1
|
Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
Collapse
Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
2
|
Kilfeather P, Khoo JH, Wagner K, Liang H, Caiazza MC, An Y, Zhang X, Chen X, Connor-Robson N, Shang Z, Wade-Martins R. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease. Cell Rep 2024; 43:113784. [PMID: 38386560 DOI: 10.1016/j.celrep.2024.113784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
The brain is spatially organized and contains unique cell types, each performing diverse functions and exhibiting differential susceptibility to neurodegeneration. This is exemplified in Parkinson's disease with the preferential loss of dopaminergic neurons of the substantia nigra pars compacta. Using a Parkinson's transgenic model, we conducted a single-cell spatial transcriptomic and dopaminergic neuron translatomic analysis of young and old mouse brains. Through the high resolving capacity of single-cell spatial transcriptomics, we provide a deep characterization of the expression features of dopaminergic neurons and 27 other cell types within their spatial context, identifying markers of healthy and aging cells, spanning Parkinson's relevant pathways. We integrate gene enrichment and genome-wide association study data to prioritize putative causative genes for disease investigation, identifying CASR as a regulator of dopaminergic calcium handling. These datasets represent the largest public resource for the investigation of spatial gene expression in brain cells in health, aging, and disease.
Collapse
Affiliation(s)
- Peter Kilfeather
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Katherina Wagner
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | | | - Natalie Connor-Robson
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| |
Collapse
|
3
|
Ament SA, Poulopoulos A. The brain's dark transcriptome: Sequencing RNA in distal compartments of neurons and glia. Curr Opin Neurobiol 2023; 81:102725. [PMID: 37196598 PMCID: PMC10524153 DOI: 10.1016/j.conb.2023.102725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 05/19/2023]
Abstract
Transcriptomic approaches are powerful strategies to map the molecular diversity of cells in the brain. Single-cell genomic atlases have now been compiled for entire mammalian brains. However, complementary techniques are only just beginning to map the subcellular transcriptomes from distal cellular compartments. We review single-cell datasets alongside subtranscriptome data from the mammalian brain to explore the development of cellular and subcellular diversity. We discuss how single-cell RNA-seq misses transcripts localized away from cell bodies, which form the 'dark transcriptome' of the brain: a collection of subtranscriptomes in dendrites, axons, growth cones, synapses, and endfeet with important roles in brain development and function. Recent advances in subcellular transcriptome sequencing are beginning to reveal these elusive pools of RNA. We outline the success stories to date in uncovering the constituent subtranscriptomes of neurons and glia, as well as present the emerging toolkit that is accelerating the pace of subtranscriptome discovery.
Collapse
Affiliation(s)
- Seth A Ament
- Department of Psychiatry, UM-MIND, and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
4
|
Vasek MJ, Mueller SM, Fass SB, Deajon-Jackson JD, Liu Y, Crosby HW, Koester SK, Yi J, Li Q, Dougherty JD. Local translation in microglial processes is required for efficient phagocytosis. Nat Neurosci 2023; 26:1185-1195. [PMID: 37277487 PMCID: PMC10580685 DOI: 10.1038/s41593-023-01353-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/03/2023] [Indexed: 06/07/2023]
Abstract
Neurons, astrocytes and oligodendrocytes locally regulate protein translation within distal processes. Here, we tested whether there is regulated local translation within peripheral microglial processes (PeMPs) from mouse brain. We show that PeMPs contain ribosomes that engage in de novo protein synthesis, and these are associated with transcripts involved in pathogen defense, motility and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the formation of PeMP phagocytic cups, the localization of lysosomal proteins within them, and phagocytosis of apoptotic cells and pathogen-like particles. Finally, PeMPs severed from their somata exhibit and require de novo local protein synthesis to effectively surround pathogen-like particles. Collectively, these data argue for regulated local translation in PeMPs and indicate a need for new translation to support dynamic microglial functions.
Collapse
Affiliation(s)
- Michael J Vasek
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shayna M Mueller
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart B Fass
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jelani D Deajon-Jackson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Haley W Crosby
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sarah K Koester
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jiwon Yi
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Qingyun Li
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
5
|
Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process. Cell Rep 2022; 41:111474. [PMID: 36261025 PMCID: PMC9624251 DOI: 10.1016/j.celrep.2022.111474] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 06/16/2022] [Accepted: 09/19/2022] [Indexed: 01/07/2023] Open
Abstract
Within eukaryotic cells, translation is regulated independent of transcription, enabling nuanced, localized, and rapid responses to stimuli. Neurons respond transcriptionally and translationally to synaptic activity. Although transcriptional responses are documented in astrocytes, here we test whether astrocytes have programmed translational responses. We show that seizure activity rapidly changes the transcripts on astrocyte ribosomes, some predicted to be downstream of BDNF signaling. In acute slices, we quantify the extent to which cues of neuronal activity activate translation in astrocytes and show that this translational response requires the presence of neurons, indicating that the response is non-cell autonomous. We also show that this induction of new translation extends into the periphery of astrocytes. Finally, synaptic proteomics show that new translation is required for changes that occur in perisynaptic astrocyte protein composition after fear conditioning. Regulation of translation in astrocytes by neuronal activity suggests an additional mechanism by which astrocytes may dynamically modulate nervous system functioning.
Collapse
|
6
|
Hobson BD, Kong L, Angelo MF, Lieberman OJ, Mosharov EV, Herzog E, Sulzer D, Sims PA. Subcellular and regional localization of mRNA translation in midbrain dopamine neurons. Cell Rep 2022; 38:110208. [PMID: 35021090 PMCID: PMC8844886 DOI: 10.1016/j.celrep.2021.110208] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/25/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Midbrain dopaminergic (mDA) neurons exhibit extensive dendritic and axonal arborizations, but local protein synthesis is not characterized in these neurons. Here, we investigate messenger RNA (mRNA) localization and translation in mDA neuronal axons and dendrites, both of which release dopamine (DA). Using highly sensitive ribosome-bound RNA sequencing and imaging approaches, we find no evidence for mRNA translation in mDA axons. In contrast, mDA neuronal dendrites in the substantia nigra pars reticulata (SNr) contain ribosomes and mRNAs encoding the major components of DA synthesis, release, and reuptake machinery. Surprisingly, we also observe dendritic localization of mRNAs encoding synaptic vesicle-related proteins, including those involved in exocytic fusion. Our results are consistent with a role for local translation in the regulation of DA release from dendrites, but not from axons. Our translatome data define a molecular signature of sparse mDA neurons in the SNr, including the enrichment of Atp2a3/SERCA3, an atypical ER calcium pump. Local translation regulates the subcellular proteome in neurons but has not been characterized in midbrain dopamine neurons, cells with large dendrites and axonal arborizations. Hobson et al. investigate messenger RNA localization and translation in midbrain dopamine neurons in the mouse brain, finding ribosomes and dopaminergic mRNAs in dendrites, but not axons.
Collapse
Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York 10032, NY, USA; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Linghao Kong
- Department of Systems Biology, Columbia University Irving Medical Center, New York 10032, NY, USA
| | - Maria Florencia Angelo
- Interdisciplinary Institute for Neuroscience, Université de Bordeaux, Bordeaux, France; Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France
| | - Ori J Lieberman
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Etienne Herzog
- Interdisciplinary Institute for Neuroscience, Université de Bordeaux, Bordeaux, France; Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York 10032, NY, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| |
Collapse
|
7
|
Wang DO. Epitranscriptomic regulation of cognitive development and decline. Semin Cell Dev Biol 2021; 129:3-13. [PMID: 34857470 DOI: 10.1016/j.semcdb.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Functional genomics and systems biology have opened new doors to previously inaccessible genomic information and holistic approaches to study complex networks of genes and proteins in the central nervous system. The advances are revolutionizing our understanding of the genetic underpinning of cognitive development and decline by facilitating identifications of novel molecular regulators and physiological pathways underlying brain function, and by associating polymorphism and mutations to cognitive dysfunction and neurological diseases. However, our current understanding of these complex gene regulatory mechanisms has yet lacked sufficient mechanistic resolution for further translational breakthroughs. Here we review recent findings from the burgeoning field of epitranscriptomics in association of cognitive functions with a special focus on the epitranscritomic regulation in subcellular locations such as chromosome, synapse, and mitochondria. Although there are important gaps in knowledge, current evidence is suggesting that this layer of RNA regulation may be of particular interest for the spatiotemporally coordinated regulation of gene networks in developing and maintaining brain function that underlie cognitive changes.
Collapse
Affiliation(s)
- Dan Ohtan Wang
- Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Yoshida Hon-machi, Kyoto 606-8501, Japan.
| |
Collapse
|
8
|
Kharod SC, Hwang DW, Das S, Yoon YJ. Spatiotemporal Insights Into RNA-Organelle Interactions in Neurons. Front Cell Dev Biol 2021; 9:663367. [PMID: 34178987 PMCID: PMC8222803 DOI: 10.3389/fcell.2021.663367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Neurons exhibit spatial compartmentalization of gene expression where localization of messenger RNAs (mRNAs) to distal processes allows for site-specific distribution of proteins through local translation. Recently, there have been reports of coordination between mRNA transport with vesicular and organellar trafficking. In this review, we will highlight the latest literature on axonal and dendritic local protein synthesis with links to mRNA-organelle cotransport followed by emerging technologies necessary to study these phenomena. Recent high-resolution imaging studies have led to insights into the dynamics of RNA-organelle interactions, and we can now peer into these intricate interactions within subcellular compartments of neurons.
Collapse
Affiliation(s)
- Shivani C Kharod
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Dong-Woo Hwang
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| |
Collapse
|
9
|
Lazebny OE, Kulikov AM, Butovskaya PR, Proshakov PA, Fokin AV, Butovskaya ML. Analysis of Aggressive Behavior in Young Russian Males Using 250 SNP Markers. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420080098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|