1
|
De Pace R, Ghosh S, Ryan VH, Sohn M, Jarnik M, Rezvan Sangsari P, Morgan NY, Dale RK, Ward ME, Bonifacino JS. Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration. Nat Neurosci 2024; 27:1087-1102. [PMID: 38600167 PMCID: PMC11156585 DOI: 10.1038/s41593-024-01619-1] [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: 05/16/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
In neurons, RNA granules are transported along the axon for local translation away from the soma. Recent studies indicate that some of this transport involves hitchhiking of RNA granules on lysosome-related vesicles. In the present study, we leveraged the ability to prevent transport of these vesicles into the axon by knockout of the lysosome-kinesin adaptor BLOC-one-related complex (BORC) to identify a subset of axonal mRNAs that depend on lysosome-related vesicles for transport. We found that BORC knockout causes depletion of a large group of axonal mRNAs mainly encoding ribosomal and mitochondrial/oxidative phosphorylation proteins. This depletion results in mitochondrial defects and eventually leads to axonal degeneration in human induced pluripotent stem cell (iPSC)-derived and mouse neurons. Pathway analyses of the depleted mRNAs revealed a mechanistic connection of BORC deficiency with common neurodegenerative disorders. These results demonstrate that mRNA transport on lysosome-related vesicles is critical for the maintenance of axonal homeostasis and that its failure causes axonal degeneration.
Collapse
Affiliation(s)
- Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mira Sohn
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Paniz Rezvan Sangsari
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Y Morgan
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
2
|
D'Sa K, Guelfi S, Vandrovcova J, Reynolds RH, Zhang D, Hardy J, Botía JA, Weale ME, Taliun SAG, Small KS, Ryten M. Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally. Sci Rep 2023; 13:13874. [PMID: 37620324 PMCID: PMC10449874 DOI: 10.1038/s41598-023-40324-0] [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: 10/07/2022] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Gaining insight into the genetic regulation of gene expression in human brain is key to the interpretation of genome-wide association studies for major neurological and neuropsychiatric diseases. Expression quantitative trait loci (eQTL) analyses have largely been used to achieve this, providing valuable insights into the genetic regulation of steady-state RNA in human brain, but not distinguishing between molecular processes regulating transcription and stability. RNA quantification within cellular fractions can disentangle these processes in cell types and tissues which are challenging to model in vitro. We investigated the underlying molecular processes driving the genetic regulation of gene expression specific to a cellular fraction using allele-specific expression (ASE). Applying ASE analysis to genomic and transcriptomic data from paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control human brains, we demonstrate that a significant proportion of genetic regulation of gene expression occurs post-transcriptionally in the cytoplasm, with genes undergoing this form of regulation more likely to be synaptic. These findings have implications for understanding the structure of gene expression regulation in human brain, and importantly the interpretation of rapidly growing single-nucleus brain RNA-sequencing and eQTL datasets, where cytoplasm-specific regulatory events could be missed.
Collapse
Affiliation(s)
- Karishma D'Sa
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, SE1 1UL, UK
- Department of Clinical and Movement Neurosciences, University College London, London, WC1N 3BG, UK
| | - Sebastian Guelfi
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- Verge Genomics, Tower Pl, South San Francisco, CA, 94080, USA
| | - Jana Vandrovcova
- Dept of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Regina H Reynolds
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
| | - David Zhang
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute at University College London, London, WC1N 3BG, UK
| | - Juan A Botía
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, 30100, Murcia, Spain
| | - Michael E Weale
- Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, SE1 1UL, UK
- Genomics Plc, Oxford, OX1 1JD, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Montréal Heart Institute, Montréal, QC, H1T 1C8, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Mina Ryten
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, WC1N 1EH, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, WC1N 3JH, UK.
| |
Collapse
|
3
|
Yang Z, Yu J, Zhang J, Song H, Ye H, Liu J, Wang N, Che P, Long G, Wang Y, Park J, Ji SJ. Facilitation of axonal transcriptome analysis with quantitative microfluidic devices. LAB ON A CHIP 2023; 23:2217-2227. [PMID: 37067243 DOI: 10.1039/d2lc01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microfluidic chambers are powerful tools for studying axonal mRNA localization and translation in neurons. In addition to specific manipulation and measurements of axons, microfluidic chambers are used for collecting axonal materials to perform axonal transcriptome analysis. However, traditional bipartite and tripartite chambers have limitations either in purity or quantity of collected axons. Here, we improved the design of traditional chambers. Moreover, we developed two new quantitative chambers, multi-compartmental quantitative bipartite chamber (MQBC) and long quantitative tripartite chamber (LQTC). Compared with the traditional chambers, MQBC and LQTC could dramatically increase the efficiency in collecting axonal RNA. Finally, we applied these chambers to do comparative axon transcriptome analysis of different types of neurons. Thus, our newly designed quantitative chambers significantly improve axon collection efficiency and facilitate axonal transcriptome analysis.
Collapse
Affiliation(s)
- Zhuoxuan Yang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jun Yu
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jian Zhang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Huixue Song
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Haixia Ye
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Jianhui Liu
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Nijia Wang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Pengfei Che
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Gaoxin Long
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Yunxuan Wang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jaewon Park
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
- OJeong Resilience Institute (OJERI), Korea University, Seoul, 02841, Korea.
| | - Sheng-Jian Ji
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| |
Collapse
|
4
|
Slota JA, Medina SJ, Frost KL, Booth SA. Neurons and Astrocytes Elicit Brain Region Specific Transcriptional Responses to Prion Disease in the Murine CA1 and Thalamus. Front Neurosci 2022; 16:918811. [PMID: 35651626 PMCID: PMC9149297 DOI: 10.3389/fnins.2022.918811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 01/14/2023] Open
Abstract
Progressive dysfunction and loss of neurons ultimately culminates in the symptoms and eventual fatality of prion disease, yet the pathways and mechanisms that lead to neuronal degeneration remain elusive. Here, we used RNAseq to profile transcriptional changes in microdissected CA1 and thalamus brain tissues from prion infected mice. Numerous transcripts were altered during clinical disease, whereas very few transcripts were reliably altered at pre-clinical time points. Prion altered transcripts were assigned to broadly defined brain cell types and we noted a strong transcriptional signature that was affiliated with reactive microglia and astrocytes. While very few neuronal transcripts were common between the CA1 and thalamus, we described transcriptional changes in both regions that were related to synaptic dysfunction. Using transcriptional profiling to compare how different neuronal populations respond during prion disease may help decipher mechanisms that lead to neuronal demise and should be investigated with greater detail.
Collapse
Affiliation(s)
- Jessy A. Slota
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Sarah J. Medina
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kathy L. Frost
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stephanie A. Booth
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Stephanie A. Booth
| |
Collapse
|
5
|
Savulescu AF, Bouilhol E, Beaume N, Nikolski M. Prediction of RNA subcellular localization: Learning from heterogeneous data sources. iScience 2021; 24:103298. [PMID: 34765919 PMCID: PMC8571491 DOI: 10.1016/j.isci.2021.103298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA subcellular localization has recently emerged as a widespread phenomenon, which may apply to the majority of RNAs. The two main sources of data for characterization of RNA localization are sequence features and microscopy images, such as obtained from single-molecule fluorescent in situ hybridization-based techniques. Although such imaging data are ideal for characterization of RNA distribution, these techniques remain costly, time-consuming, and technically challenging. Given these limitations, imaging data exist only for a limited number of RNAs. We argue that the field of RNA localization would greatly benefit from complementary techniques able to characterize location of RNA. Here we discuss the importance of RNA localization and the current methodology in the field, followed by an introduction on prediction of location of molecules. We then suggest a machine learning approach based on the integration between imaging localization data and sequence-based data to assist in characterization of RNA localization on a transcriptome level.
Collapse
Affiliation(s)
- Anca Flavia Savulescu
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Emmanuel Bouilhol
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Nicolas Beaume
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town,7925 Cape Town, South Africa
| | - Macha Nikolski
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| |
Collapse
|
6
|
Single-molecule mRNA and translation imaging in neurons. Biochem Soc Trans 2021; 49:2221-2227. [PMID: 34495323 DOI: 10.1042/bst20210313] [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: 07/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022]
Abstract
Memory-relevant neuronal plasticity is believed to require local translation of new proteins at synapses. Understanding this process has necessitated the development of tools to visualize mRNA within relevant neuronal compartments. In this review, we summarize the technical developments that now enable mRNA transcripts and their translation to be visualized at single-molecule resolution in both fixed and live cells. These tools include single-molecule fluorescence in situ hybridization (smFISH) to visualize mRNA in fixed cells, MS2/PP7 labelling for live mRNA imaging and SunTag labelling to observe the emergence of nascent polypeptides from a single translating mRNA. The application of these tools in cultured neurons and more recently in whole brains promises to revolutionize our understanding of local translation in the neuronal plasticity that underlies behavioural change.
Collapse
|
7
|
Regulation of mRNA translation in stem cells; links to brain disorders. Cell Signal 2021; 88:110166. [PMID: 34624487 DOI: 10.1016/j.cellsig.2021.110166] [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: 06/06/2021] [Revised: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022]
Abstract
Translational control of gene expression is emerging as a cardinal step in the regulation of protein abundance. Especially for embryonic (ESC) and neuronal stem cells (NSC), regulation of mRNA translation is involved in the maintenance of pluripotency but also differentiation. For neuronal stem cells this regulation is linked to the various neuronal subtypes that arise in the developing brain and is linked to numerous brain disorders. Herein, we review translational control mechanisms in ESCs and NSCs during development and differentiation, and briefly discuss their link to brain disorders.
Collapse
|
8
|
Bhatia TN, Clark RN, Needham PG, Miner KM, Jamenis AS, Eckhoff EA, Abraham N, Hu X, Wipf P, Luk KC, Brodsky JL, Leak RK. Heat Shock Protein 70 as a Sex-Skewed Regulator of α-Synucleinopathy. Neurotherapeutics 2021; 18:2541-2564. [PMID: 34528172 PMCID: PMC8804008 DOI: 10.1007/s13311-021-01114-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2021] [Indexed: 01/01/2023] Open
Abstract
The role of molecular chaperones, such as heat shock protein 70 (Hsp70), is not typically studied as a function of biological sex, but by addressing this gap we might improve our understanding of proteinopathic disorders that predominate in one sex. Therefore, we exposed male or female primary hippocampal cultures to preformed α-synuclein fibrils in a model of early-stage Lewy pathology. We first discovered that two mechanistically distinct inhibitors of Hsp70 function increased phospho-α-synuclein+ inclusions more robustly in male-derived neurons. Because Hsp70 is released into extracellular compartments and may restrict cell-to-cell transmission/amplification of α-synucleinopathy, we then tested the effects of low-endotoxin, exogenous Hsp70 (eHsp70) in primary hippocampal cultures. eHsp70 was taken up by and reduced α-synuclein+ inclusions in cells of both sexes, but pharmacological suppression of Hsp70 function attenuated the inhibitory effect of eHsp70 on perinuclear inclusions only in male neurons. In 20-month-old male mice infused with α-synuclein fibrils in the olfactory bulb, daily intranasal eHsp70 delivery also reduced inclusion numbers and the time to locate buried food. eHsp70 penetrated the limbic system and spinal cord of male mice within 3 h but was cleared within 72 h. Unexpectedly, no evidence of eHsp70 uptake from nose into brain was observed in females. A trend towards higher expression of inducible Hsp70-but not constitutive Hsp70 or Hsp40-was observed in amygdala tissues from male subjects with Lewy body disorders compared to unaffected male controls, supporting the importance of this chaperone in human disease. Women expressed higher amygdalar Hsp70 levels compared to men, regardless of disease status. Together, these data provide a new link between biological sex and a key chaperone that orchestrates proteostasis.
Collapse
Affiliation(s)
- Tarun N Bhatia
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Rachel N Clark
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Patrick G Needham
- Dept. of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristin M Miner
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Anuj S Jamenis
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Elizabeth A Eckhoff
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Nevil Abraham
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Xiaoming Hu
- Dept. of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Wipf
- Dept. of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin C Luk
- Dept. of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey L Brodsky
- Dept. of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rehana K Leak
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA.
| |
Collapse
|
9
|
Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
Collapse
Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| |
Collapse
|
10
|
Nagano S, Araki T. Axonal Transport and Local Translation of mRNA in Neurodegenerative Diseases. Front Mol Neurosci 2021; 14:697973. [PMID: 34194300 PMCID: PMC8236635 DOI: 10.3389/fnmol.2021.697973] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Since neurons have long neurites including axons, it is crucial for the axons to transport many intracellular substances such as proteins and mitochondria in order to maintain their morphology and function. In addition, mRNAs have also been shown to be transported within axons. RNA-binding proteins form complexes with mRNAs, and regulate transport of the mRNAs to axons, as well as locally translate them into proteins. Local translation of mRNAs actively occurs during the development and damage of neurons, and plays an important role in axon elongation, regeneration, and synapse formation. In recent years, it has been reported that impaired axonal transport and local translation of mRNAs may be involved in the pathogenesis of some neurodegenerative diseases. In this review, we discuss the significance of mRNA axonal transport and their local translation in amyotrophic lateral sclerosis/frontotemporal dementia, spinal muscular atrophy, Alzheimer’s disease, and fragile X syndrome.
Collapse
Affiliation(s)
- Seiichi Nagano
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, Japan.,Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| |
Collapse
|
11
|
Facilitating mGluR4 activity reverses the long-term deleterious consequences of chronic morphine exposure in male mice. Neuropsychopharmacology 2021; 46:1373-1385. [PMID: 33349673 PMCID: PMC8136479 DOI: 10.1038/s41386-020-00927-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022]
Abstract
Understanding the neurobiological underpinnings of abstinence from drugs of abuse is critical to allow better recovery and ensure relapse prevention in addicted subjects. By comparing the long-term transcriptional consequences of morphine and cocaine exposure, we identified the metabotropic glutamate receptor subtype 4 (mGluR4) as a promising pharmacological target in morphine abstinence. We evaluated the behavioral and molecular effects of facilitating mGluR4 activity in abstinent mice. Transcriptional regulation of marker genes of medium spiny neurons (MSNs) allowed best discriminating between 4-week morphine and cocaine abstinence in the nucleus accumbens (NAc). Among these markers, Grm4, encoding mGluR4, displayed down-regulated expression in the caudate putamen and NAc of morphine, but not cocaine, abstinent mice. Chronic administration of the mGluR4 positive allosteric modulator (PAM) VU0155041 (2.5 and 5 mg/kg) rescued social behavior, normalized stereotypies and anxiety and blunted locomotor sensitization in morphine abstinent mice. This treatment improved social preference but increased stereotypies in cocaine abstinent mice. Finally, the beneficial behavioral effects of VU0155041 treatment in morphine abstinent mice were correlated with restored expression of key MSN and neural activity marker genes in the NAc. This study reports that chronic administration of the mGluR4 PAM VU0155041 relieves long-term deleterious consequences of morphine exposure. It illustrates the neurobiological differences between opiate and psychostimulant abstinence and points to pharmacological repression of excessive activity of D2-MSNs in the NAc as a promising therapeutic lever in drug addiction.
Collapse
|
12
|
Di Paolo A, Farias J, Garat J, Macklin A, Ignatchenko V, Kislinger T, Sotelo Silveira J. Rat Sciatic Nerve Axoplasm Proteome Is Enriched with Ribosomal Proteins during Regeneration Processes. J Proteome Res 2021; 20:2506-2520. [PMID: 33793244 DOI: 10.1021/acs.jproteome.0c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Axons are complex subcellular compartments that are extremely long in relation to cell bodies, especially in peripheral nerves. Many processes are required and regulated during axon injury, including anterograde and retrograde transport, glia-to-axon macromolecular transfer, and local axonal protein synthesis. Many in vitro omics approaches have been used to gain insight into these processes, but few have been applied in vivo. Here we adapted the osmotic ex vivo axoplasm isolation method and analyzed the adult rat sciatic-nerve-extruded axoplasm by label-free quantitative proteomics before and after injury. 2087 proteins groups were detected in the axoplasm, revealing translation machinery and microtubule-associated proteins as the most overrepresented biological processes. Ribosomal proteins (73) were detected in the uninjured axoplasm and increased their levels after injury but not within whole sciatic nerves. Meta-analysis showed that detected ribosomal proteins were present in in vitro axonal proteomes. Because local protein synthesis is important for protein localization, we were interested in detecting the most abundant newly synthesized axonal proteins in vivo. With an MS/MS-BONCAT approach, we detected 42 newly synthesized protein groups. Overall, our work indicates that proteomics profiling is useful for local axonal interrogation and suggests that ribosomal proteins may play an important role, especially during injury.
Collapse
Affiliation(s)
- Andres Di Paolo
- Departamento de Proteínas y Ácidos Nucleicos, IIBCE, 11600 Montevideo, Uruguay.,Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay
| | | | - Joaquin Garat
- Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay
| | - Andrew Macklin
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - José Sotelo Silveira
- Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay.,Departamento de Biología Celular y Molecular, Facultad de Ciencias, 11400 Montevideo, Uruguay
| |
Collapse
|
13
|
Mofatteh M. Neurodegeneration and axonal mRNA transportation. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2021; 10:1-12. [PMID: 33815964 PMCID: PMC8012751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
The prevalence of neurodegenerative diseases is accelerating in rapidly aging global population. Novel and effective diagnostic and therapeutic methods are required to tackle the global issue of neurodegeneration in the future. A better understanding of the potential molecular mechanism causing neurodegeneration can shed light on dysfunctional processes in diseased neurons, which can pave the way to design and synthesize novel targets for early diagnosis during the asymptomatic phase of the disease. Abnormal protein aggregation is a hallmark of neurodegenerative diseases which can hamper transportation of cargoes into axons. Recent evidence suggests that disruption of local protein synthesis has been observed in neurodegenerative diseases. Because of their highly asymmetric structure, highly polarized neurons require trafficking of cargoes from the cell body to different subcellular regions to meet the extensive demands of cellular physiology. Localization of mRNAs and subsequent local translation to corresponding proteins in axons is a mechanism which allows neurons to rapidly respond to external stimuli as well as establishing neuronal networks by synthesizing proteins on demand. Axonal protein synthesis is required for axon guidance, synapse formation and plasticity, axon maintenance and regeneration in response to injury. Different types of excitatory and inhibitory neurons in the central and peripheral nervous systems have been shown to localize mRNA. Rising evidence suggests that the repertoire of localizing mRNA in axons can change during aging, indicating a connection between axonal mRNA trafficking and aging diseases such as neurodegeneration. Here, I briefly review the latest findings on the importance of mRNA localization and local translation in neurons and the consequences of their disruption in neurodegenerative diseases. In addition, I discuss recent evidence that dysregulation of mRNA localization and local protein translation can contribute to the formation of neurodegenerative diseases such as Alzheimer's disease, Amyotrophic Lateral Sclerosis, and Spinal Muscular Atrophy. In addition, I discuss recent findings on mRNAs localizing to mitochondria in neurodegeneration.
Collapse
Affiliation(s)
- Mohammad Mofatteh
- Lincoln College, University of OxfordOxford, UK
- Sir William Dunn School of Pathology, Medical Sciences Division, University of OxfordOxford, UK
| |
Collapse
|
14
|
Monday HR, Bourdenx M, Jordan BA, Castillo PE. CB 1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination. eLife 2020; 9:54812. [PMID: 32902378 PMCID: PMC7521925 DOI: 10.7554/elife.54812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/08/2020] [Indexed: 01/03/2023] Open
Abstract
Long-lasting forms of postsynaptic plasticity commonly involve protein synthesis-dependent structural changes of dendritic spines. However, the relationship between protein synthesis and presynaptic structural plasticity remains unclear. Here, we investigated structural changes in cannabinoid-receptor 1 (CB1)-mediated long-term depression of inhibitory transmission (iLTD), a form of presynaptic plasticity that involves a protein-synthesis-dependent long-lasting reduction in GABA release. We found that CB1-iLTD in acute rat hippocampal slices was associated with protein synthesis-dependent presynaptic structural changes. Using proteomics, we determined that CB1 activation in hippocampal neurons resulted in increased ribosomal proteins and initiation factors, but decreased levels of proteins involved in regulation of the actin cytoskeleton, such as ARPC2 and WASF1/WAVE1, and presynaptic release. Moreover, while CB1-iLTD increased ubiquitin/proteasome activity, ubiquitination but not proteasomal degradation was critical for structural and functional presynaptic CB1-iLTD. Thus, CB1-iLTD relies on both protein synthesis and ubiquitination to elicit structural changes that underlie long-term reduction of GABA release.
Collapse
Affiliation(s)
- Hannah R Monday
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States
| | - Mathieu Bourdenx
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, United States.,Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, United States
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, United States
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, United States
| |
Collapse
|
15
|
Kajtez J, Buchmann S, Vasudevan S, Birtele M, Rocchetti S, Pless CJ, Heiskanen A, Barker RA, Martínez‐Serrano A, Parmar M, Lind JU, Emnéus J. 3D-Printed Soft Lithography for Complex Compartmentalized Microfluidic Neural Devices. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001150. [PMID: 32832365 PMCID: PMC7435242 DOI: 10.1002/advs.202001150] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/16/2020] [Indexed: 05/18/2023]
Abstract
Compartmentalized microfluidic platforms are an invaluable tool in neuroscience research. However, harnessing the full potential of this technology remains hindered by the lack of a simple fabrication approach for the creation of intricate device architectures with high-aspect ratio features. Here, a hybrid additive manufacturing approach is presented for the fabrication of open-well compartmentalized neural devices that provides larger freedom of device design, removes the need for manual postprocessing, and allows an increase in the biocompatibility of the system. Suitability of the method for multimaterial integration allows to tailor the device architecture for the long-term maintenance of healthy human stem-cell derived neurons and astrocytes, spanning at least 40 days. Leveraging fast-prototyping capabilities at both micro and macroscale, a proof-of-principle human in vitro model of the nigrostriatal pathway is created. By presenting a route for novel materials and unique architectures in microfluidic systems, the method provides new possibilities in biological research beyond neuroscience applications.
Collapse
Affiliation(s)
- Janko Kajtez
- Department of Experimental Medical SciencesWallenberg Neuroscience CenterDivision of Neurobiology and Lund Stem Cell CenterBMC A11Lund UniversityLundS‐22184Sweden
| | - Sebastian Buchmann
- Department of Biotechnology and Biomedicine (DTU Bioengineering)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Shashank Vasudevan
- Department of Biotechnology and Biomedicine (DTU Bioengineering)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Marcella Birtele
- Department of Experimental Medical SciencesWallenberg Neuroscience CenterDivision of Neurobiology and Lund Stem Cell CenterBMC A11Lund UniversityLundS‐22184Sweden
| | - Stefano Rocchetti
- Department of Biotechnology and Biomedicine (DTU Bioengineering)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Christian Jonathan Pless
- Department of Healthcare Technology (DTU Health Tech)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Arto Heiskanen
- Department of Biotechnology and Biomedicine (DTU Bioengineering)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Roger A. Barker
- John van Geest Centre for Brain Repair & Department of NeurologyDepartment of Clinical Neurosciences and WT‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 1TNUK
| | - Alberto Martínez‐Serrano
- Department of Molecular BiologyUniversidad Autónoma de Madridand Department of Molecular NeuropathologyCenter of Molecular Biology Severo Ochoa (UAM‐CSIC)Nicolás Cabrera 1Madrid28049Spain
| | - Malin Parmar
- Department of Experimental Medical SciencesWallenberg Neuroscience CenterDivision of Neurobiology and Lund Stem Cell CenterBMC A11Lund UniversityLundS‐22184Sweden
| | - Johan Ulrik Lind
- Department of Healthcare Technology (DTU Health Tech)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| | - Jenny Emnéus
- Department of Biotechnology and Biomedicine (DTU Bioengineering)Technical University of DenmarkProduktionstorvet, Building 423Lyngby2800 Kgs.Denmark
| |
Collapse
|
16
|
Lo LHY, Lai KO. Dysregulation of protein synthesis and dendritic spine morphogenesis in ASD: studies in human pluripotent stem cells. Mol Autism 2020; 11:40. [PMID: 32460854 PMCID: PMC7251853 DOI: 10.1186/s13229-020-00349-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a brain disorder that involves changes in neuronal connections. Abnormal morphology of dendritic spines on postsynaptic neurons has been observed in ASD patients and transgenic mice that model different monogenetic causes of ASD. A number of ASD-associated genetic variants are known to disrupt dendritic local protein synthesis, which is essential for spine morphogenesis, synaptic transmission, and plasticity. Most of our understanding on the molecular mechanism underlying ASD depends on studies using rodents. However, recent advance in human pluripotent stem cells and their neural differentiation provides a powerful alternative tool to understand the cellular aspects of human neurological disorders. In this review, we summarize recent progress on studying mRNA targeting and local protein synthesis in stem cell-derived neurons, and discuss how perturbation of these processes may impact synapse development and functions that are relevant to cognitive deficits in ASD.
Collapse
Affiliation(s)
- Louisa Hoi-Ying Lo
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Kwok-On Lai
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China. .,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| |
Collapse
|
17
|
Kodavati M, Wang H, Hegde ML. Altered Mitochondrial Dynamics in Motor Neuron Disease: An Emerging Perspective. Cells 2020; 9:cells9041065. [PMID: 32344665 PMCID: PMC7226538 DOI: 10.3390/cells9041065] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria plays privotal role in diverse pathways that regulate cellular function and survival, and have emerged as a prime focus in aging and age-associated motor neuron diseases (MNDs), such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Accumulating evidence suggests that many amyloidogenic proteins, including MND-associated RNA/DNA-binding proteins fused in sarcoma (FUS) and TAR DNA binding protein (TDP)-43, are strongly linked to mitochondrial dysfunction. Animal model and patient studies have highlighted changes in mitochondrial structure, plasticity, replication/copy number, mitochondrial DNA instability, and altered membrane potential in several subsets of MNDs, and these observations are consistent with the evidence of increased excitotoxicity, induction of reactive oxygen species, and activation of intrinsic apoptotic pathways. Studies in MND rodent models also indicate that mitochondrial abnormalities begin prior to the clinical and pathological onset of the disease, suggesting a causal role of mitochondrial dysfunction. Our recent studies, which demonstrated the involvement of specific defects in DNA break-ligation mediated by DNA ligase 3 (LIG3) in FUS-associated ALS, raised a key question of its potential implication in mitochondrial DNA transactions because LIG3 is essential for both mitochondrial DNA replication and repair. This question, as well as how wild-type and mutant MND-associated factors affect mitochondria, remain to be elucidated. These new investigation avenues into the mechanistic role of mitochondrial dysfunction in MNDs are critical to identify therapeutic targets to alleviate mitochondrial toxicity and its consequences. In this article, we critically review recent advances in our understanding of mitochondrial dysfunction in diverse subgroups of MNDs and discuss challenges and future directions.
Collapse
Affiliation(s)
- Manohar Kodavati
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
| | - Haibo Wang
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
| | - Muralidhar L. Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
- Department of Neurosurgery, Weill Medical College, New York, NY 10065, USA
- Correspondence:
| |
Collapse
|
18
|
Suzuki N, Akiyama T, Warita H, Aoki M. Omics Approach to Axonal Dysfunction of Motor Neurons in Amyotrophic Lateral Sclerosis (ALS). Front Neurosci 2020; 14:194. [PMID: 32269505 PMCID: PMC7109447 DOI: 10.3389/fnins.2020.00194] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an intractable adult-onset neurodegenerative disease that leads to the loss of upper and lower motor neurons (MNs). The long axons of MNs become damaged during the early stages of ALS. Genetic and pathological analyses of ALS patients have revealed dysfunction in the MN axon homeostasis. However, the molecular pathomechanism for the degeneration of axons in ALS has not been fully elucidated. This review provides an overview of the proposed axonal pathomechanisms in ALS, including those involving the neuronal cytoskeleton, cargo transport within axons, axonal energy supply, clearance of junk protein, neuromuscular junctions (NMJs), and aberrant axonal branching. To improve understanding of the global changes in axons, the review summarizes omics analyses of the axonal compartments of neurons in vitro and in vivo, including a motor nerve organoid approach that utilizes microfluidic devices developed by this research group. The review also discusses the relevance of intra-axonal transcription factors frequently identified in these omics analyses. Local axonal translation and the relationship among these pathomechanisms should be pursued further. The development of novel strategies to analyze axon fractions provides a new approach to establishing a detailed understanding of resilience of long MN and MN pathology in ALS.
Collapse
Affiliation(s)
- Naoki Suzuki
- Department of Neurology, Tohoku University School of Medicine, Sendai, Japan.,Department of Neurology, Shodo-kai Southern Tohoku General Hospital, Miyagi, Japan
| | - Tetsuya Akiyama
- Department of Neurology, Tohoku University School of Medicine, Sendai, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University School of Medicine, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University School of Medicine, Sendai, Japan
| |
Collapse
|
19
|
Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
Collapse
Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
| |
Collapse
|
20
|
Hyvärinen T, Hagman S, Ristola M, Sukki L, Veijula K, Kreutzer J, Kallio P, Narkilahti S. Co-stimulation with IL-1β and TNF-α induces an inflammatory reactive astrocyte phenotype with neurosupportive characteristics in a human pluripotent stem cell model system. Sci Rep 2019; 9:16944. [PMID: 31729450 PMCID: PMC6858358 DOI: 10.1038/s41598-019-53414-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Astrocyte reactivation has been discovered to be an important contributor to several neurological diseases. In vitro models involving human astrocytes have the potential to reveal disease-specific mechanisms of these cells and to advance research on neuropathological conditions. Here, we induced a reactive phenotype in human induced pluripotent stem cell (hiPSC)-derived astrocytes and studied the inflammatory natures and effects of these cells on human neurons. Astrocytes responded to interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) treatment with a typical transition to polygonal morphology and a shift to an inflammatory phenotype characterized by altered gene and protein expression profiles. Astrocyte-secreted factors did not exert neurotoxic effects, whereas they transiently promoted the functional activity of neurons. Importantly, we engineered a novel microfluidic platform designed for investigating interactions between neuronal axons and reactive astrocytes that also enables the implementation of a controlled inflammatory environment. In this platform, selective stimulation of astrocytes resulted in an inflammatory niche that sustained axonal growth, further suggesting that treatment induces a reactive astrocyte phenotype with neurosupportive characteristics. Our findings show that hiPSC-derived astrocytes are suitable for modeling astrogliosis, and the developed in vitro platform provides promising novel tools for studying neuron-astrocyte crosstalk and human brain disease in a dish.
Collapse
Affiliation(s)
- Tanja Hyvärinen
- NeuroGroup, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sanna Hagman
- NeuroGroup, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mervi Ristola
- NeuroGroup, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lassi Sukki
- Micro and Nanosystems Research Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Katariina Veijula
- NeuroGroup, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Joose Kreutzer
- Micro and Nanosystems Research Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pasi Kallio
- Micro and Nanosystems Research Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Susanna Narkilahti
- NeuroGroup, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| |
Collapse
|
21
|
Nijssen J, Aguila J, Hoogstraaten R, Kee N, Hedlund E. Axon-Seq Decodes the Motor Axon Transcriptome and Its Modulation in Response to ALS. Stem Cell Reports 2019; 11:1565-1578. [PMID: 30540963 PMCID: PMC6294264 DOI: 10.1016/j.stemcr.2018.11.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 12/11/2022] Open
Abstract
Spinal motor axons traverse large distances to innervate target muscles, thus requiring local control of cellular events for proper functioning. To interrogate axon-specific processes we developed Axon-seq, a refined method incorporating microfluidics, RNA sequencing (RNA-seq), and bioinformatic quality control. We show that the axonal transcriptome is distinct from that of somas and contains fewer genes. We identified 3,500-5,000 transcripts in mouse and human stem cell-derived spinal motor axons, most of which are required for oxidative energy production and ribogenesis. Axons contained transcription factor mRNAs, e.g., Ybx1, with implications for local functions. As motor axons degenerate in amyotrophic lateral sclerosis (ALS), we investigated their response to the SOD1G93A mutation, identifying 121 ALS-dysregulated transcripts. Several of these are implicated in axonal function, including Nrp1, Dbn1, and Nek1, a known ALS-causing gene. In conclusion, Axon-seq provides an improved method for RNA-seq of axons, increasing our understanding of peripheral axon biology and identifying therapeutic targets in motor neuron disease.
Collapse
Affiliation(s)
- Jik Nijssen
- Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Julio Aguila
- Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Rein Hoogstraaten
- Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden; Department of Translational Neuroscience, Brain Center Rudolf Magnus, UMC Utrecht, Utrecht 3984 CG, Netherlands
| | - Nigel Kee
- Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden.
| |
Collapse
|
22
|
Shimba K, Sakai K, Iida S, Kotani K, Jimbo Y. Long-Term Developmental Process of the Human Cortex Revealed In Vitro by Axon-Targeted Recording Using a Microtunnel-Augmented Microelectrode Array. IEEE Trans Biomed Eng 2019; 66:2538-2545. [DOI: 10.1109/tbme.2019.2891310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
23
|
Farias J, Sotelo JR, Sotelo‐Silveira J. Toward Axonal System Biology: Genome Wide Views of Local mRNA Translation. Proteomics 2019; 19:e1900054. [DOI: 10.1002/pmic.201900054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/12/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Joaquina Farias
- Departamento de Proteínas y Ácidos NucleicosInstituto de Investigaciones Biológicas Clemente Estable Montevideo CP 11600 Uruguay
- Departamento de GenómicaInstituto de Investigaciones Biológicas Clemente Estable Montevideo CP 11600 Uruguay
| | - José Roberto Sotelo
- Departamento de Proteínas y Ácidos NucleicosInstituto de Investigaciones Biológicas Clemente Estable Montevideo CP 11600 Uruguay
| | - José Sotelo‐Silveira
- Departamento de GenómicaInstituto de Investigaciones Biológicas Clemente Estable Montevideo CP 11600 Uruguay
- Sección Biología CelularFacultad de Ciencias, Universidad de la República Montevideo CP 11400 Uruguay
| |
Collapse
|
24
|
Kamande JW, Nagendran T, Harris J, Taylor AM. Multi-compartment Microfluidic Device Geometry and Covalently Bound Poly-D-Lysine Influence Neuronal Maturation. Front Bioeng Biotechnol 2019; 7:84. [PMID: 31134192 PMCID: PMC6515982 DOI: 10.3389/fbioe.2019.00084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/03/2019] [Indexed: 12/23/2022] Open
Abstract
Multi-compartment microfluidic devices have become valuable tools for experimental neuroscientists, improving the organization of neurons and access to their distinct subcellular microenvironments for measurements and manipulations. While murine neurons are extensively used within these devices, there is a growing need to culture and maintain human neurons differentiated from stem cells within multi-compartment devices. Human neuron cultures have different metabolic demands and require longer culture times to achieve synaptic maturation. We tested different channel heights (100 μm, 400 μm, and open) to determine whether greater exposure to media for nutrient exchange might improve long-term growth of NIH-approved H9 embryonic stem cells differentiated into glutamatergic neurons. Our data showed an opposite result with both closed channel configurations having greater synaptic maturation compared to the open compartment configuration. These data suggest that restricted microenvironments surrounding neurons improve growth and maturation of neurons. We next tested whether covalently bound poly-D-lysine (PDL) might improve growth and maturation of these neurons as somata tend to cluster together on PDL adsorbed surfaces after long culture periods (>30 days). We found that covalently bound PDL greatly improved the differentiation and maturation of stem cell-derived neurons within the devices. Lastly, experimental paradigms using the multi-compartment platform show that axons of human stem cell derived neurons intrinsically regenerate in the absence of inhibitory cues and that isolated axons form presynaptic terminals when presented with synaptic targets.
Collapse
Affiliation(s)
- Joyce W Kamande
- UNC/NC State Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Tharkika Nagendran
- UNC/NC State Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Joseph Harris
- Xona Microfluidics, LLC, Temecula, CA, United States
| | - Anne Marion Taylor
- UNC/NC State Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Xona Microfluidics, LLC, Temecula, CA, United States
| |
Collapse
|
25
|
Paranjape SR, Nagendran T, Poole V, Harris J, Taylor AM. Compartmentalization of Human Stem Cell-Derived Neurons within Pre-Assembled Plastic Microfluidic Chips. J Vis Exp 2019. [PMID: 31107446 DOI: 10.3791/59250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Use of microfluidic devices to compartmentalize cultured neurons has become a standard method in neuroscience. This protocol shows how to use a pre-assembled multi-compartment chip made in a cyclic olefin copolymer (COC) to compartmentalize neurons differentiated from human stem cells. The footprint of these COC chips are the same as a standard microscope slide and are equally compatible with high resolution microscopy. Neurons are differentiated from human neural stem cells (NSCs) into glutamatergic neurons within the chip and maintained for 5 weeks, allowing sufficient time for these neurons to develop synapses and dendritic spines. Further, we demonstrate multiple common experimental procedures using these multi-compartment chips, including viral labeling, establishing microenvironments, axotomy, and immunocytochemistry.
Collapse
Affiliation(s)
- Smita R Paranjape
- UNC Neuroscience Center; UNC/NC State Joint Department of Biomedical Engineering
| | - Tharkika Nagendran
- UNC Neuroscience Center; UNC/NC State Joint Department of Biomedical Engineering
| | | | | | - Anne Marion Taylor
- UNC Neuroscience Center; UNC/NC State Joint Department of Biomedical Engineering; Xona Microfluidics, LLC;
| |
Collapse
|
26
|
Bott CJ, Johnson CG, Yap CC, Dwyer ND, Litwa KA, Winckler B. Nestin in immature embryonic neurons affects axon growth cone morphology and Semaphorin3a sensitivity. Mol Biol Cell 2019; 30:1214-1229. [PMID: 30840538 PMCID: PMC6724523 DOI: 10.1091/mbc.e18-06-0361] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/21/2019] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Correct wiring in the neocortex requires that responses to an individual guidance cue vary among neurons in the same location, and within the same neuron over time. Nestin is an atypical intermediate filament expressed strongly in neural progenitors and is thus used widely as a progenitor marker. Here we show a subpopulation of embryonic cortical neurons that transiently express nestin in their axons. Nestin expression is thus not restricted to neural progenitors, but persists for 2-3 d at lower levels in newborn neurons. We found that nestin-expressing neurons have smaller growth cones, suggesting that nestin affects cytoskeletal dynamics. Nestin, unlike other intermediate filament subtypes, regulates cdk5 kinase by binding the cdk5 activator p35. Cdk5 activity is induced by the repulsive guidance cue Semaphorin3a (Sema3a), leading to axonal growth cone collapse in vitro. Therefore, we tested whether nestin-expressing neurons showed altered responses to Sema3a. We find that nestin-expressing newborn neurons are more sensitive to Sema3a in a roscovitine-sensitive manner, whereas nestin knockdown results in lowered sensitivity to Sema3a. We propose that nestin functions in immature neurons to modulate cdk5 downstream of the Sema3a response. Thus, the transient expression of nestin could allow temporal and/or spatial modulation of a neuron's response to Sema3a, particularly during early axon guidance.
Collapse
Affiliation(s)
- C. J. Bott
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - C. G. Johnson
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - C. C. Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - N. D. Dwyer
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - K. A. Litwa
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - B. Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| |
Collapse
|
27
|
Nagendran T, Poole V, Harris J, Taylor AM. Use of Pre-Assembled Plastic Microfluidic Chips for Compartmentalizing Primary Murine Neurons. J Vis Exp 2018. [PMID: 30451222 PMCID: PMC6420830 DOI: 10.3791/58421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Microfabricated methods to compartmentalize neurons have become essential tools for many neuroscientists. This protocol describes the use of a commercially available pre-assembled plastic chip for compartmentalizing cultured primary rat hippocampal neurons. These plastic chips, contained within the footprint of a standard microscope slide, are compatible with high-resolution, live, and fluorescence imaging. This protocol demonstrates how to retrograde label neurons via isolated axons using a modified rabies virus encoding a fluorescent protein, create isolated microenvironments within one compartment, and perform axotomy and immunocytochemistry on-chip. Neurons are cultured for >3 weeks within the plastic chips, illustrating the compatibility of these chips for long-term neuronal cultures.
Collapse
Affiliation(s)
- Tharkika Nagendran
- UNC Neuroscience Center; UNC/NC State Joint Department of Biomedical Engineering, UNC
| | | | | | - Anne Marion Taylor
- UNC Neuroscience Center; UNC/NC State Joint Department of Biomedical Engineering, UNC; Xona Microfluidics, LLC;
| |
Collapse
|
28
|
Pujol CN, Pellissier LP, Clément C, Becker JAJ, Le Merrer J. Back-translating behavioral intervention for autism spectrum disorders to mice with blunted reward restores social abilities. Transl Psychiatry 2018; 8:197. [PMID: 30242222 PMCID: PMC6155047 DOI: 10.1038/s41398-018-0247-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 12/12/2022] Open
Abstract
The mu opioid receptor (MOR) plays a critical role in modulating social behavior in humans and animals. Accordingly, MOR null mice display severe alterations in their social repertoire as well as multiple other behavioral deficits, recapitulating core and secondary symptoms of autism spectrum disorder (ASD). Such behavioral profile suggests that MOR dysfunction, and beyond this, altered reward processes may contribute to ASD etiopathology. Interestingly, the only treatments that proved efficacy in relieving core symptoms of ASD, early behavioral intervention programs, rely principally on positive reinforcement to ameliorate behavior. The neurobiological underpinnings of their beneficial effects, however, remain poorly understood. Here we back-translated applied behavior analysis (ABA)-based behavioral interventions to mice lacking the MOR (Oprm1-/-), as a model of autism with blunted reward processing. By associating a positive reinforcement, palatable food reward, to daily encounter with a wild-type congener, we were able to rescue durably social interaction and preference in Oprm1-/- mice. Along with behavioral improvements, the expression of marker genes of neuronal activity and plasticity as well as genes of the oxytocin/vasopressin system were remarkably normalized in the reward/social circuitry. Our study provides further evidence for a critical involvement of reward processes in driving social behavior and opens new perspectives regarding therapeutic intervention in ASD.
Collapse
Affiliation(s)
- Camille N. Pujol
- 0000 0001 2157 9291grid.11843.3fMédecine Translationelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Inserm U-964, CNRS UMR-7104, Université de Strasbourg, Illkirch, France ,0000 0004 0383 2080grid.461890.2Present Address: Département de Neurosciences, Institut de Génomique fonctionnelle, Inserm U-661, CNRS UMR 5203, 34094 Montpellier, France
| | - Lucie P. Pellissier
- 0000 0001 2182 6141grid.12366.30Physiologie de la Reproduction et des Comportements, INRA UMR-0085, CNRS UMR-7247, IFCE, Université de Tours, Inserm, Nouzilly, France ,0000 0004 0383 2080grid.461890.2Present Address: Département de Neurosciences, Institut de Génomique fonctionnelle, Inserm U-661, CNRS UMR 5203, 34094 Montpellier, France
| | - Céline Clément
- 0000 0001 2157 9291grid.11843.3fLaboratoire Interuniversitaire en Sciences de l’Education et de la Communication, EA 2310, Université de Strasbourg, Strasbourg, France
| | - Jérôme A. J. Becker
- 0000 0001 2157 9291grid.11843.3fMédecine Translationelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Inserm U-964, CNRS UMR-7104, Université de Strasbourg, Illkirch, France ,0000 0001 2182 6141grid.12366.30Physiologie de la Reproduction et des Comportements, INRA UMR-0085, CNRS UMR-7247, IFCE, Université de Tours, Inserm, Nouzilly, France ,0000 0004 0383 2080grid.461890.2Present Address: Département de Neurosciences, Institut de Génomique fonctionnelle, Inserm U-661, CNRS UMR 5203, 34094 Montpellier, France
| | - Julie Le Merrer
- Médecine Translationelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Inserm U-964, CNRS UMR-7104, Université de Strasbourg, Illkirch, France. .,Physiologie de la Reproduction et des Comportements, INRA UMR-0085, CNRS UMR-7247, IFCE, Université de Tours, Inserm, Nouzilly, France.
| |
Collapse
|
29
|
Olesnicky EC, Wright EG. Drosophila as a Model for Assessing the Function of RNA-Binding Proteins during Neurogenesis and Neurological Disease. J Dev Biol 2018; 6:E21. [PMID: 30126171 PMCID: PMC6162566 DOI: 10.3390/jdb6030021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
An outstanding question in developmental neurobiology is how RNA processing events contribute to the regulation of neurogenesis. RNA processing events are increasingly recognized as playing fundamental roles in regulating multiple developmental events during neurogenesis, from the asymmetric divisions of neural stem cells, to the generation of complex and diverse neurite morphologies. Indeed, both asymmetric cell division and neurite morphogenesis are often achieved by mechanisms that generate asymmetric protein distributions, including post-transcriptional gene regulatory mechanisms such as the transport of translationally silent messenger RNAs (mRNAs) and local translation of mRNAs within neurites. Additionally, defects in RNA splicing have emerged as a common theme in many neurodegenerative disorders, highlighting the importance of RNA processing in maintaining neuronal circuitry. RNA-binding proteins (RBPs) play an integral role in splicing and post-transcriptional gene regulation, and mutations in RBPs have been linked with multiple neurological disorders including autism, dementia, amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Fragile X syndrome (FXS), and X-linked intellectual disability disorder. Despite their widespread nature and roles in neurological disease, the molecular mechanisms and networks of regulated target RNAs have been defined for only a small number of specific RBPs. This review aims to highlight recent studies in Drosophila that have advanced our knowledge of how RBP dysfunction contributes to neurological disease.
Collapse
Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
| |
Collapse
|
30
|
Maciel R, Bis DM, Rebelo AP, Saghira C, Züchner S, Saporta MA. The human motor neuron axonal transcriptome is enriched for transcripts related to mitochondrial function and microtubule-based axonal transport. Exp Neurol 2018; 307:155-163. [PMID: 29935168 DOI: 10.1016/j.expneurol.2018.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 06/05/2018] [Accepted: 06/15/2018] [Indexed: 10/28/2022]
Abstract
Local axonal translation of specific mRNA species plays an important role in axon maintenance, plasticity during development and recovery from injury. Recently, disrupted axonal mRNA transport and translation have been linked to neurodegenerative disorders. To identify mRNA species that are actively transported to axons and play an important role in axonal physiology, we mapped the axonal transcriptome of human induced pluripotent stem cell (iPSC)-derived motor neurons using permeable inserts to obtain large amounts of enriched axonal material for RNA isolation and sequencing. Motor neurons from healthy subjects were used to determine differences in gene expression profiles between neuronal somatodendritic and axonal compartments. Our results demonstrate that several transcripts were enriched in either the axon or neuronal bodies. Gene ontology analysis demonstrated enrichment in the axonal compartment for transcripts associated with mitochondrial electron transport, microtubule-based axonal transport and ER-associated protein catabolism. These results suggest that local translation of mRNAs is required to meet the high-energy demand of axons and to support microtubule-based axonal transport. Interestingly, several transcripts related to human genetic disorders associated with axonal degeneration (inherited axonopathies) were identified among the mRNA species enriched in motor axons.
Collapse
Affiliation(s)
- Renata Maciel
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Dana M Bis
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Adriana P Rebelo
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Cima Saghira
- Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stephan Züchner
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario A Saporta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| |
Collapse
|
31
|
Chuang CF, King CE, Ho BW, Chien KY, Chang YC. Unbiased Proteomic Study of the Axons of Cultured Rat Cortical Neurons. J Proteome Res 2018; 17:1953-1966. [DOI: 10.1021/acs.jproteome.8b00069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | | | - Kun-Yi Chien
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan
- Clinical Proteomics Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan City 33305, Taiwan
| | | |
Collapse
|
32
|
Van Driesche SJ, Martin KC. New frontiers in RNA transport and local translation in neurons. Dev Neurobiol 2018; 78:331-339. [DOI: 10.1002/dneu.22574] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Sarah J. Van Driesche
- Department of Biological Chemistry; University of California; Los Angeles California
| | - Kelsey C. Martin
- Department of Biological Chemistry; University of California; Los Angeles California
| |
Collapse
|
33
|
Jorfi M, D'Avanzo C, Kim DY, Irimia D. Three-Dimensional Models of the Human Brain Development and Diseases. Adv Healthc Mater 2018; 7:10.1002/adhm.201700723. [PMID: 28845922 PMCID: PMC5762251 DOI: 10.1002/adhm.201700723] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 06/24/2017] [Indexed: 01/07/2023]
Abstract
Deciphering the human brain pathophysiology remains one of the greatest challenges of the 21st century. Neurological disorders represent a significant proportion of diseases burden; however, the complexity of the brain physiology makes it challenging to model its diseases. Simple in vitro models have been very useful for precise measurements in controled conditions. However, existing models are limited in their ability to replicate complex interactions between various cells in the brain. Studying human brain requires sophisticated models to reconstitute the tangled architecture and functions of brain cells. Recently, advances in the development of three-dimensional (3D) brain cell culture models have begun to recapitulate various aspects of the human brain physiology in vitro and replicate basic disease processes of Alzheimer's disease, amyotrophic lateral sclerosis, and microcephaly. In this review, we discuss the progress, advantages, limitations, and future directions of 3D cell culture systems for modeling the human brain development and diseases.
Collapse
Affiliation(s)
- Mehdi Jorfi
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 02129, USA
| | - Carla D'Avanzo
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 02129, USA
| | - Doo Yeon Kim
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 02129, USA
| | - Daniel Irimia
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, 02129, USA
| |
Collapse
|
34
|
Costa CJ, Willis DE. To the end of the line: Axonal mRNA transport and local translation in health and neurodegenerative disease. Dev Neurobiol 2017; 78:209-220. [PMID: 29115051 DOI: 10.1002/dneu.22555] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/20/2017] [Accepted: 11/01/2017] [Indexed: 12/14/2022]
Abstract
Axons and growth cones, by their very nature far removed from the cell body, encounter unique environments and require distinct populations of proteins. It seems only natural, then, that they have developed mechanisms to locally synthesize a host of proteins required to perform their specialized functions. Acceptance of this ability has taken decades; however, there is now consensus that axons do indeed have the capacity for local translation, and that this capacity is even retained into adulthood. Accumulating evidence supports the role of locally synthesized proteins in the proper development, maintenance, and function of neurons, and newly emerging studies also suggest that disruption in this process has implications in a number of neurodevelopmental and neurodegenerative diseases. Here, we briefly review the long history of axonal mRNA localization and local translation, and the role that these locally synthesized proteins play in normal neuronal function. Additionally, we highlight the emerging evidence that dysregulation in these processes contributes to a wide range of pathophysiology, including neuropsychiatric disorders, Alzheimer's, and motor neuron diseases such as spinal muscular atrophy and Amyotrophic Lateral Sclerosis. © 2017 Wiley Periodicals, Inc. Develop. Neurobiol 78: 209-220, 2018.
Collapse
Affiliation(s)
| | - Dianna E Willis
- Burke Medical Research Institute, White Plains, New York, 10605.,Brain & Mind Research Institute, Weill Cornell Medicine, New York, New York
| |
Collapse
|
35
|
Lee MR, Schwandt ML, Sankar V, Suchankova P, Sun H, Leggio L. Effect of alcohol use disorder on oxytocin peptide and receptor mRNA expression in human brain: A post-mortem case-control study. Psychoneuroendocrinology 2017; 85:14-19. [PMID: 28787642 DOI: 10.1016/j.psyneuen.2017.07.481] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022]
Abstract
Animal and human evidence supports a role for oxytocin in alcohol-seeking behaviors. There is interest, therefore, in targeting the oxytocin pathway as a new pharmacologic approach to treat alcohol use disorder. To this end, it is important to understand the effect of alcohol use disorder on endogenous oxytocin in brain regions that are relevant for the initiation and maintenance of alcohol use disorder. We examined human post-mortem brain tissue from males with alcohol use disorder (n=11) compared to nonalcohol dependent male controls (n=16). We a priori targeted five brain regions that in rodent studies, are projection areas for oxytocin neurons: nucleus accumbens, amygdala, hippocampus, ventral tegmental area and prefrontal cortex. Fold change in mRNA levels of oxytocin peptide and receptor were measured in each of the brain regions studied. Fold change for oxytocin peptide mRNA was significantly elevated in the prefrontal cortex of subjects with alcohol use disorder compared to controls (uncorrected p=0.0001; FDR-corrected p=0.001). For the entire sample of 27 subjects, there was a significant positive correlation between the fold change in oxytocin peptide mRNA in the prefrontal cortex and both daily alcohol intake (r2=0.38; p=0.002) and drinks per week (r2=0.24; p=0.02). Results are discussed in light of the previous animal and human literature on changes in the endogenous oxytocin system as an effect of chronic alcohol exposure.
Collapse
Affiliation(s)
- Mary R Lee
- Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA.
| | - Melanie L Schwandt
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - Vignesh Sankar
- Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - Petra Suchankova
- Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA; Department of Pharmacology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Hui Sun
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA
| | - Lorenzo Leggio
- Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism and National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD, USA; Center for Alcohol and Addiction Studies, Department of Behavioral and Social Sciences, Brown University, Providence, RI, USA
| |
Collapse
|
36
|
Mitochondrial health maintenance in axons. Biochem Soc Trans 2017; 45:1045-1052. [DOI: 10.1042/bst20170023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023]
Abstract
Neurons are post-mitotic cells that must function throughout the life of an organism. The high energetic requirements and Ca2+ spikes of synaptic transmission place a burden on neuronal mitochondria. The removal of older mitochondria and the replenishment of the functional mitochondrial pool in axons with freshly synthesized components are therefore important parts of neuronal maintenance. Although the mechanism of mitochondrial protein import and dynamics is studied in great detail, the length of neurons poses additional challenges to those processes. In this mini-review, I briefly cover the basics of mitochondrial biogenesis and proceed to explain the interdependence of mitochondrial transport and mitochondrial health. I then extrapolate recent findings in yeast and mammalian cultured cells to neurons, making a case for axonal translation as a contributor to mitochondrial biogenesis in neurons.
Collapse
|
37
|
Kar AN, Lee SJ, Twiss JL. Expanding Axonal Transcriptome Brings New Functions for Axonally Synthesized Proteins in Health and Disease. Neuroscientist 2017; 24:111-129. [PMID: 28593814 DOI: 10.1177/1073858417712668] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intra-axonal protein synthesis has been shown to play critical roles in both development and repair of axons. Axons provide long-range connectivity in the nervous system, and disruption of their function and/or structure is seen in several neurological diseases and disorders. Axonally synthesized proteins or losses in axonally synthesized proteins contribute to neurodegenerative diseases, neuropathic pain, viral transport, and survival of axons. Increasing sensitivity of RNA detection and quantitation coupled with methods to isolate axons to purity has shown that a surprisingly complex transcriptome exists in axons. This extends across different species, neuronal populations, and physiological conditions. These studies have helped define the repertoire of neuronal mRNAs that can localize into axons and imply previously unrecognized functions for local translation in neurons. Here, we review the current state of transcriptomics studies of isolated axons, contrast axonal mRNA profiles between different neuronal types and growth states, and discuss how mRNA transport into and translation within axons contribute to neurological disorders.
Collapse
Affiliation(s)
- Amar N Kar
- 1 Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Seung Joon Lee
- 1 Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Jeffery L Twiss
- 1 Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,2 Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
| |
Collapse
|