegenerative diseases and single-cell RNA sequencing: Opportunities and challenges. iScience 2023; 26:107833. [PMID: 37736042 PMCID: PMC10509354 DOI: 10.1016/j.isci.2023.107833] [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: 06/19/2023] [Revised: 07/18/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
Neurodegeneration, characterized by the progressive deterioration in neuronal structure or function, presents an elusive mechanism. The use of single-cell RNA sequencing (scRNA-seq) technology in the clinic is becoming increasingly prevalent in recent decades. This technology offers unparalleled cell-level insights into neurodegenerative diseases, establishing itself as a potent tool for elucidating these diseases underlying mechanisms. Here, we made a deep investigation for scRNA-seq research in neurodegenerative diseases using bibliometric analysis from 2009 to 2022. We observed a robust upward trajectory in the number of publications on this subject. The United States stood out as the principal contributor to this expanding field. Specifically, the University of California System exhibited notable research prowess in this field. Alzheimer disease and Parkinson disease were the diseases most frequently investigated. Key research hotspots include the creation of a molecular brain atlas and identification of vulnerable neuronal subpopulations and potential therapeutic targets at the transcriptomic level.
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Affiliation(s)
- Wei Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Tianhua Li
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Zheng Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yaxin Yin
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Sitao Zhang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Chaodong Wang
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xinli Hu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shibao Lu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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16
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Zhu S, Deen MC, Zhu Y, Gilormini PA, Chen X, Davis OB, Chin MY, Henry AG, Vocadlo DJ. A Fixable Fluorescence-Quenched Substrate for Quantitation of Lysosomal Glucocerebrosidase Activity in Both Live and Fixed Cells. Angew Chem Int Ed Engl 2023; 62:e202309306. [PMID: 37582679 DOI: 10.1002/anie.202309306] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
Fluorogenic substrates are emerging tools that enable studying enzymatic processes within their native cellular environments. However, fluorogenic substrates that function within live cells are generally incompatible with cellular fixation, preventing their tandem application with fundamental cell biology methods such as immunocytochemistry. Here we report a simple approach to enable the chemical fixation of a dark-to-light substrate, LysoFix-GBA, which enables quantification of glucocerebrosidase (GCase) activity in both live and fixed cells. LysoFix-GBA enables measuring responses to both chemical and genetic perturbations to lysosomal GCase activity. Further, LysoFix-GBA permits simple multiplexed co-localization studies of GCase activity with subcellular protein markers. This tool will aid studying the role of GCase activity in Parkinson's Disease, creating new therapeutic approaches targeting the GCase pathway. This approach also lays the foundation for an approach to create fixable substrates for other lysosomal enzymes.
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Affiliation(s)
- Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yanping Zhu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Xi Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Oliver B Davis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Marcus Y Chin
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Anastasia G Henry
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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17
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Xu X, Chen J, Zhao H, Pi Y, Lin G, Hu L. Single-Cell RNA-seq Analysis of a Human Embryonic Stem Cell to Endothelial Cell System Based on Transcription Factor Overexpression. Stem Cell Rev Rep 2023; 19:2497-2509. [PMID: 37537495 DOI: 10.1007/s12015-023-10598-y] [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] [Accepted: 07/17/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Human embryonic stem cell (hESC)-derived endothelial cells (ECs) possess therapeutic potential in many diseases. Cytokine supplementation induction and transcription factor overexpression have become two mainstream methods of hESC-EC induction. Single-cell RNA-seq technology has been widely used to analyse dynamic processes during hESC-EC induction and components of induced endothelial cells. However, studies that used single-cell RNA-seq are mainly based on cytokine supplementation methods. In this study, we used a high-efficiency human embryonic stem cell-endothelial cell line (hESC-EC) called the "FLI1-PKC system" as a research model and employed single-cell RNA sequencing (scRNA-seq) to investigate the transcriptional landscape and cellular dynamics. METHODS The high-efficiency hESC-EC induction (FLI1-PKC) system was established in our previous study. We applied single-cell RNA sequencing (scRNA-seq) of the differentiated cells at different time points and investigated the gene expression profiles. RESULTS The FLI1-PKC induction system can directionally differentiate hESCs into mature endothelial cells with all the requisite functions. Unlike other hES-EC induction protocols, the FLI1-PKC method follows a different induction route; nonetheless, the transcriptome of induced endothelial cells (iECs) remains the same. The elevated number of activated transcription factors may explain why the FLI1-PKC system is more effective than other hES-EC protocols. CONCLUSION Our study has presented a single-cell transcriptional overview of a high-efficiency hESC-EC induction system, which can be used as a model and reference for further improvement in other hESC induction systems.
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Affiliation(s)
- XiangWang Xu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
| | - JunRu Chen
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China
| | - Hao Zhao
- Xiangya Hospital of Central South University, Changsha, Human, China
| | - YuZe Pi
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, National Engineering and Research Center of Human Stem Cell, Changsha, 410008, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China.
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, National Engineering and Research Center of Human Stem Cell, Changsha, 410008, Hunan, China.
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18
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Williamson MG, Madureira M, McGuinness W, Heon-Roberts R, Mock ED, Naidoo K, Cramb KML, Caiazza MC, Malpartida AB, Lavelle M, Savory K, Humble SW, Patterson R, Davis JB, Connor-Robson N, Ryan BJ, Wade-Martins R. Mitochondrial dysfunction and mitophagy defects in LRRK2-R1441C Parkinson's disease models. Hum Mol Genet 2023; 32:2808-2821. [PMID: 37384414 PMCID: PMC10481106 DOI: 10.1093/hmg/ddad102] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
Mutations in the Leucine-Rich Repeat Kinase 2 (LRRK2) gene have been identified as one of the most common genetic causes of Parkinson's disease (PD). The LRRK2 PD-associated mutations LRRK2G2019S and LRRK2R1441C, located in the kinase domain and in the ROC-COR domain, respectively, have been demonstrated to impair mitochondrial function. Here, we sought to further our understanding of mitochondrial health and mitophagy by integrating data from LRRK2R1441C rat primary cortical and human induced pluripotent stem cell-derived dopamine (iPSC-DA) neuronal cultures as models of PD. We found that LRRK2R1441C neurons exhibit decreased mitochondrial membrane potential, impaired mitochondrial function and decreased basal mitophagy levels. Mitochondrial morphology was altered in LRRK2R1441C iPSC-DA but not in cortical neuronal cultures or aged striatal tissue, indicating a cell-type-specific phenotype. Additionally, LRRK2R1441C but not LRRK2G2019S neurons demonstrated decreased levels of the mitophagy marker pS65Ub in response to mitochondrial damage, which could disrupt degradation of damaged mitochondria. This impaired mitophagy activation and mitochondrial function were not corrected by the LRRK2 inhibitor MLi-2 in LRRK2R1441C iPSC-DA neuronal cultures. Furthermore, we demonstrate LRRK2 interaction with MIRO1, a protein necessary to stabilize and to anchor mitochondria for transport, occurs at mitochondria, in a genotype-independent manner. Despite this, we found that degradation of MIRO1 was impaired in LRRK2R1441C cultures upon induced mitochondrial damage, suggesting a divergent mechanism from the LRRK2G2019S mutation.
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Affiliation(s)
- Matthew G Williamson
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Marta Madureira
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
- ICBAS, Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira, 228, Porto 4050-313, Portugal
| | - William McGuinness
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Elliot D Mock
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Kalina Naidoo
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Kaitlyn M L Cramb
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Maria-Claudia Caiazza
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Ana B Malpartida
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
| | - Martha Lavelle
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Katrina Savory
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Stewart W Humble
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
- National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda, MD, 20892, USA
| | - Ryan Patterson
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda, MD, 20892, USA
| | - John B Davis
- Oxford Drug Discovery Institute, Centre of Medicines Discovery, University of Oxford, NDM Research Building, Old Road Campus, Oxford OX3 7FZ, UK
| | - Natalie Connor-Robson
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J Ryan
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Richard Wade-Martins
- Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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19
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Pozojevic J, Spielmann M. Single-Cell Sequencing in Neurodegenerative Disorders. Mol Diagn Ther 2023; 27:553-561. [PMID: 37552451 PMCID: PMC10435411 DOI: 10.1007/s40291-023-00668-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/09/2023]
Abstract
Neurodegenerative disorders are typically characterized by late onset progressive damage to specific (sub)populations of cells of the nervous system that are essential for mobility, coordination, strength, sensation, and cognition. Addressing this selective cellular vulnerability has become feasible with the emergence of single-cell-omics technologies, which now represent the state-of-the-art approach to profile heterogeneity of complex tissues including human post-mortem brain at unprecedented resolution. In this review, we briefly recapitulate the experimental workflow of single-cell RNA sequencing and summarize the recent knowledge acquired with it in the most common neurodegenerative diseases: Parkinson's, Alzheimer's, Huntington's disease, and multiple sclerosis. We also discuss the possibility of applying single-cell approaches in the diagnostics and therapy of neurodegenerative disorders, as well as the limitations. While we are currently at the point of deeply exploring the transcriptomic changes in the affected cells, further technological developments hold a promise of manipulating the affected pathways once we understand them better.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany.
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.
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20
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Beccano-Kelly DA, Cherubini M, Mousba Y, Cramb KM, Giussani S, Caiazza MC, Rai P, Vingill S, Bengoa-Vergniory N, Ng B, Corda G, Banerjee A, Vowles J, Cowley S, Wade-Martins R. Calcium dysregulation combined with mitochondrial failure and electrophysiological maturity converge in Parkinson's iPSC-dopamine neurons. iScience 2023; 26:107044. [PMID: 37426342 PMCID: PMC10329047 DOI: 10.1016/j.isci.2023.107044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/30/2022] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Parkinson's disease (PD) is characterized by a progressive deterioration of motor and cognitive functions. Although death of dopamine neurons is the hallmark pathology of PD, this is a late-stage disease process preceded by neuronal dysfunction. Here we describe early physiological perturbations in patient-derived induced pluripotent stem cell (iPSC)-dopamine neurons carrying the GBA-N370S mutation, a strong genetic risk factor for PD. GBA-N370S iPSC-dopamine neurons show an early and persistent calcium dysregulation notably at the mitochondria, followed by reduced mitochondrial membrane potential and oxygen consumption rate, indicating mitochondrial failure. With increased neuronal maturity, we observed decreased synaptic function in PD iPSC-dopamine neurons, consistent with the requirement for ATP and calcium to support the increase in electrophysiological activity over time. Our work demonstrates that calcium dyshomeostasis and mitochondrial failure impair the higher electrophysiological activity of mature neurons and may underlie the vulnerability of dopamine neurons in PD.
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Affiliation(s)
- Dayne A. Beccano-Kelly
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Marta Cherubini
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Yassine Mousba
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Kaitlyn M.L. Cramb
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Stefania Giussani
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Maria Claudia Caiazza
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Pavandeep Rai
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Siv Vingill
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Nora Bengoa-Vergniory
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Bryan Ng
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Gabriele Corda
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
| | - Abhirup Banerjee
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford OX3 7DQ, UK
| | - Jane Vowles
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- The James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sally Cowley
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- The James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Richard Wade-Martins
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, United Kingdom
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX3 7BN, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
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21
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Antunes AS, Martins-de-Souza D. Single-Cell RNA Sequencing and Its Applications in the Study of Psychiatric Disorders. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:329-339. [PMID: 37519459 PMCID: PMC10382703 DOI: 10.1016/j.bpsgos.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/19/2022] [Accepted: 03/25/2022] [Indexed: 10/18/2022] Open
Abstract
Neuroscience is currently one of the most challenging research fields owing to the enormous complexity of the mammalian nervous system. We are yet to understand precise transcriptional programs that govern cell fate during neurodevelopment, resolve the connectome of the mammalian brain, and determine the etiology of various neurodegenerative and psychiatric disorders. Technological advances in the past decade, notably single-cell RNA sequencing, have enabled huge progress in our understanding of such features. Our current knowledge of the transcriptome is largely derived from bulk RNA sequencing, which reveals only the average gene expression of millions of cells, potentially missing out on minor transcriptome differences between cells detectable only at single-cell resolution. Since 2009, several single-cell RNA sequencing techniques have emerged that enable the accurate classification of neuronal and glial cell subtypes beyond classical molecular markers and electrophysiological features and allow the identification of previously unknown cell types. Furthermore, it enables the interrogation of molecular and disease-relevant mechanisms and offers further possibilities for the discovery of new drug targets and disease biomarkers. This review intends to familiarize the reader with the main single-cell RNA sequencing techniques developed throughout the past decade and discusses their application in the fields of brain cell taxonomy, neurodevelopment, and psychiatric disorders.
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Affiliation(s)
- André S.L.M. Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
- D'Or Institute for Research and Education, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
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22
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Hu J, Zhang D, Tian K, Ren C, Li H, Lin C, Huang X, Liu J, Mao W, Zhang J. Small-molecule LRRK2 inhibitors for PD therapy: Current achievements and future perspectives. Eur J Med Chem 2023; 256:115475. [PMID: 37201428 DOI: 10.1016/j.ejmech.2023.115475] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that orchestrates a diverse array of cellular processes, including vesicle transport, autophagy, lysosome degradation, neurotransmission, and mitochondrial activity. Hyperactivation of LRRK2 triggers vesicle transport dysfunction, neuroinflammation, accumulation of α-synuclein, mitochondrial dysfunction, and the loss of cilia, ultimately leading to Parkinson's disease (PD). Therefore, targeting LRRK2 protein is a promising therapeutic strategy for PD. The clinical translation of LRRK2 inhibitors was historically impeded by issues surrounding tissue specificity. Recent studies have identified LRRK2 inhibitors that have no effect on peripheral tissues. Currently, there are four small-molecule LRRK2 inhibitors undergoing clinical trials. This review provides a summary of the structure and biological functions of LRRK2, along with an overview of the binding modes and structure-activity relationships (SARs) of small-molecule inhibitors targeting LRRK2. It offers valuable references for developing novel drugs targeting LRRK2.
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Affiliation(s)
- Jiarui Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changyu Ren
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Heng Li
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoli Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wuyu Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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23
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Ren J, Lv Y, Tian Q, Sun L, Miao P, Yang X, Xu LX, Feng CX, Li M, Gu Q, Feng X, Ding X. Suppression of Microglial ERO1a Alleviates Inflammation and Enhances the Efficacy of Rehabilitative Training After Ischemic Stroke. Mol Neurobiol 2023:10.1007/s12035-023-03333-8. [PMID: 37100971 DOI: 10.1007/s12035-023-03333-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/28/2023] [Indexed: 04/28/2023]
Abstract
Microglia mediated inflammation plays a crucial role in cellular events and functional recovery post ischemic stroke. In the current study, we profiled the proteome changes of microglia treated with oxygen and glucose deprivation (OGD). Bioinformatics analysis identified that differentially expressed proteins (DEPs) were enriched in pathways associated with oxidate phosphorylation and mitochondrial respiratory chain at both 6h and 24h post OGD. We next focused on one validated target named endoplasmic reticulum oxidoreductase 1 alpha (ERO1a) to study its role in stroke pathophysiology. We showed that over-expression of microglial ERO1a exacerbated inflammation, cell apoptosis and behavioral outcomes post middle cerebral artery occlusion (MCAO). In contrast, suppression of microglial ERO1a significantly reduced activation of both microglia and astrocyte, along with cell apoptosis. Furthermore, knocking down microglial ERO1a improved the efficacy of rehabilitative training and enhanced the mTOR activity in spared corticospinal neurons. Our study provided novel insights into the identification of therapeutic targets and the design of rehabilitative protocols to treat ischemic stroke and other traumatic CNS injuries.
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Affiliation(s)
- Jing Ren
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China
| | - Yuan Lv
- Department of Neonatology, Northern Jiangsu People's Hospital, Yangzhou, 225000, China
- Clinical Medical College, Yangzhou University, Northan Jiangsu People's Hospital, Yangzhou, 225000, China
| | - Qiuyan Tian
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Li Sun
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China
| | - Po Miao
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China
| | - Xiaofeng Yang
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China
| | - Li-Xiao Xu
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Chen-Xi Feng
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Mei Li
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Qin Gu
- Department of Rehabilitation, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Xing Feng
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China.
| | - Xin Ding
- Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, Jiangsu, China.
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24
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Wang L, Liu L, Han C, Jiang H, Ma K, Guo S, Xia Y, Wan F, Huang J, Xiong N, Wang T. Histone Deacetylase 4 Inhibition Reduces Rotenone-Induced Alpha-Synuclein Accumulation via Autophagy in SH-SY5Y Cells. Brain Sci 2023; 13:brainsci13040670. [PMID: 37190635 DOI: 10.3390/brainsci13040670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
(1) Background: Parkinson's disease (PD) is the most common movement disorder. Imbalanced protein homeostasis and α-syn aggregation are involved in PD pathogenesis. Autophagy is related to the occurrence and development of PD and can be regulated by histone deacetylases (HDACs). Various inhibitors of HDACs exert neuroprotective effects within in vitro and in vivo models of PD. HDAC4, a class Ⅱ HDAC, colocalizes with α-synuclein and ubiquitin in Lewy bodies and also accumulates in the nuclei of dopaminergic neurons in PD models. (2) Methods: In the present study, the gene expression profile of HDACs from two previously reported datasets in the GEO database was analyzed, and the RNA levels of HDAC4 in brain tissues were compared between PD patients and healthy controls. In vitro, SH-SY5Y cells transfected with HDAC4 shRNA or pretreated with mc1568 were treated with 1 μM of rotenone for 24 h. Then, the levels of α-syn, LC3, and p62 were detected using Western blot analysis and immunofluorescent staining, and cell viabilities were detected using Cell Counting Kit-8 (CCK-8). (3) Results: HDAC4 was highly expressed in PD substantia nigra and locus coeruleus. Mc1568, an inhibitor of HDAC4, decreased α-synuclein levels in rotenone-treated SH-SY5Y cells in a concentration-dependent manner and activated autophagy, which was impaired by rotenone. The knockdown of HDAC4 reversed rotenone-induced α-syn accumulation in SH-SY5Y cells and protected the neurons by enhancing autophagy. (4) Conclusions: HDAC4 is a potential therapeutic target for PD. The inhibition of HDAC4 by mc1568 or a gene block can reduce α-syn levels by regulating the autophagy process in PD. Mc1568 is a promising therapeutic agent for PD and other disorders related to α-syn accumulation.
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Affiliation(s)
- Luxi Wang
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ling Liu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chao Han
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Haiyang Jiang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kai Ma
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shiyi Guo
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yun Xia
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Fang Wan
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jinsha Huang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Nian Xiong
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tao Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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25
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Xu Y, Wei S, Zhu L, Huang C, Yang T, Wang S, Zhang Y, Duan Y, Li X, Wang Z, Pan W. Low expression of the intestinal metabolite butyric acid and the corresponding memory pattern regulate HDAC4 to promote apoptosis in rat hippocampal neurons. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114660. [PMID: 36812872 DOI: 10.1016/j.ecoenv.2023.114660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
After intensive research on the gut-brain axis, intestinal dysbiosis is considered to be one of the important pathways of cognitive decline. Microbiota transplantation has long been thought to reverse the behavioral changes in the brain caused by colony dysregulation, but in our study, microbiota transplantation seemed to improve only behavioral brain function, and there was no reasonable explanation for the high level of hippocampal neuron apoptosis that remained. Butyric acid is one of the short-chain fatty acids of intestinal metabolites and is mainly used as an edible flavoring. It is commonly used in butter, cheese and fruit flavorings, and is a natural product of bacterial fermentation of dietary fiber and resistant starch in the colon, acting similarly to the small-molecule HDAC inhibitor TSA. The effect of butyric acid on HDAC levels in hippocampal neurons in the brain remains unclear. Therefore, this study used rats with low bacterial abundance, conditional knockout mice, microbiota transplantation, 16S rDNA amplicon sequencing, and behavioral assays to demonstrate the regulatory mechanism of short-chain fatty acids on the acetylation of hippocampal histones. The results showed that disturbance of short-chain fatty acid metabolism led to high HDAC4 expression in the hippocampus and regulated H4K8ac, H4K12ac, and H4K16ac to promote increased neuronal apoptosis. However, microbiota transplantation did not change the pattern of low butyric acid expression, resulting in maintained high HDAC4 expression in hippocampal neurons with continued neuronal apoptosis. Overall, our study shows that low levels of butyric acid in vivo can promote HDAC4 expression through the gut-brain axis pathway, leading to hippocampal neuronal apoptosis, and demonstrates that butyric acid has great potential value for neuroprotection in the brain. In this regard, we suggest that patients with chronic dysbiosis should pay attention to changes in the levels of SCFAs in their bodies, and if deficiencies occur, they should be promptly supplemented through diet and other means to avoid affecting brain health.
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Affiliation(s)
- Yongjie Xu
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China; Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China; Department of Medical Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Sijia Wei
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Liying Zhu
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China; Department of Medical Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Changyudong Huang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Tingting Yang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Shuang Wang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Yiqiong Zhang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Yunfeng Duan
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China
| | - Xing Li
- Guizhou University of Traditional Chinese Medicine, Guiyang 550004, Guizhou, PR China.
| | - Zhengrong Wang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China; Department of Medical Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China.
| | - Wei Pan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China; Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, PR China; Department of Medical Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, Guizhou, PR China.
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26
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Bogetofte H, Ryan BJ, Jensen P, Schmidt SI, Vergoossen DLE, Barnkob MB, Kiani LN, Chughtai U, Heon-Roberts R, Caiazza MC, McGuinness W, Márquez-Gómez R, Vowles J, Bunn FS, Brandes J, Kilfeather P, Connor JP, Fernandes HJR, Caffrey TM, Meyer M, Cowley SA, Larsen MR, Wade-Martins R. Post-translational proteomics platform identifies neurite outgrowth impairments in Parkinson's disease GBA-N370S dopamine neurons. Cell Rep 2023; 42:112180. [PMID: 36870058 DOI: 10.1016/j.celrep.2023.112180] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/04/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Variants at the GBA locus, encoding glucocerebrosidase, are the strongest common genetic risk factor for Parkinson's disease (PD). To understand GBA-related disease mechanisms, we use a multi-part-enrichment proteomics and post-translational modification (PTM) workflow, identifying large numbers of dysregulated proteins and PTMs in heterozygous GBA-N370S PD patient induced pluripotent stem cell (iPSC) dopamine neurons. Alterations in glycosylation status show disturbances in the autophagy-lysosomal pathway, which concur with upstream perturbations in mammalian target of rapamycin (mTOR) activation in GBA-PD neurons. Several native and modified proteins encoded by PD-associated genes are dysregulated in GBA-PD neurons. Integrated pathway analysis reveals impaired neuritogenesis in GBA-PD neurons and identify tau as a key pathway mediator. Functional assays confirm neurite outgrowth deficits and identify impaired mitochondrial movement in GBA-PD neurons. Furthermore, pharmacological rescue of glucocerebrosidase activity in GBA-PD neurons improves the neurite outgrowth deficit. Overall, this study demonstrates the potential of PTMomics to elucidate neurodegeneration-associated pathways and potential drug targets in complex disease models.
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Affiliation(s)
- Helle Bogetofte
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense C, Denmark; Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Brent J Ryan
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK.
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Sissel I Schmidt
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense C, Denmark
| | - Dana L E Vergoossen
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Mike B Barnkob
- Centre for Cellular Immunotherapy of Haematological Cancer Odense (CITCO), Department of Clinical Immunology, Odense University Hospital, University of Southern Denmark, 5000 Odense C, Denmark
| | - Lisa N Kiani
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Uroosa Chughtai
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - William McGuinness
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Ricardo Márquez-Gómez
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Vowles
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Fiona S Bunn
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Janine Brandes
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Peter Kilfeather
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Jack P Connor
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Hugo J R Fernandes
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Tara M Caffrey
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense C, Denmark; Department of Neurology, Odense University Hospital, 5000 Odense C, Denmark
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK.
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27
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Colussi C, Aceto G, Ripoli C, Bertozzi A, Li Puma DD, Paccosi E, D'Ascenzo M, Grassi C. Cytoplasmic HDAC4 recovers synaptic function in the 3×Tg mouse model of Alzheimer's disease. Neuropathol Appl Neurobiol 2023; 49:e12861. [PMID: 36331820 PMCID: PMC10099707 DOI: 10.1111/nan.12861] [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: 05/24/2022] [Revised: 08/26/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
AIMS Early dysfunction in Alzheimer's disease (AD) is characterised by alterations of synapse structure and function leading to dysmorphic neurites, decreased spine density, impaired synaptic plasticity and cognitive deficits. The class II member HDAC4, which recently emerged as a crucial factor in shaping synaptic plasticity and memory, was found to be altered in AD. We investigated how the modulation of HDAC4 may contribute to counteracting AD pathogenesis. METHODS Using a cytoplasmic HDAC4 mutant (HDAC4SD ), we studied the recovery of synaptic function in hippocampal tissue and primary neurons from the triple-transgenic mouse model of AD (3×Tg-AD). RESULTS Here, we report that in wild-type mice, HDAC4 is localised at synapses and interacts with postsynaptic proteins, whereas in the 3×Tg-AD, it undergoes nuclear import, reducing its interaction with synaptic proteins. Of note, HDAC4 delocalisation was induced by both amyloid-β and tau accumulation. Overexpression of the HDAC4SD mutant in CA1 pyramidal neurons of organotypic hippocampal slices obtained from 3×Tg-AD mice increased dendritic length and promoted the enrichment of N-cadherin, GluA1, PSD95 and CaMKII proteins at the synaptic level compared with AD neurons transfected with the empty vector. Moreover, HDAC4 overexpression recovered the level of SUMO2/3ylation of PSD95 in AD hippocampal tissue, and in AD organotypic hippocampal slices, the HDAC4SD rescued spine density and synaptic transmission. CONCLUSIONS These results highlight a new role of cytoplasmic HDAC4 in providing a structural and enzymatic regulation of postsynaptic proteins. Our findings suggest that controlling HDAC4 localisation may represent a promising strategy to rescue synaptic function in AD, potentially leading to memory improvement.
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Affiliation(s)
- Claudia Colussi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giuseppe Aceto
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Cristian Ripoli
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alessia Bertozzi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy
| | - Domenica Donatella Li Puma
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Elena Paccosi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy
| | - Marcello D'Ascenzo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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28
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Wu S, Hernandez Villegas NC, Sirkis DW, Thomas-Wright I, Wade-Martins R, Schekman R. Unconventional secretion of α-synuclein mediated by palmitoylated DNAJC5 oligomers. eLife 2023; 12:e85837. [PMID: 36626307 PMCID: PMC9876576 DOI: 10.7554/elife.85837] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Alpha-synuclein (α-syn), a major component of Lewy bodies found in Parkinson's disease (PD) patients, has been found exported outside of cells and may mediate its toxicity via cell-to-cell transmission. Here, we reconstituted soluble, monomeric α-syn secretion by the expression of DnaJ homolog subfamily C member 5 (DNAJC5) in HEK293T cells. DNAJC5 undergoes palmitoylation and anchors on the membrane. Palmitoylation is essential for DNAJC5-induced α-syn secretion, and the secretion is not limited by substrate size or unfolding. Cytosolic α-syn is actively translocated and sequestered in an endosomal membrane compartment in a DNAJC5-dependent manner. Reduction of α-syn secretion caused by a palmitoylation-deficient mutation in DNAJC5 can be reversed by a membrane-targeting peptide fusion-induced oligomerization of DNAJC5. The secretion of endogenous α-syn mediated by DNAJC5 is also found in a human neuroblastoma cell line, SH-SY5Y, differentiated into neurons in the presence of retinoic acid, and in human-induced pluripotent stem cell-derived midbrain dopamine neurons. We propose that DNAJC5 forms a palmitoylated oligomer to accommodate and export α-syn.
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Affiliation(s)
- Shenjie Wu
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | | | - Daniel W Sirkis
- Memory and Aging Center, Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Iona Thomas-Wright
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Richard Wade-Martins
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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29
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Wakhloo D, Oberhauser J, Madira A, Mahajani S. From cradle to grave: neurogenesis, neuroregeneration and neurodegeneration in Alzheimer's and Parkinson's diseases. Neural Regen Res 2022; 17:2606-2614. [PMID: 35662189 PMCID: PMC9165389 DOI: 10.4103/1673-5374.336138] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/16/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022] Open
Abstract
Two of the most common neurodegenerative disorders - Alzheimer's and Parkinson's diseases - are characterized by synaptic dysfunction and degeneration that culminate in neuronal loss due to abnormal protein accumulation. The intracellular aggregation of hyper-phosphorylated tau and the extracellular aggregation of amyloid beta plaques form the basis of Alzheimer's disease pathology. The major hallmark of Parkinson's disease is the loss of dopaminergic neurons in the substantia nigra pars compacta, following the formation of Lewy bodies, which consists primarily of alpha-synuclein aggregates. However, the discrete mechanisms that contribute to neurodegeneration in these disorders are still poorly understood. Both neuronal loss and impaired adult neurogenesis have been reported in animal models of these disorders. Yet these findings remain subject to frequent debate due to a lack of conclusive evidence in post mortem brain tissue from human patients. While some publications provide significant findings related to axonal regeneration in Alzheimer's and Parkinson's diseases, they also highlight the limitations and obstacles to the development of neuroregenerative therapies. In this review, we summarize in vitro and in vivo findings related to neurogenesis, neuroregeneration and neurodegeneration in the context of Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Debia Wakhloo
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jane Oberhauser
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Angela Madira
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Sameehan Mahajani
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
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30
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Bancroft EA, De La Mora M, Pandey G, Zarate SM, Srinivasan R. Extracellular S100B inhibits A-type voltage-gated potassium currents and increases L-type voltage-gated calcium channel activity in dopaminergic neurons. Glia 2022; 70:2330-2347. [PMID: 35916350 PMCID: PMC10738449 DOI: 10.1002/glia.24254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/11/2022]
Abstract
Parkinson's disease (PD) is associated with an increase in secreted S100B within the midbrain and cerebrospinal fluid. In addition, S100B overexpression in mice accelerates the loss of substantia nigra pars compacta dopaminergic (DA) neurons, suggesting a role for this protein in PD pathogenesis. We found that in the mouse SNc, S100B labeled astrocytic processes completely envelop the somata of tyrosine hydroxylase (TH) expressing DA neurons only in male mice. These data suggest that an increase in S100B secretion by astrocytes within the midbrain could play a role in DA dysfunction during early PD. We therefore asked if acute exposure to extracellular S100B alters the activity of identified TH expressing DA neurons in primary mouse midbrain cultures. Acute exposure to 50 pM S100B specifically inhibited A-type voltage-gated potassium currents in TH+ , but not TH- neurons. This was accompanied by ~2-fold increases in the frequency of both intrinsic firing, as well as L-type voltage-gated calcium channel (VGCC)-mediated calcium fluxes only in TH+ neurons. Further, exposure to 100 μM 4-aminopyridine (4-AP), an A-type voltage-gated potassium channel inhibitor, mimicked the S100B mediated increase in intrinsic firing and L-type VGCC-mediated calcium fluxes in TH+ neurons. Taken together, our finding that extracellular S100B alters the activity of native DA neurons via an inhibition of A-type voltage-gated potassium channels has important implications for understanding the pathophysiology of early PD.
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Affiliation(s)
- Eric A. Bancroft
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Martha De La Mora
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Gauri Pandey
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
- Texas A&M Institute for Neuroscience (TAMIN), College Station, Texas, USA
| | - Sara M. Zarate
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Rahul Srinivasan
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
- Texas A&M Institute for Neuroscience (TAMIN), College Station, Texas, USA
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31
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Vijayaragavan K, Cannon BJ, Tebaykin D, Bossé M, Baranski A, Oliveria JP, Bukhari SA, Mrdjen D, Corces MR, McCaffrey EF, Greenwald NF, Sigal Y, Marquez D, Khair Z, Bruce T, Goldston M, Bharadwaj A, Montine KS, Angelo RM, Montine TJ, Bendall SC. Single-cell spatial proteomic imaging for human neuropathology. Acta Neuropathol Commun 2022; 10:158. [PMID: 36333818 PMCID: PMC9636771 DOI: 10.1186/s40478-022-01465-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimer's disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves broadly as a methodology for spatial proteomic analysis of archival human neuropathology. TEASER: Multiplex Ion beam Imaging enables deep spatial phenotyping of human neuropathology-associated cellular and disease features.
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Affiliation(s)
| | - Bryan J Cannon
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bossé
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - J P Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Syed A Bukhari
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Erin F McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Diana Marquez
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Trevor Bruce
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mako Goldston
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kathleen S Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - R Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
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32
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Cuevas-Diaz Duran R, González-Orozco JC, Velasco I, Wu JQ. Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. Front Cell Dev Biol 2022; 10:884748. [PMID: 36353512 PMCID: PMC9637968 DOI: 10.3389/fcell.2022.884748] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/06/2022] [Indexed: 08/10/2023] Open
Abstract
Neurodegenerative diseases affect millions of people worldwide and there are currently no cures. Two types of common neurodegenerative diseases are Alzheimer's (AD) and Parkinson's disease (PD). Single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq) have become powerful tools to elucidate the inherent complexity and dynamics of the central nervous system at cellular resolution. This technology has allowed the identification of cell types and states, providing new insights into cellular susceptibilities and molecular mechanisms underlying neurodegenerative conditions. Exciting research using high throughput scRNA-seq and snRNA-seq technologies to study AD and PD is emerging. Herein we review the recent progress in understanding these neurodegenerative diseases using these state-of-the-art technologies. We discuss the fundamental principles and implications of single-cell sequencing of the human brain. Moreover, we review some examples of the computational and analytical tools required to interpret the extensive amount of data generated from these assays. We conclude by highlighting challenges and limitations in the application of these technologies in the study of AD and PD.
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Affiliation(s)
| | | | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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33
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van den Hurk M, Lau S, Marchetto MC, Mertens J, Stern S, Corti O, Brice A, Winner B, Winkler J, Gage FH, Bardy C. Druggable transcriptomic pathways revealed in Parkinson's patient-derived midbrain neurons. NPJ Parkinsons Dis 2022; 8:134. [PMID: 36258029 PMCID: PMC9579158 DOI: 10.1038/s41531-022-00400-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Complex genetic predispositions accelerate the chronic degeneration of midbrain substantia nigra neurons in Parkinson’s disease (PD). Deciphering the human molecular makeup of PD pathophysiology can guide the discovery of therapeutics to slow the disease progression. However, insights from human postmortem brain studies only portray the latter stages of PD, and there is a lack of data surrounding molecular events preceding the neuronal loss in patients. We address this gap by identifying the gene dysregulation of live midbrain neurons reprogrammed in vitro from the skin cells of 42 individuals, including sporadic and familial PD patients and matched healthy controls. To minimize bias resulting from neuronal reprogramming and RNA-seq methods, we developed an analysis pipeline integrating PD transcriptomes from different RNA-seq datasets (unsorted and sorted bulk vs. single-cell and Patch-seq) and reprogramming strategies (induced pluripotency vs. direct conversion). This PD cohort’s transcriptome is enriched for human genes associated with known clinical phenotypes of PD, regulation of locomotion, bradykinesia and rigidity. Dysregulated gene expression emerges strongest in pathways underlying synaptic transmission, metabolism, intracellular trafficking, neural morphogenesis and cellular stress/immune responses. We confirmed a synaptic impairment with patch-clamping and identified pesticides and endoplasmic reticulum stressors as the most significant gene-chemical interactions in PD. Subsequently, we associated the PD transcriptomic profile with candidate pharmaceuticals in a large database and a registry of current clinical trials. This study highlights human transcriptomic pathways that can be targeted therapeutically before the irreversible neuronal loss. Furthermore, it demonstrates the preclinical relevance of unbiased large transcriptomic assays of reprogrammed patient neurons.
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Affiliation(s)
- Mark van den Hurk
- grid.430453.50000 0004 0565 2606South Australian Health and Medical Research Institute (SAHMRI), Laboratory for Human Neurophysiology and Genetics, Adelaide, SA Australia
| | - Shong Lau
- grid.250671.70000 0001 0662 7144Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA USA
| | - Maria C. Marchetto
- grid.266100.30000 0001 2107 4242Department of Anthropology, University of California San Diego, La Jolla, CA USA
| | - Jerome Mertens
- grid.250671.70000 0001 0662 7144Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA USA ,grid.5771.40000 0001 2151 8122Neural Aging Laboratory, Institute of Molecular Biology, CMBI, Leopold-Franzens-University Innsbruck, Innsbruck, Tyrol Austria
| | - Shani Stern
- grid.250671.70000 0001 0662 7144Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA USA ,grid.18098.380000 0004 1937 0562Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Olga Corti
- grid.425274.20000 0004 0620 5939Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, DMU BioGeM, Paris, France
| | - Alexis Brice
- grid.425274.20000 0004 0620 5939Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, DMU BioGeM, Paris, France
| | - Beate Winner
- grid.411668.c0000 0000 9935 6525Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany ,grid.411668.c0000 0000 9935 6525Center of Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany ,grid.411668.c0000 0000 9935 6525Department of Molecular Neurology, University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Winkler
- grid.411668.c0000 0000 9935 6525Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany ,grid.411668.c0000 0000 9935 6525Center of Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany ,grid.411668.c0000 0000 9935 6525Department of Molecular Neurology, University Hospital Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Fred H. Gage
- grid.250671.70000 0001 0662 7144Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA USA
| | - Cedric Bardy
- grid.430453.50000 0004 0565 2606South Australian Health and Medical Research Institute (SAHMRI), Laboratory for Human Neurophysiology and Genetics, Adelaide, SA Australia ,grid.1014.40000 0004 0367 2697Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA Australia
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Sheta R, Teixeira M, Idi W, Pierre M, de Rus Jacquet A, Emond V, Zorca CE, Vanderperre B, Durcan TM, Fon EA, Calon F, Chahine M, Oueslati A. Combining NGN2 programming and dopaminergic patterning for a rapid and efficient generation of hiPSC-derived midbrain neurons. Sci Rep 2022; 12:17176. [PMID: 36229560 PMCID: PMC9562300 DOI: 10.1038/s41598-022-22158-4] [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: 01/27/2022] [Accepted: 10/10/2022] [Indexed: 01/04/2023] Open
Abstract
The use of human derived induced pluripotent stem cells (hiPSCs) differentiated to dopaminergic (DA) neurons offers a valuable experimental model to decorticate the cellular and molecular mechanisms of Parkinson's disease (PD) pathogenesis. However, the existing approaches present with several limitations, notably the lengthy time course of the protocols and the high variability in the yield of DA neurons. Here we report on the development of an improved approach that combines neurogenin-2 programming with the use of commercially available midbrain differentiation kits for a rapid, efficient, and reproducible directed differentiation of hiPSCs to mature and functional induced DA (iDA) neurons, with minimum contamination by other brain cell types. Gene expression analysis, associated with functional characterization examining neurotransmitter release and electrical recordings, support the functional identity of the iDA neurons to A9 midbrain neurons. iDA neurons showed selective vulnerability when exposed to 6-hydroxydopamine, thus providing a viable in vitro approach for modeling PD and for the screening of small molecules with neuroprotective proprieties.
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Affiliation(s)
- Razan Sheta
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Maxime Teixeira
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Walid Idi
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Marion Pierre
- grid.23856.3a0000 0004 1936 8390CERVO Brain Research Center, 2601, rue de La Canardière, Quebec City, Canada
| | - Aurelie de Rus Jacquet
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Vincent Emond
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada
| | - Cornelia E. Zorca
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Benoît Vanderperre
- grid.38678.320000 0001 2181 0211Département des sciences biologiques, Université du Québec à Montréal, Montreal, QC Canada ,Centre d’Excellence en Recherche sur les Maladies Orphelines – Fondation Courtois (CERMO-FC), Montreal, Canada
| | - Thomas M. Durcan
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Edward A. Fon
- grid.14709.3b0000 0004 1936 8649McGill Parkinson Program and Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Frédéric Calon
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Faculty of Pharmacy, Université Laval, Quebec City, Canada
| | - Mohamed Chahine
- grid.23856.3a0000 0004 1936 8390CERVO Brain Research Center, 2601, rue de La Canardière, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Abid Oueslati
- grid.411081.d0000 0000 9471 1794CHU de Québec Research Center, Axe Neurosciences, Quebec City, Canada ,grid.23856.3a0000 0004 1936 8390Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
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Drouin-Ouellet J, Legault EM, Nilsson F, Pircs K, Bouquety J, Petit F, Shrigley S, Birtele M, Pereira M, Storm P, Sharma Y, Bruzelius A, Vuono R, Kele M, Stoker TB, Ottosson DR, Falk A, Jakobsson J, Barker RA, Parmar M. Age-related pathological impairments in directly reprogrammed dopaminergic neurons derived from patients with idiopathic Parkinson's disease. Stem Cell Reports 2022; 17:2203-2219. [PMID: 36150382 PMCID: PMC9561608 DOI: 10.1016/j.stemcr.2022.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 12/23/2022] Open
Abstract
We have developed an efficient approach to generate functional induced dopaminergic (DA) neurons from adult human dermal fibroblasts. When performing DA neuronal conversion of patient fibroblasts with idiopathic Parkinson's disease (PD), we could specifically detect disease-relevant pathology in these cells. We show that the patient-derived neurons maintain age-related properties of the donor and exhibit lower basal chaperone-mediated autophagy compared with healthy donors. Furthermore, stress-induced autophagy resulted in an age-dependent accumulation of macroautophagic structures. Finally, we show that these impairments in patient-derived DA neurons leads to an accumulation of phosphorylated alpha-synuclein, the classical hallmark of PD pathology. This pathological phenotype is absent in neurons generated from induced pluripotent stem cells from the same patients. Taken together, our results show that direct neural reprogramming can be used for obtaining patient-derived DA neurons, which uniquely function as a cellular model to study age-related pathology relevant to idiopathic PD.
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Affiliation(s)
| | - Emilie M Legault
- Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Fredrik Nilsson
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Karolina Pircs
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Julie Bouquety
- Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Florence Petit
- Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Shelby Shrigley
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Marcella Birtele
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Maria Pereira
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Petter Storm
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Yogita Sharma
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Andreas Bruzelius
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Romina Vuono
- Wellcome-MRC Cambridge Stem Cell Institute & John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Forvie Site, Cambridge CB2 0PY, UK; Medway School of Pharmacy, University of Kent, Chatham Maritime, Chatham ME4 4TB, UK
| | - Malin Kele
- Department of Neuroscience, Karolinska institutet, Stockholm, Sweden
| | - Thomas B Stoker
- Wellcome-MRC Cambridge Stem Cell Institute & John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Forvie Site, Cambridge CB2 0PY, UK
| | - Daniella Rylander Ottosson
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska institutet, Stockholm, Sweden
| | - Johan Jakobsson
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden
| | - Roger A Barker
- Wellcome-MRC Cambridge Stem Cell Institute & John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Forvie Site, Cambridge CB2 0PY, UK
| | - Malin Parmar
- Department of Experimental Medical Science, Wallenberg Neuroscience Center, Division of Neurobiology and Lund Stem Cell Center, Lund University, BMC A11 and B10, S-221 84 Lund, Sweden.
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Kumar A, Rhee M. Transcriptomic networks of gba3 governing specification of the dopaminergic neurons in zebrafish embryos. Genes Genomics 2022; 44:1543-1554. [PMID: 36181626 DOI: 10.1007/s13258-022-01317-x] [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: 12/27/2021] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Molecular networks associated with dopaminergic (DA) neurogenesis remain undefined within mammalian models. To address this issue, the transient zebrafish model lmx1al: EGFP was generated, which expresses GFP in the DA precursor cells as well as in the DA neurons of the ventral diencephalon (VD). We found that the novel pseudogene gba3 has not been well studied in zebrafish neurogenesis. OBJECTIVE Crucial networks associated with gba3 transcripts were investigated because the biological functions of these networks have not been reported in DA neurogenesis in zebrafish. METHODS RNA isolation and sequencing were employed with GFP-expressing cells from 20-, 22-, and 24 h post-fertilization (hpf), while subsequent transcriptomic analysis generated differentially expressed genes with DA neurogenesis (DEG-DA) list. Hierarchical cluster analysis provided absolute guidance for the collection of gba3, an essential transcript that is strictly spatiotemporally expressed during DA neurogenesis, which was proven with whole-mount in situ hybridization (WISH) and knockdown and rescue of the gba3 transcripts in zebrafish embryos. RESULTS The gba3 transcripts were restricted to the midbrain at 24 hpf and the midbrain and pectoral fins at 30 hpf in zebrafish embryos. Functional studies with knockdown of gba3 found a diminished state in the midbrain and midbrain-hindbrain boundary (MHB) and an underdeveloped condition in the anteroposterior and dorsolateral axis relative to the wild type (WT) at 24 hpf. However, it was recovered after forced expression of gba3 transcripts at 24 hpf. Molecular markers for the DA precursors and mature neurons lmx1al, nurr1, th, and pitx3 were analyzed in the gba3 MOs. The levels of transcripts lmx1al, nurr1, and th were significantly reduced in the midbrain ventral diencephalon (VD) and hindbrain of gba3 morphants compared to the WT at 24 hpf, while expression patterns of pitx3 transcripts showed no differences in the identical regions between gba3 MOs and the controls. CONCLUSIONS We discuss transcriptional networks in which transcripts of gba3 plausibly govern the specification of dopaminergic neurogenesis in zebrafish embryos.
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Affiliation(s)
- Ajeet Kumar
- Department of Biological Sciences, Graduate School, BK21 plus program, Chungnam National University, Daejeon, 34134, South Korea. .,Laboratory of Neural Stem Cell Biology, Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea.
| | - Myungchull Rhee
- Department of Biological Sciences, Graduate School, BK21 plus program, Chungnam National University, Daejeon, 34134, South Korea.
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Arena G, Sharma K, Agyeah G, Krüger R, Grünewald A, Fitzgerald JC. Neurodegeneration and Neuroinflammation in Parkinson's Disease: a Self-Sustained Loop. Curr Neurol Neurosci Rep 2022; 22:427-440. [PMID: 35674870 PMCID: PMC9174445 DOI: 10.1007/s11910-022-01207-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Neuroinflammation plays a significant role in Parkinson's disease (PD) etiology along with mitochondrial dysfunction and impaired proteostasis. In this context, mechanisms related to immune response can act as modifiers at different steps of the neurodegenerative process and justify the growing interest in anti-inflammatory agents as potential disease-modifying treatments in PD. The discovery of inherited gene mutations in PD has allowed researchers to develop cellular and animal models to study the mechanisms of the underlying biology, but the original cause of neuroinflammation in PD is still debated to date. RECENT FINDINGS Cell autonomous alterations in neuronal cells, including mitochondrial damage and protein aggregation, could play a role, but recent findings also highlighted the importance of intercellular communication at both local and systemic level. This has given rise to debate about the role of non-neuronal cells in PD and reignited intense research into the gut-brain axis and other non-neuronal interactions in the development of the disease. Whatever the original trigger of neuroinflammation in PD, what appears quite clear is that the aberrant activation of glial cells and other components of the immune system creates a vicious circle in which neurodegeneration and neuroinflammation nourish each other. In this review, we will provide an up-to-date summary of the main cellular alterations underlying neuroinflammation in PD, including those induced by environmental factors (e.g. the gut microbiome) and those related to the genetic background of affected patients. Starting from the lesson provided by familial forms of PD, we will discuss pathophysiological mechanisms linked to inflammation that could also play a role in idiopathic forms. Finally, we will comment on the potential clinical translatability of immunobiomarkers identified in PD patient cohorts and provide an update on current therapeutic strategies aimed at overcoming or preventing inflammation in PD.
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Affiliation(s)
- G Arena
- Luxembourg Center for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - K Sharma
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - G Agyeah
- Luxembourg Center for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - R Krüger
- Luxembourg Center for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
| | - A Grünewald
- Luxembourg Center for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - J C Fitzgerald
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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A versatile fluorescence-quenched substrate for quantitative measurement of glucocerebrosidase activity within live cells. Proc Natl Acad Sci U S A 2022; 119:e2200553119. [PMID: 35858317 PMCID: PMC9304032 DOI: 10.1073/pnas.2200553119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Loss of activity of the lysosomal glycosidase β-glucocerebrosidase (GCase) causes the lysosomal storage disease Gaucher disease (GD) and has emerged as the greatest genetic risk factor for the development of both Parkinson disease (PD) and dementia with Lewy bodies. There is significant interest into how GCase dysfunction contributes to these diseases, however, progress toward a full understanding is complicated by presence of endogenous cellular factors that influence lysosomal GCase activity. Indeed, such factors are thought to contribute to the high degree of variable penetrance of GBA mutations among patients. Robust methods to quantitatively measure GCase activity within lysosomes are therefore needed to advance research in this area, as well as to develop clinical assays to monitor disease progression and assess GCase-directed therapeutics. Here, we report a selective fluorescence-quenched substrate, LysoFQ-GBA, which enables measuring endogenous levels of lysosomal GCase activity within living cells. LysoFQ-GBA is a sensitive tool for studying chemical or genetic perturbations of GCase activity using either fluorescence microscopy or flow cytometry. We validate the quantitative nature of measurements made with LysoFQ-GBA using various cell types and demonstrate that it accurately reports on both target engagement by GCase inhibitors and the GBA allele status of cells. Furthermore, through comparisons of GD, PD, and control patient-derived tissues, we show there is a close correlation in the lysosomal GCase activity within monocytes, neuronal progenitor cells, and neurons. Accordingly, analysis of clinical blood samples using LysoFQ-GBA may provide a surrogate marker of lysosomal GCase activity in neuronal tissue.
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Li D, Huang LT, Zhang CP, Li Q, Wang JH. Insights Into the Role of Platelet-Derived Growth Factors: Implications for Parkinson’s Disease Pathogenesis and Treatment. Front Aging Neurosci 2022; 14:890509. [PMID: 35847662 PMCID: PMC9283766 DOI: 10.3389/fnagi.2022.890509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease (PD), the second most common neurodegenerative disease after Alzheimer’s disease, commonly occurs in the elderly population, causing a significant medical and economic burden to the aging society worldwide. At present, there are few effective methods that achieve satisfactory clinical results in the treatment of PD. Platelet-derived growth factors (PDGFs) and platelet-derived growth factor receptors (PDGFRs) are important neurotrophic factors that are expressed in various cell types. Their unique structures allow for specific binding that can effectively regulate vital functions in the nervous system. In this review, we summarized the possible mechanisms by which PDGFs/PDGFRs regulate the occurrence and development of PD by affecting oxidative stress, mitochondrial function, protein folding and aggregation, Ca2+ homeostasis, and cell neuroinflammation. These modes of action mainly depend on the type and distribution of PDGFs in different nerve cells. We also summarized the possible clinical applications and prospects for PDGF in the treatment of PD, especially in genetic treatment. Recent advances have shown that PDGFs have contradictory roles within the central nervous system (CNS). Although they exert neuroprotective effects through multiple pathways, they are also associated with the disruption of the blood–brain barrier (BBB). Our recommendations based on our findings include further investigation of the contradictory neurotrophic and neurotoxic effects of the PDGFs acting on the CNS.
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Affiliation(s)
- Dan Li
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Le-Tian Huang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cheng-pu Zhang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Li
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Qiang Li,
| | - Jia-He Wang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Jia-He Wang,
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Ketogenic therapy for Parkinson's disease: A systematic review and synthesis without meta-analysis of animal and human trials. Maturitas 2022; 163:46-61. [PMID: 35714419 DOI: 10.1016/j.maturitas.2022.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The aim of the present systematic review was to assess the efficacy of ketogenic therapy in Parkinson's disease (PD), using all available data from randomized controlled trials (RCTs) on humans and animal studies with PD models. DESIGN Systematic review of in vivo studies. METHODS Studies related to the research question were identified through searches in PubMed, Cochrane Central Register of Controlled Trials (CENTRAL), Scopus, clinicaltrials.gov and the gray literature, from inception until November 2021. Rayyan was employed to screen and identify all studies fulfilling the inclusion criteria. Cochrane's revised Risk of Bias 2.0 and SYRCLE tools evaluated bias in RCTs and animal studies, respectively. An effect direction plot was developed to synthesize the evidence of the RCTs. RESULTS Twelve studies were identified and included in the qualitative synthesis (4 RCTs and 8 animal trials). Interventions included ketogenic diets (KDs), supplementation with medium-chain triglyceride (MCT) oil, caprylic acid administration and ketone ester drinks. The animal research used zebrafish and rodents, and PD was toxin-induced. Based on the available RCTs, ketogenic therapy does not improve motor coordination and functioning, cognitive impairment, anthropometrics, blood lipids and glycemic control, exercise performance or voice disorders in patients with PD. The evidence is scattered and heterogenous, with single trials assessing different outcomes; thus, a synthesis of the evidence cannot be conclusive regarding the efficacy of ketogenic therapy. On the other hand, animal studies tend to demonstrate more promising results, with marked improvements in locomotor activity, dopaminergic activity, redox status, and inflammatory markers. CONCLUSIONS Although animal studies indicate promising results, research on the effect of ketogenic therapy in PD is still in its infancy, with RCTs conducted on humans being heterogeneous and lacking PD-specific outcomes. More studies are required to recommend or refute the use of ketogenic therapy in PD.
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Yoshikawa M, Ishikawa C, Li H, Kudo T, Shiba D, Shirakawa M, Murtani M, Takahashi S, Aizawa S, Shiga T. Comparing effects of microgravity and amyotrophic lateral sclerosis in the mouse ventral lumbar spinal cord. Mol Cell Neurosci 2022; 121:103745. [PMID: 35660087 DOI: 10.1016/j.mcn.2022.103745] [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: 03/14/2022] [Revised: 05/24/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022] Open
Abstract
Microgravity (MG) exposure and motor neuron diseases, such as amyotrophic lateral sclerosis (ALS), lead to motor deficits, including muscle atrophy and loss of neuronal activity. Abnormalities in motor neurons and muscles caused by MG exposure can be recovered by subsequent ground exercise. In contrast, the degeneration that occurs in ALS is irreversible. A common phenotype between MG exposure and ALS pathology is motor system abnormality, but the causes may be different. In this study, to elucidate the motor system that is affected by each condition, we investigated the effects of MG and the human SOD1 ALS mutation on gene expression in various cell types of the mouse ventral lumbar spinal cord, which is rich in motor neurons innervating the lower limb. To identify cell types affected by MG or ALS pathogenesis, we analyzed differentially expressed genes with known cell-type markers, which were determined from previous single-cell studies of the spinal cord in MG-exposed and SOD1G93A mice, an ALS mouse model. Differentially expressed genes were observed in MG mice in various spinal cord cell types, including neurons, microglia, astrocytes, oligodendrocytes, oligodendrocyte precursor cells, meningeal cells/Schwann cells, and vascular cells. We also examined neuronal populations in the spinal cord. Gene expression in putative excitatory and inhibitory neurons changed more than that in cholinergic motor neurons of the spinal cord in both MG and SOD1G93A mice. Many putative neuron types, especially visceral motor neurons, and axon initial segments (AIS) were affected in MG mice. In contrast, the effect on neurons and AIS in SOD1G93A mice was slight at P30 but progressed with aging. Interestingly, changes in dopaminergic system-related genes were specifically altered in the spinal cord of MG mice. These results indicate that MG and ALS pathology in various cell types contribute to motor neuron degeneration. Furthermore, there were more alterations in neurons in MG-exposed mice than in SOD1G93A mice. A large number of differentially expressed genes (DEGs) in MG mice represent more than SOD1G93A mice with ALS pathology. Elucidation of MG pathogenesis may provide more insight into the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Masaaki Yoshikawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan.
| | - Chihiro Ishikawa
- Laboratory of Neurobiology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Haiyan Li
- Laboratory of Neurobiology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takashi Kudo
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Dai Shiba
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Ibaraki 305-8505, Japan
| | - Masaki Shirakawa
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Ibaraki 305-8505, Japan
| | - Masafumi Murtani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Shin Aizawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Takashi Shiga
- Laboratory of Neurobiology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan; Department of Neurobiology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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Zou J, Deng F, Wang M, Zhang Z, Liu Z, Zhang X, Hua R, Chen K, Zou X, Hao J. scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data. Brief Bioinform 2022; 23:6590434. [PMID: 35598331 DOI: 10.1093/bib/bbac180] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
Differential expression (DE) gene detection in single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data is a key step to understand the biological question investigated. Filtering genes is suggested to improve the performance of DE methods, but the influence of filtering genes has not been demonstrated. Furthermore, the optimal methods for different scRNA-seq datasets are divergent, and different datasets should benefit from data-specific DE gene detection strategies. However, existing tools did not take gene filtering into consideration. There is a lack of metrics for evaluating the optimal method on experimental datasets. Based on two new metrics, we propose single-cell Consensus Optimization of Differentially Expressed gene detection, an R package to automatically optimize DE gene detection for each experimental scRNA-seq dataset.
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Affiliation(s)
- Jiawei Zou
- School of Life Sciences and Biotechnology, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fulan Deng
- School of Materials Science and Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Miaochen Wang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth Peopleȉs Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology
| | - Zhen Zhang
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth Peopleȉs Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology
| | - Zheqi Liu
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth Peopleȉs Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology
| | - Xiaobin Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Cardiovascular Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Hua
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xin Zou
- Jinshan Hospital Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
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Li Y, Gu Z, Lin S, Chen L, Dzreyan V, Eid M, Demyanenko S, He B. Histone Deacetylases as Epigenetic Targets for Treating Parkinson's Disease. Brain Sci 2022; 12:672. [PMID: 35625059 PMCID: PMC9140162 DOI: 10.3390/brainsci12050672] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is a chronic progressive neurodegenerative disease that is increasingly becoming a global threat to the health and life of the elderly worldwide. Although there are some drugs clinically available for treating PD, these treatments can only alleviate the symptoms of PD patients but cannot completely cure the disease. Therefore, exploring other potential mechanisms to develop more effective treatments that can modify the course of PD is still highly desirable. Over the last two decades, histone deacetylases, as an important group of epigenetic targets, have attracted much attention in drug discovery. This review focused on the current knowledge about histone deacetylases involved in PD pathophysiology and their inhibitors used in PD studies. Further perspectives related to small molecules that can inhibit or degrade histone deacetylases to treat PD were also discussed.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China; (Y.L.); (Z.G.); (S.L.); (L.C.)
| | - Zhicheng Gu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China; (Y.L.); (Z.G.); (S.L.); (L.C.)
| | - Shuxian Lin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China; (Y.L.); (Z.G.); (S.L.); (L.C.)
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China; (Y.L.); (Z.G.); (S.L.); (L.C.)
| | - Valentina Dzreyan
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, Stachki Ave. 194/1, 344090 Rostov-on-Don, Russia; (V.D.); (M.E.)
| | - Moez Eid
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, Stachki Ave. 194/1, 344090 Rostov-on-Don, Russia; (V.D.); (M.E.)
| | - Svetlana Demyanenko
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, Stachki Ave. 194/1, 344090 Rostov-on-Don, Russia; (V.D.); (M.E.)
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China; (Y.L.); (Z.G.); (S.L.); (L.C.)
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44
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Huang J, Liu L, Qin L, Huang H, Li X. Single-Cell Transcriptomics Uncovers Cellular Heterogeneity, Mechanisms, and Therapeutic Targets for Parkinson’s Disease. Front Genet 2022; 13:686739. [PMID: 35601482 PMCID: PMC9114673 DOI: 10.3389/fgene.2022.686739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: This study aimed to exploit cellular heterogeneity for revealing mechanisms and identifying therapeutic targets for Parkinson’s disease (PD) via single-cell transcriptomics. Methods: Single-cell RNA sequencing (scRNA-seq) data on midbrain specimens from PD and healthy individuals were obtained from the GSE157783 dataset. After quality control and preprocessing, the principal component analysis (PCA) was presented. Cells were clustered with the Seurat package. Cell clusters were labeled by matching marker genes and annotations of the brain in the CellMarker database. The ligand–receptor networks were established, and the core cell cluster was selected. Biological functions of differentially expressed genes in core cell clusters were analyzed. Upregulated marker genes were identified between PD and healthy individuals, which were measured in 18 PD patients’ and 18 healthy individuals’ blood specimens through RT-qPCR and Western blotting. Results: The first nine PCs were determined, which can better represent the overall change. Five cell clusters were identified, including oligodendrocytes, astrocytes, neurons, microglial cells, and endothelial cells. Among them, endothelial cells were the core cell cluster in the ligand–receptor network. Marker genes of endothelial cells possessed various biological functions. Among them, five marker genes (ANGPT2, APOD, HSP90AA1, HSPA1A, and PDE1C) were upregulated in PD patients’ than in healthy individuals’ endothelial cells, which were confirmed in PD patients’ than in healthy individuals’ blood specimens. Conclusion: Our findings revealed that the cellular heterogeneity of PD and endothelial cells could play a major role in cell-to-cell communications. Five upregulated marker genes of endothelial cells could be underlying therapeutic targets of PD, which deserve more in-depth clinical research.
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Affiliation(s)
- Jianjun Huang
- Department of Neurology, Youjiang Medical University for Nationalities, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Li Liu, ; Jianjun Huang,
| | - Li Liu
- Department of Cardiology, Youjiang Medical University for Nationalities, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Li Liu, ; Jianjun Huang,
| | - Lingling Qin
- Department of Medical Quality Management, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Hehua Huang
- Department of Anatomy, Youjiang Medical University for Nationalities, Baise, China
| | - Xue Li
- Department of Electrophysiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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45
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Dhanwani R, Lima-Junior JR, Sethi A, Pham J, Williams G, Frazier A, Xu Y, Amara AW, Standaert DG, Goldman JG, Litvan I, Alcalay RN, Peters B, Sulzer D, Arlehamn CSL, Sette A. Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures. NPJ Parkinsons Dis 2022; 8:30. [PMID: 35314697 PMCID: PMC8938520 DOI: 10.1038/s41531-022-00282-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) is a multi-stage neurodegenerative disorder with largely unknown etiology. Recent findings have identified PD-associated autoimmune features including roles for T cells. To further characterize the role of T cells in PD, we performed RNA sequencing on PBMC and peripheral CD4 and CD8 memory T cell subsets derived from PD patients and age-matched healthy controls. When the groups were stratified by their T cell responsiveness to alpha-synuclein (α-syn) as a proxy for an ongoing inflammatory autoimmune response, the study revealed a broad differential gene expression profile in memory T cell subsets and a specific PD associated gene signature. We identified significant enrichment of transcriptomic signatures previously associated with PD, including for oxidative stress, phosphorylation, autophagy of mitochondria, cholesterol metabolism and inflammation, and the chemokine signaling proteins CX3CR1, CCR5, and CCR1. In addition, we identified genes in these peripheral cells that have previously been shown to be involved in PD pathogenesis and expressed in neurons, such as LRRK2, LAMP3, and aquaporin. Together, these findings suggest that features of circulating T cells with α-syn-specific responses in PD patients provide insights into the interactive processes that occur during PD pathogenesis and suggest potential intervention targets.
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Affiliation(s)
- Rekha Dhanwani
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - João Rodrigues Lima-Junior
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ashu Sethi
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Gregory Williams
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yaqian Xu
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, Columbia University, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Amy W Amara
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - David G Standaert
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Jennifer G Goldman
- Shirley Ryan AbilityLab, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Irene Litvan
- Department of Neuroscience, University of California San Diego, La Jolla, CA, 92093, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - David Sulzer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Neurology, Columbia University, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, 10032, USA.,Departments of Psychiatry and Pharmacology, Columbia University, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Cecilia S Lindestam Arlehamn
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA. .,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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46
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Udayar V, Chen Y, Sidransky E, Jagasia R. Lysosomal dysfunction in neurodegeneration: emerging concepts and methods. Trends Neurosci 2022; 45:184-199. [PMID: 35034773 PMCID: PMC8854344 DOI: 10.1016/j.tins.2021.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 02/06/2023]
Abstract
The understanding of lysosomes has come a long way since the initial discovery of their role in degrading cellular waste. The lysosome is now recognized as a highly dynamic organelle positioned at the crossroads of cell signaling, transcription, and metabolism. Underscoring its importance is the observation that, in addition to rare monogenic lysosomal storage disorders, genes regulating lysosomal function are implicated in common sporadic neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Developing therapies for these disorders is particularly challenging, largely due to gaps in knowledge of the underlying molecular and cellular processes. In this review, we discuss technological advances that have propelled deeper understanding of the lysosome in neurodegeneration, from elucidating the functions of lysosome-related disease risk variants at the level of the organelle, cell, and tissue, to the development of disease-specific biological models that recapitulate disease manifestations. Finally, we identify key questions to be addressed to successfully bridge the gap to the clinic.
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Affiliation(s)
- Vinod Udayar
- Roche Pharmaceutical Research and Early Development, Neuroscience and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Yu Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ravi Jagasia
- Roche Pharmaceutical Research and Early Development, Neuroscience and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
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47
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CNS Redox Homeostasis and Dysfunction in Neurodegenerative Diseases. Antioxidants (Basel) 2022; 11:antiox11020405. [PMID: 35204286 PMCID: PMC8869494 DOI: 10.3390/antiox11020405] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022] Open
Abstract
A single paragraph of about 200 words maximum. Neurodegenerative diseases (ND), such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis, pose a global challenge in the aging population due to the lack of treatments for their cure. Despite various disease-specific clinical symptoms, ND have some fundamental common pathological mechanisms involving oxidative stress and neuroinflammation. The present review focuses on the major causes of central nervous system (CNS) redox homeostasis imbalance comprising mitochondrial dysfunction and endoplasmic reticulum (ER) stress. Mitochondrial disturbances, leading to reduced mitochondrial function and elevated reactive oxygen species (ROS) production, are thought to be a major contributor to the pathogenesis of ND. ER dysfunction has been implicated in ND in which protein misfolding evidently causes ER stress. The consequences of ER stress ranges from an increase in ROS production to altered calcium efflux and proinflammatory signaling in glial cells. Both pathological pathways have links to ferroptotic cell death, which has been implicated to play an important role in ND. Pharmacological targeting of these pathological pathways may help alleviate or slow down neurodegeneration.
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48
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Bioengineered models of Parkinson's disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment. Cell Mol Life Sci 2022; 79:78. [PMID: 35044538 PMCID: PMC8908880 DOI: 10.1007/s00018-021-04047-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 01/21/2023]
Abstract
Three-dimensional (3D) in vitro culture systems using human induced pluripotent stem cells (hiPSCs) are useful tools to model neurodegenerative disease biology in physiologically relevant microenvironments. Though many successful biomaterials-based 3D model systems have been established for other neurogenerative diseases, such as Alzheimer's disease, relatively few exist for Parkinson's disease (PD) research. We employed tissue engineering approaches to construct a 3D silk scaffold-based platform for the culture of hiPSC-dopaminergic (DA) neurons derived from healthy individuals and PD patients harboring LRRK2 G2019S or GBA N370S mutations. We then compared results from protein, gene expression, and metabolic analyses obtained from two-dimensional (2D) and 3D culture systems. The 3D platform enabled the formation of dense dopamine neuronal network architectures and developed biological profiles both similar and distinct from 2D culture systems in healthy and PD disease lines. PD cultures developed in 3D platforms showed elevated levels of α-synuclein and alterations in purine metabolite profiles. Furthermore, computational network analysis of transcriptomic networks nominated several novel molecular interactions occurring in neurons from patients with mutations in LRRK2 and GBA. We conclude that the brain-like 3D system presented here is a realistic platform to interrogate molecular mechanisms underlying PD biology.
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49
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Khan AH, Lee LK, Smith DJ. Single-cell analysis of gene expression in the substantia nigra pars compacta of a pesticide-induced mouse model of Parkinson's disease. Transl Neurosci 2022; 13:255-269. [PMID: 36117858 PMCID: PMC9438968 DOI: 10.1515/tnsci-2022-0237] [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: 05/26/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022] Open
Abstract
Exposure to pesticides in humans increases the risk of Parkinson’s disease (PD), but the mechanisms remain poorly understood. To elucidate these pathways, we dosed C57BL/6J mice with a combination of the pesticides maneb and paraquat. Behavioral analysis revealed motor deficits consistent with PD. Single-cell RNA sequencing of substantia nigra pars compacta revealed both cell-type-specific genes and genes expressed differentially between pesticide and control, including Fam241b, Emx2os, Bivm, Gm1439, Prdm15, and Rai2. Neurons had the largest number of significant differentially expressed genes, but comparable numbers were found in astrocytes and less so in oligodendrocytes. In addition, network analysis revealed enrichment in functions related to the extracellular matrix. These findings emphasize the importance of support cells in pesticide-induced PD and refocus our attention away from neurons as the sole agent of this disorder.
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Affiliation(s)
- Arshad H. Khan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Box 951735, 23-151 A CHS, Los Angeles, CA 90095-1735, United States of America
| | - Lydia K. Lee
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-6928, United States of America
| | - Desmond J. Smith
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Box 951735, 23-151 A CHS, Los Angeles, CA 90095-1735, United States of America
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50
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Allen GE, Dhanda AS, Julian LM. Emerging Methods in Modeling Brain Development and Disease with Human Pluripotent Stem Cells. Methods Mol Biol 2022; 2515:319-342. [PMID: 35776361 DOI: 10.1007/978-1-0716-2409-8_20] [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] [Indexed: 06/15/2023]
Abstract
The Nobel Prize-winning discovery that human somatic cells can be readily reprogrammed into pluripotent cells has revolutionized our potential to understand the human brain. The rapid technological progression of this field has made it possible to easily obtain human neural cells and even intact tissues, offering invaluable resources to model human brain development. In this chapter, we present a brief history of hPSC-based approaches to study brain development and then, provide new insights into neurological diseases, focusing on those driven by aberrant cell death. Furthermore, we will shed light on the latest technologies and highlight the methods that researchers can use to employ established hPSC approaches in their research. Our intention is to demonstrate that hPSC-based modeling is a technical approach accessible to all researchers who seek a deeper understanding of the human brain.
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Affiliation(s)
- George E Allen
- Department of Biological Sciences; Centre for Cell Biology, Development, and Disease, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Aaron S Dhanda
- Department of Biological Sciences; Centre for Cell Biology, Development, and Disease, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Lisa M Julian
- Department of Biological Sciences; Centre for Cell Biology, Development, and Disease, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada.
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