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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. SCIENCE ADVANCES 2024; 10:eadp6039. [PMID: 39028813 PMCID: PMC11259177 DOI: 10.1126/sciadv.adp6039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing Sox4 or Sox11 remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation.
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Affiliation(s)
- Natalí B. Rasetto
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Damiana Giacomini
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Ariel A. Berardino
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Tomás Vega Waichman
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Maximiliano S. Beckel
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Daniela J. Di Bella
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juliana Brown
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - M. Georgina Davies-Sala
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Chiara Gerhardinger
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dieter Chichung Lie
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Paola Arlotta
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ariel Chernomoretz
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
- University of Buenos Aires, School of Science, Phys Dept and INFINA (CONICET-UBA), Buenos Aires, Argentina
| | - Alejandro F. Schinder
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
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2
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Guo X, Hong P, Xiong S, Yan Y, Xie H, Guan JS. Kdm4a is an activity downregulated barrier to generate engrams for memory separation. Nat Commun 2024; 15:5887. [PMID: 39003305 PMCID: PMC11246488 DOI: 10.1038/s41467-024-50218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/01/2024] [Indexed: 07/15/2024] Open
Abstract
Memory engrams are a subset of learning activated neurons critical for memory recall, consolidation, extinction and separation. While the transcriptional profile of engrams after learning suggests profound neural changes underlying plasticity and memory formation, little is known about how memory engrams are selected and allocated. As epigenetic factors suppress memory formation, we developed a CRISPR screening in the hippocampus to search for factors controlling engram formation. We identified histone lysine-specific demethylase 4a (Kdm4a) as a negative regulator for engram formation. Kdm4a is downregulated after neural activation and controls the volume of mossy fiber boutons. Mechanistically, Kdm4a anchors to the exonic region of Trpm7 gene loci, causing the stalling of nascent RNAs and allowing burst transcription of Trpm7 upon the dismissal of Kdm4a. Furthermore, the YTH domain containing protein 2 (Ythdc2) recruits Kdm4a to the Trpm7 gene and stabilizes nascent RNAs. Reducing the expression of Kdm4a in the hippocampus via genetic manipulation or artificial neural activation facilitated the ability of pattern separation in rodents. Our work indicates that Kdm4a is a negative regulator of engram formation and suggests a priming state to generate a separate memory.
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Affiliation(s)
- Xiuxian Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Pengfei Hong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Songhai Xiong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuze Yan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hong Xie
- Institute of Photonic Chips, School of Artificial Intelligence Science and Technology, University of Shanghai for Science and Technology, Shanghai, China.
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, China.
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3
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Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A. A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593308. [PMID: 38766140 PMCID: PMC11100777 DOI: 10.1101/2024.05.10.593308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage1-3. As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days4,5, the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptor Drd2, a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.
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Affiliation(s)
- Dominik Szabó
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Vedran Franke
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Eleanor J. Paul
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alexander Kukalev
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Ulrich G. Pfisterer
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ibai Irastorza-Azcarate
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Andrea M. Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Samuel Demharter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Luna Zea-Redondo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Jose P. Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Sant Joan d’Alacant, Spain
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Mark A. Ungless
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Toronto, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
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4
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Zheng F, Dahlmanns M, Kessler P, Alzheimer C. Increase in activin A may counteract decline in synaptic plasticity with age. Front Aging Neurosci 2024; 16:1382492. [PMID: 38646448 PMCID: PMC11026702 DOI: 10.3389/fnagi.2024.1382492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Activin A, a member of the transforming growth factor β (TGF-β) family, is widely recognized for its neurotrophic and neuroprotective function in the developing and injured brain, respectively. Moreover, in the healthy adult brain, activin A has been shown to tune signal processing at excitatory synapses in a fashion that improves cognitive performance. Because its level in human cerebrospinal fluid rises with age, we wondered whether activin A has a role in mitigating the gradual cognitive decline that healthy individuals experience in late-life. To interrogate the role of activin A in synaptic plasticity in the aging brain, we used an established transgenic mouse line, in which expression of a dominant-negative mutant of activin receptor IB (dnActRIB) serves to disrupt activin receptor signaling in a forebrain-specific fashion. In brain slices of young adult dnActRIB mice (2-4 months old), the NMDA receptor-dependent and -independent forms of long-term potentiation (LTP) at the Schaffer collateral-CA1 pyramidal cell synapse of the hippocampus were equally impaired relative to the extent of LTP measured in the wild-type preparation. Unexpectedly, the difference between the genotypes disappeared when the two forms of LTP were re-examined in slices from middle-aged mice (13-16 months old). Since the level of activin A and endogenous ActRIB both displayed a significant elevation in middle-aged hippocampus, we reasoned that with such a rise, the dominant-negative effect of the mutant receptors could be overcome. Substantiating this idea, we found that administration of recombinant activin A was indeed capable of restoring full-blown LTP in slices from young dnActRIB mice. Our data suggest that, beginning in the middle-aged brain, endogenous activin receptor signaling appears to become strengthened in an attempt to stave off cognitive decline. If further corroborated, this concept would also hold promise for new therapeutic venues to preserve cognitive functions in the aged brain.
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Affiliation(s)
- Fang Zheng
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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5
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Lissek T. Aging as a Consequence of the Adaptation-Maladaptation Dilemma. Adv Biol (Weinh) 2024; 8:e2300654. [PMID: 38299389 DOI: 10.1002/adbi.202300654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Indexed: 02/02/2024]
Abstract
In aging, the organism is unable to counteract certain harmful influences over its lifetime which leads to progressive dysfunction and eventually death, thus delineating aging as one failed process of adaptation to a set of aging stimuli. A central problem in understanding aging is hence to explain why the organism cannot adapt to these aging stimuli. The adaptation-maladaptation theory of aging proposes that in aging adaptation processes such as adaptive transcription, epigenetic remodeling, and metabolic plasticity drive dysfunction themselves over time (maladaptation) and thereby cause aging-related disorders such as cancer and metabolic dysregulation. The central dilemma of aging is thus that the set of adaptation mechanisms that the body uses to deal with internal and external stressors acts as a stressor itself and cannot be effectively counteracted. The only available option for the organism to decrease maladaptation may be a program to progressively reduce the output of adaptive cascades (e.g., via genomic methylation) which then leads to reduced physiological adaptation capacity and syndromes like frailty, immunosenescence, and cognitive decline. The adaptation-maladaptation dilemma of aging entails that certain biological mechanisms can simultaneously protect against aging as well as drive aging. The key to longevity may lie in uncoupling adaptation from maladaptation.
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Affiliation(s)
- Thomas Lissek
- Interdisciplinary Center for Neurosciences, Heidelberg University, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
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6
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Kupke J, Klimmt J, Mudlaff F, Schwab M, Lutsik P, Plass C, Sticht C, Oliveira AMM. Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1. Neuropsychopharmacology 2024:10.1038/s41386-024-01843-0. [PMID: 38499720 DOI: 10.1038/s41386-024-01843-0] [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: 09/13/2023] [Revised: 02/04/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Epigenetic factors are well-established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role of DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
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Affiliation(s)
- 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, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Julien Klimmt
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Franziska Mudlaff
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Integrated Program in Neuroscience, McGill University, Montreal, QC, H3A 2B4, Canada
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC, H3G 1A4, Canada
| | - Maximilian Schwab
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Carsten Sticht
- Next Generation Sequencing Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - 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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7
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Dunton KL, Hedrick NG, Meamardoost S, Ren C, Howe JR, Wang J, Root CM, Gunawan R, Komiyama T, Zhang Y, Hwang EJ. Divergent Learning-Related Transcriptional States of Cortical Glutamatergic Neurons. J Neurosci 2024; 44:e0302232023. [PMID: 38238073 PMCID: PMC10919205 DOI: 10.1523/jneurosci.0302-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 03/08/2024] Open
Abstract
Experience-dependent gene expression reshapes neural circuits, permitting the learning of knowledge and skills. Most learning involves repetitive experiences during which neurons undergo multiple stages of functional and structural plasticity. Currently, the diversity of transcriptional responses underlying dynamic plasticity during repetition-based learning is poorly understood. To close this gap, we analyzed single-nucleus transcriptomes of L2/3 glutamatergic neurons of the primary motor cortex after 3 d motor skill training or home cage control in water-restricted male mice. "Train" and "control" neurons could be discriminated with high accuracy based on expression patterns of many genes, indicating that recent experience leaves a widespread transcriptional signature across L2/3 neurons. These discriminating genes exhibited divergent modes of coregulation, differentiating neurons into discrete clusters of transcriptional states. Several states showed gene expressions associated with activity-dependent plasticity. Some of these states were also prominent in the previously published reference, suggesting that they represent both spontaneous and task-related plasticity events. Markedly, however, two states were unique to our dataset. The first state, further enriched by motor training, showed gene expression suggestive of late-stage plasticity with repeated activation, which is suitable for expected emergent neuronal ensembles that stably retain motor learning. The second state, equally found in both train and control mice, showed elevated levels of metabolic pathways and norepinephrine sensitivity, suggesting a response to common experiences specific to our experimental conditions, such as water restriction or circadian rhythm. Together, we uncovered divergent transcriptional responses across L2/3 neurons, each potentially linked with distinct features of repetition-based motor learning such as plasticity, memory, and motivation.
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Affiliation(s)
- Katie L Dunton
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Nathan G Hedrick
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo 14260, New York
| | - Chi Ren
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - James R Howe
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla 92093, California
- Neurosciences Graduate Program, University of California San Diego, La Jolla 92093, California
| | - Jing Wang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Cory M Root
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla 92093, California
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo 14260, New York
| | - Takaki Komiyama
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Eun Jung Hwang
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
- Cell Biology and Anatomy, Chicago Medical School, Stanson Toshok Center for Brain Function and Repair, Rosalind Franklin University of Medicine and Science, North Chicago 60064, Illinois
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8
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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565477. [PMID: 38260428 PMCID: PMC10802403 DOI: 10.1101/2023.11.03.565477] [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
The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing Sox4 or Sox11 remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.
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9
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Yelhekar TD, Meng M, Doupe J, Lin Y. All IEGs Are Not Created Equal-Molecular Sorting Within the Memory Engram. ADVANCES IN NEUROBIOLOGY 2024; 38:81-109. [PMID: 39008012 DOI: 10.1007/978-3-031-62983-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
When neurons are recruited to form the memory engram, they are driven to activate the expression of a series of immediate-early genes (IEGs). While these IEGs have been used relatively indiscriminately to identify the so-called engram neurons, recent research has demonstrated that different IEG ensembles can be physically and functionally distinct within the memory engram. This inherent heterogeneity of the memory engram is driven by the diversity in the functions and distributions of different IEGs. This process, which we call molecular sorting, is analogous to sorting the entire population of engram neurons into different sub-engrams molecularly defined by different IEGs. In this chapter, we will describe the molecular sorting process by systematically reviewing published work on engram ensemble cells defined by the following four major IEGs: Fos, Npas4, Arc, and Egr1. By comparing and contrasting these likely different components of the memory engram, we hope to gain a better understanding of the logic and significance behind the molecular sorting process for memory functions.
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Affiliation(s)
- Tushar D Yelhekar
- Department of Psychiatry, O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meizhen Meng
- Department of Psychiatry, O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Neuroscience Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joslyn Doupe
- Neuroscience Graduate Program, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Yingxi Lin
- Department of Psychiatry, O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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10
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Fuentes-Ramos M, Barco Á. Unveiling Transcriptional and Epigenetic Mechanisms Within Engram Cells: Insights into Memory Formation and Stability. ADVANCES IN NEUROBIOLOGY 2024; 38:111-129. [PMID: 39008013 DOI: 10.1007/978-3-031-62983-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Memory traces for behavioral experiences, such as fear conditioning or taste aversion, are believed to be stored through biophysical and molecular changes in distributed neuronal ensembles across various brain regions. These ensembles are known as engrams, and the cells that constitute them are referred to as engram cells. Recent advancements in techniques for labeling and manipulating neural activity have facilitated the study of engram cells throughout different memory phases, including acquisition, allocation, long-term storage, retrieval, and erasure. In this chapter, we will explore the application of next-generation sequencing methods to engram research, shedding new light on the contribution of transcriptional and epigenetic mechanisms to engram formation and stability.
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Affiliation(s)
- Miguel Fuentes-Ramos
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Alicante, Spain
| | - Ángel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Alicante, Spain.
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11
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Dahlmanns M, Valero-Aracama MJ, Dahlmanns JK, Zheng F, Alzheimer C. Tonic activin signaling shapes cellular and synaptic properties of CA1 neurons mainly in dorsal hippocampus. iScience 2023; 26:108001. [PMID: 37829200 PMCID: PMC10565779 DOI: 10.1016/j.isci.2023.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/07/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
Dorsal and ventral hippocampus serve different functions in cognition and affective behavior, but the underpinnings of this diversity at the cellular and synaptic level are not well understood. We found that the basal level of activin A, a member of the TGF-β family, which regulates hippocampal circuits in a behaviorally relevant fashion, is much higher in dorsal than in ventral hippocampus. Using transgenic mice with a forebrain-specific disruption of activin receptor signaling, we identified the pronounced dorsal-ventral gradient of activin A as a major factor determining the distinct neurophysiologic signatures of dorsal and ventral hippocampus, ranging from pyramidal cell firing, tuning of frequency-dependent synaptic facilitation, to long-term potentiation (LTP), long-term depression (LTD), and de-potentiation. Thus, the strong activin A tone in dorsal hippocampus appears crucial to establish cellular and synaptic phenotypes that are tailored specifically to the respective network operations in dorsal and ventral hippocampus.
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Affiliation(s)
- Marc Dahlmanns
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Maria Jesus Valero-Aracama
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jana Katharina Dahlmanns
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Fang Zheng
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christian Alzheimer
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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12
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Yang M, Singh A, McDougle M, Décarie-Spain L, Kanoski S, de Lartigue G. Separate orexigenic hippocampal ensembles shape dietary choice by enhancing contextual memory and motivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561580. [PMID: 37873148 PMCID: PMC10592764 DOI: 10.1101/2023.10.09.561580] [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
The hippocampus (HPC), traditionally known for its role in learning and memory, has emerged as a controller of food intake. While prior studies primarily associated the HPC with food intake inhibition, recent research suggests a critical role in appetitive processes. We hypothesized that orexigenic HPC neurons differentially respond to fats and/or sugars, potent natural reinforcers that contribute to obesity development. Results uncover previously-unrecognized, spatially-distinct neuronal ensembles within the dorsal HPC (dHPC) that are responsive to separate nutrient signals originating from the gut. Using activity-dependent genetic capture of nutrient-responsive HPC neurons, we demonstrate a causal role of both populations in promoting nutrient-specific preference through different mechanisms. Sugar-responsive neurons encode an appetitive spatial memory engram for meal location, whereas fat-responsive neurons selectively enhance the preference and motivation for fat intake. Collectively, these findings uncover a neural basis for the exquisite specificity in processing macronutrient signals from a meal that shape dietary choices.
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13
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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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14
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Soon HR, Gaunt JR, Bansal VA, Lenherr C, Sze SK, Ch’ng TH. Seizure enhances SUMOylation and zinc-finger transcriptional repression in neuronal nuclei. iScience 2023; 26:107707. [PMID: 37694138 PMCID: PMC10483055 DOI: 10.1016/j.isci.2023.107707] [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: 04/10/2023] [Revised: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
A single episode of pilocarpine-induced status epilepticus can trigger the development of spontaneous recurrent seizures in a rodent model for epilepsy. The initial seizure-induced events in neuronal nuclei that lead to long-term changes in gene expression and cellular responses likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear proteome via tandem mass tag mass spectrometry and observed robust enrichment of nuclear proteins associated with the SUMOylation pathway. In parallel with nuclear proteome, we characterized nuclear gene expression by RNA sequencing which provided insights into seizure-driven transcriptional regulation and dynamics. Strikingly, we saw widespread downregulation of zinc-finger transcription factors, specifically proteins that harbor Krüppel-associated box (KRAB) domains. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.
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Affiliation(s)
- Hui Rong Soon
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
| | - Jessica Ruth Gaunt
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Vibhavari Aysha Bansal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Clara Lenherr
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Centre for Discovery Brain Science, The University of Edinburgh, Edinburgh, UK
| | - Siu Kwan Sze
- Faculty of Applied Health Sciences, Brock University, St. Catherines, ON, Canada
| | - Toh Hean Ch’ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
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15
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Valero-Aracama MJ, Zheng F, Alzheimer C. Dorsal-Ventral Gradient of Activin Regulates Strength of GABAergic Inhibition along Longitudinal Axis of Mouse Hippocampus in an Activity-Dependent Fashion. Int J Mol Sci 2023; 24:13145. [PMID: 37685952 PMCID: PMC10487617 DOI: 10.3390/ijms241713145] [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: 07/13/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The functional and neurophysiological distinction between the dorsal and ventral hippocampus affects also GABAergic inhibition. In line with this notion, ventral CA1 pyramidal cells displayed a more dynamic and effective response to inhibitory input compared to their dorsal counterparts. We posit that this difference is effected by the dorsal-ventral gradient of activin A, a member of the transforming growth factor-β family, which is increasingly recognized for its modulatory role in brain regions involved in cognitive functions and affective behavior. Lending credence to this hypothesis, we found that in slices from transgenic mice expressing a dominant-negative mutant of activin receptor IB (dnActRIB), inhibitory transmission was enhanced only in CA1 neurons of the dorsal hippocampus, where the basal activin A level is much higher than in the ventral hippocampus. We next asked how a rise in endogenous activin A would affect GABAergic inhibition along the longitudinal axis of the hippocampus. We performed ex vivo recordings in wild-type and dnActRIB mice after overnight exposure to an enriched environment (EE), which engenders a robust increase in activin A levels in both dorsal and ventral hippocampi. Compared to control mice from standard cages, the behaviorally induced surge in activin A produced a decline in ventral inhibition, an effect that was absent in slices from dnActRIB mice. Underscoring the essential role of activin in the EE-associated modulation of ventral inhibition, this effect was mimicked by acute application of recombinant activin A in control slices. In summary, both genetic and behavioral manipulations of activin receptor signaling affected the dorsal-ventral difference in synaptic inhibition, suggesting that activin A regulates the strength of GABAergic inhibition in a region-specific fashion.
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16
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Shi HJ, Wang S, Wang XP, Zhang RX, Zhu LJ. Hippocampus: Molecular, Cellular, and Circuit Features in Anxiety. Neurosci Bull 2023; 39:1009-1026. [PMID: 36680709 PMCID: PMC10264315 DOI: 10.1007/s12264-023-01020-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/13/2022] [Indexed: 01/22/2023] Open
Abstract
Anxiety disorders are currently a major psychiatric and social problem, the mechanisms of which have been only partially elucidated. The hippocampus serves as a major target of stress mediators and is closely related to anxiety modulation. Yet so far, its complex anatomy has been a challenge for research on the mechanisms of anxiety regulation. Recent advances in imaging, virus tracking, and optogenetics/chemogenetics have permitted elucidation of the activity, connectivity, and function of specific cell types within the hippocampus and its connected brain regions, providing mechanistic insights into the elaborate organization of the hippocampal circuitry underlying anxiety. Studies of hippocampal neurotransmitter systems, including glutamatergic, GABAergic, cholinergic, dopaminergic, and serotonergic systems, have contributed to the interpretation of the underlying neural mechanisms of anxiety. Neuropeptides and neuroinflammatory factors are also involved in anxiety modulation. This review comprehensively summarizes the hippocampal mechanisms associated with anxiety modulation, based on molecular, cellular, and circuit properties, to provide tailored targets for future anxiety treatment.
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Affiliation(s)
- Hu-Jiang Shi
- Key Laboratory of Developmental Genes and Human Diseases, MOE, Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Shuang Wang
- Key Laboratory of Developmental Genes and Human Diseases, MOE, Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xin-Ping Wang
- Key Laboratory of Developmental Genes and Human Diseases, MOE, Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Rui-Xin Zhang
- Key Laboratory of Developmental Genes and Human Diseases, MOE, Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Li-Juan Zhu
- Key Laboratory of Developmental Genes and Human Diseases, MOE, Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, 210009, China.
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 201108, China.
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17
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Parylak SL, Qiu F, Linker SB, Gallina IS, Lim CK, Preciado D, McDonald AH, Zhou X, Gage FH. Neuronal activity-related transcription is blunted in immature compared to mature dentate granule cells. Hippocampus 2023; 33:412-423. [PMID: 36811254 PMCID: PMC10985790 DOI: 10.1002/hipo.23515] [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: 09/26/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023]
Abstract
Immature dentate granule cells (DGCs) generated in the hippocampus during adulthood are believed to play a unique role in dentate gyrus (DG) function. Although immature DGCs have hyperexcitable membrane properties in vitro, the consequences of this hyperexcitability in vivo remain unclear. In particular, the relationship between experiences that activate the DG, such as exploration of a novel environment (NE), and downstream molecular processes that modify DG circuitry in response to cellular activation is unknown in this cell population. We first performed quantification of immediate early gene (IEG) proteins in immature (5-week-old) and mature (13-week-old) DGCs from mice exposed to a NE. Paradoxically, we observed lower IEG protein expression in hyperexcitable immature DGCs. We then isolated nuclei from active and inactive immature DGCs and performed single-nuclei RNA-Sequencing. Compared to mature nuclei collected from the same animal, immature DGC nuclei showed less activity-induced transcriptional change, even though they were classified as active based on expression of ARC protein. These results demonstrate that the coupling of spatial exploration, cellular activation, and transcriptional change differs between immature and mature DGCs, with blunted activity-induced changes in immature cells.
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Affiliation(s)
- Sarah L Parylak
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Fan Qiu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Iryna S Gallina
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Christina K Lim
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - David Preciado
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Aidan H McDonald
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Xavier Zhou
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
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18
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Chen P, Guo Z, Zhou B. Insight into the role of adult hippocampal neurogenesis in aging and Alzheimer's disease. Ageing Res Rev 2023; 84:101828. [PMID: 36549424 DOI: 10.1016/j.arr.2022.101828] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and seriously affects the quality of life of the elderly. Neurodegeneration is closely related to hippocampal dysfunction in AD patients. The hippocampus is key to creating new memories and is also one of the first areas of the brain to deteriorate with age. Mammalian neurogenesis occurs mainly in the hippocampus. Recent studies have confirmed that neurogenesis in the hippocampus is sustainable but decreases with age, which seriously affects the learning and memory function of AD patients. At present, our understanding of neurogenesis is still relatively shallow, especially pertaining to the influence and role of neurogenesis during aging and cognitive deficits in AD patients. Interestingly, many recent studies have described the characteristics of neurogenesis in animal models. This article reviews the progress of neurogenesis research in the context of aging and AD to provide new insights into neurogenesis.
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Affiliation(s)
- Peng Chen
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - ZhiLei Guo
- Department of Pharmacy, Wuhan Fourth Hospital, Wuhan, Hubei, China.
| | - Benhong Zhou
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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19
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Vanrobeys Y, Mukherjee U, Langmack L, Bahl E, Lin LC, Michaelson JJ, Abel T, Chatterjee S. Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524576. [PMID: 36711475 PMCID: PMC9882356 DOI: 10.1101/2023.01.18.524576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Memory consolidation involves discrete patterns of transcriptional events in the hippocampus. Despite the emergence of single-cell transcriptomic profiling techniques, defining learning-responsive gene expression across subregions of the hippocampus has remained challenging. Here, we utilized unbiased spatial sequencing to elucidate transcriptome-wide changes in gene expression in the hippocampus following learning, enabling us to define molecular signatures unique to each hippocampal subregion. We find that each subregion of the hippocampus exhibits distinct yet overlapping transcriptomic signatures. Although the CA1 region exhibited increased expression of genes related to transcriptional regulation, the DG showed upregulation of genes associated with protein folding. We demonstrate the functional relevance of subregion-specific gene expression by genetic manipulation of a transcription factor selectively in the CA1 hippocampal subregion, leading to long-term memory deficits. This work demonstrates the power of using spatial molecular approaches to reveal transcriptional events during memory consolidation.
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Affiliation(s)
- Yann Vanrobeys
- 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
| | - 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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20
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Dahlmanns M, Dahlmanns JK, Schmidt CC, Valero-Aracama MJ, Zheng F, Alzheimer C. Environmental enrichment recruits activin A to recalibrate neural activity in mouse hippocampus. Cereb Cortex 2023; 33:663-675. [PMID: 35257169 DOI: 10.1093/cercor/bhac092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/03/2023] Open
Abstract
The TGF-β family member activin A modulates neural underpinnings of cognitive and affective functions in an activity-dependent fashion. We have previously shown that exploration of a novel and enriched environment (EE) strongly enhanced activin signaling. Whereas the many beneficial effects of EE are amply documented, the underlying mechanisms remain largely elusive. Here, we examined the hypothesis that EE recruits activin to regulate synaptic plasticity in a coordinated, cognition-promoting manner. Elevated activin levels after EE enhanced CA1 pyramidal cell excitability, facilitated synaptic transmission, and promoted long-term potentiation. These EE-induced changes were largely absent in mice expressing a dominant-negative mutant of activin receptor IB. We then interrogated the impact of activin on network oscillations and functional connectivity, using high-speed Ca 2+ imaging to study spike routing within networks formed by dissociated primary hippocampal cultures. Activin facilitated Ca2+ signaling, enhanced the network strength, and shortened the weighted characteristic path length. In the slice preparation, activin promoted theta oscillations during cholinergic stimulation. Thus, we advance activin as an activity-dependent and very early molecular effector that translates behavioral stimuli experienced during EE exposure into a set of synchronized changes in neuronal excitability, synaptic plasticity, and network activity that are all tuned to improve cognitive functions.
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Affiliation(s)
- Marc Dahlmanns
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jana Katharina Dahlmanns
- Department of Psychiatry and Psychotherapy, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Carla C Schmidt
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Maria Jesus Valero-Aracama
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Fang Zheng
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christian Alzheimer
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
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21
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Cinalli DA, Cohen SJ, Calubag M, Oz G, Zhou L, Stackman RW. DREADD-inactivation of dorsal CA1 pyramidal neurons in mice impairs retrieval of object and spatial memories. Hippocampus 2023; 33:6-17. [PMID: 36468186 DOI: 10.1002/hipo.23484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/02/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022]
Abstract
The hippocampus, a medial temporal lobe brain region, is critical for the consolidation of information from short-term memory into long-term episodic memory and for spatial memory that enables navigation. Hippocampal damage in humans has been linked to amnesia and memory loss, characteristic of Alzheimer's disease and other dementias. Numerous studies indicate that the rodent hippocampus contributes significantly to long-term memory for spatial and nonspatial information. For example, muscimol-induced depression of CA1 neuronal activity in the dorsal hippocampus impairs the encoding, consolidation, and retrieval of nonspatial object memory in mice. Here, a chemogenetic designer receptor exclusively activated by designer drugs (DREADDs) approach was used to test the selective involvement of CA1 pyramidal neurons in memory retrieval for objects and for spatial location in a cohort of male C57BL/6J mice. Activation of the inhibitory (hM4Di) DREADDs receptor expressed in CA1 neurons significantly impaired the retrieval of object memory in the spontaneous object recognition task and of spatial memory in the Morris water maze. Silencing of CA1 neuronal activity in hM4Di-expressing mice was confirmed by comparing Fos expression in vehicle- and clozapine-N-oxide-treated mice after exploration of a novel environment. Histological analyses revealed that expression of the hM4Di receptor was limited to CA1 neurons of the dorsal hippocampus. These results suggest that a common subset of CA1 neurons (i.e., those expressing hM4Di receptors) in mouse hippocampus contributed to the retrieval of long-term memory for nonspatial and spatial information. Our findings support the view that the contribution of the rodent hippocampus is like that of the primate hippocampus, specifically essential for global memory. Our results further validate mice as a suitable model system to study the neurobiological mechanisms of human episodic memory, but also in developing treatments and understanding the underlying causes of diseases affecting long-term memory, such as Alzheimer's disease.
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Affiliation(s)
- David A Cinalli
- Department of Psychology, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, Florida, USA
| | - Sarah J Cohen
- Jupiter Life Science Initiative, John D. MacArthur Campus, Florida Atlantic University, Jupiter, Florida, USA
| | - Mariah Calubag
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
| | - Goksu Oz
- Department of Psychology, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, Florida, USA.,Florida Atlantic University and Max Planck Florida Institute Joint Integrative Biology - Neuroscience Ph.D. Program, Florida Atlantic University, Jupiter, Florida, USA.,International Max Planck Research School for Synapses and Circuits, Florida Atlantic University and Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
| | - Lylybell Zhou
- Alexander W. Dreyfoos High School of the Arts, West Palm Beach, Florida, USA
| | - Robert W Stackman
- Department of Psychology, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, Florida, USA.,Jupiter Life Science Initiative, John D. MacArthur Campus, Florida Atlantic University, Jupiter, Florida, USA.,Florida Atlantic University and Max Planck Florida Institute Joint Integrative Biology - Neuroscience Ph.D. Program, Florida Atlantic University, Jupiter, Florida, USA.,International Max Planck Research School for Synapses and Circuits, Florida Atlantic University and Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
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22
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Lissek T. Activity-Dependent Induction of Younger Biological Phenotypes. Adv Biol (Weinh) 2022; 6:e2200119. [PMID: 35976161 DOI: 10.1002/adbi.202200119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/11/2022] [Indexed: 01/28/2023]
Abstract
In several mammalian species, including humans, complex stimulation patterns such as cognitive and physical exercise lead to improvements in organ function, organism health and performance, as well as possibly longer lifespans. A framework is introduced here in which activity-dependent transcriptional programs, induced by these environmental stimuli, move somatic cells such as neurons and muscle cells toward a state that resembles younger cells to allow remodeling and adaptation of the organism. This cellular adaptation program targets several process classes that are heavily implicated in aging, such as mitochondrial metabolism, cell-cell communication, and epigenetic information processing, and leads to functional improvements in these areas. The activity-dependent gene program (ADGP) can be seen as a natural, endogenous cellular reprogramming mechanism that provides deep insight into the principles of inducible improvements in cell and organism function and can guide the development of therapeutic approaches for longevity. Here, these ADGPs are analyzed, exemplary critical molecular nexus points such as cAMP response element-binding protein, myocyte enhancer factor 2, serum response factor, and c-Fos are identified, and it is explored how one may leverage them to prevent, attenuate, and reverse human aging-related decline of body function.
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Affiliation(s)
- Thomas Lissek
- Interdisciplinary Center for Neurosciences, Heidelberg University, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
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23
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Gil-Marti B, Barredo CG, Pina-Flores S, Trejo JL, Turiegano E, Martin FA. The elusive transcriptional memory trace. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac008. [PMID: 38596710 PMCID: PMC10913820 DOI: 10.1093/oons/kvac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 04/11/2024]
Abstract
Memory is the brain faculty to store and remember information. It is a sequential process in which four different phases can be distinguished: encoding or learning, consolidation, storage and reactivation. Since the discovery of the first Drosophila gene essential for memory formation in 1976, our knowledge of its mechanisms has progressed greatly. The current view considers the existence of engrams, ensembles of neuronal populations whose activity is temporally coordinated and represents the minimal correlate of experience in brain circuits. In order to form and maintain the engram, protein synthesis and, probably, specific transcriptional program(s) is required. The immediate early gene response during learning process has been extensively studied. However, a detailed description of the transcriptional response for later memory phases was technically challenging. Recent advances in transcriptomics have allowed us to tackle this biological problem. This review summarizes recent findings in this field, and discusses whether or not it is possible to identify a transcriptional trace for memory.
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Affiliation(s)
- Beatriz Gil-Marti
- Molecular Physiology of Behavior Laboratory, Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Spanish National Research Council (CSIC), 28002 Madrid, Spain
- Department of Biology, Autonomous University of Madrid, 28049 Madrid, Spain
| | - Celia G Barredo
- Molecular Physiology of Behavior Laboratory, Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Spanish National Research Council (CSIC), 28002 Madrid, Spain
| | - Sara Pina-Flores
- Molecular Physiology of Behavior Laboratory, Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Spanish National Research Council (CSIC), 28002 Madrid, Spain
| | - Jose Luis Trejo
- Neurogenesis of the Adult Animal Laboratory. Department of Translational Neuroscience, Cajal Institute, Spanish National Research Council (CSIC), 28049, Madrid, Spain
| | - Enrique Turiegano
- Department of Biology, Autonomous University of Madrid, 28049 Madrid, Spain
| | - Francisco A Martin
- Molecular Physiology of Behavior Laboratory, Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Spanish National Research Council (CSIC), 28002 Madrid, Spain
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24
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The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning. Proc Natl Acad Sci U S A 2022; 119:e2116797119. [PMID: 35613054 PMCID: PMC9295763 DOI: 10.1073/pnas.2116797119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Memory formation relies on a plethora of functions, including epigenetic modifications. Over recent years, multiple studies have indicated the potential of HDAC inhibitors (HDACis) as cognitive enhancers, but their mode of action is not fully understood. Here, we tested whether HDACi treatment improves memory formation via “cognitive epigenetic priming,” stipulating that HDACis—without inherent target specificity—specifically enhance naturally occurring plasticity processes. We found that combining HDACis with fear learning, but not either treatment alone, enhances synaptic plasticity as well as memory-promoting transcriptional signaling in the hippocampus, a brain area recruited by fear learning, but not in unrelated areas. These results lend experimental support to the theory of cognitive epigenetic priming. Long-term memory formation relies on synaptic plasticity, neuronal activity-dependent gene transcription, and epigenetic modifications. Multiple studies have shown that HDAC inhibitor (HDACi) treatments can enhance individual aspects of these processes and thereby act as putative cognitive enhancers. However, their mode of action is not fully understood. In particular, it is unclear how systemic application of HDACis, which are devoid of substrate specificity, can target pathways that promote memory formation. In this study, we explore the electrophysiological, transcriptional, and epigenetic responses that are induced by CI-994, a class I HDACi, combined with contextual fear conditioning (CFC) in mice. We show that CI-994–mediated improvement of memory formation is accompanied by enhanced long-term potentiation in the hippocampus, a brain region recruited by CFC, but not in the striatum, a brain region not primarily implicated in fear learning. Furthermore, using a combination of bulk and single-cell RNA-sequencing, we find that, when paired with CFC, HDACi treatment engages synaptic plasticity-promoting gene expression more strongly in the hippocampus, specifically in the dentate gyrus (DG). Finally, using chromatin immunoprecipitation-sequencing (ChIP-seq) of DG neurons, we show that the combined action of HDACi application and conditioning is required to elicit enhancer histone acetylation in pathways that underlie improved memory performance. Together, these results indicate that systemic HDACi administration amplifies brain region-specific processes that are naturally induced by learning.
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25
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Ortega-de San Luis C, Ryan TJ. Understanding the physical basis of memory: Molecular mechanisms of the engram. J Biol Chem 2022; 298:101866. [PMID: 35346687 PMCID: PMC9065729 DOI: 10.1016/j.jbc.2022.101866] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/18/2022] Open
Abstract
Memory, defined as the storage and use of learned information in the brain, is necessary to modulate behavior and critical for animals to adapt to their environments and survive. Despite being a cornerstone of brain function, questions surrounding the molecular and cellular mechanisms of how information is encoded, stored, and recalled remain largely unanswered. One widely held theory is that an engram is formed by a group of neurons that are active during learning, which undergoes biochemical and physical changes to store information in a stable state, and that are later reactivated during recall of the memory. In the past decade, the development of engram labeling methodologies has proven useful to investigate the biology of memory at the molecular and cellular levels. Engram technology allows the study of individual memories associated with particular experiences and their evolution over time, with enough experimental resolution to discriminate between different memory processes: learning (encoding), consolidation (the passage from short-term to long-term memories), and storage (the maintenance of memory in the brain). Here, we review the current understanding of memory formation at a molecular and cellular level by focusing on insights provided using engram technology.
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Affiliation(s)
- Clara Ortega-de San Luis
- School of Biochemistry and Immunology and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland.
| | - Tomás J Ryan
- School of Biochemistry and Immunology and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland; Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, Victoria, Australia; Child & Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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26
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Chen QN, Ding XL, Guo XX, Zhou G, Guan JS. Suv39h1 regulates memory stability by inhibiting the expression of Shank1 in hippocampal newborn neurons. Eur J Neurosci 2022; 55:1424-1441. [PMID: 35181969 DOI: 10.1111/ejn.15626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 11/28/2022]
Abstract
Adult newborn neurons are involved in memory encoding and extinction, but the neural mechanism is unclear. We found the adult newborn neurons at 4 weeks are recruited by learning and subjected to epigenetic regulations, consequently reducing their ability to be re-recruited later. After removal of the epigenetic blockage, Suv39h1 KO mice showed an increased recruiting number of aged newborn neurons and enhanced flexibility in learning tasks. Besides NRXN1, we found SHANK1, the synaptic scaffold protein, is one of the major targets of Suv39h1, regulating memory stability. Expression of Shank1 is transiently engaged to enhance synaptogenesis during learning and is strongly suppressed by Suv39h1 from 5 hours after learning. Exogenously overexpression of Shank1 in dentate gyrus increased the density of mushroom spines and decreased the persistency of old memories. Our study indicated the activity-regulated epigenetic modification in newly matured newborn neurons in hippocampus insulates temporally distinct experiences and stabilizes old memories.
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Affiliation(s)
- Qi-Nan Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Lu Ding
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiu-Xian Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Gang Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
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27
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Mazurkiewicz M, Kambham A, Pace B, Skwarzynska D, Wagley P, Burnsed J. Neuronal activity mapping during exploration of a novel environment. Brain Res 2022; 1776:147748. [PMID: 34896333 PMCID: PMC8728889 DOI: 10.1016/j.brainres.2021.147748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 02/03/2023]
Abstract
Whole-brain mapping is an effective approach to investigate which brain areas are activated by the exploration of a novel environment. Previous studies analyzing neuronal activity promoted by novelty focused mostly on one specific area instead of the whole brain and measured activation using cfos immunohistochemistry. In this study, we utilized TRAP2 mice exposed to a novel and familiar environment to examine neuronal activity in exploratory, learning, and memory circuits. We analyzed the behavior of mice during environment exploration. Brain tissue was processed using tissue clarification and neurons active during exploration of an environment were mapped based on the cfos expression. Neuronal activity after each experience were quantified in regions of interest. We observed increased exploratory behavior in mice exposed to a novel environment in comparison to familiar (170.5 s ± 6.47 vs. 112.5 s ± 9.54, p = 0.0001). Neuronal activity was significantly increased in the dentate gyrus (115.56 ± 53.84 vs. 32.24 ± 12.32, p = 0.02) during the exploration of a novel environment. Moreover, examination of the remaining regions of interest showed some increase in the number of active neurons in the novel condition, however, those differences were not statistically significant. Brief exposure to a novel environment results in increased exploratory behavior and significant neuronal activity in the dentate gyrus.
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Affiliation(s)
| | - Anvitha Kambham
- Department of Pediatrics, University of Virginia, Charlottesville, VA
| | - Belle Pace
- Department of Pediatrics, University of Virginia, Charlottesville, VA
| | - Daria Skwarzynska
- Department of Pediatrics, University of Virginia, Charlottesville, VA
| | - Pravin Wagley
- Department of Pediatrics, University of Virginia, Charlottesville, VA
| | - Jennifer Burnsed
- Department of Pediatrics, University of Virginia, Charlottesville, VA;,Department of Neurology, University of Virginia, Charlottesville, VA
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28
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Jiang Y, VanDongen AMJ. Selective increase of correlated activity in Arc-positive neurons after chemically induced long-term potentiation in cultured hippocampal neurons. eNeuro 2021; 8:ENEURO.0540-20.2021. [PMID: 34782348 PMCID: PMC8658543 DOI: 10.1523/eneuro.0540-20.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022] Open
Abstract
The activity-dependent expression of immediate-early genes (IEGs) has been utilised to label memory traces. However, their roles in engram specification are incompletely understood. Outstanding questions remain as to whether expression of IEGs can interplay with network properties such as functional connectivity and also if neurons expressing different IEGs are functionally distinct. In order to connect IEG expression at the cellular level with changes in functional-connectivity, we investigated the expression of 2 IEGs, Arc and c-Fos, in cultured hippocampal neurons. Primary neuronal cultures were treated with a chemical cocktail (4-aminopyridine, bicuculline, and forskolin) to increase neuronal activity, IEG expression, and induce chemical long-term potentiation. Neuronal firing is assayed by intracellular calcium imaging using GCaMP6m and expression of IEGs is assessed by immunofluorescence staining. We noted an emergent network property of refinement in network activity, characterized by a global downregulation of correlated activity, together with an increase in correlated activity between subsets of specific neurons. Subsequently, we show that Arc expression correlates with the effects of refinement, as the increase in correlated activity occurs specifically between Arc-positive neurons. The expression patterns of the IEGs c-Fos and Arc strongly overlap, but Arc was more selectively expressed than c-Fos. A subpopulation of neurons positive for both Arc and c-Fos shows increased correlated activity, while correlated firing between Arc+/cFos- neurons is reduced. Our results relate neuronal activity-dependent expression of the IEGs Arc and c-Fos on the individual cellular level to changes in correlated activity of the neuronal network.SIGNIFICANCEEstablishing a stable long-lasting memory requires neuronal network-level changes in connection strengths in a subset of neurons, which together constitute a memory trace or engram. Two genes, c-Fos and Arc, have been implicated to play critical roles in the formation of the engram. They have been studied extensively at the cellular/molecular level, and have been used as markers of memory traces in mice. We have correlated Arc and c-Fos cellular expression with refinement of correlated neuronal activity following pharmacological activation of networks formed by cultured hippocampal neurons. Whereas there is a global loss of correlated activity, Arc-positive neurons show selectively increased correlated activity. Arc is more selectively expressed than c-Fos, but the two genes act together in encoding information about changes in correlated firing.
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Affiliation(s)
- Yuheng Jiang
- Program for Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore 169857
| | - Antonius M J VanDongen
- Program for Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore 169857
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29
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Denoth-Lippuner A, Jaeger BN, Liang T, Royall LN, Chie SE, Buthey K, Machado D, Korobeynyk VI, Kruse M, Munz CM, Gerbaulet A, Simons BD, Jessberger S. Visualization of individual cell division history in complex tissues using iCOUNT. Cell Stem Cell 2021; 28:2020-2034.e12. [PMID: 34525348 PMCID: PMC8577829 DOI: 10.1016/j.stem.2021.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022]
Abstract
The division potential of individual stem cells and the molecular consequences of successive rounds of proliferation remain largely unknown. Here, we developed an inducible cell division counter (iCOUNT) that reports cell division events in human and mouse tissues in vitro and in vivo. Analyzing cell division histories of neural stem/progenitor cells (NSPCs) in the developing and adult brain, we show that iCOUNT can provide novel insights into stem cell behavior. Further, we use single-cell RNA sequencing (scRNA-seq) of iCOUNT-labeled NSPCs and their progenies from the developing mouse cortex and forebrain-regionalized human organoids to identify functionally relevant molecular pathways that are commonly regulated between mouse and human cells, depending on individual cell division histories. Thus, we developed a tool to characterize the molecular consequences of repeated cell divisions of stem cells that allows an analysis of the cellular principles underlying tissue formation, homeostasis, and repair.
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Affiliation(s)
- Annina Denoth-Lippuner
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Tong Liang
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Lars N Royall
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Stefanie E Chie
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Kilian Buthey
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Diana Machado
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Vladislav I Korobeynyk
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Merit Kruse
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Clara M Munz
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland.
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30
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Damphousse CC, Medeiros J, Marrone DF. Functional Integration of Adult-Generated Neurons in Diabetic Goto-Kakizaki Rats. Front Behav Neurosci 2021; 15:734359. [PMID: 34675787 PMCID: PMC8523851 DOI: 10.3389/fnbeh.2021.734359] [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: 07/01/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Adult-born neurons in the dentate gyrus (DG) make important contributions to learning as they integrate into neuronal networks. Neurogenesis is dramatically reduced by a number of conditions associated with cognitive impairment, including type 2 diabetes mellitus (T2DM). Increasing neurogenesis may thus provide a therapeutic target for ameliorating diabetes-associated cognitive impairments, but only if new neurons remain capable of normal function. To address the capacity for adult-generated neurons to incorporate into functional circuits in the hyperglycemic DG, we measured Egr1 expression in granule cells (GCs), BrdU labeled four weeks prior, in Goto-Kakizaki (GK) rats, an established model of T2DM, and age-matched Wistars. The results indicate that while fewer GCs are generated in the DG of GK rats, GCs that survive readily express Egr1 in response to spatial information. These data demonstrate that adult-generated GCs in the hyperglycemic DG remain functionally competent and support neurogenesis as a viable therapeutic target.
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Affiliation(s)
| | - Jaclyn Medeiros
- Department of Psychology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Diano F Marrone
- Department of Psychology, Wilfrid Laurier University, Waterloo, ON, Canada
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31
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Wang IF, Wang Y, Yang YH, Huang GJ, Tsai KJ, Shen CKJ. Activation of a hippocampal CREB-pCREB-miRNA-MEF2 axis modulates individual variation of spatial learning and memory capability. Cell Rep 2021; 36:109477. [PMID: 34348143 DOI: 10.1016/j.celrep.2021.109477] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
Phenotypic variation is a fundamental prerequisite for cell and organism evolution by natural selection. Whereas the role of stochastic gene expression in phenotypic diversity of genetically identical cells is well studied, not much is known regarding the relationship between stochastic gene expression and individual behavioral variation in animals. We demonstrate that a specific miRNA (miR-466f-3p) is upregulated in the hippocampus of a portion of individual inbred mice upon a Morris water maze task. Significantly, miR-466f-3p positively regulates the neuron morphology, function and spatial learning, and memory capability of mice. Mechanistically, miR-466f-3p represses translation of MEF2A, a negative regulator of learning/memory. Finally, we show that varied upregulation of hippocampal miR-466f-3p results from randomized phosphorylation of hippocampal cyclic AMP (cAMP)-response element binding (CREB) in individuals. This finding of modulation of spatial learning and memory via a randomized hippocampal signaling axis upon neuronal stimulation represents a demonstration of how variation in tissue gene expression lead to varied animal behavior.
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Affiliation(s)
- I-Fang Wang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yihan Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hua Yang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Guo-Jen Huang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou 33302, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan.
| | - Che-Kun James Shen
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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32
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Zocher S, Overall RW, Lesche M, Dahl A, Kempermann G. Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. Nat Commun 2021; 12:3892. [PMID: 34162876 PMCID: PMC8222384 DOI: 10.1038/s41467-021-23993-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that experiencing a stimulus-rich environment counteracts age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is critical to neuronal function. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the stimulating effects of environmental enrichment on hippocampal plasticity at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.
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Affiliation(s)
- Sara Zocher
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Mathias Lesche
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
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33
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Giorgi C, Marinelli S. Roles and Transcriptional Responses of Inhibitory Neurons in Learning and Memory. Front Mol Neurosci 2021; 14:689952. [PMID: 34211369 PMCID: PMC8239217 DOI: 10.3389/fnmol.2021.689952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Increasing evidence supports a model whereby memories are encoded by sparse ensembles of neurons called engrams, activated during memory encoding and reactivated upon recall. An engram consists of a network of cells that undergo long-lasting modifications of their transcriptional programs and connectivity. Ground-breaking advancements in this field have been made possible by the creative exploitation of the characteristic transcriptional responses of neurons to activity, allowing both engram labeling and manipulation. Nevertheless, numerous aspects of engram cell-type composition and function remain to be addressed. As recent transcriptomic studies have revealed, memory encoding induces persistent transcriptional and functional changes in a plethora of neuronal subtypes and non-neuronal cells, including glutamatergic excitatory neurons, GABAergic inhibitory neurons, and glia cells. Dissecting the contribution of these different cellular classes to memory engram formation and activity is quite a challenging yet essential endeavor. In this review, we focus on the role played by the GABAergic inhibitory component of the engram through two complementary lenses. On one hand, we report on available physiological evidence addressing the involvement of inhibitory neurons to different stages of memory formation, consolidation, storage and recall. On the other, we capitalize on a growing number of transcriptomic studies that profile the transcriptional response of inhibitory neurons to activity, revealing important clues on their potential involvement in learning and memory processes. The picture that emerges suggests that inhibitory neurons are an essential component of the engram, likely involved in engram allocation, in tuning engram excitation and in storing the memory trace.
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Affiliation(s)
- Corinna Giorgi
- CNR, Institute of Molecular Biology and Pathology, Rome, Italy.,European Brain Research Institute (EBRI), Fondazione Rita Levi-Montalcini, Rome, Italy
| | - Silvia Marinelli
- European Brain Research Institute (EBRI), Fondazione Rita Levi-Montalcini, Rome, Italy
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34
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Fuentes-Ramos M, Alaiz-Noya M, Barco A. Transcriptome and epigenome analysis of engram cells: Next-generation sequencing technologies in memory research. Neurosci Biobehav Rev 2021; 127:865-875. [PMID: 34097980 DOI: 10.1016/j.neubiorev.2021.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/19/2022]
Abstract
Transcription and epigenetic changes are integral components of the neuronal response to stimulation and have been postulated to be drivers or substrates for enduring changes in animal behavior, including learning and memory. Memories are thought to be deposited in neuronal assemblies called engrams, i.e., groups of cells that undergo persistent physical or chemical changes during learning and are selectively reactivated to retrieve the memory. Despite the research progress made in recent years, the identity of specific epigenetic changes, if any, that occur in these cells and subsequently contribute to the persistence of memory traces remains unknown. The analysis of these changes is challenging due to the difficulty of exploring molecular alterations that only occur in a relatively small percentage of cells embedded in a complex tissue. In this review, we discuss the recent advances in this field and the promise of next-generation sequencing (NGS) and epigenome editing methods for overcoming these challenges and address long-standing questions concerning the role of epigenetic mechanisms in memory encoding, maintenance and expression.
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Affiliation(s)
- Miguel Fuentes-Ramos
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Marta Alaiz-Noya
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain.
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35
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Epigenomically Bistable Regions across Neuron-Specific Genes Govern Neuron Eligibility to a Coding Ensemble in the Hippocampus. Cell Rep 2021; 31:107789. [PMID: 32579919 PMCID: PMC7440841 DOI: 10.1016/j.celrep.2020.107789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/12/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Sensory inputs activate sparse neuronal ensembles in the dentate gyrus of the hippocampus, but how eligibility of individual neurons to recruitment is determined remains elusive. We identify thousands of largely bistable (CpG methylated or unmethylated) regions within neuronal gene bodies, established during mouse dentate gyrus development. Reducing DNA methylation and the proportion of the methylated epialleles at bistable regions compromises novel context-induced neuronal activation. Conversely, increasing methylation and the frequency of the methylated epialleles at bistable regions enhances intrinsic excitability. Single-nucleus profiling reveals enrichment of specific epialleles related to a subset of primarily exonic, bistable regions in activated neurons. Genes displaying both differential methylation and expression in activated neurons define a network of proteins regulating neuronal excitability and structural plasticity. We propose a model in which bistable regions create neuron heterogeneity and constellations of exonic methylation, which may contribute to cell-specific gene expression, excitability, and eligibility to a coding ensemble. Odell et al. show regions within neuronal genes with bistable DNA methylation states that are associated with gene expression, excitability, and activation in the dentate gyrus of the hippocampus. These data suggest that the methylation state of bistable regions dictates, via modulating gene expression, neuron eligibility to a coding ensemble.
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36
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Wang JM, Woodruff AL, Dunn MJ, Fillinger RJ, Bennett RJ, Anderson MZ. Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits. mBio 2021; 12:e00586-21. [PMID: 33879584 PMCID: PMC8092256 DOI: 10.1128/mbio.00586-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences and to link these differences to phenotypic traits. C. albicans adapts primarily through clonal evolution, and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Strikingly, strain-specific gene expression was prevalent in some strain backgrounds. Association of gene expression with phenotypic data by differential analysis, linear correlation, and assembly of gene networks connected both previously characterized and novel genes with 23 C. albicans traits. Construction of de novo gene modules produced a gene atlas incorporating 67% of C. albicans genes and revealed correlations between expression modules and important phenotypes such as systemic virulence. Furthermore, targeted investigation of two modules that have novel roles in growth and filamentation supported our bioinformatic predictions. Together, these studies reveal widespread transcriptional variation across C. albicans isolates and identify genetic and epigenetic links to phenotypic variation based on coexpression network analysis.IMPORTANCE Infectious fungal species are often treated uniformly despite clear evidence of genotypic and phenotypic heterogeneity being widespread across strains. Identifying the genetic basis for this phenotypic diversity is extremely challenging because of the tens or hundreds of thousands of variants that may distinguish two strains. Here, we use transcriptional profiling to determine differences in gene expression that can be linked to phenotypic variation among a set of 21 Candida albicans isolates. Analysis of this transcriptional data set uncovered clear trends in gene expression characteristics for this species and new genes and pathways that were associated with variation in pathogenic processes. Direct investigation confirmed functional predictions for a number of new regulators associated with growth and filamentation, demonstrating the utility of these approaches in linking genes to important phenotypes.
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Affiliation(s)
- Joshua M Wang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Andrew L Woodruff
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew J Dunn
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Fillinger
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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37
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Molecular and cellular mechanisms of engram allocation and maintenance. Brain Res Bull 2021; 170:274-282. [PMID: 33647419 DOI: 10.1016/j.brainresbull.2021.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/29/2021] [Accepted: 02/18/2021] [Indexed: 01/19/2023]
Abstract
Understanding how we learn and remember has been a long-standing question in neuroscience. Technological developments of the past 15 years have allowed for dramatically increased access to the neurons that hold the physical representation of memory, also known as a memory trace or engram. Such developments have tremendously facilitated advancement of the memory field, since they made possible interrogation of the cellular and molecular mechanisms underlying memory formation with unprecedented cellular specificity. Here, we discuss the studies that have investigated rules governing neuronal recruitment to a particular memory engram. Furthermore, we provide an overview of the evidence that functional and structural changes associated with memory consolidation occur in engram neurons. Moreover, we summarize the expanding literature showing that transcriptional regulatory factors such as transcription factors and epigenetic mechanisms play an important role in the maintained allocation of behaviorally-selected neurons to an engram. Together, these studies have begun elucidating how neuronal networks are selected and modified in order to support memory formation and storage.
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Lipovsek M, Bardy C, Cadwell CR, Hadley K, Kobak D, Tripathy SJ. Patch-seq: Past, Present, and Future. J Neurosci 2021; 41:937-946. [PMID: 33431632 PMCID: PMC7880286 DOI: 10.1523/jneurosci.1653-20.2020] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/11/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Single-cell transcriptomic approaches are revolutionizing neuroscience. Integrating this wealth of data with morphology and physiology, for the comprehensive study of neuronal biology, requires multiplexing gene expression data with complementary techniques. To meet this need, multiple groups in parallel have developed "Patch-seq," a modification of whole-cell patch-clamp protocols that enables mRNA sequencing of cell contents after electrophysiological recordings from individual neurons and morphologic reconstruction of the same cells. In this review, we first outline the critical technical developments that enabled robust Patch-seq experimental efforts and analytical solutions to interpret the rich multimodal data generated. We then review recent applications of Patch-seq that address novel and long-standing questions in neuroscience. These include the following: (1) targeted study of specific neuronal populations based on their anatomic location, functional properties, lineage, or a combination of these factors; (2) the compilation and integration of multimodal cell type atlases; and (3) the investigation of the molecular basis of morphologic and functional diversity. Finally, we highlight potential opportunities for further technical development and lines of research that may benefit from implementing the Patch-seq technique. As a multimodal approach at the intersection of molecular neurobiology and physiology, Patch-seq is uniquely positioned to directly link gene expression to brain function.
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Affiliation(s)
- Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI), Adelaide 5000, SA, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park 5042, SA, Australia
| | - Cathryn R Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, California 94143
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Shreejoy J Tripathy
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Feurle P, Abentung A, Cera I, Wahl N, Ablinger C, Bucher M, Stefan E, Sprenger S, Teis D, Fischer A, Laighneach A, Whitton L, Morris DW, Apostolova G, Dechant G. SATB2-LEMD2 interaction links nuclear shape plasticity to regulation of cognition-related genes. EMBO J 2021; 40:e103701. [PMID: 33319920 PMCID: PMC7849313 DOI: 10.15252/embj.2019103701] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
SATB2 is a schizophrenia risk gene and is genetically associated with human intelligence. How it affects cognition at molecular level is currently unknown. Here, we show that interactions between SATB2, a chromosomal scaffolding protein, and the inner nuclear membrane protein LEMD2 orchestrate the response of pyramidal neurons to neuronal activation. Exposure to novel environment in vivo causes changes in nuclear shape of CA1 hippocampal neurons via a SATB2-dependent mechanism. The activity-driven plasticity of the nuclear envelope requires not only SATB2, but also its protein interactor LEMD2 and the ESCRT-III/VPS4 membrane-remodeling complex. Furthermore, LEMD2 depletion in cortical neurons, similar to SATB2 ablation, affects neuronal activity-dependent regulation of multiple rapid and delayed primary response genes. In human genetic data, LEMD2-regulated genes are enriched for de novo mutations reported in intellectual disability and schizophrenia and are, like SATB2-regulated genes, enriched for common variants associated with schizophrenia and cognitive function. Hence, interactions between SATB2 and the inner nuclear membrane protein LEMD2 influence gene expression programs in pyramidal neurons that are linked to cognitive ability and psychiatric disorder etiology.
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Affiliation(s)
- Patrick Feurle
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Andreas Abentung
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Isabella Cera
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Nico Wahl
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Cornelia Ablinger
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Michael Bucher
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Simon Sprenger
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - Andre Fischer
- Department of Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GoettingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical CenterGoettingenGermany
| | - Aodán Laighneach
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Laura Whitton
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Derek W Morris
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Galina Apostolova
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Georg Dechant
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
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Pléau C, Peret A, Pearlstein E, Scalfati T, Vigier A, Marti G, Michel FJ, Marissal T, Crépel V. Dentate Granule Cells Recruited in the Home Environment Display Distinctive Properties. Front Cell Neurosci 2021; 14:609123. [PMID: 33519383 PMCID: PMC7843370 DOI: 10.3389/fncel.2020.609123] [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: 09/22/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
The dentate granule cells (DGCs) play a crucial role in learning and memory. Many studies have described the role and physiological properties of these sparsely active neurons using different behavioral contexts. However, the morpho-functional features of DGCs recruited in mice maintained in their home cage (without training), considered as a baseline condition, have not yet been established. Using fosGFP transgenic mice, we observed ex vivo that DGCs recruited in animals maintained in the home cage condition are mature neurons that display a longer dendritic tree and lower excitability compared with non-activated cells. The higher GABAA receptor-mediated shunting inhibition contributes to the lower excitability of DGCs activated in the home environment by shifting the input resistance towards lower values. Remarkably, that shunting inhibition is neither observed in non-activated DGCs nor in DGCs activated during training in virtual reality. In short, our results suggest that strong shunting inhibition and reduced excitability could constitute a distinctive neural signature of mature DGCs recruited in the context of the home environment.
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Affiliation(s)
- Claire Pléau
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
| | - Angélique Peret
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
| | | | - Thomas Scalfati
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
| | - Alexandre Vigier
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
| | | | | | - Thomas Marissal
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
| | - Valérie Crépel
- INMED, INSERM UMR1249, Aix-Marseille University, Marseille, France
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41
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Sullivan KE, Kendrick RM, Cembrowski MS. Elucidating memory in the brain via single-cell transcriptomics. J Neurochem 2020; 157:982-992. [PMID: 33230878 DOI: 10.1111/jnc.15250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 01/17/2023]
Abstract
Elucidating the neural mechanisms of memory in the brain is a central goal of neuroscience. Here, we discuss modern-day transcriptomics methodologies, and how they are well-poised to revolutionize our insight into memory mechanisms at unprecedented resolution and throughput. Focusing on the hippocampus and amygdala, two regions extensively examined in memory research, we show how single-cell transcriptomics technologies have been leveraged to understand the naïve state of these brain regions. Building upon this foundation, we show that these technologies can be applied to single-trial learning paradigms to comprehensively identify molecules and cells that participate in the encoding and retrieval of memory. Transcriptomics also provides an opportunity to understand the cell-type organization of the human hippocampus and amygdala, and due to conservation of these brain regions between humans and rodents, to infer behavioral and causal contributions in the human brain by leveraging rodent cell-type homologies and interventions. Ultimately, such transcriptomic technologies are poised to usher in a qualitatively novel understanding of memory in the brain.
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Affiliation(s)
- Kaitlin E Sullivan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Rennie M Kendrick
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada.,Institute of Applied Mathematics, University of British Columbia, Vancouver, Canada
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42
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Marco A, Meharena HS, Dileep V, Raju RM, Davila-Velderrain J, Zhang AL, Adaikkan C, Young JZ, Gao F, Kellis M, Tsai LH. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nat Neurosci 2020; 23:1606-1617. [PMID: 33020654 PMCID: PMC7686266 DOI: 10.1038/s41593-020-00717-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
The epigenome and three-dimensional (3D) genomic architecture are emerging as key factors in the dynamic regulation of different transcriptional programs required for neuronal functions. In this study, we used an activity-dependent tagging system in mice to determine the epigenetic state, 3D genome architecture and transcriptional landscape of engram cells over the lifespan of memory formation and recall. Our findings reveal that memory encoding leads to an epigenetic priming event, marked by increased accessibility of enhancers without the corresponding transcriptional changes. Memory consolidation subsequently results in spatial reorganization of large chromatin segments and promoter-enhancer interactions. Finally, with reactivation, engram neurons use a subset of de novo long-range interactions, where primed enhancers are brought in contact with their respective promoters to upregulate genes involved in local protein translation in synaptic compartments. Collectively, our work elucidates the comprehensive transcriptional and epigenomic landscape across the lifespan of memory formation and recall in the hippocampal engram ensemble.
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Affiliation(s)
- Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ravikiran M Raju
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jose Davila-Velderrain
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy Letao Zhang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chinnakkaruppan Adaikkan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jennie Z Young
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fan Gao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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43
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Linker SB, Randolph-Moore L, Kottilil K, Qiu F, Jaeger BN, Barron J, Gage FH. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. Genome Res 2020; 30:1643-1654. [PMID: 33122305 PMCID: PMC7605253 DOI: 10.1101/gr.262196.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
Abstract
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5′ gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type–specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
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Affiliation(s)
- Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lynne Randolph-Moore
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kalyani Kottilil
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fan Qiu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculty of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Jerika Barron
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94143, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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44
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Jaeger BN, Yángüez E, Gesuita L, Denoth-Lippuner A, Kruse M, Karayannis T, Jessberger S. Miniaturization of Smart-seq2 for Single-Cell and Single-Nucleus RNA Sequencing. STAR Protoc 2020; 1:100081. [PMID: 33000004 PMCID: PMC7501729 DOI: 10.1016/j.xpro.2020.100081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This protocol presents a plate-based workflow to perform RNA sequencing analysis of single cells/nuclei using Smart-seq2. We describe (1) the dissociation procedures for cell/nucleus isolation from the mouse brain and human organoids, (2) the flow sorting of single cells/nuclei into 384-well plates, and (3) the preparation of libraries following miniaturization of the Smart-seq2 protocol using a liquid-handling robot. This pipeline allows for the reliable, high-throughput, and cost-effective preparation of mouse and human samples for full-length deep single-cell/nucleus RNA sequencing. For complete details on the use and execution of this protocol, please refer to Bowers et al. (2020).
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Affiliation(s)
- Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Emilio Yángüez
- Functional Genomic Center Zurich, ETH and University of Zurich, Zurich, Switzerland
| | - Lorenzo Gesuita
- Laboratory of Neural Circuit Assembly, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Annina Denoth-Lippuner
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Merit Kruse
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Theofanis Karayannis
- Laboratory of Neural Circuit Assembly, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
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Nguyen PT, Dorman LC, Pan S, Vainchtein ID, Han RT, Nakao-Inoue H, Taloma SE, Barron JJ, Molofsky AB, Kheirbek MA, Molofsky AV. Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity. Cell 2020; 182:388-403.e15. [PMID: 32615087 DOI: 10.1016/j.cell.2020.05.050] [Citation(s) in RCA: 297] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/20/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022]
Abstract
Synapse remodeling is essential to encode experiences into neuronal circuits. Here, we define a molecular interaction between neurons and microglia that drives experience-dependent synapse remodeling in the hippocampus. We find that the cytokine interleukin-33 (IL-33) is expressed by adult hippocampal neurons in an experience-dependent manner and defines a neuronal subset primed for synaptic plasticity. Loss of neuronal IL-33 or the microglial IL-33 receptor leads to impaired spine plasticity, reduced newborn neuron integration, and diminished precision of remote fear memories. Memory precision and neuronal IL-33 are decreased in aged mice, and IL-33 gain of function mitigates age-related decreases in spine plasticity. We find that neuronal IL-33 instructs microglial engulfment of the extracellular matrix (ECM) and that its loss leads to impaired ECM engulfment and a concomitant accumulation of ECM proteins in contact with synapses. These data define a cellular mechanism through which microglia regulate experience-dependent synapse remodeling and promote memory consolidation.
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Affiliation(s)
- Phi T Nguyen
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Leah C Dorman
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Simon Pan
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Ilia D Vainchtein
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rafael T Han
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Hiromi Nakao-Inoue
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sunrae E Taloma
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jerika J Barron
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Ari B Molofsky
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mazen A Kheirbek
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA
| | - Anna V Molofsky
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
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Stephens GS, Fu CH, St Romain CP, Zheng Y, Botterill JJ, Scharfman HE, Liu Y, Chin J. Genes Bound by ΔFosB in Different Conditions With Recurrent Seizures Regulate Similar Neuronal Functions. Front Neurosci 2020; 14:472. [PMID: 32536852 PMCID: PMC7268090 DOI: 10.3389/fnins.2020.00472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Seizure incidence is increased in Alzheimer’s disease (AD) patients and mouse models, and treatment with the antiseizure drug levetiracetam improves cognition. We reported that one mechanism by which seizures can exert persistent effects on cognition is through accumulation of ΔFosB, a transcription factor with a long half-life. Even the infrequent seizures that spontaneously occur in transgenic mice expressing human amyloid precursor protein (APP) lead to persistent increases in ΔFosB in the hippocampus, similar to what we observed in patients with AD or temporal lobe epilepsy. ΔFosB epigenetically regulates expression of target genes, however, whether ΔFosB targets the same genes when induced by seizures in different neurological conditions is not clear. We performed ChIP-sequencing to assess the repertoire of ΔFosB target genes in APP mice and in pilocarpine-treated wildtype mice (Pilo mice), a pharmacological model of epilepsy. These mouse models allowed us to compare AD, in which seizures occur in the context of high levels of amyloid beta, and epilepsy, in which recurrent seizures occur without AD-specific pathophysiology. Network profiling of genes bound by ΔFosB in APP mice, Pilo mice, and respective control mice revealed that functional domains modulated by ΔFosB in the hippocampus are expanded and diversified in APP and Pilo mice (vs. respective controls). Domains of interest in both disease contexts involved neuronal excitability and neurotransmission, neurogenesis, chromatin remodeling, and cellular stress and neuroinflammation. To assess the gene targets bound by ΔFosB regardless of seizure etiology, we focused on 442 genes with significant ΔFosB binding in both APP and Pilo mice (vs. respective controls). Functional analyses identified pathways that regulate membrane potential, glutamatergic signaling, calcium homeostasis, complement activation, neuron-glia population maintenance, and chromatin dynamics. RNA-sequencing and qPCR measurements in independent mice detected altered expression of several ΔFosB targets shared in APP and Pilo mice. Our findings indicate that seizure-induced ΔFosB can bind genes in patterns that depend on seizure etiology, but can bind other genes regardless of seizure etiology. Understanding the factors that underlie these differences, such as chromatin accessibility and/or abundance of co-factors, could reveal novel insights into the control of gene expression in disorders with recurrent seizures.
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Affiliation(s)
- Gabriel S Stephens
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Chia-Hsuan Fu
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Corey P St Romain
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Yi Zheng
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Justin J Botterill
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States
| | - Helen E Scharfman
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States.,Departments of Child & Adolescent Psychiatry, Neuroscience & Physiology, and Psychiatry, New York University Neuroscience Institute, New York University Langone Health, New York, NY, United States
| | - Yin Liu
- Department of Neurobiology and Anatomy, University of Texas Medical School at Houston, Houston, TX, United States
| | - Jeannie Chin
- Memory and Brain Research Center, Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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von Wittgenstein J, Zheng F, Wittmann MT, Balta EA, Ferrazzi F, Schäffner I, Häberle BM, Valero-Aracama MJ, Koehl M, Miranda CJ, Kaspar BK, Ekici AB, Reis A, Abrous DN, Alzheimer C, Lie DC. Sox11 is an Activity-Regulated Gene with Dentate-Gyrus-Specific Expression Upon General Neural Activation. Cereb Cortex 2020; 30:3731-3743. [PMID: 32080705 DOI: 10.1093/cercor/bhz338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 01/21/2023] Open
Abstract
Neuronal activity initiates transcriptional programs that shape long-term changes in plasticity. Although neuron subtypes differ in their plasticity response, most activity-dependent transcription factors (TFs) are broadly expressed across neuron subtypes and brain regions. Thus, how region- and neuronal subtype-specific plasticity are established on the transcriptional level remains poorly understood. We report that in young adult (i.e., 6-8 weeks old) mice, the developmental TF SOX11 is induced in neurons within 6 h either by electroconvulsive stimulation or by exploration of a novel environment. Strikingly, SOX11 induction was restricted to the dentate gyrus (DG) of the hippocampus. In the novel environment paradigm, SOX11 was observed in a subset of c-FOS expressing neurons (ca. 15%); whereas around 75% of SOX11+ DG granule neurons were c-FOS+, indicating that SOX11 was induced in an activity-dependent fashion in a subset of neurons. Environmental enrichment or virus-mediated overexpression of SOX11 enhanced the excitability of DG granule cells and downregulated the expression of different potassium channel subunits, whereas conditional Sox11/4 knock-out mice presented the opposite phenotype. We propose that Sox11 is regulated in an activity-dependent fashion, which is specific to the DG, and speculate that activity-dependent Sox11 expression may participate in the modulation of DG neuron plasticity.
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Affiliation(s)
- Julia von Wittgenstein
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.,Department of Biology, Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Fang Zheng
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marie-Theres Wittmann
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.,Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Elli-Anna Balta
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Iris Schäffner
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Benjamin M Häberle
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Maria J Valero-Aracama
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Muriel Koehl
- Neurocentre Magendie U1215, INSERM and Université de Bordeaux, Bordeaux 33000, France
| | - Carlos J Miranda
- The Research Institute, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Brian K Kaspar
- The Research Institute, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Djoher Nora Abrous
- Neurocentre Magendie U1215, INSERM and Université de Bordeaux, Bordeaux 33000, France
| | - Christian Alzheimer
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - D Chichung Lie
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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Roopra A. MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. PLoS Comput Biol 2020; 16:e1007800. [PMID: 32251445 PMCID: PMC7162552 DOI: 10.1371/journal.pcbi.1007800] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 04/16/2020] [Accepted: 03/19/2020] [Indexed: 01/26/2023] Open
Abstract
Transcriptomic profiling is an immensely powerful hypothesis generating tool. However, accurately predicting the transcription factors (TFs) and cofactors that drive transcriptomic differences between samples is challenging. A number of algorithms draw on ChIP-seq tracks to define TFs and cofactors behind gene changes. These approaches assign TFs and cofactors to genes via a binary designation of 'target', or 'non-target' followed by Fisher Exact Tests to assess enrichment of TFs and cofactors. ENCODE archives 2314 ChIP-seq tracks of 684 TFs and cofactors assayed across a 117 human cell lines under a multitude of growth and maintenance conditions. The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. When compared to other TF mining resources, MAGIC displayed favourable performance in predicting TFs and cofactors that drive gene changes in 4 settings: 1) A cell line expressing or lacking single TF, 2) Breast tumors divided along PAM50 designations 3) Whole brain samples from WT mice or mice lacking a single TF in a particular neuronal subtype 4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels. In summary, MAGIC is a standalone application that produces meaningful predictions of TFs and cofactors in transcriptomic experiments.
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Affiliation(s)
- Avtar Roopra
- Dept. of Neuroscience, 5507 WIMR, University of Wisconsin-Madison, Madison, United States of America
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Huynh LM, Burns MP, Taub DD, Blackman MR, Zhou J. Chronic Neurobehavioral Impairments and Decreased Hippocampal Expression of Genes Important for Brain Glucose Utilization in a Mouse Model of Mild TBI. Front Endocrinol (Lausanne) 2020; 11:556380. [PMID: 33071972 PMCID: PMC7531511 DOI: 10.3389/fendo.2020.556380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022] Open
Abstract
Glucose is an essential cellular fuel for maintaining normal brain functions. Traumatic brain injury (TBI) decreases brain glucose utilization in both human and experimental animals during the acute or subacute phase of TBI. It remains unclear as to how the damages affect brain glucose utilization and its association with persistent neurobehavioral impairments in the chronic phase of mild TBI (mTBI). Accordingly, we compared expression of selected genes important to brain glucose utilization in different brain regions of mice during the chronic phase in mTBI vs. sham operated mice. These genes included hexokinase-1 (HK1), phosphofructokinase (PFK), pyruvate kinase (PK), pyruvate dehydrogenase (PDH), capillary glucose transporter (Glut-1), neuron glucose transporter (Glut-3), astrocyte lactate transpor1 (MCT-1), neuron lactate transporter (MCT-2), lactate receptor (GPR81), and Hexokinase isoform-2 (HK2). Young adult male C57BL/6J mice were brain injured with repetitive closed-head concussions. Morris water maze (MWM), elevated plus maze (EPM), and neurological severity score test (NSS) were performed for evaluation of mice neurobehavioral impairments at 2, 4, and 6 months post mTBI. Two days after completion of the last behavioral test, the frontal cortex, hippocampus, brainstem, hypothalamus, and cerebellum were collected for gene expression measurements. The expression of the mRNAs encoding PK, and PDH, two critical enzymes in glucose metabolism, was decreased at all-time points only in the hippocampus, but was unchanged in the brainstem, hypothalamus, and cortex in mTBI mice. mTBI mice also exhibited the following behavioral alterations: (1) decreased spatial learning and memory 2, 4, and 6 months after the injury, (2) increased proportion of time spent on open vs. closed arms determined by EPM, and (3) accelerated reduction in motor activity observed at 4 months, two months earlier than observed in the sham group, during the EPM testing. There were no significant differences in NSS between injury and sham groups at any of the three time points. Thus, mTBI in male mice led to persistent decreased hippocampal expression of mRNAs that encode critical glucose utilization related enzymes in association with long-term impairments in selected neurobehavioral outcomes.
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Affiliation(s)
- Linda M. Huynh
- Research Service, Washington DC VA Medical Center, Washington, DC, United States
| | - Mark P. Burns
- Department of Neuroscience, Georgetown University School of Medicine, Washington, DC, United States
| | - Daniel D. Taub
- Research Service, Washington DC VA Medical Center, Washington, DC, United States
- Department of Biochemistry and Molecular and Cell Biology, Georgetown University School of Medicine, Washington, DC, United States
| | - Marc R. Blackman
- Research Service, Washington DC VA Medical Center, Washington, DC, United States
- Department of Medicine, George Washington University School of Medicine, Washington, DC, United States
- Department of Medicine, Georgetown University School of Medicine, Washington, DC, United States
| | - June Zhou
- Research Service, Washington DC VA Medical Center, Washington, DC, United States
- *Correspondence: June Zhou
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50
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Single-cell transcriptomics as a framework and roadmap for understanding the brain. J Neurosci Methods 2019; 326:108353. [PMID: 31351971 DOI: 10.1016/j.jneumeth.2019.108353] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/05/2019] [Accepted: 07/07/2019] [Indexed: 12/31/2022]
Abstract
A framework for interpreting and guiding experimental examination of the brain is essential for neuroscience. Recently, single-cell RNA sequencing and single-molecule fluorescent in situ hybridization have emerged as key technologies to generate such a framework at a single-cell resolution. These technologies provide a powerful complement for understanding gene expression in the brain: RNA sequencing enables genome-wide high-throughput quantification of gene expression, and in situ hybridization yields spatial registration of gene expression at a cellular resolution. Here, I discuss the insight that each of these technologies individually provide, and how they can be paired in principle and practice to resolve the cell-type-specific spatial organization of the brain. I further discuss the potential of cutting-edge spatial transcriptomics technologies that leverage the advantages of both techniques within the same assay, as well as how transcriptomic assays can be linked with higher-order features of brain structure and function. Such current and forthcoming transcriptomic technologies will have immense impact in generating an underlying logic of the nervous system, and will guide experiments and interpretations across molecular, cellular, circuit, and behavioural neuroscience.
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