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Brito DVC, Kupke J, Sokolov R, Cambridge S, Both M, Bengtson CP, Rozov A, Oliveira AMM. Biphasic Npas4 expression promotes inhibitory plasticity and suppression of fear memory consolidation in mice. Mol Psychiatry 2024:10.1038/s41380-024-02454-3. [PMID: 38347124 DOI: 10.1038/s41380-024-02454-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
Long-term memories are believed to be encoded by unique transcriptional signatures in the brain. The expression of immediate early genes (IEG) promotes structural and molecular changes required for memory consolidation. Recent evidence has shown that the brain is equipped with mechanisms that not only promote, but actively constrict memory formation. However, it remains unknown whether IEG expression may play a role in memory suppression. Here we uncovered a novel function of the IEG neuronal PAS domain protein 4 (Npas4), as an inducible memory suppressor gene of highly salient aversive experiences. Using a contextual fear conditioning paradigm, we found that low stimulus salience leads to monophasic Npas4 expression, while highly salient learning induces a biphasic expression of Npas4 in the hippocampus. The later phase requires N-methyl-D-aspartate (NMDA) receptor activity and is independent of dopaminergic neurotransmission. Our in vivo pharmacological and genetic manipulation experiments suggested that the later phase of Npas4 expression restricts the consolidation of a fear memory and promote behavioral flexibility, by facilitating fear extinction and the contextual specificity of fear responses. Moreover, immunofluorescence and electrophysiological analysis revealed a concomitant increase in synaptic input from cholecystokinin (CCK)-expressing interneurons. Our results demonstrate how salient experiences evoke unique temporal patterns of IEG expression that fine-tune memory consolidation. Moreover, our study provides evidence for inducible gene expression associated with memory suppression as a possible mechanism to balance the consolidation of highly salient memories, and thereby to evade the formation of maladaptive behavior.
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Affiliation(s)
- David V C Brito
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Janina Kupke
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Rostilav Sokolov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
- Federal Center of Brain Research and Neurotechnology, 117513, Moscow, Russia
- Institute of Neuroscience, Lobachevsky State University of Nizhniy Novgorod, Nizhny, Novgorod, Russia
| | - Sidney Cambridge
- Anatomy II, Dr. Senckenberg Anatomy, Goethe-University Frankfurt, 60590, Frankfurt am Main, Germany
| | - Martin Both
- Institute of Physiology and Pathophysiology, Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - C Peter Bengtson
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
| | - Andrei Rozov
- Federal Center of Brain Research and Neurotechnology, 117513, Moscow, Russia
- Institute of Physiology and Pathophysiology, Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
- OpenLab of Neurobiology, Kazan Federal University, 420008, Kazan, Russia
| | - Ana M M Oliveira
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany.
- Department of Molecular and Cellular Cognition Research, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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Bahl E, Chatterjee S, Mukherjee U, Elsadany M, Vanrobaeys Y, Lin LC, McDonough M, Resch J, Giese KP, Abel T, Michaelson JJ. Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data. Nat Commun 2024; 15:779. [PMID: 38278804 PMCID: PMC10817898 DOI: 10.1038/s41467-023-44503-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/15/2023] [Indexed: 01/28/2024] Open
Abstract
Neuronal activity-dependent transcription directs molecular processes that regulate synaptic plasticity, brain circuit development, behavioral adaptation, and long-term memory. Single cell RNA-sequencing technologies (scRNAseq) are rapidly developing and allow for the interrogation of activity-dependent transcription at cellular resolution. Here, we present NEUROeSTIMator, a deep learning model that integrates transcriptomic signals to estimate neuronal activation in a way that we demonstrate is associated with Patch-seq electrophysiological features and that is robust against differences in species, cell type, and brain region. We demonstrate this method's ability to accurately detect neuronal activity in previously published studies of single cell activity-induced gene expression. Further, we applied our model in a spatial transcriptomic study to identify unique patterns of learning-induced activity across different brain regions in male mice. Altogether, our findings establish NEUROeSTIMator as a powerful and broadly applicable tool for measuring neuronal activation, whether as a critical covariate or a primary readout of interest.
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Affiliation(s)
- Ethan Bahl
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
| | - Utsav Mukherjee
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, USA
| | - Muhammad Elsadany
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
| | - Miriam McDonough
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Molecular Medicine, University of Iowa, Iowa City, IA, USA
| | - Jon Resch
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Ted Abel
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Neuroscience & Pharmacology, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA.
- Department of Communication Sciences & Disorders, University of Iowa, Iowa City, IA, USA.
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53
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Jiang C, Huang H, Yang X, Le Q, Liu X, Ma L, Wang F. Targeting mitochondrial dynamics of morphine-responsive dopaminergic neurons ameliorates opiate withdrawal. J Clin Invest 2024; 134:e171995. [PMID: 38236644 PMCID: PMC10904060 DOI: 10.1172/jci171995] [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: 05/03/2023] [Accepted: 01/11/2024] [Indexed: 03/02/2024] Open
Abstract
Converging studies demonstrate the dysfunction of the dopaminergic neurons following chronic opioid administration. However, the therapeutic strategies targeting opioid-responsive dopaminergic ensembles that contribute to the development of opioid withdrawal remain to be elucidated. Here, we used the neuronal activity-dependent Tet-Off system to label dopaminergic ensembles in response to initial morphine exposure (Mor-Ens) in the ventral tegmental area (VTA). Fiber optic photometry recording and transcriptome analysis revealed downregulated spontaneous activity and dysregulated mitochondrial respiratory, ultrastructure, and oxidoreductase signal pathways after chronic morphine administration in these dopaminergic ensembles. Mitochondrial fragmentation and the decreased mitochondrial fusion gene mitofusin 1 (Mfn1) were found in these ensembles after prolonged opioid withdrawal. Restoration of Mfn1 in the dopaminergic Mor-Ens attenuated excessive oxidative stress and the development of opioid withdrawal. Administration of Mdivi-1, a mitochondrial fission inhibitor, ameliorated the mitochondrial fragmentation and maladaptation of the neuronal plasticity in these Mor-Ens, accompanied by attenuated development of opioid withdrawal after chronic morphine administration, without affecting the analgesic effect of morphine. These findings highlighted the plastic architecture of mitochondria as a potential therapeutic target for opioid analgesic-induced substance use disorders.
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Affiliation(s)
- Changyou Jiang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Han Huang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Xiao Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Qiumin Le
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Xing Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Lan Ma
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Feifei Wang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Basic Medical Sciences, Departments of Neurosurgery and Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
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Boor SA, Meisel JD, Kim DH. Neuroendocrine gene expression coupling of interoceptive bacterial food cues to foraging behavior of C. elegans. eLife 2024; 12:RP91120. [PMID: 38231572 PMCID: PMC10945577 DOI: 10.7554/elife.91120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Animal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematode Caenorhabditis elegans, distinct cues from bacterial food - interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria - act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression of daf-7 from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, the C. elegans ortholog of mammalian anaplastic lymphoma kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrine daf-7 expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors in C. elegans. Our data suggest that the expression of daf-7 from the ASJ neurons contributes to and is correlated with an internal state of 'unmet need' that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.
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Affiliation(s)
- Sonia A Boor
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical SchoolBostonUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Joshua D Meisel
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
| | - Dennis H Kim
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical SchoolBostonUnited States
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55
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Huang LC, McKeown CR, He HY, Ta AC, Cline HT. BRCA1 and ELK-1 regulate neural progenitor cell fate in the optic tectum in response to visual experience in Xenopus laevis tadpoles. Proc Natl Acad Sci U S A 2024; 121:e2316542121. [PMID: 38198524 PMCID: PMC10801852 DOI: 10.1073/pnas.2316542121] [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: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
In developing Xenopus tadpoles, the optic tectum begins to receive patterned visual input while visuomotor circuits are still undergoing neurogenesis and circuit assembly. This visual input regulates neural progenitor cell fate decisions such that maintaining tadpoles in the dark increases proliferation, expanding the progenitor pool, while visual stimulation promotes neuronal differentiation. To identify regulators of activity-dependent neural progenitor cell fate, we profiled the transcriptomes of proliferating neural progenitor cells and newly differentiated neurons using RNA-Seq. We used advanced bioinformatic analysis of 1,130 differentially expressed transcripts to identify six differentially regulated transcriptional regulators, including Breast Cancer 1 (BRCA1) and the ETS-family transcription factor, ELK-1, which are predicted to regulate the majority of the other differentially expressed transcripts. BRCA1 is known for its role in cancers, but relatively little is known about its potential role in regulating neural progenitor cell fate. ELK-1 is a multifunctional transcription factor which regulates immediate early gene expression. We investigated the potential functions of BRCA1 and ELK-1 in activity-regulated neurogenesis in the tadpole visual system using in vivo time-lapse imaging to monitor the fate of GFP-expressing SOX2+ neural progenitor cells in the optic tectum. Our longitudinal in vivo imaging analysis showed that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 and ELK-1 expression. These studies provide insight into the potential mechanisms by which neural activity affects neural progenitor cell fate.
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Affiliation(s)
- Lin-Chien Huang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Caroline R. McKeown
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hai-Yan He
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Aaron C. Ta
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hollis T. Cline
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
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56
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Ma Y, Bendl J, Hartley BJ, Fullard JF, Abdelaal R, Ho SM, Kosoy R, Gochman P, Rapoport J, Hoffman GE, Brennand KJ, Roussos P. Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders. Biol Psychiatry 2024; 95:187-198. [PMID: 37454787 PMCID: PMC10787819 DOI: 10.1016/j.biopsych.2023.07.003] [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: 10/12/2022] [Revised: 06/07/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Converging evidence from large-scale genetic and postmortem studies highlights the role of aberrant neurotransmission and genetic regulation in brain-related disorders. However, identifying neuronal activity-regulated transcriptional programs in the human brain and understanding how changes contribute to disease remain challenging. METHODS To better understand how the activity-dependent regulome contributes to risk for brain-related disorders, we profiled the transcriptomic and epigenomic changes following neuronal depolarization in human induced pluripotent stem cell-derived glutamatergic neurons (NGN2) from 6 patients with schizophrenia and 5 control participants. RESULTS Multiomic data integration associated global patterns of chromatin accessibility with gene expression and identified enhancer-promoter interactions in glutamatergic neurons. Within 1 hour of potassium chloride-induced depolarization, independent of diagnosis, glutamatergic neurons displayed substantial activity-dependent changes in the expression of genes regulating synaptic function. Depolarization-induced changes in the regulome revealed significant heritability enrichment for schizophrenia and Parkinson's disease, adding to mounting evidence that sequence variation within activation-dependent regulatory elements contributes to the genetic risk for brain-related disorders. Gene coexpression network analysis elucidated interactions among activity-dependent and disease-associated genes and pointed to a key driver (NAV3) that interacted with multiple genes involved in axon guidance. CONCLUSIONS Overall, we demonstrated that deciphering the activity-dependent regulome in glutamatergic neurons reveals novel targets for advanced diagnosis and therapy.
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Affiliation(s)
- Yixuan Ma
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brigham J Hartley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rawan Abdelaal
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - Seok-Man Ho
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York
| | - Roman Kosoy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Judith Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, New York, New York.
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, New York; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, New York.
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Ling E, Nemesh J, Goldman M, Kamitaki N, Reed N, Handsaker RE, Genovese G, Vogelgsang JS, Gerges S, Kashin S, Ghosh S, Esposito JM, French K, Meyer D, Lutservitz A, Mullally CD, Wysoker A, Spina L, Neumann A, Hogan M, Ichihara K, Berretta S, McCarroll SA. Concerted neuron-astrocyte gene expression declines in aging and schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574148. [PMID: 38260461 PMCID: PMC10802483 DOI: 10.1101/2024.01.07.574148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a striking relationship between people's cortical neurons and cortical astrocytes. We used single-nucleus RNA-seq to analyze the prefrontal cortex of 191 human donors ages 22-97 years, including healthy individuals and persons with schizophrenia. Latent-factor analysis of these data revealed that in persons whose cortical neurons more strongly expressed genes for synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the Synaptic Neuron-and-Astrocyte Program (SNAP). In schizophrenia and aging - two conditions that involve declines in cognitive flexibility and plasticity 1,2 - cells had divested from SNAP: astrocytes, glutamatergic (excitatory) neurons, and GABAergic (inhibitory) neurons all reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy persons of similar age, may underlie many aspects of normal human interindividual differences and be an important point of convergence for multiple kinds of pathophysiology.
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Affiliation(s)
- Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nolan Kamitaki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Nora Reed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert E. Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan S. Vogelgsang
- McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alyssa Lutservitz
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher D. Mullally
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Liv Spina
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marina Hogan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kiku Ichihara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Berretta
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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58
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Zhang X, Haeri M, Swerdlow RH, Wang N. Loss of Adaptive DNA Breaks in Alzheimer's Disease Brains. J Alzheimers Dis 2024; 97:1861-1875. [PMID: 38306051 PMCID: PMC10894583 DOI: 10.3233/jad-231303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
Background DNA breaks accumulate in Alzheimer's disease (AD) brains. While their role as true genomic lesions is recognized, DNA breaks also support cognitive function by facilitating the expression of activity-dependent immediate early genes. This process involves TOP2B, a DNA topoisomerase that catalyzes the formation of DNA double-strand breaks. Objective To characterize how AD impacts adaptive DNA breaks at nervous system genes. Methods We leveraged the ability of DNA single- and double-strand breaks to activate poly(ADP-ribose) polymerases (PARPs) that conjugate poly(ADP-ribose) (PAR) to adjacent proteins. To characterize the genomic sites harboring DNA breaks in AD brains, nuclei extracted from 3 AD and 3 non-demented autopsy brains (frontal cortex, all male donors, age 78 to 91 years of age) were analyzed through CUT&RUN in which we targeted PAR with subsequent DNA sequencing. Results Although the AD brains contained 19.9 times more PAR peaks than the non-demented brains, PAR peaks at nervous system genes were profoundly lost in AD brains, and the expression of these genes was downregulated. This result is consistent with our previous CUT&RUN targeting γH2AX, which marks DNA double-strand breaks. In addition, TOP2B expression was significantly decreased in the AD brains. Conclusions Although AD brains contain a net increase in DNA breaks, adaptive DNA breaks at nervous system genes are lost in AD brains. This could potentially reflect diminished TOP2B expression and contribute to impaired neuron function and cognition in AD patients.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mohammad Haeri
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ning Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
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Avarlaid A, Esvald E, Koppel I, Parkman A, Zhuravskaya A, Makeyev EV, Tuvikene J, Timmusk T. An 840 kb distant upstream enhancer is a crucial regulator of catecholamine-dependent expression of the Bdnf gene in astrocytes. Glia 2024; 72:90-110. [PMID: 37632136 PMCID: PMC10952894 DOI: 10.1002/glia.24463] [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: 10/12/2022] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Brain-derived neurotrophic factor (BDNF) plays a fundamental role in the developing and adult nervous system, contributing to neuronal survival, differentiation, and synaptic plasticity. Dysregulation of BDNF synthesis, secretion or signaling has been associated with many neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Although the transcriptional regulation of the Bdnf gene has been extensively studied in neurons, less is known about the regulation and function of BDNF in non-neuronal cells. The most abundant type of non-neuronal cells in the brain, astrocytes, express BDNF in response to catecholamines. However, genetic elements responsible for this regulation have not been identified. Here, we investigated four potential Bdnf enhancer regions and based on reporter gene assays, CRISPR/Cas9 engineering and CAPTURE-3C-sequencing we conclude that a region 840 kb upstream of the Bdnf gene regulates catecholamine-dependent expression of Bdnf in rodent astrocytes. We also provide evidence that this regulation is mediated by CREB and AP1 family transcription factors. This is the first report of an enhancer coordinating the transcription of Bdnf gene in non-neuronal cells.
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Affiliation(s)
- Annela Avarlaid
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Eli‐Eelika Esvald
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
| | - Indrek Koppel
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Annabel Parkman
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
| | - Anna Zhuravskaya
- Centre for Developmental NeurobiologyKing's College LondonLondonUK
| | | | - Jürgen Tuvikene
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
| | - Tõnis Timmusk
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Protobios LLCTallinnEstonia
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Atta-Ur-Rahman. Protein Folding and Molecular Basis of Memory: Molecular Vibrations and Quantum Entanglement as Basis of Consciousness. Curr Med Chem 2024; 31:258-265. [PMID: 37424348 DOI: 10.2174/0929867331666230707123345] [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: 04/30/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/11/2023]
Affiliation(s)
- Atta-Ur-Rahman
- Kings College, University of Cambridge, Cambridge CB2 1st, United Kingdom
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Rocks D, Purisic E, Gallo EF, Greally JM, Suzuki M, Kundakovic M. Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572697. [PMID: 38187614 PMCID: PMC10769422 DOI: 10.1101/2023.12.20.572697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Sex differences are found in brain structure and function across species, and across brain disorders in humans1-3. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan4. Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk5-7. However, due to limited molecular studies in female rodents8, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor9, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation1 in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eric Purisic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eduardo F. Gallo
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - John M. Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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Salery M, Godino A, Xu YQ, Fullard JF, Durand-de Cuttoli R, LaBanca AR, Holt LM, Russo SJ, Roussos P, Nestler EJ. Transcriptional correlates of cocaine-associated learning in striatal ARC ensembles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571585. [PMID: 38168167 PMCID: PMC10760161 DOI: 10.1101/2023.12.13.571585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Learned associations between the rewarding effects of drugs and the context in which they are experienced underlie context-induced relapse. Previous work demonstrates the importance of sparse neuronal populations - called neuronal ensembles - in associative learning and cocaine seeking, but it remains unknown whether the encoding vs. retrieval of cocaine-associated memories involves similar or distinct mechanisms of ensemble activation and reactivation in nucleus accumbens (NAc). We use ArcCreER T2 mice to establish that mostly distinct NAc ensembles are recruited by initial vs. repeated exposures to cocaine, which are then differentially reactivated and exert distinct effects during cocaine-related memory retrieval. Single-nuclei RNA-sequencing of these ensembles demonstrates predominant recruitment of D1 medium spiny neurons and identifies transcriptional properties that are selective to cocaine-recruited NAc neurons and could explain distinct excitability features. These findings fundamentally advance our understanding of how cocaine drives pathological memory formation during repeated exposures.
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Zhang X, Haeri M, Swerdlow RH, Wang N. Loss of Adaptive DNA Breaks in Alzheimer's Disease Brains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.566423. [PMID: 38168316 PMCID: PMC10760021 DOI: 10.1101/2023.12.11.566423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background DNA breaks accumulate in Alzheimer's disease (AD) brains. While their role as true genomic lesions is recognized, DNA breaks also support cognitive function by facilitating the expression of activity-dependent immediate early genes (IEGs). This process involves TOP2B, a DNA topoisomerase that catalyzes the formation of DNA double-strand breaks (DSBs). Objective To characterize how AD impacts adaptive DNA breaks at nervous system genes. Methods We leveraged the ability of DNA single- and double-strand breaks to activate poly(ADP-ribose) polymerases (PARPs) that conjugate poly(ADP-ribose) (PAR) to adjacent proteins. To characterize the genomic sites harboring DNA breaks in AD brains, nuclei extracted from 3 AD and 3 non-demented (ND) autopsy brains (frontal cortex, all male donors, age 78 to 91 years of age) were analyzed through CUT&RUN in which we targeted PAR with subsequent DNA sequencing. Results Although the AD brains contained 19.9 times more PAR peaks than the ND brains, PAR peaks at nervous system genes were profoundly lost in AD brains, and the expression of these genes was downregulated. This result is consistent with our previous CUT&RUN targeting γH2AX, which marks DNA double-strand breaks (DSBs). In addition, TOP2B expression was significantly decreased in the AD brains. Conclusion Although AD brains contain a net increase in DNA breaks, adaptive DNA breaks at nervous system genes are lost in AD brains. This could potentially reflect diminished TOP2B expression and contribute to impaired neuron function and cognition in AD patients.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mohammad Haeri
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ning Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
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Langlieb J, Sachdev NS, Balderrama KS, Nadaf NM, Raj M, Murray E, Webber JT, Vanderburg C, Gazestani V, Tward D, Mezias C, Li X, Flowers K, Cable DM, Norton T, Mitra P, Chen F, Macosko EZ. The molecular cytoarchitecture of the adult mouse brain. Nature 2023; 624:333-342. [PMID: 38092915 PMCID: PMC10719111 DOI: 10.1038/s41586-023-06818-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types and their positions within individual anatomical structures remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq1,2-a recently developed spatial transcriptomics method with near-cellular resolution-across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signalling, elucidated region-specific specializations in activity-regulated gene expression and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource ( www.BrainCellData.org ), should find diverse applications across neuroscience, including the construction of new genetic tools and the prioritization of specific cell types and circuits in the study of brain diseases.
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Affiliation(s)
| | | | | | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mukund Raj
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | - Daniel Tward
- Departments of Computational Medicine and Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Dylan M Cable
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Partha Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell and Regenerative Biology, Cambridge, MA, USA.
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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66
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Liu X, Wang F, Le Q, Ma L. Cellular and molecular basis of drug addiction: The role of neuronal ensembles in addiction. Curr Opin Neurobiol 2023; 83:102813. [PMID: 37972536 DOI: 10.1016/j.conb.2023.102813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Addiction has been conceptualized as a disease of learning and memory. Learned associations between environmental cues and unconditioned rewards induced by drug administration, which play a critical role in addiction, have been shown to be encoded in sparsely distributed populations of neurons called neuronal ensembles. This review aims to highlight how synaptic remodeling and alterations in signaling pathways that occur specifically in neuronal ensembles contribute to the pathogenesis of addiction. Furthermore, a causal link between transcriptional and epigenetic modifications in neuronal ensembles and the development of the addictive state is proposed. Translational studies of molecular and cellular changes in neuronal ensembles that contribute to drug-seeking behavior, will allow the identification of molecular and circuit targets and interventions for substance use disorders.
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Affiliation(s)
- Xing Liu
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, and Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Feifei Wang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, and Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China.
| | - Qiumin Le
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, and Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
| | - Lan Ma
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, and Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, China
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Yang L, Zhang Q, Wu XQ, Qiu XY, Fei F, Lai NX, Zheng YY, Zhang MD, Zhang QY, Wang Y, Wang F, Xu CL, Ruan YP, Wang Y, Chen Z. Chemogenetic inhibition of subicular seizure-activated neurons alleviates cognitive deficit in male mouse epilepsy model. Acta Pharmacol Sin 2023; 44:2376-2387. [PMID: 37488426 PMCID: PMC10692337 DOI: 10.1038/s41401-023-01129-z] [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: 04/07/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023] Open
Abstract
Cognitive deficit is a common comorbidity in temporal lobe epilepsy (TLE) and is not well controlled by current therapeutics. How epileptic seizure affects cognitive performance remains largely unclear. In this study we investigated the role of subicular seizure-activated neurons in cognitive impairment in TLE. A bipolar electrode was implanted into hippocampal CA3 in male mice for kindling stimulation and EEG recording; a special promoter with enhanced synaptic activity-responsive element (E-SARE) was used to label seizure-activated neurons in the subiculum; the activity of subicular seizure-activated neurons was manipulated using chemogenetic approach; cognitive function was assessed in object location memory (OLM) and novel object recognition (NOR) tasks. We showed that chemogenetic inhibition of subicular seizure-activated neurons (mainly CaMKIIα+ glutamatergic neurons) alleviated seizure generalization and improved cognitive performance, but inhibition of seizure-activated GABAergic interneurons had no effect on seizure and cognition. For comparison, inhibition of the whole subicular CaMKIIα+ neuron impaired cognitive function in naïve mice in basal condition. Notably, chemogenetic inhibition of subicular seizure-activated neurons enhanced the recruitment of cognition-responsive c-fos+ neurons via increasing neural excitability during cognition tasks. Our results demonstrate that subicular seizure-activated neurons contribute to cognitive impairment in TLE, suggesting seizure-activated neurons as the potential therapeutic target to alleviate cognitive impairment in TLE.
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Affiliation(s)
- Lin Yang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qi Zhang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xue-Qing Wu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiao-Yun Qiu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Fan Fei
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- Zhejiang Rehabilitation Medical Center, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310013, China
| | - Nan-Xi Lai
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yu-Yi Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Meng-di Zhang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qing-Yang Zhang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu Wang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Fei Wang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Ceng-Lin Xu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Ye-Ping Ruan
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yi Wang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
- Zhejiang Rehabilitation Medical Center, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310013, China.
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- Epilepsy Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
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Ma L, Wang F, Li Y, Wang J, Chang Q, Du Y, Sadan J, Zhao Z, Fan G, Yao B, Chen JF. Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation. Nat Commun 2023; 14:7829. [PMID: 38030616 PMCID: PMC10687003 DOI: 10.1038/s41467-023-43497-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
How early life experience is translated into storable epigenetic information leading to behavioral changes remains poorly understood. Here we found that Zika virus (ZIKV) induced-maternal immune activation (MIA) imparts offspring with anxiety- and depression-like behavior. By integrating bulk and single-nucleus RNA sequencing (snRNA-seq) with genome-wide 5hmC (5-hydroxymethylcytosine) profiling and 5mC (5-methylcytosine) profiling in prefrontal cortex (PFC) of ZIKV-affected male offspring mice, we revealed an overall loss of 5hmC and an increase of 5mC levels in intragenic regions, associated with transcriptional changes in neuropsychiatric disorder-related genes. In contrast to their rapid initiation and inactivation in normal conditions, immediate-early genes (IEGs) remain a sustained upregulation with enriched expression in excitatory neurons, which is coupled with increased 5hmC and decreased 5mC levels of IEGs in ZIKV-affected male offspring. Thus, MIA induces maladaptive methylome remodeling in brain and selectively regulates neuronal activity gene methylation linking to emotional behavioral abnormalities in offspring.
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Affiliation(s)
- Li Ma
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Feng Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jing Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Qing Chang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Yuanning Du
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jotham Sadan
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Zhen Zhao
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA.
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Boor SA, Meisel JD, Kim DH. Neuroendocrine Gene Expression Coupling of Interoceptive Bacterial Food Cues to Foraging Behavior of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.15.549072. [PMID: 37503081 PMCID: PMC10369937 DOI: 10.1101/2023.07.15.549072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Animal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematode Caenorhabditis elegans, distinct cues from bacterial food - interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria - act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression of daf-7 from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, the C. elegans ortholog of mammalian Anaplastic Lymphoma Kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrine daf-7 expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors in C. elegans. Our data suggest that the expression of daf-7 from the ASJ neurons contributes to and is correlated with an internal state of "unmet need" that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.
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Affiliation(s)
- Sonia A. Boor
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joshua D. Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Dennis H. Kim
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115
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70
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Rummel CK, Gagliardi M, Ahmad R, Herholt A, Jimenez-Barron L, Murek V, Weigert L, Hausruckinger A, Maidl S, Hauger B, Raabe FJ, Fürle C, Trastulla L, Turecki G, Eder M, Rossner MJ, Ziller MJ. Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants. Cell 2023; 186:5165-5182.e33. [PMID: 37852259 DOI: 10.1016/j.cell.2023.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/12/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
Abstract
Schizophrenia (SCZ) is a highly heritable mental disorder with thousands of associated genetic variants located mostly in the noncoding space of the genome. Translating these associations into insights regarding the underlying pathomechanisms has been challenging because the causal variants, their mechanisms of action, and their target genes remain largely unknown. We implemented a massively parallel variant annotation pipeline (MVAP) to perform SCZ variant-to-function mapping at scale in disease-relevant neural cell types. This approach identified 620 functional variants (1.7%) that operate in a highly developmental context and neuronal-activity-dependent manner. Multimodal integration of epigenomic and CRISPRi screening data enabled us to link these functional variants to target genes, biological processes, and ultimately alterations of neuronal physiology. These results provide a multistage prioritization strategy to map functional single-nucleotide polymorphism (SNP)-to-gene-to-endophenotype relations and offer biological insights into the context-dependent molecular processes modulated by SCZ-associated genetic variation.
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Affiliation(s)
- Christine K Rummel
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster 48149, Germany
| | - Ruhel Ahmad
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alexander Herholt
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Laura Jimenez-Barron
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Vanessa Murek
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Liesa Weigert
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | | | - Susanne Maidl
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Hauger
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Florian J Raabe
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany
| | | | - Lucia Trastulla
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Technische Universität München Medical Graduate Center Experimental Medicine, Munich 80333, Germany
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Matthias Eder
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Michael J Ziller
- Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Center for Soft Nanoscience, University of Münster, Münster 48149, Germany.
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71
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife 2023; 12:RP89993. [PMID: 37938195 PMCID: PMC10631760 DOI: 10.7554/elife.89993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 hr) enriched for inducible transcription factors and later changes (4 hr) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 hr, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 hr after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - David Reid
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
- Civitan International Research Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
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Fleury S, Kolaric R, Espera J, Ha Q, Tomaio J, Gether U, Sørensen AT, Mingote S. Role of Dopamine Neurons in Familiarity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564006. [PMID: 37961265 PMCID: PMC10634822 DOI: 10.1101/2023.10.25.564006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Dopamine neurons signal the salience of environmental stimuli, influencing learning and motivation. However, research has not yet identified whether dopamine neurons also modulate the salience of memory content. Dopamine neuron activity in the ventral tegmental area (VTA) increases in response to novel objects and diminishes as objects become familiar through repeated presentations. We proposed that the declined rate of dopamine neuron activity during familiarization affects the salience of a familiar object's memory. This, in turn, influences the degree to which an animal distinguishes between familiar and novel objects in a subsequent novel object recognition (NOR) test. As such, a single familiarization session may not sufficiently reduce dopamine activity, allowing the memory of a familiar object to maintain its salience and potentially attenuating NOR. In contrast, multiple familiarization sessions could lead to more pronounced dopamine activity suppression, strengthening NOR. Our data in mice reveals that, compared to a single session, multiple sessions result in decreased VTA dopamine neuron activation, as indicated by c-Fos measurements, and enhanced novelty discrimination. Critically, when VTA dopamine neurons are chemogenetically inhibited during a single familiarization session, NOR improves, mirroring the effects of multiple familiarization sessions. In summary, our findings highlight the pivotal function of dopamine neurons in familiarity and suggest a role in modulating the salience of memory content.
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Affiliation(s)
- Sixtine Fleury
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Rhonda Kolaric
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Justin Espera
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Quan Ha
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Jacquelyn Tomaio
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Andreas Toft Sørensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Susana Mingote
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
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Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.
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74
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Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, Osteen J, Lucero J, Lin L, Yang Q, Zhu Q, Zemke N, Espinoza S, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Hodge RD, Linnarsson S, Bakken T, Levi B, Keene CD, Shang J, Lein E, Wang A, Behrens MM, Ecker JR, Ren B. A comparative atlas of single-cell chromatin accessibility in the human brain. Science 2023; 382:eadf7044. [PMID: 37824643 PMCID: PMC10852054 DOI: 10.1126/science.adf7044] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer's disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.
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Affiliation(s)
- Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Zihan Wang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Henry Jiao
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Chenxu Zhu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Colin Kern
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Nora Emerson
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia Osteen
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Qian Yang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Quan Zhu
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Nathan Zemke
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Sarah Espinoza
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Jingbo Shang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Joseph R Ecker
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
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Barber KR, Vizcarra VS, Zilch A, Majuta L, Diezel CC, Culver OP, Hughes BW, Taniguchi M, Streicher JM, Vanderah TW, Riegel AC. The Role of Ryanodine Receptor 2 in Drug-Associated Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560743. [PMID: 37873212 PMCID: PMC10592901 DOI: 10.1101/2023.10.03.560743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Type-2 ryanodine receptor (RyR2) ion channels facilitate the release of Ca 2+ from stores and serve an important function in neuroplasticity. The role for RyR2 in hippocampal-dependent learning and memory is well established and chronic hyperphosphorylation of RyR2 (RyR2P) is associated with pathological calcium leakage and cognitive disorders, including Alzheimer's disease. By comparison, little is known about the role of RyR2 in the ventral medial prefrontal cortex (vmPFC) circuitry important for working memory, decision making, and reward seeking. Here, we evaluated the basal expression and localization of RyR2 and RyR2P in the vmPFC. Next, we employed an operant model of sucrose, cocaine, or morphine self-administration (SA) followed by a (reward-free) recall test, to reengage vmPFC neurons and reactivate reward-seeking and re-evaluated the expression and localization of RyR2 and RyR2P in vmPFC. Under basal conditions, RyR2 was expressed in pyramidal cells but not regularly detected in PV/SST interneurons. On the contrary, RyR2P was rarely observed in PFC somata and was restricted to a different subcompartment of the same neuron - the apical dendrites of layer-5 pyramidal cells. Chronic SA of drug (cocaine or morphine) and nondrug (sucrose) rewards produced comparable increases in RyR2 protein expression. However, recalling either drug reward impaired the usual localization of RyR2P in dendrites and markedly increased its expression in somata immunoreactive for Fos, a marker of highly activated neurons. These effects could not be explained by chronic stress or drug withdrawal and instead appeared to require a recall experience associated with prior drug SA. In addition to showing the differential distribution of RyR2/RyR2P and affirming the general role of vmPFC in reward learning, this study provides information on the propensity of addictive drugs to redistribute RyR2P ion channels in a neuronal population engaged in drug-seeking. Hence, focusing on the early impact of addictive drugs on RyR2 function may serve as a promising approach to finding a treatment for substance use disorders.
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76
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Hammack RJ, Fischer VE, Andrade MA, Toney GM. Presence of a remote fear memory engram in the central amygdala. Learn Mem 2023; 30:250-259. [PMID: 37802546 PMCID: PMC10561632 DOI: 10.1101/lm.053833.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023]
Abstract
Fear memory formation and recall are highly regulated processes, with the central amygdala (CeA) contributing to fear memory-related behaviors. We recently reported that a remote fear memory engram is resident in the anterior basolateral amygdala (aBLA). However, the extent to which downstream neurons in the CeA participate in this engram is unknown. We tested the hypothesis that CeA neurons activated during fear memory formation are reactivated during remote memory retrieval such that a CeA engram participates in remote fear memory recall and its associated behavior. Using contextual fear conditioning in TRAP2;Ai14 mice, we identified, by persistent Cre-dependent tdTomato expression (i.e., "TRAPing"), CeA neurons that were c-fos-activated during memory formation. Twenty-one days later, we quantified neurons activated during remote memory recall using Fos immunohistochemistry. Dual labeling was used to identify the subpopulation of CeA neurons that was both activated during memory formation and reactivated during recall. Compared with their context-conditioned (no shock) controls, fear-conditioned (electric shock) mice (n = 5/group) exhibited more robust fear memory-related behavior (freezing) as well as larger populations of activated (tdTomato+) and reactivated (dual-labeled) CeA neurons. Most neurons in both groups were mainly located in the capsular CeA subdivision (CeAC). Notably, however, only the size of the TRAPed population distributed throughout the CeA was significantly correlated with time spent freezing during remote fear memory recall. Our findings indicate that fear memory formation robustly activates CeA neurons and that a subset located mainly in the CeAC may contribute to both remote fear memory storage/retrieval and the resulting fear-like behavior.
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Affiliation(s)
- Robert J Hammack
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Victoria E Fischer
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Mary Ann Andrade
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Glenn M Toney
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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77
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Vanrobaeys Y, Mukherjee U, Langmack L, Beyer SE, Bahl E, Lin LC, Michaelson JJ, Abel T, Chatterjee S. Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation. Nat Commun 2023; 14:6100. [PMID: 37773230 PMCID: PMC10541893 DOI: 10.1038/s41467-023-41715-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Memory consolidation involves discrete patterns of transcriptional events in the hippocampus. Despite the emergence of single-cell transcriptomic profiling techniques, mapping the transcriptomic signature across subregions of the hippocampus has remained challenging. Here, we utilized unbiased spatial sequencing to delineate transcriptome-wide gene expression changes across subregions of the dorsal hippocampus of male mice following learning. We find that each subregion of the hippocampus exhibits distinct yet overlapping transcriptomic signatures. The CA1 region exhibited increased expression of genes related to transcriptional regulation, while the DG showed upregulation of genes associated with protein folding. Importantly, our approach enabled us to define the transcriptomic signature of learning within two less-defined hippocampal subregions, CA1 stratum radiatum, and oriens. We demonstrated that CA1 subregion-specific expression of a transcription factor subfamily has a critical functional role in the consolidation of long-term memory. This work demonstrates the power of spatial molecular approaches to reveal simultaneous transcriptional events across the hippocampus during memory consolidation.
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Affiliation(s)
- Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, 52242, USA
| | - Lucy Langmack
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Biochemistry and Molecular Biology Graduate Program, University of Iowa, Iowa City, IA, USA
| | - Stacy E Beyer
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Li-Chun Lin
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
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Savell KE, Madangopal R, Saravanan P, Palaganas RG, Woods KD, Thompson DJ, Drake OR, Brenner MB, Weber SJ, Van Leer E, Choi JH, Martin TL, Martin JC, Steinberg MK, Austin JW, Charendoff CI, Hope BT. MultipleXed Population Selection and Enrichment single nucleus RNA sequencing (XPoSE-seq) enables sample identity retention during transcriptional profiling of rare populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559834. [PMID: 38196637 PMCID: PMC10775316 DOI: 10.1101/2023.09.27.559834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Single nucleus RNA-sequencing is critical in deciphering tissue heterogeneity and identifying rare populations. However, current high throughput techniques are not optimized for rare target populations and require tradeoffs in design due to feasibility. We provide a novel snRNA pipeline, MulipleXed Population Selection and Enrichment snRNA-sequencing (XPoSE-seq), to enable targeted snRNA-seq experiments and in-depth transcriptomic characterization of rare target populations while retaining individual sample identity.
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Affiliation(s)
- Katherine E Savell
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Rajtarun Madangopal
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Padmashri Saravanan
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Ryan G Palaganas
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Kareem D Woods
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Drake J Thompson
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Olivia R Drake
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Megan B Brenner
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Sophia J Weber
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Elise Van Leer
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Jae H Choi
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Toni L Martin
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | | | | | | | | | - Bruce T Hope
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
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79
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Bijoch Ł, Klos J, Pękała M, Fiołna K, Kaczmarek L, Beroun A. Diverse processing of pharmacological and natural rewards by the central amygdala. Cell Rep 2023; 42:113036. [PMID: 37616162 DOI: 10.1016/j.celrep.2023.113036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/03/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The central amygdala (CeA) with its medial (CeM) and lateral (CeL) nuclei is the brain hub for processing stimuli with emotional context. CeL nucleus gives a strong inhibitory input to the CeM, and this local circuitry assigns values (positive or negative) to incoming stimuli, guiding appropriate behavior (approach or avoid). However, the particular involvement of CeA in processing such emotionally relevant information and adaptations of the CeA circuitry are not yet well understood. In this study, we examined synaptic plasticity in the CeA after exposure to two types of rewards, pharmacological (cocaine) and natural (sugar). We found that both rewards engage CeM, where they generate silent synapses resulting in the strengthening of the network. However, only cocaine triggers plasticity in the CeL, which leads to the weakening of its excitatory inputs. Finally, chemogenetic inhibition of CeM attenuates animal preference for sugar, while activation delays cocaine-induced increase in locomotor activity.
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Affiliation(s)
- Łukasz Bijoch
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neuronal Plasticity, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland
| | - Joanna Klos
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neuronal Plasticity, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland
| | - Martyna Pękała
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland
| | - Kristina Fiołna
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neuronal Plasticity, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland; Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland
| | - Leszek Kaczmarek
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland
| | - Anna Beroun
- Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Laboratory of Neuronal Plasticity, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, L. Pasteura 3, 02-093 Warsaw, Poland.
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80
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Tsukahara T, Kethireddy S, Bonefas K, Chen A, Sutton BLM, Dou Y, Iwase S, Sutton MA. Division of labor among H3K4 Methyltransferases Defines Distinct Facets of Homeostatic Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558734. [PMID: 37790395 PMCID: PMC10542164 DOI: 10.1101/2023.09.20.558734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Heterozygous mutations in any of the six H3K4 methyltransferases (KMT2s) result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of this enzyme family in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionarily conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies: KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.
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Affiliation(s)
- Takao Tsukahara
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Saini Kethireddy
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan
| | - Katherine Bonefas
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Brendan LM Sutton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Yali Dou
- Department of Medicine and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Shigeki Iwase
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Michael A. Sutton
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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81
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Chatterjee S, Park BJ, Vanrobaeys Y, Heiney SA, Rhone AE, Nourski KV, Langmack L, Mukherjee U, Kovach CK, Kocsis Z, Kikuchi Y, Petkov CI, Hefti MM, Bahl E, Michaelson JJ, Kawasaki H, Oya H, Howard MA, Nickl-Jockschat T, Lin LC, Abel T. Activity-induced gene expression in the human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558812. [PMID: 37790527 PMCID: PMC10542502 DOI: 10.1101/2023.09.21.558812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Activity-induced gene expression underlies synaptic plasticity and brain function. Here, using molecular sequencing techniques, we define activity-dependent transcriptomic and epigenomic changes at the tissue and single-cell level in the human brain following direct electrical stimulation of the anterior temporal lobe in patients undergoing neurosurgery. Genes related to transcriptional regulation and microglia-specific cytokine activity displayed the greatest induction pattern, revealing a precise molecular signature of neuronal activation in the human brain.
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Affiliation(s)
- Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Brian J. Park
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Shane A. Heiney
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Neural Circuits and Behavior Core, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ariane E. Rhone
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Kirill V. Nourski
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Lucy Langmack
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Christopher K. Kovach
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Zsuzsanna Kocsis
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Yukiko Kikuchi
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Christopher I. Petkov
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Biosciences Institute, Newcastle University Medical School, Newcastle upon Tyne, UK
| | - Marco M. Hefti
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Ethan Bahl
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Hiroyuki Oya
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Matthew A. Howard
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Thomas Nickl-Jockschat
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Li-Chun Lin
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Iowa NeuroBank Core, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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82
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Lee H, Boor SA, Hilbert ZA, Meisel JD, Park J, Wang Y, McKeown R, Fischer SEJ, Andersen EC, Kim DH. Genetic Variants That Modify the Neuroendocrine Regulation of Foraging Behavior in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.556976. [PMID: 37745484 PMCID: PMC10515746 DOI: 10.1101/2023.09.09.556976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The molecular mechanisms underlying diversity in animal behavior are not well understood. A major experimental challenge is determining the contribution of genetic variants that affect neuronal gene expression to differences in behavioral traits. The neuroendocrine TGF-beta ligand, DAF-7, regulates diverse behavioral responses of Caenorhabditis elegans to bacterial food and pathogens. The dynamic neuron-specific expression of daf-7 is modulated by environmental and endogenous bacteria-derived cues. Here, we investigated natural variation in the expression of daf-7 from the ASJ pair of chemosensory neurons and identified common variants in gap-2, encoding a GTPase-Activating Protein homologous to mammalian SynGAP proteins, which modify daf-7 expression cell-non-autonomously and promote exploratory foraging behavior in a DAF-7-dependent manner. Our data connect natural variation in neuron-specific gene expression to differences in behavior and suggest that genetic variation in neuroendocrine signaling pathways mediating host-microbe interactions may give rise to diversity in animal behavior.
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Affiliation(s)
- Harksun Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School; Boston, 02115, USA
| | - Sonia A. Boor
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School; Boston, 02115, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, 02139, USA
| | - Zoë A. Hilbert
- Department of Biology, Massachusetts Institute of Technology; Cambridge, 02139, USA
| | - Joshua D. Meisel
- Department of Biology, Massachusetts Institute of Technology; Cambridge, 02139, USA
| | - Jaeseok Park
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School; Boston, 02115, USA
| | - Ye Wang
- Department of Molecular Biosciences, Northwestern University; Evanston, 60208, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University; Evanston, 60208, USA
| | - Sylvia E. J. Fischer
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School; Boston, 02115, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University; Evanston, 60208, USA
| | - Dennis H. Kim
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School; Boston, 02115, USA
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83
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Ulloa Severino FP, Lawal OO, Sakers K, Wang S, Kim N, Friedman AD, Johnson SA, Sriworarat C, Hughes RH, Soderling SH, Kim IH, Yin HH, Eroglu C. Training-induced circuit-specific excitatory synaptogenesis in mice is required for effort control. Nat Commun 2023; 14:5522. [PMID: 37684234 PMCID: PMC10491649 DOI: 10.1038/s41467-023-41078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Synaptogenesis is essential for circuit development; however, it is unknown whether it is critical for the establishment and performance of goal-directed voluntary behaviors. Here, we show that operant conditioning via lever-press for food reward training in mice induces excitatory synapse formation onto a subset of anterior cingulate cortex neurons projecting to the dorsomedial striatum (ACC→DMS). Training-induced synaptogenesis is controlled by the Gabapentin/Thrombospondin receptor α2δ-1, which is an essential neuronal protein for proper intracortical excitatory synaptogenesis. Using germline and conditional knockout mice, we found that deletion of α2δ-1 in the adult ACC→DMS circuit diminishes training-induced excitatory synaptogenesis. Surprisingly, this manipulation does not impact learning but results in a significant increase in effort exertion without affecting sensitivity to reward value or changing contingencies. Bidirectional optogenetic manipulation of ACC→DMS neurons rescues or phenocopies the behaviors of the α2δ-1 cKO mice, highlighting the importance of synaptogenesis within this cortico-striatal circuit in regulating effort exertion.
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Affiliation(s)
- Francesco Paolo Ulloa Severino
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA.
- Cajal Institute (CSIC), Madrid, 28001, Spain.
| | | | - Kristina Sakers
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shiyi Wang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Namsoo Kim
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA
| | | | - Sarah Anne Johnson
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | | | - Ryan H Hughes
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA
| | - Il Hwan Kim
- Department of Anatomy & Neurobiology, University of Tennessee Health and Science Center, Memphis, TN, 38103, USA
| | - Henry H Yin
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA.
| | - Cagla Eroglu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27710, USA.
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84
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Roethler O, Zohar E, Cohen-Kashi Malina K, Bitan L, Gabel HW, Spiegel I. Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex. Neuron 2023; 111:2693-2708.e8. [PMID: 37354902 DOI: 10.1016/j.neuron.2023.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)-in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.
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Affiliation(s)
- Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Zohar
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Harrison Wren Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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85
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Yip KYT, Gräff J. Tissue clearing applications in memory engram research. Front Behav Neurosci 2023; 17:1181818. [PMID: 37700912 PMCID: PMC10493294 DOI: 10.3389/fnbeh.2023.1181818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/26/2023] [Indexed: 09/14/2023] Open
Abstract
A memory engram is thought to be the physical substrate of the memory trace within the brain, which is generally depicted as a neuronal ensemble activated by learning to fire together during encoding and retrieval. It has been postulated that engram cell ensembles are functionally interconnected across multiple brain regions to store a single memory as an "engram complex", but visualizing this engram complex across the whole brain has for long been hindered by technical limitations. With the recent development of tissue clearing techniques, advanced light-sheet microscopy, and automated 3D image analysis, it has now become possible to generate a brain-wide map of engram cells and thereby to visualize the "engram complex". In this review, we first provide a comprehensive summary of brain-wide engram mapping studies to date. We then compile a guide on implementing the optimal tissue clearing technique for engram tagging approaches, paying particular attention to visualize engram reactivation as a critical mnemonic property, for which whole-brain multiplexed immunostaining becomes a challenging prerequisite. Finally, we highlight the potential of tissue clearing to simultaneously shed light on both the circuit connectivity and molecular underpinnings of engram cells in a single snapshot. In doing so, novel brain regions and circuits can be identified for subsequent functional manipulation, thus providing an opportunity to robustly examine the "engram complex" underlying memory storage.
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Affiliation(s)
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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86
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Gu X, Nardone C, Kamitaki N, Mao A, Elledge SJ, Greenberg ME. The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation. Science 2023; 381:eadh5021. [PMID: 37616343 PMCID: PMC10617673 DOI: 10.1126/science.adh5021] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs mechanistically is unclear. Here, we found that midnolin promoted the destruction of many nuclear proteins, including transcription factors encoded by the immediate-early genes. Diverse stimuli induced midnolin, and its overexpression was sufficient to cause the degradation of its targets by a mechanism that did not require ubiquitination. Instead, midnolin associated with the proteasome via an α helix, used its Catch domain to bind a region within substrates that can form a β strand, and used a ubiquitin-like domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.
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Affiliation(s)
- Xin Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Aoyue Mao
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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87
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543489. [PMID: 37333110 PMCID: PMC10274686 DOI: 10.1101/2023.06.02.543489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 h) enriched for inducible transcription factors and later changes (4 h) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 h, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 h after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Reid
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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88
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Singh M, Zhao Y, Gastaldi VD, Wojcik SM, Curto Y, Kawaguchi R, Merino RM, Garcia-Agudo LF, Taschenberger H, Brose N, Geschwind D, Nave KA, Ehrenreich H. Erythropoietin re-wires cognition-associated transcriptional networks. Nat Commun 2023; 14:4777. [PMID: 37604818 PMCID: PMC10442354 DOI: 10.1038/s41467-023-40332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/18/2023] [Indexed: 08/23/2023] Open
Abstract
Recombinant human erythropoietin (rhEPO) has potent procognitive effects, likely hematopoiesis-independent, but underlying mechanisms and physiological role of brain-expressed EPO remained obscure. Here, we provide transcriptional hippocampal profiling of male mice treated with rhEPO. Based on ~108,000 single nuclei, we unmask multiple pyramidal lineages with their comprehensive molecular signatures. By temporal profiling and gene regulatory analysis, we build developmental trajectory of CA1 pyramidal neurons derived from multiple predecessor lineages and elucidate gene regulatory networks underlying their fate determination. With EPO as 'tool', we discover populations of newly differentiating pyramidal neurons, overpopulating to ~200% upon rhEPO with upregulation of genes crucial for neurodifferentiation, dendrite growth, synaptogenesis, memory formation, and cognition. Using a Cre-based approach to visually distinguish pre-existing from newly formed pyramidal neurons for patch-clamp recordings, we learn that rhEPO treatment differentially affects excitatory and inhibitory inputs. Our findings provide mechanistic insight into how EPO modulates neuronal functions and networks.
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Affiliation(s)
- Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany.
| | - Ying Zhao
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Vinicius Daguano Gastaldi
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Sonja M Wojcik
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Yasmina Curto
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ricardo M Merino
- Max Planck Institute for Dynamics and Self-Organization and Campus Institute for Dynamics of Biological Networks, Georg-August-University, Göttingen, Germany
| | | | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany.
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89
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Dobryakova YV, Gerasimov K, Spivak YS, Korotkova T, Koryagina A, Deryabina A, Markevich VA, Bolshakov AP. The Induction of Long-Term Potentiation by Medial Septum Activation under Urethane Anesthesia Can Alter Gene Expression in the Hippocampus. Int J Mol Sci 2023; 24:12970. [PMID: 37629149 PMCID: PMC10454684 DOI: 10.3390/ijms241612970] [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: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
We studied changes in the expression of early genes in hippocampal cells in response to stimulation of the dorsal medial septal area (dMSA), leading to long-term potentiation in the hippocampus. Rats under urethane anesthesia were implanted with stimulating electrodes in the ventral hippocampal commissure and dMSA and a recording electrode in the CA1 area of the hippocampus. We found that high-frequency stimulation (HFS) of the dMSA led to the induction of long-term potentiation in the synapses formed by the ventral hippocampal commissure on the hippocampal CA1 neurons. One hour after dMSA HFS, we collected the dorsal and ventral hippocampi on both the ipsilateral (damaged by the implanted electrode) and contralateral (intact) sides and analyzed the expression of genes by qPCR. The dMSA HFS led to an increase in the expression of bdnf and cyr61 in the ipsilateral hippocampi and egr1 in the ventral contralateral hippocampus. Thus, dMSA HFS under the conditions of degeneration of the cholinergic neurons in the medial septal area prevented the described increase in gene expression. The changes in cyr61 expression appeared to be dependent on the muscarinic M1 receptors. Our data suggest that the induction of long-term potentiation by dMSA activation enhances the expression of select early genes in the hippocampus.
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Affiliation(s)
| | | | | | | | | | | | | | - Alexey P. Bolshakov
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia (K.G.)
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90
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Song J, Dikwella N, Sinske D, Roselli F, Knöll B. SRF deletion results in earlier disease onset in a mouse model of amyotrophic lateral sclerosis. JCI Insight 2023; 8:e167694. [PMID: 37339001 PMCID: PMC10445689 DOI: 10.1172/jci.insight.167694] [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: 12/02/2022] [Accepted: 06/16/2023] [Indexed: 06/22/2023] Open
Abstract
Changes in neuronal activity modulate the vulnerability of motoneurons (MNs) in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). So far, the molecular basis of neuronal activity's impact in ALS is poorly understood. Herein, we investigated the impact of deleting the neuronal activity-stimulated transcription factor (TF) serum response factor (SRF) in MNs of SOD1G93A mice. SRF was present in vulnerable MMP9+ MNs. Ablation of SRF in MNs induced an earlier disease onset starting around 7-8 weeks after birth, as revealed by enhanced weight loss and decreased motor ability. This earlier disease onset in SRF-depleted MNs was accompanied by a mild elevation of neuroinflammation and neuromuscular synapse degeneration, whereas overall MN numbers and mortality were unaffected. In SRF-deficient mice, MNs showed impaired induction of autophagy-encoding genes, suggesting a potentially new SRF function in transcriptional regulation of autophagy. Complementary, constitutively active SRF-VP16 enhanced autophagy-encoding gene transcription and autophagy progression in cells. Furthermore, SRF-VP16 decreased ALS-associated aggregate induction. Chemogenetic modulation of neuronal activity uncovered SRF as having important TF-mediating activity-dependent effects, which might be beneficial to reduce ALS disease burden. Thus, our data identify SRF as a gene regulator connecting neuronal activity with the cellular autophagy program initiated in degenerating MNs.
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Affiliation(s)
- Jialei Song
- Institute of Neurobiochemistry and
- Department of Neurology, Ulm University, Ulm, Germany
| | - Natalie Dikwella
- Institute of Neurobiochemistry and
- Department of Neurology, Ulm University, Ulm, Germany
| | | | - Francesco Roselli
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases-Ulm (DZNE-Ulm), Ulm, Germany
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91
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Tzeplaeff L, Seguin J, Le Gras S, Megat S, Cosquer B, Plassard D, Dieterlé S, Paiva I, Picchiarelli G, Decraene C, Alcala-Vida R, Cassel JC, Merienne K, Dupuis L, Boutillier AL. Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes. Prog Neurobiol 2023; 227:102483. [PMID: 37327984 DOI: 10.1016/j.pneurobio.2023.102483] [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: 12/13/2022] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. Yet, the mechanisms linking FUS mislocalization to hippocampal function and memory formation are still not characterized. Herein, we show that in these mice, the hippocampus paradoxically displays nuclear FUS accumulation. Multi-omic analyses showed that FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in a hippocampal-dependent spatial memory task and displayed decreased dendritic spine density. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events. These data call for further investigation in the neurological phenotype of FUS-related diseases and open therapeutic strategies towards epigenetic drugs.
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Affiliation(s)
- Laura Tzeplaeff
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France; Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France
| | - Jonathan Seguin
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Stéphanie Le Gras
- Université de Strasbourg, CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Salim Megat
- Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France
| | - Brigitte Cosquer
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Damien Plassard
- Université de Strasbourg, CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | | | - Isabel Paiva
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | | | - Charles Decraene
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Rafael Alcala-Vida
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Jean-Christophe Cassel
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Karine Merienne
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Luc Dupuis
- Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France.
| | - Anne-Laurence Boutillier
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France.
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92
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Caglayan E, Ayhan F, Liu Y, Vollmer RM, Oh E, Sherwood CC, Preuss TM, Yi SV, Konopka G. Molecular features driving cellular complexity of human brain evolution. Nature 2023; 620:145-153. [PMID: 37468639 PMCID: PMC11161302 DOI: 10.1038/s41586-023-06338-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
Human-specific genomic changes contribute to the unique functionalities of the human brain1-5. The cellular heterogeneity of the human brain6,7 and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.
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Affiliation(s)
- Emre Caglayan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Fatma Ayhan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuxiang Liu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rachael M Vollmer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emily Oh
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chet C Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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93
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Zhao Z, Parra OP, Musella F, Scrutton-Alvarado N, Fujita SI, Alber F, Yang Y, Yamada T. Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549737. [PMID: 37503219 PMCID: PMC10370079 DOI: 10.1101/2023.07.19.549737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dynamic regulation of gene expression plays a key role in establishing the diverse neuronal cell types in the brain. Recent findings in genome biology suggest that three-dimensional (3D) genome organization has important, but mechanistically poorly understood functions in gene transcription. Beyond local genomic interactions between promoters and enhancers, we find that cerebellar granule neurons undergoing differentiation in vivo exhibit striking increases in long-distance genomic interactions between transcriptionally active genomic loci, which are separated by tens of megabases within a chromosome or located on different chromosomes. Among these interactions, we identify a nuclear subcompartment enriched for near-megabase long enhancers and their associated neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes are differentially recruited to this enhancer-dense subcompartment to help shape the transcriptional identities of granule neuron subtypes in the cerebellum. SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D genome modeling and imaging approaches, reveal that the enhancer-dense subcompartment forms prominent nuclear structures, which we term mega-enhancer bodies. These novel nuclear bodies reside in the nuclear periphery, away from other transcriptionally active structures, including nuclear speckles located in the nuclear interior. Together, our findings define additional layers of higher-order 3D genome organization closely linked to neuronal maturation and identity in the brain.
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94
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Morè L, Privitera L, Cooper DD, Tsogka M, Arthur JSC, Frenguelli BG. MSK1 is required for the beneficial synaptic and cognitive effects of enriched experience across the lifespan. Aging (Albany NY) 2023; 15:6031-6072. [PMID: 37432063 PMCID: PMC10373962 DOI: 10.18632/aging.204833] [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: 02/28/2023] [Accepted: 05/31/2023] [Indexed: 07/12/2023]
Abstract
Positive experiences, such as social interaction, cognitive training and physical exercise, have been shown to ameliorate some of the harms to cognition associated with ageing. Animal models of positive interventions, commonly known as environmental enrichment, strongly influence neuronal morphology and synaptic function and enhance cognitive performance. While the profound structural and functional benefits of enrichment have been appreciated for decades, little is known as to how the environment influences neurons to respond and adapt to these positive sensory experiences. We show that adult and aged male wild-type mice that underwent a 10-week environmental enrichment protocol demonstrated improved performance in a variety of behavioural tasks, including those testing spatial working and spatial reference memory, and an enhancement in hippocampal LTP. Aged animals in particular benefitted from enrichment, performing spatial memory tasks at levels similar to healthy adult mice. Many of these benefits, including in gene expression, were absent in mice with a mutation in an enzyme, MSK1, which is activated by BDNF, a growth factor implicated in rodent and human cognition. We conclude that enrichment is beneficial across the lifespan and that MSK1 is required for the full extent of these experience-induced improvements of cognitive abilities, synaptic plasticity and gene expression.
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Affiliation(s)
- Lorenzo Morè
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Lucia Privitera
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel D. Cooper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Marianthi Tsogka
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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95
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Das S, Lituma PJ, Castillo PE, Singer RH. Maintenance of a short-lived protein required for long-term memory involves cycles of transcription and local translation. Neuron 2023; 111:2051-2064.e6. [PMID: 37100055 PMCID: PMC10330212 DOI: 10.1016/j.neuron.2023.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/03/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Activity-dependent expression of immediate early genes (IEGs) is critical for long-term synaptic remodeling and memory. It remains unknown how IEGs are maintained for memory despite rapid transcript and protein turnover. To address this conundrum, we monitored Arc, an IEG essential for memory consolidation. Using a knockin mouse where endogenous Arc alleles were fluorescently tagged, we performed real-time imaging of Arc mRNA dynamics in individual neurons in cultures and brain tissue. Unexpectedly, a single burst stimulation was sufficient to induce cycles of transcriptional reactivation in the same neuron. Subsequent transcription cycles required translation, whereby new Arc proteins engaged in autoregulatory positive feedback to reinduce transcription. The ensuing Arc mRNAs preferentially localized at sites marked by previous Arc protein, assembling a "hotspot" of translation, and consolidating "hubs" of dendritic Arc. These cycles of transcription-translation coupling sustain protein expression and provide a mechanism by which a short-lived event may support long-term memory.
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Affiliation(s)
- Sulagna Das
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Program in RNA Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
| | - Pablo J Lituma
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Program in RNA Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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96
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Lavertu-Jolin M, Chattopadhyaya B, Chehrazi P, Carrier D, Wünnemann F, Leclerc S, Dumouchel F, Robertson D, Affia H, Saba K, Gopal V, Patel AB, Andelfinger G, Pineyro G, Di Cristo G. Acan downregulation in parvalbumin GABAergic cells reduces spontaneous recovery of fear memories. Mol Psychiatry 2023; 28:2946-2963. [PMID: 37131076 PMCID: PMC10615765 DOI: 10.1038/s41380-023-02085-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/04/2023]
Abstract
While persistence of fear memories is essential for survival, a failure to inhibit fear in response to harmless stimuli is a feature of anxiety disorders. Extinction training only temporarily suppresses fear memory recovery in adults, but it is highly effective in juvenile rodents. Maturation of GABAergic circuits, in particular of parvalbumin-positive (PV+) cells, restricts plasticity in the adult brain, thus reducing PV+ cell maturation could promote the suppression of fear memories following extinction training in adults. Epigenetic modifications such as histone acetylation control gene accessibility for transcription and help couple synaptic activity to changes in gene expression. Histone deacetylase 2 (Hdac2), in particular, restrains both structural and functional synaptic plasticity. However, whether and how Hdac2 controls the maturation of postnatal PV+ cells is not well understood. Here, we show that PV+- cell specific Hdac2 deletion limits spontaneous fear memory recovery in adult mice, while enhancing PV+ cell bouton remodeling and reducing perineuronal net aggregation around PV+ cells in prefrontal cortex and basolateral amygdala. Prefrontal cortex PV+ cells lacking Hdac2, show reduced expression of Acan, a critical perineuronal net component, which is rescued by Hdac2 re-expression. Pharmacological inhibition of Hdac2 before extinction training is sufficient to reduce both spontaneous fear memory recovery and Acan expression in wild-type adult mice, while these effects are occluded in PV+-cell specific Hdac2 conditional knockout mice. Finally, a brief knock-down of Acan expression mediated by intravenous siRNA delivery before extinction training but after fear memory acquisition is sufficient to reduce spontaneous fear recovery in wild-type mice. Altogether, these data suggest that controlled manipulation of PV+ cells by targeting Hdac2 activity, or the expression of its downstream effector Acan, promotes the long-term efficacy of extinction training in adults.
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Affiliation(s)
- Marisol Lavertu-Jolin
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | | | - Pegah Chehrazi
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Denise Carrier
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
| | - Florian Wünnemann
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Heidelberg University, Faculty of Medicine & Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Séverine Leclerc
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
| | - Félix Dumouchel
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Derek Robertson
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
| | - Hicham Affia
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
| | - Kamal Saba
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vijaya Gopal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Anant Bahadur Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gregor Andelfinger
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Graçiela Pineyro
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada
- Department of Pharmacology, Université de Montréal, Montréal, QC, Canada
| | - Graziella Di Cristo
- Centre de Recherche, CHU Sainte-Justine (CHUSJ), Montréal, QC, Canada.
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada.
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97
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Ko B, Yoo JY, Yoo T, Choi W, Dogan R, Sung K, Um D, Lee SB, Kim HJ, Lee S, Beak ST, Park SK, Paik SB, Kim TK, Kim JH. Npas4-mediated dopaminergic regulation of safety memory consolidation. Cell Rep 2023; 42:112678. [PMID: 37379214 DOI: 10.1016/j.celrep.2023.112678] [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: 10/05/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
Amygdala circuitry encodes associations between conditioned stimuli and aversive unconditioned stimuli and also controls fear expression. However, whether and how non-threatening information for unpaired conditioned stimuli (CS-) is discretely processed remains unknown. The fear expression toward CS- is robust immediately after fear conditioning but then becomes negligible after memory consolidation. The synaptic plasticity of the neural pathway from the lateral to the anterior basal amygdala gates the fear expression of CS-, depending upon neuronal PAS domain protein 4 (Npas4)-mediated dopamine receptor D4 (Drd4) synthesis, which is precluded by stress exposure or corticosterone injection. Herein, we show cellular and molecular mechanisms that regulate the non-threatening (safety) memory consolidation, supporting the fear discrimination.
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Affiliation(s)
- BumJin Ko
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jong-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Taesik Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Woochul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Rumeysa Dogan
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kibong Sung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dahun Um
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Su Been Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sangjun Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seung Tae Beak
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Se-Bum Paik
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea.
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98
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Rummel CK, Gagliardi M, Herholt A, Ahmad R, Murek V, Weigert L, Hausruckinger A, Maidl S, Jimenez-Barron L, Trastulla L, Eder M, Rossner M, Ziller MJ. Cell type and condition specific functional annotation of schizophrenia associated non-coding genetic variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.545266. [PMID: 37425902 PMCID: PMC10326990 DOI: 10.1101/2023.06.27.545266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Schizophrenia (SCZ) is a highly polygenic disease and genome wide association studies have identified thousands of genetic variants that are statistically associated with this psychiatric disorder. However, our ability to translate these associations into insights on the disease mechanisms has been challenging since the causal genetic variants, their molecular function and their target genes remain largely unknown. In order to address these questions, we established a functional genomics pipeline in combination with induced pluripotent stem cell technology to functionally characterize ~35,000 non-coding genetic variants associated with schizophrenia along with their target genes. This analysis identified a set of 620 (1.7%) single nucleotide polymorphisms as functional on a molecular level in a highly cell type and condition specific fashion. These results provide a high-resolution map of functional variant-gene combinations and offer comprehensive biological insights into the developmental context and stimulation dependent molecular processes modulated by SCZ associated genetic variation.
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Affiliation(s)
- Christine K. Rummel
- Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Ruhel Ahmad
- Max Planck Institute of Psychiatry, Munich, Germany
| | | | | | | | | | - Laura Jimenez-Barron
- Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Lucia Trastulla
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Mathias Eder
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Moritz Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Michael J. Ziller
- Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry, University of Münster, Münster, Germany
- Center for Soft Nanoscience, University of Münster, Münster, Germany
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99
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Chandra R, Farah F, Muñoz-Lobato F, Bokka A, Benedetti KL, Brueggemann C, Saifuddin MFA, Miller JM, Li J, Chang E, Varshney A, Jimenez V, Baradwaj A, Nassif C, Alladin S, Andersen K, Garcia AJ, Bi V, Nordquist SK, Dunn RL, Garcia V, Tokalenko K, Soohoo E, Briseno F, Kaur S, Harris M, Guillen H, Byrd D, Fung B, Bykov AE, Odisho E, Tsujimoto B, Tran A, Duong A, Daigle KC, Paisner R, Zuazo CE, Lin C, Asundi A, Churgin MA, Fang-Yen C, Bremer M, Kato S, VanHoven MK, L'Étoile ND. Sleep is required to consolidate odor memory and remodel olfactory synapses. Cell 2023; 186:2911-2928.e20. [PMID: 37269832 PMCID: PMC10354834 DOI: 10.1016/j.cell.2023.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 02/02/2023] [Accepted: 05/05/2023] [Indexed: 06/05/2023]
Abstract
Animals with complex nervous systems demand sleep for memory consolidation and synaptic remodeling. Here, we show that, although the Caenorhabditis elegans nervous system has a limited number of neurons, sleep is necessary for both processes. In addition, it is unclear if, in any system, sleep collaborates with experience to alter synapses between specific neurons and whether this ultimately affects behavior. C. elegans neurons have defined connections and well-described contributions to behavior. We show that spaced odor-training and post-training sleep induce long-term memory. Memory consolidation, but not acquisition, requires a pair of interneurons, the AIYs, which play a role in odor-seeking behavior. In worms that consolidate memory, both sleep and odor conditioning are required to diminish inhibitory synaptic connections between the AWC chemosensory neurons and the AIYs. Thus, we demonstrate in a living organism that sleep is required for events immediately after training that drive memory consolidation and alter synaptic structures.
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Affiliation(s)
- Rashmi Chandra
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Fatima Farah
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Fernando Muñoz-Lobato
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anirudh Bokka
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Kelli L Benedetti
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal Brueggemann
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mashel Fatema A Saifuddin
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia M Miller
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joy Li
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Eric Chang
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Aruna Varshney
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Vanessa Jimenez
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Anjana Baradwaj
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Cibelle Nassif
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Sara Alladin
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Kristine Andersen
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Angel J Garcia
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Veronica Bi
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Sarah K Nordquist
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Raymond L Dunn
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Vanessa Garcia
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Kateryna Tokalenko
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Emily Soohoo
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Fabiola Briseno
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Sukhdeep Kaur
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Malcolm Harris
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Hazel Guillen
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Decklin Byrd
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Brandon Fung
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Andrew E Bykov
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Emma Odisho
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Bryan Tsujimoto
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Alan Tran
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Alex Duong
- Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Kevin C Daigle
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebekka Paisner
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Carlos E Zuazo
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christine Lin
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aarati Asundi
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew A Churgin
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martina Bremer
- Department of Mathematics and Statistics, San José State University, San José, CA 95192, USA
| | - Saul Kato
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Miri K VanHoven
- Department of Biological Sciences, San José State University, San José, CA 95192, USA.
| | - Noëlle D L'Étoile
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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100
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Ghaffari LT, Trotti D, Haeusler AR. Differential response of C9orf72 transcripts following neuronal depolarization. iScience 2023; 26:106959. [PMID: 37332610 PMCID: PMC10272498 DOI: 10.1016/j.isci.2023.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
The (G4C2)n nucleotide repeat expansion (NRE) mutation in C9orf72 is the most common genetic cause of ALS and FTD. The biological functions of C9orf72 are becoming understood, but it is unclear if this gene is regulated in a neural-specific manner. Neuronal activity is a crucial modifier of biological processes in health and neurodegenerative disease contexts. Here, we show that prolonged membrane depolarization in healthy human iPSC-cortical neurons leads to a significant downregulation of a transcript variant 3 (V3) of C9orf72, with a concomitant increase in variant 2 (V2), which leads to total C9orf72 RNA transcript levels remaining unchanged. However, the same response is not observed in cortical neurons derived from patients with the C9-NRE mutation. These findings reveal the impact of depolarization on C9orf72 transcripts, and how this response diverges in C9-NRE-carriers, which may have important implications in the underlying unique clinical associations of C9-NRE transcripts and disease pathogenesis.
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Affiliation(s)
- Layla T. Ghaffari
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Aaron R. Haeusler
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
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