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Chen C, Masotti M, Shepard N, Promes V, Tombesi G, Arango D, Manzoni C, Greggio E, Hilfiker S, Kozorovitskiy Y, Parisiadou L. LRRK2 mediates haloperidol-induced changes in indirect pathway striatal projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597594. [PMID: 38895420 PMCID: PMC11185612 DOI: 10.1101/2024.06.06.597594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Haloperidol is used to manage psychotic symptoms in several neurological disorders through mechanisms that involve antagonism of dopamine D2 receptors that are highly expressed in the striatum. Significant side effects of haloperidol, known as extrapyramidal symptoms, lead to motor deficits similar to those seen in Parkinson's disease and present a major challenge in clinical settings. The underlying molecular mechanisms responsible for these side effects remain poorly understood. Parkinson's disease-associated LRRK2 kinase has an important role in striatal physiology and a known link to dopamine D2 receptor signaling. Here, we systematically explore convergent signaling of haloperidol and LRRK2 through pharmacological or genetic inhibition of LRRK2 kinase, as well as knock-in mouse models expressing pathogenic mutant LRRK2 with increased kinase activity. Behavioral assays show that LRRK2 kinase inhibition ameliorates haloperidol-induced motor changes in mice. A combination of electrophysiological and anatomical approaches reveals that LRRK2 kinase inhibition interferes with haloperidol-induced changes, specifically in striatal neurons of the indirect pathway. Proteomic studies and targeted intracellular pathway analyses demonstrate that haloperidol induces a similar pattern of intracellular signaling as increased LRRK2 kinase activity. Our study suggests that LRRK2 kinase plays a key role in striatal dopamine D2 receptor signaling underlying the undesirable motor side effects of haloperidol. This work opens up new therapeutic avenues for dopamine-related disorders, such as psychosis, also furthering our understanding of Parkinson's disease pathophysiology. Summary Chen et al. demonstrate that haloperidol mediated changes in the striatal indirect pathway neurons and circuits are linked to Parkinson's disease associated LRRK2. Inhibiting LRRK2 kinase activity ameliorates the motoric side effects of haloperidol, suggesting a potential approach to alleviating the unwanted side effects of antipsychotics.
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Khudayberdiev S, Weiss K, Heinze A, Colombaretti D, Trausch N, Linne U, Rust MB. The actin-binding protein CAP1 represses MRTF-SRF-dependent gene expression in mouse cerebral cortex. Sci Signal 2024; 17:eadj0032. [PMID: 38713765 DOI: 10.1126/scisignal.adj0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Serum response factor (SRF) is an essential transcription factor for brain development and function. Here, we explored how an SRF cofactor, the actin monomer-sensing myocardin-related transcription factor MRTF, is regulated in mouse cortical neurons. We found that MRTF-dependent SRF activity in vitro and in vivo was repressed by cyclase-associated protein CAP1. Inactivation of the actin-binding protein CAP1 reduced the amount of actin monomers in the cytoplasm, which promoted nuclear MRTF translocation and MRTF-SRF activation. This function was independent of cofilin1 and actin-depolymerizing factor, and CAP1 loss of function in cortical neurons was not compensated by endogenous CAP2. Transcriptomic and proteomic analyses of cerebral cortex lysates from wild-type and Cap1 knockout mice supported the role of CAP1 in repressing MRTF-SRF-dependent signaling in vivo. Bioinformatic analysis identified likely MRTF-SRF target genes, which aligned with the transcriptomic and proteomic results. Together with our previous studies that implicated CAP1 in axonal growth cone function as well as the morphology and plasticity of excitatory synapses, our findings establish CAP1 as a crucial actin regulator in the brain relevant for formation of neuronal networks.
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Affiliation(s)
- Sharof Khudayberdiev
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Kerstin Weiss
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Anika Heinze
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Dalila Colombaretti
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Nathan Trausch
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
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3
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Bao S, Romero JM, Belfort BD, Arenkiel BR. Signaling mechanisms underlying activity-dependent integration of adult-born neurons in the mouse olfactory bulb. Genesis 2024; 62:e23595. [PMID: 38553878 PMCID: PMC10987073 DOI: 10.1002/dvg.23595] [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: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Adult neurogenesis has fascinated the field of neuroscience for decades given the prospects of harnessing mechanisms that facilitate the rewiring and/or replacement of adult brain tissue. The subgranular zone of the hippocampus and the subventricular zone of the lateral ventricle are the two main areas in the brain that exhibit ongoing neurogenesis. Of these, adult-born neurons within the olfactory bulb have proven to be a powerful model for studying circuit plasticity, providing a broad and accessible avenue into neuron development, migration, and continued circuit integration within adult brain tissue. This review focuses on some of the recognized molecular and signaling mechanisms underlying activity-dependent adult-born neuron development. Notably, olfactory activity and behavioral states contribute to adult-born neuron plasticity through sensory and centrifugal inputs, in which calcium-dependent transcriptional programs, local translation, and neuropeptide signaling play important roles. This review also highlights areas of needed continued investigation to better understand the remarkable phenomenon of adult-born neuron integration.
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Affiliation(s)
- Suyang Bao
- Development, Disease Models, and Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin D.W. Belfort
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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4
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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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5
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Privitera M, von Ziegler LM, Floriou-Servou A, Duss SN, Zhang R, Waag R, Leimbacher S, Sturman O, Roessler FK, Heylen A, Vermeiren Y, Van Dam D, De Deyn PP, Germain PL, Bohacek J. Noradrenaline release from the locus coeruleus shapes stress-induced hippocampal gene expression. eLife 2024; 12:RP88559. [PMID: 38477670 DOI: 10.7554/elife.88559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Exposure to an acute stressor triggers a complex cascade of neurochemical events in the brain. However, deciphering their individual impact on stress-induced molecular changes remains a major challenge. Here, we combine RNA sequencing with selective pharmacological, chemogenetic, and optogenetic manipulations to isolate the contribution of the locus coeruleus-noradrenaline (LC-NA) system to the acute stress response in mice. We reveal that NA release during stress exposure regulates a large and reproducible set of genes in the dorsal and ventral hippocampus via β-adrenergic receptors. For a smaller subset of these genes, we show that NA release triggered by LC stimulation is sufficient to mimic the stress-induced transcriptional response. We observe these effects in both sexes, and independent of the pattern and frequency of LC activation. Using a retrograde optogenetic approach, we demonstrate that hippocampus-projecting LC neurons directly regulate hippocampal gene expression. Overall, a highly selective set of astrocyte-enriched genes emerges as key targets of LC-NA activation, most prominently several subunits of protein phosphatase 1 (Ppp1r3c, Ppp1r3d, Ppp1r3g) and type II iodothyronine deiodinase (Dio2). These results highlight the importance of astrocytic energy metabolism and thyroid hormone signaling in LC-mediated hippocampal function and offer new molecular targets for understanding how NA impacts brain function in health and disease.
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Affiliation(s)
- Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Runzhong Zhang
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Sebastian Leimbacher
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Fabienne K Roessler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Annelies Heylen
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yannick Vermeiren
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Division of Human Nutrition and Health, Chair Group of Nutritional Biology, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Debby Van Dam
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, Netherlands
| | - Peter P De Deyn
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, Netherlands
- Department of Neurology, Memory Clinic of Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Pierre-Luc Germain
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
- Laboratory of Statistical Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
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6
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Català-Solsona J, Lutzu S, Lituma PJ, Fábregas-Ordoñez C, Siedlecki D, Giménez-Llort L, Miñano-Molina AJ, Saura CA, Castillo PE, Rodriguez-Álvarez J. Nr4a2 blocks oAβ-mediated synaptic plasticity dysfunction and ameliorates spatial memory deficits in the APP Sw,Ind mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577010. [PMID: 38328087 PMCID: PMC10849715 DOI: 10.1101/2024.01.24.577010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Alzheimer's disease AD is associated with disruptions in neuronal communication, especially in brain regions crucial for learning and memory, such as the hippocampus. The amyloid hypothesis suggests that the accumulation of amyloid-beta oligomers (oAβ) contributes to synaptic dysfunction by internalisation of synaptic AMPA receptors. Recently, it has been reported that Nr4a2, a member of the Nr4a family of orphan nuclear receptors, plays a role in hippocampal synaptic plasticity by regulating BDNF and synaptic AMPA receptors. Here, we demonstrate that oAβ inhibits activity-dependent Nr4a2 activation in hippocampal neurons, indicating a potential link between oAβ and Nr4a2 down-regulation. Furthermore, we have observed a reduction in Nr4a2 protein levels in postmortem hippocampal tissue samples from early AD stages. Pharmacological activation of Nr4a2 proves effective in preventing oAβ-mediated synaptic depression in the hippocampus. Notably, Nr4a2 overexpression in the hippocampus of AD mouse models ameliorates spatial learning and memory deficits. In conclusion, the findings suggest that oAβ may contribute to early cognitive impairment in AD by blocking Nr4a2 activation, leading to synaptic dysfunction. Thus, our results further support that Nr4a2 activation is a potential therapeutic target to mitigate oAβ-induced synaptic and cognitive impairments in the early stages of Alzheimer's disease.
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7
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Sha Q, Fu Z, Escobar Galvis ML, Madaj Z, Underwood MD, Steiner JA, Dwork A, Simpson N, Galfalvy H, Rozoklija G, Achtyes ED, Mann JJ, Brundin L. Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls. Mol Psychiatry 2024; 29:134-145. [PMID: 37938766 PMCID: PMC11078738 DOI: 10.1038/s41380-023-02311-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Suicide rates have increased steadily world-wide over the past two decades, constituting a serious public health crisis that creates a significant burden to affected families and the society as a whole. Suicidal behavior involves a multi-factorial etiology, including psychological, social and biological factors. Since the molecular neural mechanisms of suicide remain vastly uncharacterized, we examined transcriptional- and methylation profiles of postmortem brain tissue from subjects who died from suicide as well as their neurotypical healthy controls. We analyzed temporal pole tissue from 61 subjects, largely free from antidepressant and antipsychotic medication, using RNA-sequencing and DNA-methylation profiling using an array that targets over 850,000 CpG sites. Expression of NPAS4, a key regulator of inflammation and neuroprotection, was significantly downregulated in the suicide decedent group. Moreover, we identified a total of 40 differentially methylated regions in the suicide decedent group, mapping to seven genes with inflammatory function. There was a significant association between NPAS4 DNA methylation and NPAS4 expression in the control group that was absent in the suicide decedent group, confirming its dysregulation. NPAS4 expression was significantly associated with the expression of multiple inflammatory factors in the brain tissue. Overall, gene sets and pathways closely linked to inflammation were significantly upregulated, while specific pathways linked to neuronal development were suppressed in the suicide decedent group. Excitotoxicity as well as suppressed oligodendrocyte function were also implicated in the suicide decedents. In summary, we have identified central nervous system inflammatory mechanisms that may be active during suicidal behavior, along with oligodendrocyte dysfunction and altered glutamate neurotransmission. In these processes, NPAS4 might be a master regulator, warranting further studies to validate its role as a potential biomarker or therapeutic target in suicidality.
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Affiliation(s)
- Qiong Sha
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhen Fu
- Bioinformatics & Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Zach Madaj
- Bioinformatics & Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Mark D Underwood
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Jennifer A Steiner
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Andrew Dwork
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Norman Simpson
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Hanga Galfalvy
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Mental Health Data Science, New York State Psychiatric Institute, New York, NY, USA
| | - Gorazd Rozoklija
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Eric D Achtyes
- Pine Rest Christian Mental Health Services, Grand Rapids, MI, USA
- Department of Psychiatry, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - J John Mann
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Lena Brundin
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA.
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8
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Gu X, Nardone C, Kamitaki N, Mao A, Elledge SJ, Greenberg ME. The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation. Science 2023; 381:eadh5021. [PMID: 37616343 PMCID: PMC10617673 DOI: 10.1126/science.adh5021] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs mechanistically is unclear. Here, we found that midnolin promoted the destruction of many nuclear proteins, including transcription factors encoded by the immediate-early genes. Diverse stimuli induced midnolin, and its overexpression was sufficient to cause the degradation of its targets by a mechanism that did not require ubiquitination. Instead, midnolin associated with the proteasome via an α helix, used its Catch domain to bind a region within substrates that can form a β strand, and used a ubiquitin-like domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.
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Affiliation(s)
- Xin Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Aoyue Mao
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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9
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Song J, Dikwella N, Sinske D, Roselli F, Knöll B. SRF deletion results in earlier disease onset in a mouse model of amyotrophic lateral sclerosis. JCI Insight 2023; 8:e167694. [PMID: 37339001 PMCID: PMC10445689 DOI: 10.1172/jci.insight.167694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/16/2023] [Indexed: 06/22/2023] Open
Abstract
Changes in neuronal activity modulate the vulnerability of motoneurons (MNs) in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). So far, the molecular basis of neuronal activity's impact in ALS is poorly understood. Herein, we investigated the impact of deleting the neuronal activity-stimulated transcription factor (TF) serum response factor (SRF) in MNs of SOD1G93A mice. SRF was present in vulnerable MMP9+ MNs. Ablation of SRF in MNs induced an earlier disease onset starting around 7-8 weeks after birth, as revealed by enhanced weight loss and decreased motor ability. This earlier disease onset in SRF-depleted MNs was accompanied by a mild elevation of neuroinflammation and neuromuscular synapse degeneration, whereas overall MN numbers and mortality were unaffected. In SRF-deficient mice, MNs showed impaired induction of autophagy-encoding genes, suggesting a potentially new SRF function in transcriptional regulation of autophagy. Complementary, constitutively active SRF-VP16 enhanced autophagy-encoding gene transcription and autophagy progression in cells. Furthermore, SRF-VP16 decreased ALS-associated aggregate induction. Chemogenetic modulation of neuronal activity uncovered SRF as having important TF-mediating activity-dependent effects, which might be beneficial to reduce ALS disease burden. Thus, our data identify SRF as a gene regulator connecting neuronal activity with the cellular autophagy program initiated in degenerating MNs.
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Affiliation(s)
- Jialei Song
- Institute of Neurobiochemistry and
- Department of Neurology, Ulm University, Ulm, Germany
| | - Natalie Dikwella
- Institute of Neurobiochemistry and
- Department of Neurology, Ulm University, Ulm, Germany
| | | | - Francesco Roselli
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases-Ulm (DZNE-Ulm), Ulm, Germany
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10
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Ghaffari LT, Trotti D, Haeusler AR. Differential response of C9orf72 transcripts following neuronal depolarization. iScience 2023; 26:106959. [PMID: 37332610 PMCID: PMC10272498 DOI: 10.1016/j.isci.2023.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
The (G4C2)n nucleotide repeat expansion (NRE) mutation in C9orf72 is the most common genetic cause of ALS and FTD. The biological functions of C9orf72 are becoming understood, but it is unclear if this gene is regulated in a neural-specific manner. Neuronal activity is a crucial modifier of biological processes in health and neurodegenerative disease contexts. Here, we show that prolonged membrane depolarization in healthy human iPSC-cortical neurons leads to a significant downregulation of a transcript variant 3 (V3) of C9orf72, with a concomitant increase in variant 2 (V2), which leads to total C9orf72 RNA transcript levels remaining unchanged. However, the same response is not observed in cortical neurons derived from patients with the C9-NRE mutation. These findings reveal the impact of depolarization on C9orf72 transcripts, and how this response diverges in C9-NRE-carriers, which may have important implications in the underlying unique clinical associations of C9-NRE transcripts and disease pathogenesis.
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Affiliation(s)
- Layla T. Ghaffari
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Aaron R. Haeusler
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
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11
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Català-Solsona J, Lituma PJ, Lutzu S, Siedlecki-Wullich D, Fábregas-Ordoñez C, Miñano-Molina AJ, Saura CA, Castillo PE, Rodriguez-Álvarez J. Activity-Dependent Nr4a2 Induction Modulates Synaptic Expression of AMPA Receptors and Plasticity via a Ca 2+/CRTC1/CREB Pathway. J Neurosci 2023; 43:3028-3041. [PMID: 36931707 PMCID: PMC10146469 DOI: 10.1523/jneurosci.1341-22.2023] [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: 07/08/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Transcription factors have a pivotal role in synaptic plasticity and the associated modification of neuronal networks required for memory formation and consolidation. The nuclear receptors subfamily 4 group A (Nr4a) have emerged as possible modulators of hippocampal synaptic plasticity and cognitive functions. However, the molecular and cellular mechanisms underlying Nr4a2-mediated hippocampal synaptic plasticity are not completely known. Here, we report that neuronal activity enhances Nr4a2 expression and function in cultured mouse hippocampal neurons (both sexes) by an ionotropic glutamate receptor/Ca2+/cAMP response element-binding protein/CREB-regulated transcription factor 1 (iGluR/Ca2+/CREB/CRTC1) pathway. Nr4a2 activation mediates BDNF production and increases expression of iGluRs, thereby affecting LTD at CA3-CA1 synapses in acute mouse hippocampal slices (both sexes). Together, our results indicate that the iGluR/Ca2+/CREB/CRTC1 pathway mediates activity-dependent expression of Nr4a2, which is involved in glutamatergic synaptic plasticity by increasing BDNF and synaptic GluA1-AMPARs. Therefore, Nr4a2 activation could be a therapeutic approach for brain disorders associated with dysregulated synaptic plasticity.SIGNIFICANCE STATEMENT A major factor that regulates fast excitatory synaptic transmission and plasticity is the modulation of synaptic AMPARs. However, despite decades of research, the underlying mechanisms of this modulation remain poorly understood. Our study identified a molecular pathway that links neuronal activity with AMPAR modulation and hippocampal synaptic plasticity through the activation of Nr4a2, a member of the nuclear receptor subfamily 4. Since several compounds have been described to activate Nr4a2, our study not only provides mechanistic insights into the molecular pathways related to hippocampal synaptic plasticity and learning, but also identifies Nr4a2 as a potential therapeutic target for pathologic conditions associated with dysregulation of glutamatergic synaptic function.
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Affiliation(s)
- Judit Català-Solsona
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
| | - Pablo J Lituma
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461
| | - Stefano Lutzu
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461
| | - Dolores Siedlecki-Wullich
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
| | - Cristina Fábregas-Ordoñez
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
| | - Alfredo J Miñano-Molina
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
| | - Carlos A Saura
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461
- Department of Psychiatry & Behavioral Sciences, Albert Einstein College of Medicine, New York, New York 10461
| | - José Rodriguez-Álvarez
- Institut de Neurociències and Departamento Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, 28031, Spain
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461
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12
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Porter RS, Iwase S. Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression. Biochem Soc Trans 2023; 51:703-713. [PMID: 36929379 PMCID: PMC10959270 DOI: 10.1042/bst20220889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
The disruption of chromatin-regulating genes is associated with many neurocognitive syndromes. While most of these genes are ubiquitously expressed across various cell-types, many chromatin regulators act upon activity regulated genes (ARGs) that play central roles in synaptic development and plasticity. Recent literature suggests a link between ARG expression disruption in neurons with the human phenotypes observed in various neurocognitive syndromes. Advances in chromatin biology have demonstrated how chromatin structure, from nucleosome occupancy to higher-order structures such as topologically associated domains, impacts the kinetics of transcription. This review discusses the dynamics of these various levels of chromatin structure and their influence on the expression of ARGs.
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Affiliation(s)
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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13
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Zha C, Sossin WS. The molecular diversity of plasticity mechanisms underlying memory: An evolutionary perspective. J Neurochem 2022; 163:444-460. [PMID: 36326567 DOI: 10.1111/jnc.15717] [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: 06/23/2022] [Revised: 08/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Experience triggers molecular cascades in organisms (learning) that lead to alterations (memory) to allow the organism to change its behavior based on experience. Understanding the molecular mechanisms underlying memory, particularly in the nervous system of animals, has been an exciting scientific challenge for neuroscience. We review what is known about forms of neuronal plasticity that underlie memory highlighting important issues in the field: (1) the importance of being able to measure how neurons are activated during learning to identify the form of plasticity that underlies memory, (2) the many distinct forms of plasticity important for memories that naturally decay both within and between organisms, and (3) unifying principles underlying the formation and maintenance of long-term memories. Overall, the diversity of molecular mechanisms underlying memories that naturally decay contrasts with more unified molecular mechanisms implicated in long-lasting changes. Despite many advances, important questions remain as to which mechanisms of neuronal plasticity underlie memory.
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Affiliation(s)
- Congyao Zha
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Wayne S Sossin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
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14
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Musazzi L, Tornese P, Sala N, Lee FS, Popoli M, Ieraci A. Acute stress induces an aberrant increase of presynaptic release of glutamate and cellular activation in the hippocampus of BDNF Val/Met mice. J Cell Physiol 2022; 237:3834-3844. [PMID: 35908196 PMCID: PMC9796250 DOI: 10.1002/jcp.30833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/15/2022] [Accepted: 07/11/2022] [Indexed: 01/01/2023]
Abstract
Stressful life events are considered major risk factors for the development of several psychiatric disorders, though people differentially cope with stress. The reasons for this are still largely unknown but could be accounted for by individual genetic variants, previous life events, or the kind of stressors. The human brain-derived neurotrophic factor (BDNF) Val66Met variant, which was found to impair intracellular trafficking and activity-dependent secretion of BDNF, has been associated with increased susceptibility to develop several neuropsychiatric disorders, although there is still some controversial evidence. On the other hand, acute stress has been consistently demonstrated to promote the release of glutamate in cortico-limbic regions and altered glutamatergic transmission has been reported in psychiatric disorders. However, it is not known if the BDNF Val66Met single-nucleotide polymorphism (SNP) affects the stress-induced presynaptic glutamate release. In this study, we exposed adult male BDNFVal/Val and BDNFVal/Met knock-in mice to 30 min of acute restraint stress. Plasma corticosterone levels, glutamate release, protein, and gene expression in the hippocampus were analyzed immediately after the end of the stress session. Acute restraint stress similarly increased plasma corticosterone levels and nuclear glucocorticoid receptor levels and phosphorylation in both BDNFVal/Val and BDNFVal/Met mice. However, acute restraint stress induced higher increases in hippocampal presynaptic release of glutamate, phosphorylation of cAMP-response element binding protein (CREB), and levels of the immediate early gene c-fos of BDNFVal/Met compared to BFNFVal/Val mice. Moreover, acute restraint stress selectively increased phosphorylation levels of synapsin I at Ser9 and at Ser603 in BDNFVal/Val and BDNFVal/Met mice, respectively. In conclusion, we report here that the BDNF Val66Met SNP knock-in mice display an altered response to acute restraint stress in terms of hippocampal glutamate release, CREB phosphorylation, and neuronal activation, compared to wild-type animals. Taken together, these results could partially explain the enhanced vulnerability to stressful events of Met carriers reported in both preclinical and clinical studies.
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Affiliation(s)
- Laura Musazzi
- Department of Medicine and SurgeryUniversity of Milano‐BicoccaMonzaItaly
| | - Paolo Tornese
- Dipartimento di Scienze FarmaceuticheUniversity of MilanMilanItaly
| | - Nathalie Sala
- Dipartimento di Scienze FarmaceuticheUniversity of MilanMilanItaly
| | - Francis S. Lee
- Department of PsychiatryWeill Cornell Medical CollegeNew YorkNew YorkUSA
| | - Maurizio Popoli
- Dipartimento di Scienze FarmaceuticheUniversity of MilanMilanItaly
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15
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Pettit NL, Yap EL, Greenberg ME, Harvey CD. Fos ensembles encode and shape stable spatial maps in the hippocampus. Nature 2022; 609:327-334. [PMID: 36002569 PMCID: PMC9452297 DOI: 10.1038/s41586-022-05113-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/14/2022] [Indexed: 12/24/2022]
Abstract
In the hippocampus, spatial maps are formed by place cells while contextual memories are thought to be encoded as engrams1-6. Engrams are typically identified by expression of the immediate early gene Fos, but little is known about the neural activity patterns that drive, and are shaped by, Fos expression in behaving animals7-10. Thus, it is unclear whether Fos-expressing hippocampal neurons also encode spatial maps and whether Fos expression correlates with and affects specific features of the place code11. Here we measured the activity of CA1 neurons with calcium imaging while monitoring Fos induction in mice performing a hippocampus-dependent spatial learning task in virtual reality. We find that neurons with high Fos induction form ensembles of cells with highly correlated activity, exhibit reliable place fields that evenly tile the environment and have more stable tuning across days than nearby non-Fos-induced cells. Comparing neighbouring cells with and without Fos function using a sparse genetic loss-of-function approach, we find that neurons with disrupted Fos function have less reliable activity, decreased spatial selectivity and lower across-day stability. Our results demonstrate that Fos-induced cells contribute to hippocampal place codes by encoding accurate, stable and spatially uniform maps and that Fos itself has a causal role in shaping these place codes. Fos ensembles may therefore link two key aspects of hippocampal function: engrams for contextual memories and place codes that underlie cognitive maps.
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Affiliation(s)
- Noah L Pettit
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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16
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Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity. Nat Commun 2022; 13:2929. [PMID: 35614043 PMCID: PMC9132991 DOI: 10.1038/s41467-022-30511-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/04/2022] [Indexed: 01/02/2023] Open
Abstract
In mammals, chemoperception relies on a diverse set of neuronal sensors able to detect chemicals present in the environment, and to adapt to various levels of stimulation. The contribution of endogenous and external factors to these neuronal identities remains to be determined. Taking advantage of the parallel coding lines present in the olfactory system, we explored the potential variations of neuronal identities before and after olfactory experience. We found that at rest, the transcriptomic profiles of mouse olfactory sensory neuron populations are already divergent, specific to the olfactory receptor they express, and are associated with the sequence of these latter. These divergent profiles further evolve in response to the environment, as odorant exposure leads to reprogramming via the modulation of transcription. These findings highlight a broad range of sensory neuron identities that are present at rest and that adapt to the experience of the individual, thus adding to the complexity and flexibility of sensory coding.
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17
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Pumo GM, Kitazawa T, Rijli FM. Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits 2022; 16:911023. [PMID: 35664458 PMCID: PMC9158562 DOI: 10.3389/fncir.2022.911023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity generated before the onset of sensory transduction has a key role in wiring developing sensory circuits. From axonal targeting, to synapse formation and elimination, to the balanced integration of neurons into developing circuits, this type of activity is implicated in a variety of cellular processes. However, little is known about its molecular mechanisms of action, especially at the level of genome regulation. Conversely, sensory experience-dependent activity implements well-characterized transcriptional and epigenetic chromatin programs that underlie heterogeneous but specific genomic responses that shape both postnatal circuit development and neuroplasticity in the adult. In this review, we focus on our knowledge of the developmental processes regulated by spontaneous activity and the underlying transcriptional mechanisms. We also review novel findings on how chromatin regulates the specificity and developmental induction of the experience-dependent program, and speculate their relevance for our understanding of how spontaneous activity may act at the genomic level to instruct circuit assembly and prepare developing neurons for sensory-dependent connectivity refinement and processing.
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Affiliation(s)
- Gabriele M. Pumo
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| | - Taro Kitazawa
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M. Rijli
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
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18
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Grabowska A, Sas-Nowosielska H, Wojtas B, Holm-Kaczmarek D, Januszewicz E, Yushkevich Y, Czaban I, Trzaskoma P, Krawczyk K, Gielniewski B, Martin-Gonzalez A, Filipkowski RK, Olszynski KH, Bernas T, Szczepankiewicz AA, Sliwinska MA, Kanhema T, Bramham CR, Bokota G, Plewczynski D, Wilczynski GM, Magalska A. Activation-induced chromatin reorganization in neurons depends on HDAC1 activity. Cell Rep 2022; 38:110352. [PMID: 35172152 DOI: 10.1016/j.celrep.2022.110352] [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: 02/09/2021] [Revised: 11/09/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Spatial chromatin organization is crucial for transcriptional regulation and might be particularly important in neurons since they dramatically change their transcriptome in response to external stimuli. We show that stimulation of neurons causes condensation of large chromatin domains. This phenomenon can be observed in vitro in cultured rat hippocampal neurons as well as in vivo in the amygdala and hippocampal neurons. Activity-induced chromatin condensation is an active, rapid, energy-dependent, and reversible process. It involves calcium-dependent pathways but is independent of active transcription. It is accompanied by the redistribution of posttranslational histone modifications and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that the histone deacetylase HDAC1 is the key regulator of this process. Our results suggest that HDAC1-dependent chromatin reorganization constitutes an important level of transcriptional regulation in neurons.
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Affiliation(s)
- Agnieszka Grabowska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Hanna Sas-Nowosielska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dagmara Holm-Kaczmarek
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Elzbieta Januszewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Yana Yushkevich
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Pawel Trzaskoma
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ana Martin-Gonzalez
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, San Juan de Alicante, 03550 Alicante, Spain
| | - Robert Kuba Filipkowski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Krzysztof Hubert Olszynski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Tytus Bernas
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Department of Anatomy and Neurology, VCU School of Medicine, Richmond, VA 23284, USA
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Malgorzata Alicja Sliwinska
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Grzegorz Bokota
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Adriana Magalska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland.
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19
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Hermey G. Deciphering the transcriptomic signature of synaptic activity. Neural Regen Res 2022; 17:82-84. [PMID: 34100431 PMCID: PMC8451554 DOI: 10.4103/1673-5374.315229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Guido Hermey
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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20
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Català-Solsona J, Miñano-Molina AJ, Rodríguez-Álvarez J. Nr4a2 Transcription Factor in Hippocampal Synaptic Plasticity, Memory and Cognitive Dysfunction: A Perspective Review. Front Mol Neurosci 2021; 14:786226. [PMID: 34880728 PMCID: PMC8645690 DOI: 10.3389/fnmol.2021.786226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Long-lasting changes of synaptic efficacy are largely mediated by activity-induced gene transcription and are essential for neuronal plasticity and memory. In this scenario, transcription factors have emerged as pivotal players underlying synaptic plasticity and the modification of neural networks required for memory formation and consolidation. Hippocampal synaptic dysfunction is widely accepted to underlie the cognitive decline observed in some neurodegenerative disorders including Alzheimer’s disease. Therefore, understanding the molecular pathways regulating gene expression profiles may help to identify new synaptic therapeutic targets. The nuclear receptor 4A subfamily (Nr4a) of transcription factors has been involved in a variety of physiological processes within the hippocampus, ranging from inflammation to neuroprotection. Recent studies have also pointed out a role for the activity-dependent nuclear receptor subfamily 4, group A, member 2 (Nr4a2/Nurr1) in hippocampal synaptic plasticity and cognitive functions, although the underlying molecular mechanisms are still poorly understood. In this review, we highlight the specific effects of Nr4a2 in hippocampal synaptic plasticity and memory formation and we discuss whether the dysregulation of this transcription factor could contribute to hippocampal synaptic dysfunction, altogether suggesting the possibility that Nr4a2 may emerge as a novel synaptic therapeutic target in brain pathologies associated to cognitive dysfunctions.
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Affiliation(s)
- Judit Català-Solsona
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Alfredo J Miñano-Molina
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - José Rodríguez-Álvarez
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, United States
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21
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Mason MRJ, Erp S, Wolzak K, Behrens A, Raivich G, Verhaagen J. The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity. Hum Mol Genet 2021; 31:1242-1262. [PMID: 34718572 PMCID: PMC9029231 DOI: 10.1093/hmg/ddab315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular, the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first-regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4 and 14 days after axotomy, Jun upregulates 11, 23 and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the downregulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.
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Affiliation(s)
- Matthew R J Mason
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Susan Erp
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Kim Wolzak
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Gennadij Raivich
- UCL Institute for Women's Health, Maternal and Fetal Medicine, Perinatal Brain Repair Group, London, WC1E 6HX, United Kingdom
| | - Joost Verhaagen
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Meibergdreef 47, 1105, BA, Amsterdam, The Netherlands.,Center for Neurogenomics and Cognition Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081HV, Amsterdam, The Netherlands
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22
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Vallés AS, Barrantes FJ. Dendritic spine membrane proteome and its alterations in autistic spectrum disorder. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:435-474. [PMID: 35034726 DOI: 10.1016/bs.apcsb.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dendritic spines are small protrusions stemming from the dendritic shaft that constitute the primary specialization for receiving and processing excitatory neurotransmission in brain synapses. The disruption of dendritic spine function in several neurological and neuropsychiatric diseases leads to severe information-processing deficits with impairments in neuronal connectivity and plasticity. Spine dysregulation is usually accompanied by morphological alterations to spine shape, size and/or number that may occur at early pathophysiological stages and not necessarily be reflected in clinical manifestations. Autism spectrum disorder (ASD) is one such group of diseases involving changes in neuronal connectivity and abnormal morphology of dendritic spines on postsynaptic neurons. These alterations at the subcellular level correlate with molecular changes in the spine proteome, with alterations in the copy number, topography, or in severe cases in the phenotype of the molecular components, predominantly of those proteins involved in spine recognition and adhesion, reflected in abnormally short lifetimes of the synapse and compensatory increases in synaptic connections. Since cholinergic neurotransmission participates in the regulation of cognitive function (attention, memory, learning processes, cognitive flexibility, social interactions) brain acetylcholine receptors are likely to play an important role in the dysfunctional synapses in ASD, either directly or indirectly via the modulatory functions exerted on other neurotransmitter receptor proteins and spine-resident proteins.
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Affiliation(s)
- Ana Sofía Vallés
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (UNS-CONICET), Bahía Blanca, Argentina
| | - Francisco J Barrantes
- Instituto de Investigaciones Biomédicas (BIOMED), UCA-CONICET, Buenos Aires, Argentina.
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23
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Baker MR, Wong RY. Npas4a expression in the teleost forebrain is associated with stress coping style differences in fear learning. Sci Rep 2021; 11:12074. [PMID: 34103598 PMCID: PMC8187387 DOI: 10.1038/s41598-021-91495-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
Learning to anticipate potentially dangerous contexts is an adaptive behavioral response to coping with stressors. An animal's stress coping style (e.g. proactive-reactive axis) is known to influence how it encodes salient events. However, the neural and molecular mechanisms underlying these stress coping style differences in learning are unknown. Further, while a number of neuroplasticity-related genes have been associated with alternative stress coping styles, it is unclear if these genes may bias the development of conditioned behavioral responses to stressful stimuli, and if so, which brain regions are involved. Here, we trained adult zebrafish to associate a naturally aversive olfactory cue with a given context. Next, we investigated if expression of two neural plasticity and neurotransmission-related genes (npas4a and gabbr1a) were associated with the contextual fear conditioning differences between proactive and reactive stress coping styles. Reactive zebrafish developed a stronger conditioned fear response and showed significantly higher npas4a expression in the medial and lateral zones of the dorsal telencephalon (Dm, Dl), and the supracommissural nucleus of the ventral telencephalon (Vs). Our findings suggest that the expression of activity-dependent genes like npas4a may be differentially expressed across several interconnected forebrain regions in response to fearful stimuli and promote biases in fear learning among different stress coping styles.
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Affiliation(s)
- Matthew R Baker
- Department of Biology, University of Nebraska at Omaha, Omaha, USA
| | - Ryan Y Wong
- Department of Biology, University of Nebraska at Omaha, Omaha, USA.
- Department of Psychology, University of Nebraska at Omaha, 6001 Dodge St, Omaha, NE, 68182, USA.
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24
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Garay PM, Chen A, Tsukahara T, Rodríguez Díaz JC, Kohen R, Althaus JC, Wallner MA, Giger RJ, Jones KS, Sutton MA, Iwase S. RAI1 Regulates Activity-Dependent Nascent Transcription and Synaptic Scaling. Cell Rep 2021; 32:108002. [PMID: 32783930 PMCID: PMC7418709 DOI: 10.1016/j.celrep.2020.108002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Long-lasting forms of synaptic plasticity such as synaptic scaling are critically dependent on transcription. Activity-dependent transcriptional dynamics in neurons, however, remain incompletely characterized because most previous efforts relied on measurement of steady-state mRNAs. Here, we use nascent RNA sequencing to profile transcriptional dynamics of primary neuron cultures undergoing network activity shifts. We find pervasive transcriptional changes, in which ∼45% of expressed genes respond to network activity shifts. We further link retinoic acid-induced 1 (RAI1), the Smith-Magenis syndrome gene, to the transcriptional program driven by reduced network activity. Remarkable agreement among nascent transcriptomes, dynamic chromatin occupancy of RAI1, and electrophysiological properties of Rai1-deficient neurons demonstrates the essential roles of RAI1 in suppressing synaptic upscaling in the naive network, while promoting upscaling triggered by activity silencing. These results highlight the utility of bona fide transcription profiling to discover mechanisms of activity-dependent chromatin remodeling that underlie normal and pathological synaptic plasticity. BrU-seq reveals nascent transcription during synaptic up- or downscaling Smith-Magenis syndrome protein RAI1 regulates upscaling-associated transcription RAI1 departs chromatin in response to network activity shifts RAI1 blocks upscaling in naive networks and promotes inactivity-induced upscaling
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Affiliation(s)
- Patricia M Garay
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Takao Tsukahara
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Rafi Kohen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Christian Althaus
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Margarete A Wallner
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roman J Giger
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kevin S Jones
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michael A Sutton
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Shigeki Iwase
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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25
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Defteralı Ç, Moreno-Estellés M, Crespo C, Díaz-Guerra E, Díaz-Moreno M, Vergaño-Vera E, Nieto-Estévez V, Hurtado-Chong A, Consiglio A, Mira H, Vicario C. Neural stem cells in the adult olfactory bulb core generate mature neurons in vivo. Stem Cells 2021; 39:1253-1269. [PMID: 33963799 DOI: 10.1002/stem.3393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 04/20/2021] [Indexed: 01/05/2023]
Abstract
Although previous studies suggest that neural stem cells (NSCs) exist in the adult olfactory bulb (OB), their location, identity, and capacity to generate mature neurons in vivo has been little explored. Here, we injected enhanced green fluorescent protein (EGFP)-expressing retroviral particles into the OB core of adult mice to label dividing cells and to track the differentiation/maturation of any neurons they might generate. EGFP-labeled cells initially expressed adult NSC markers on days 1 to 3 postinjection (dpi), including Nestin, GLAST, Sox2, Prominin-1, and GFAP. EGFP+ -doublecortin (DCX) cells with a migratory morphology were also detected and their abundance increased over a 7-day period. Furthermore, EGFP-labeled cells progressively became NeuN+ neurons, they acquired neuronal morphologies, and they became immunoreactive for OB neuron subtype markers, the most abundant representing calretinin expressing interneurons. OB-NSCs also generated glial cells, suggesting they could be multipotent in vivo. Significantly, the newly generated neurons established and received synaptic contacts, and they expressed presynaptic proteins and the transcription factor pCREB. By contrast, when the retroviral particles were injected into the subventricular zone (SVZ), nearly all (98%) EGFP+ -cells were postmitotic when they reached the OB core, implying that the vast majority of proliferating cells present in the OB are not derived from the SVZ. Furthermore, we detected slowly dividing label-retaining cells in this region that could correspond to the population of resident NSCs. This is the first time NSCs located in the adult OB core have been shown to generate neurons that incorporate into OB circuits in vivo.
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Affiliation(s)
- Çağla Defteralı
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mireia Moreno-Estellés
- Unidad de Neurobiología Molecular, Área de Biología Celular y del Desarrollo, CNM-ISCIII, Majadahonda, Spain.,Instituto de Biomedicina de Valencia-CSIC (IBV-CSIC), Valencia, Spain
| | - Carlos Crespo
- Departamento de Biología Celular, Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina (BIOTECMED), Universitat de Valencia, Valencia, Spain
| | - Eva Díaz-Guerra
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Díaz-Moreno
- Unidad de Neurobiología Molecular, Área de Biología Celular y del Desarrollo, CNM-ISCIII, Majadahonda, Spain
| | - Eva Vergaño-Vera
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Vanesa Nieto-Estévez
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Anahí Hurtado-Chong
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonella Consiglio
- Institute of Biomedicine, Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Barcelona, Spain.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Helena Mira
- Unidad de Neurobiología Molecular, Área de Biología Celular y del Desarrollo, CNM-ISCIII, Majadahonda, Spain.,Instituto de Biomedicina de Valencia-CSIC (IBV-CSIC), Valencia, Spain
| | - Carlos Vicario
- Instituto Cajal-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,CIBERNED-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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26
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Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
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27
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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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28
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Effects of L-DOPA on Gene Expression in the Frontal Cortex of Rats with Unilateral Lesions of Midbrain Dopaminergic Neurons. eNeuro 2021; 8:ENEURO.0234-20.2020. [PMID: 33257528 PMCID: PMC7877460 DOI: 10.1523/eneuro.0234-20.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/15/2020] [Accepted: 11/11/2020] [Indexed: 11/21/2022] Open
Abstract
The development of Parkinson’s disease (PD) causes dysfunction of the frontal cortex, which contributes to the hallmark motor symptoms and is regarded as one of the primary causes of the affective and cognitive impairments observed in PD. Treatment with L-3,4-dihydroxyphenylalanine (L-DOPA) alleviates motor symptoms but has mixed efficacy in restoring normal cognitive functions, which is further complicated by the psychoactive effects of the drug. We investigated how L-DOPA affects gene expression in the frontal cortex in an animal model of unilateral PD. We performed RNA sequencing (RNA-Seq) analysis of gene expression in the frontal cortex of rats with 6-hydroxydopamine (6-OHDA)-induced unilateral dopaminergic lesions treated with L-DOPA, for two weeks. The analysis of variance identified 48 genes with a significantly altered transcript abundance after L-DOPA treatment. We also performed a weighted gene coexpression network analysis (WGCNA), which resulted in the detection of five modules consisting of genes with similar expression patterns. The analyses led to three primary observations. First, the changes in gene expression induced by L-DOPA were bilateral, although only one hemisphere was lesioned. Second, the changes were not restricted to neurons but also appeared to affect immune or endothelial cells. Finally, comparisons with databases of drug-induced gene expression signatures revealed multiple nonspecific effects, indicating that a part of the observed response is a common pattern activated by multiple types of drugs in different target tissues. Taken together, our results identify cellular mechanisms in the frontal cortex that are involved in the response to L-DOPA treatment.
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29
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Martorell-Ribera J, Venuto MT, Otten W, Brunner RM, Goldammer T, Rebl A, Gimsa U. Time-Dependent Effects of Acute Handling on the Brain Monoamine System of the Salmonid Coregonus maraena. Front Neurosci 2020; 14:591738. [PMID: 33343287 PMCID: PMC7746803 DOI: 10.3389/fnins.2020.591738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
The immediate stress response involves the activation of the monoaminergic neurotransmitter systems including serotonin, dopamine and noradrenaline in particular areas of the fish brain. We chose maraena whitefish as a stress-sensitive salmonid species to investigate the influence of acute and chronic handling on the neurochemistry of monoamines in the brain. Plasma cortisol was quantified to assess the activation of the stress axis. In addition, we analyzed the expression of 37 genes related to the monoamine system to identify genes that could be used as markers of neurophysiological stress effects. Brain neurochemistry responded to a single handling (1 min netting and chasing) with increased serotonergic activity 3 h post-challenge. This was accompanied by a modulated expression of monoaminergic receptor genes in the hindbrain and a significant increase of plasma cortisol. The initial response was compensated by an increased monoamine synthesis at 24 h post-challenge, combined with the modulated expression of serotonin-receptor genes and plasma cortisol concentrations returning to control levels. After 10 days of repeated handling (1 min per day), we detected a slightly increased noradrenaline synthesis and a down-regulated expression of dopamine-receptor genes without effect on plasma cortisol levels. In conclusion, the changes in serotonergic neurochemistry and selected gene-expression profiles, together with the initial plasma cortisol variation, indicate an acute response and a subsequent recovery phase with signs of habituation after 10 days of daily exposure to handling. Based on the basal expression patterns of particular genes and their significant regulation upon handling conditions, we suggest a group of genes as potential biomarkers that indicate handling stress on the brain monoamine systems.
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Affiliation(s)
- Joan Martorell-Ribera
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Marzia Tindara Venuto
- Glycobiology Group, Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Winfried Otten
- Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ronald M Brunner
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Tom Goldammer
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Alexander Rebl
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ulrike Gimsa
- Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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30
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Reshetnikov VV, Kisaretova PE, Ershov NI, Shulyupova AS, Oshchepkov DY, Klimova NV, Ivanchihina AV, Merkulova TI, Bondar NP. Genes associated with cognitive performance in the Morris water maze: an RNA-seq study. Sci Rep 2020; 10:22078. [PMID: 33328525 PMCID: PMC7744575 DOI: 10.1038/s41598-020-78997-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Learning and memory are among higher-order cognitive functions that are based on numerous molecular processes including changes in the expression of genes. To identify genes associated with learning and memory formation, here, we used the RNA-seq (high-throughput mRNA sequencing) technology to compare hippocampal transcriptomes between mice with high and low Morris water maze (MWM) cognitive performance. We identified 88 differentially expressed genes (DEGs) and 24 differentially alternatively spliced transcripts between the high- and low-MWM-performance mice. Although the sets of DEGs and differentially alternatively spliced transcripts did not overlap, both were found to be enriched with genes related to the same type of biological processes: trans-synaptic signaling, cognition, and glutamatergic transmission. These findings were supported by the results of weighted-gene co-expression network analysis (WGCNA) revealing the enrichment of MWM-cognitive-performance-correlating gene modules with very similar Gene Ontology terms. High-MWM-performance mice manifested mostly higher expression of the genes associated with glutamatergic transmission and long-term potentiation implementation, which are processes necessary for memory acquisition and consolidation. In this set, there were genes participating in the regulation of trans-synaptic signaling, primarily AMPA receptor signaling (Nrn1, Nptx1, Homer3, Prkce, Napa, Camk2b, Syt7, and Nrgn) and calcium turnover (Hpca, Caln1, Orai2, Cpne4, and Cpne9). In high-MWM-performance mice, we also demonstrated significant upregulation of the “flip” splice variant of Gria1 and Gria2 transcripts encoding subunits of AMPA receptor. Altogether, our data helped to identify specific genes in the hippocampus that are associated with learning and long-term memory. We hypothesized that the differences in MWM cognitive performance between the mouse groups are linked with increased long-term potentiation, which is mainly mediated by increased glutamatergic transmission, primarily AMPA receptor signaling.
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Affiliation(s)
- Vasiliy V Reshetnikov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Polina E Kisaretova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Nikita I Ershov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Anastasia S Shulyupova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Dmitry Yu Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Natalia V Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | | | - Tatiana I Merkulova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Natalia P Bondar
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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31
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Pérez-Lluch S, Klein CC, Breschi A, Ruiz-Romero M, Abad A, Palumbo E, Bekish L, Arnan C, Guigó R. bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage. PLoS Genet 2020; 16:e1009245. [PMID: 33370262 PMCID: PMC7793246 DOI: 10.1371/journal.pgen.1009245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 01/08/2021] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Natural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With the aim to identify NATs with potential regulatory function during fly development, we generated RNA-Seq data in Drosophila developing tissues and found bsAS, one of the most highly expressed lncRNAs in the fly wing. bsAS is antisense to bs/DSRF, a gene involved in wing development and neural processes. bsAS plays a crucial role in the tissue specific regulation of the expression of the bs/DSRF isoforms. This regulation is essential for the correct determination of cell fate during Drosophila development, as bsAS knockouts show highly aberrant phenotypes. Regulation of bs isoform usage by bsAS is mediated by specific physical interactions between the promoters of these two genes, which suggests a regulatory mechanism involving the collision of RNA polymerases transcribing in opposite directions. Evolutionary analysis suggests that bsAS NAT emerged simultaneously to the long-short isoform structure of bs, preceding the emergence of wings in insects.
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Affiliation(s)
- Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Cecilia C. Klein
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alessandra Breschi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Amaya Abad
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Lyazzat Bekish
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
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32
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Denkena J, Zaisser A, Merz B, Klinger B, Kuhl D, Blüthgen N, Hermey G. Neuronal activity regulates alternative exon usage. Mol Brain 2020; 13:148. [PMID: 33172478 PMCID: PMC7656758 DOI: 10.1186/s13041-020-00685-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/09/2020] [Indexed: 01/18/2023] Open
Abstract
Neuronal activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. A large number of genes regulated by different neuronal plasticity inducing pathways have been identified, but altered gene expression levels represent only part of the complexity of the activity-regulated transcriptional program. Alternative splicing, the differential inclusion and exclusion of exonic sequence in mRNA, is an additional mechanism that is thought to define the activity-dependent transcriptome. Here, we present a genome wide microarray-based survey to identify exons with increased expression levels at 1, 4 or 8 h following neuronal activity in the murine hippocampus provoked by generalized seizures. We used two different bioinformatics approaches to identify alternative activity-induced exon usage and to predict alternative splicing, ANOSVA (ANalysis Of Splicing VAriation) which we here adjusted to accommodate data from different time points and FIRMA (Finding Isoforms using Robust Multichip Analysis). RNA sequencing, in situ hybridization and reverse transcription PCR validate selected activity-dependent splicing events of previously described and so far undescribed activity-regulated transcripts, including Homer1a, Homer1d, Ania3, Errfi1, Inhba, Dclk1, Rcan1, Cda, Tpm1 and Krt75. Taken together, our survey significantly adds to the comprehensive understanding of the complex activity-dependent neuronal transcriptomic signature. In addition, we provide data sets that will serve as rich resources for future comparative expression analyses.
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Affiliation(s)
- Johanna Denkena
- Institute for Theoretical Biology and Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany.,Integrative Research Institute Life Sciences, Humboldt Universität Berlin, 10115, Berlin, Germany
| | - Andrea Zaisser
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Barbara Merz
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Bertram Klinger
- Institute for Theoretical Biology and Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany.,Integrative Research Institute Life Sciences, Humboldt Universität Berlin, 10115, Berlin, Germany
| | - Dietmar Kuhl
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology and Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany.,Integrative Research Institute Life Sciences, Humboldt Universität Berlin, 10115, Berlin, Germany
| | - Guido Hermey
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany.
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33
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Nishi M. Effects of Early-Life Stress on the Brain and Behaviors: Implications of Early Maternal Separation in Rodents. Int J Mol Sci 2020; 21:E7212. [PMID: 33003605 PMCID: PMC7584021 DOI: 10.3390/ijms21197212] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 01/06/2023] Open
Abstract
Early-life stress during the prenatal and postnatal periods affects the formation of neural networks that influence brain function throughout life. Previous studies have indicated that maternal separation (MS), a typical rodent model equivalent to early-life stress and, more specifically, to child abuse and/or neglect in humans, can modulate the hypothalamic-pituitary-adrenal (HPA) axis, affecting subsequent neuronal function and emotional behavior. However, the neural basis of the long-lasting effects of early-life stress on brain function has not been clarified. In the present review, we describe the alterations in the HPA-axis activity-focusing on serum corticosterone (CORT)-and in the end products of the HPA axis as well as on the CORT receptor in rodents. We then introduce the brain regions activated during various patterns of MS, including repeated MS and single exposure to MS at various stages before weaning, via an investigation of c-Fos expression, which is a biological marker of neuronal activity. Furthermore, we discuss the alterations in behavior and gene expression in the brains of adult mice exposed to MS. Finally, we ask whether MS repeats itself and whether intergenerational transmission of child abuse and neglect is possible.
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Affiliation(s)
- Mayumi Nishi
- Department of Anatomy and Cell Biology, Nara Medical University, Kashihara 634-8521, Japan
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34
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Borodinova AA, Balaban PM. Epigenetic Regulation as a Basis for Long-Term Changes in the Nervous System: In Search of Specificity Mechanisms. BIOCHEMISTRY (MOSCOW) 2020; 85:994-966. [DOI: 10.1134/s0006297920090023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Adaptive long-term changes in the functioning of nervous system (plasticity, memory) are not written in the genome, but are directly associated with the changes in expression of many genes comprising epigenetic regulation. Summarizing the known data regarding the role of epigenetics in regulation of plasticity and memory, we would like to highlight several key aspects. (i) Different chromatin remodeling complexes and DNA methyltransferases can be organized into high-order multiprotein repressor complexes that are cooperatively acting as the “molecular brake pads”, selectively restricting transcriptional activity of specific genes at rest. (ii) Relevant physiological stimuli induce a cascade of biochemical events in the activated neurons resulting in translocation of different signaling molecules (protein kinases, NO-containing complexes) to the nucleus. (iii) Stimulus-specific nitrosylation and phosphorylation of different epigenetic factors is linked to a decrease in their enzymatic activity or changes in intracellular localization that results in temporary destabilization of the repressor complexes. (iv) Removing “molecular brakes” opens a “critical time window” for global and local epigenetic changes, triggering specific transcriptional programs and modulation of synaptic connections efficiency. It can be assumed that the reversible post-translational histone modifications serve as the basis of plastic changes in the neural network. On the other hand, DNA methylation and methylation-dependent 3D chromatin organization can serve a stable molecular basis for long-term maintenance of plastic changes and memory.
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35
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Runge K, Cardoso C, de Chevigny A. Dendritic Spine Plasticity: Function and Mechanisms. Front Synaptic Neurosci 2020. [DOI: 10.3389/fnsyn.2020.00036
expr 823669561 + 872784217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
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36
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Runge K, Cardoso C, de Chevigny A. Dendritic Spine Plasticity: Function and Mechanisms. Front Synaptic Neurosci 2020; 12:36. [PMID: 32982715 PMCID: PMC7484486 DOI: 10.3389/fnsyn.2020.00036] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
Dendritic spines are small protrusions studding neuronal dendrites, first described in 1888 by Ramón y Cajal using his famous Golgi stainings. Around 50 years later the advance of electron microscopy (EM) confirmed Cajal's intuition that spines constitute the postsynaptic site of most excitatory synapses in the mammalian brain. The finding that spine density decreases between young and adult ages in fixed tissues suggested that spines are dynamic. It is only a decade ago that two-photon microscopy (TPM) has unambiguously proven the dynamic nature of spines, through the repeated imaging of single spines in live animals. Spine dynamics comprise formation, disappearance, and stabilization of spines and are modulated by neuronal activity and developmental age. Here, we review several emerging concepts in the field that start to answer the following key questions: What are the external signals triggering spine dynamics and the molecular mechanisms involved? What is, in return, the role of spine dynamics in circuit-rewiring, learning, and neuropsychiatric disorders?
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Affiliation(s)
- Karen Runge
- Institut de Neurobiologie de la Méditerranée (INMED) INSERM U1249, Aix-Marseille University, Marseille, France
| | - Carlos Cardoso
- Institut de Neurobiologie de la Méditerranée (INMED) INSERM U1249, Aix-Marseille University, Marseille, France
| | - Antoine de Chevigny
- Institut de Neurobiologie de la Méditerranée (INMED) INSERM U1249, Aix-Marseille University, Marseille, France
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37
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Vukojevic V, Mastrandreas P, Arnold A, Peter F, Kolassa IT, Wilker S, Elbert T, de Quervain DJF, Papassotiropoulos A, Stetak A. Evolutionary conserved role of neural cell adhesion molecule-1 in memory. Transl Psychiatry 2020; 10:217. [PMID: 32632143 PMCID: PMC7338365 DOI: 10.1038/s41398-020-00899-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 01/17/2023] Open
Abstract
The neural cell adhesion molecule 1 (NCAM-1) has been implicated in several brain-related biological processes, including neuronal migration, axonal branching, fasciculation, and synaptogenesis, with a pivotal role in synaptic plasticity. Here, we investigated the evolutionary conserved role of NCAM-1 in learning and memory. First, we investigated sustained changes in ncam-1 expression following aversive olfactory conditioning in C. elegans using molecular genetic methods. Furthermore, we examined the link between epigenetic signatures of the NCAM1 gene and memory in two human samples of healthy individuals (N = 568 and N = 319) and in two samples of traumatized individuals (N = 350 and N = 463). We found that olfactory conditioning in C. elegans induced ncam-1 expression and that loss of ncam-1 function selectively impaired associative long-term memory, without causing acquisition, sensory, or short-term memory deficits. Reintroduction of the C. elegans or human NCAM1 fully rescued memory impairment, suggesting a conserved role of NCAM1 for memory. In parallel, DNA methylation of the NCAM1 promoter in two independent healthy Swiss cohorts was associated with memory performance. In two independent Sub-Saharan populations of conflict zone survivors who had faced severe trauma, DNA methylation at an alternative promoter of the NCAM1 gene was associated with traumatic memories. Our results support a role of NCAM1 in associative memory in nematodes and humans, and might, ultimately, be helpful in elucidating diagnostic markers or suggest novel therapy targets for memory-related disorders, like PTSD.
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Affiliation(s)
- Vanja Vukojevic
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland.
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
- University of Basel, Psychiatric University Clinics, Wilhelm Klein-Strasse 27, CH-4012, Basel, Switzerland.
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland.
| | - Pavlina Mastrandreas
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland.
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland.
| | - Andreas Arnold
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland
| | - Fabian Peter
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland
| | - Iris-T Kolassa
- Ulm University, Clinical & Biological Psychology, Institute for Psychology & Education, Albert-Einstein-Allee 47, D-89069, Ulm, Germany
| | - Sarah Wilker
- Ulm University, Clinical & Biological Psychology, Institute for Psychology & Education, Albert-Einstein-Allee 47, D-89069, Ulm, Germany
- University Bielefeld, Department for Psychology and Sports Science, P.O. Box 100131, D-33501, Bielefeld, Germany
| | - Thomas Elbert
- University of Konstanz, Clinical Psychology & Behavioural Neuroscience, D-78457, Konstanz, Germany
| | - Dominique J-F de Quervain
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland
- University of Basel, Department of Psychology, Division of Cognitive Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland
| | - Andreas Papassotiropoulos
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland.
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
- University of Basel, Psychiatric University Clinics, Wilhelm Klein-Strasse 27, CH-4012, Basel, Switzerland.
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland.
| | - Attila Stetak
- University of Basel, Department of Psychology, Division of Molecular Neuroscience, Birmannsgasse 8, CH-4055, Basel, Switzerland
- University of Basel, Department Biozentrum, Life Sciences Training Facility, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
- University of Basel, Psychiatric University Clinics, Wilhelm Klein-Strasse 27, CH-4012, Basel, Switzerland
- University of Basel, Transfaculty Research Platform, Birmannsgasse 8, CH-4055, Basel, Switzerland
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Marchisella F, Paladini MS, Guidi A, Begni V, Brivio P, Spero V, Calabrese F, Molteni R, Riva MA. Chronic treatment with the antipsychotic drug blonanserin modulates the responsiveness to acute stress with anatomical selectivity. Psychopharmacology (Berl) 2020; 237:1783-1793. [PMID: 32296859 DOI: 10.1007/s00213-020-05498-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022]
Abstract
RATIONALE Patients diagnosed with schizophrenia typically receive life-long treatments with antipsychotic drugs (APDs). However, the impact of chronic APDs treatment on neuroplastic mechanisms in the brain remains largely elusive. OBJECTIVE Here, we focused on blonanserin, a second-generation antipsychotic (SGA) that acts as an antagonist at dopamine D2, D3, and serotonin 5-HT2A receptors, and represents an important tool for the treatment of schizophrenia. METHODS We used rats to investigate the ability of chronic treatment blonanserin to modulate the activity of brain structures relevant for schizophrenia, under baseline conditions or in response to an acute forced swim session (FSS). We measured the expression of different immediate early genes (IEGs), including c-Fos, Arc/Arg 3.1, Zif268 and Npas4. RESULTS Blonanserin per se produced limited changes in the expression of these genes under basal conditions, while, as expected, FSS produced a significant elevation of IEGs transcription in different brain regions. The response of blonanserin-treated rats to FSS show anatomical and gene-selective differences. Indeed, the upregulation of IEGs was greatly reduced in the striatum, a brain structure enriched in dopamine receptors, whereas the upregulation of some genes (Zif268, Npas4) was largely preserved in other regions, such as the prefrontal cortex and the ventral hippocampus. CONCLUSIONS Taken together, our findings show that chronic exposure to blonanserin modulates selective IEGs with a specific anatomical profile. Moreover, the differential activation of specific brain regions under challenging conditions may contribute to specific clinical features of the drug.
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Affiliation(s)
- Francesca Marchisella
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy
| | - Maria Serena Paladini
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy
| | - Alice Guidi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy
| | - Paola Brivio
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy
| | - Vittoria Spero
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy
| | - Francesca Calabrese
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy
| | - Raffaella Molteni
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20129, Milan, Italy.
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133, Milan, Italy
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39
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Servili E, Trus M, Sajman J, Sherman E, Atlas D. Elevated basal transcription can underlie timothy channel association with autism related disorders. Prog Neurobiol 2020; 191:101820. [PMID: 32437834 DOI: 10.1016/j.pneurobio.2020.101820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 03/18/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023]
Abstract
Timothy syndrome (TS) is a neurodevelopmental disorder caused by mutations in the pore-forming subunit α11.2 of the L-type voltage-gated Ca2+-channel Cav1.2, at positions G406R or G402S. Although both mutations cause cardiac arrhythmias, only Cav1.2G406R is associated with the autism-spectrum-disorder (ASD). We show that transcriptional activation by Cav1.2G406R and Cav1.2G402S is driven by membrane depolarization through the Ras/ERK/CREB pathway in a process called excitation-transcription (ET) coupling, as previously shown for wt Cav1.2. This process requires the presence of the intracellular β-subunit of the channel. We found that only the autism-associated mutant Cav1.2G406R, as opposed to the non-autistic mutated channel Cav1.2G402S, exhibits a depolarization-independent CREB phosphorylation, and spontaneous transcription of cFos and MeCP2. A leftward voltage-shift typical of Cav1.2G406R activation, increases channel opening at subthreshold potentials, resulting in an enhanced channel activity, as opposed to a rightward shift in Cav1.2G402S. We suggest that the enhanced spontaneous Cav1.2G406R activity accounts for the increase in basal transcriptional activation. This uncontroled transcriptional activation may result in the manifestation of long-term dysregulations such as autism. Thus, gating changes provide a mechanistic framework for understanding the molecular events underlying the autistic phenomena caused by the G406R Timothy mutation. They might clarify whether a constitutive transcriptional activation accompanies other VGCC that exhibit a leftward voltage-shift of activation and are also associated with long-term cognitive disorders.
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Affiliation(s)
- Evrim Servili
- Dept. of Biological Chemistry, Institute of Life Sciences, Israel
| | - Michael Trus
- Dept. of Biological Chemistry, Institute of Life Sciences, Israel
| | - Julia Sajman
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Daphne Atlas
- Dept. of Biological Chemistry, Institute of Life Sciences, Israel.
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40
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Koltun B, Ironi S, Gershoni-Emek N, Barrera I, Hleihil M, Nanguneri S, Sasmal R, Agasti SS, Nair D, Rosenblum K. Measuring mRNA translation in neuronal processes and somata by tRNA-FRET. Nucleic Acids Res 2020; 48:e32. [PMID: 31974573 PMCID: PMC7102941 DOI: 10.1093/nar/gkaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023] Open
Abstract
In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. Here, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and transport of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA mobility in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of long-term potentiation (LTP) in culture revealed up-regulation of mRNA translation with a similar effect in dendrites and somata, which appeared to be GluR-dependent 6 h post-activation. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.
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Affiliation(s)
- Bella Koltun
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Sivan Ironi
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Iliana Barrera
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Mohammad Hleihil
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Ranjan Sasmal
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Sarit S Agasti
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.,Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel
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41
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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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42
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Rigby MJ, Ding Y, Farrugia MA, Feig M, Cortese GP, Mitchell H, Burger C, Puglielli L. The endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 are differentially regulated to adjust engagement of the secretory pathway. J Neurochem 2020; 154:404-423. [PMID: 31945187 DOI: 10.1111/jnc.14958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 01/13/2023]
Abstract
Nε-lysine acetylation of nascent glycoproteins within the endoplasmic reticulum (ER) lumen regulates the efficiency of the secretory pathway. The ER acetylation machinery consists of the membrane transporter, acetyl-CoA transporter 1 (AT-1/SLC33A1), and two acetyltransferases, ATase1/NAT8B and ATase2/NAT8. Dysfunctional ER acetylation is associated with severe neurological diseases with duplication of AT-1/SLC33A1 being associated with autism spectrum disorder, intellectual disability, and dysmorphism. Neuron-specific AT-1 over-expression in the mouse alters neuron morphology and function, causing an autism-like phenotype, indicating that ER acetylation plays a key role in neurophysiology. As such, characterizing the molecular mechanisms that regulate the acetylation machinery could reveal critical information about its biology. By using structure-biochemistry approaches, we discovered that ATase1 and ATase2 share enzymatic properties but differ in that ATase1 is post-translationally regulated via acetylation. Furthermore, gene expression studies revealed that the promoters of AT-1, ATase1, and ATase2 contain functional binding sites for the neuron-related transcription factors cAMP response element-binding protein and the immediate-early genes c-FOS and c-JUN, and that ATase1 and ATase2 exhibit additional modes of transcriptional regulation relevant to aging and Alzheimer's disease. In vivo rodent gene expression experiments revealed that Atase2 is specifically induced following activity-dependent events. Finally, over-expression of either ATase1 or ATase2 was sufficient to increase the engagement of the secretory pathway in PC12 cells. Our results indicate important regulatory roles for ATase1 and ATase2 in neuron function with induction of ATase2 expression potentially serving as a critical event that adjusts the efficiency of the secretory pathway for activity-dependent neuronal functions.
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Affiliation(s)
- Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Yun Ding
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark A Farrugia
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Giuseppe P Cortese
- Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Corinna Burger
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA.,Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.,Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, USA
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43
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Förstner P, Knöll B. Interference of neuronal activity-mediated gene expression through serum response factor deletion enhances mortality and hyperactivity after traumatic brain injury. FASEB J 2020; 34:3855-3873. [PMID: 31930559 DOI: 10.1096/fj.201902257rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022]
Abstract
Traumatic brain injury (TBI) is one of the most frequent causes of brain injury and mortality in young adults with detrimental sequelae such as cognitive impairments, epilepsy, and attention-deficit hyperactivity disorder. TBI modulates the neuronal excitability resulting in propagation of a neuronal activity-driven gene expression program. However, the impact of such neuronal activity mediated gene expression in TBI has been poorly studied. In this study we analyzed mouse mutants of the prototypical neuronal activity-dependent transcription factor SRF (serum response factor) in a weight-drop TBI model. Neuron-restricted SRF deletion elevated TBI inflicted mortality suggesting a neuroprotective SRF function during TBI. Behavioral inspection uncovered elevated locomotor activity in Srf mutant mice after TBI in contrast to hypoactivity observed in wild-type littermates. This indicates an SRF role in modulation of TBI-associated alterations in locomotor activity. Finally, induction of a neuronal activity induced gene expression program composed of immediate early genes (IEGs) such as Egr1, Egr2, Egr3, Npas4, Atf3, Arc, Ptgs2, and neuronal pentraxins (Nptx2) was compromised upon SRF depletion. Overall, our data show a role of neuronal activity-mediated gene transcription during TBI and suggest a molecular link between TBI and such post-TBI neurological comorbidities involving hyperactivity phenotypes.
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Affiliation(s)
- Philip Förstner
- Institute of Physiological Chemistry, Ulm University, Ulm, Germany
| | - Bernd Knöll
- Institute of Physiological Chemistry, Ulm University, Ulm, Germany
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44
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Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proc Natl Acad Sci U S A 2019; 116:26980-26990. [PMID: 31806754 PMCID: PMC6936480 DOI: 10.1073/pnas.1911413116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Single-cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell-type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically and functionally identified neurons in 2 small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology. Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
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45
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Fernandez-Albert J, Lipinski M, Lopez-Cascales MT, Rowley MJ, Martin-Gonzalez AM, Del Blanco B, Corces VG, Barco A. Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus. Nat Neurosci 2019; 22:1718-1730. [PMID: 31501571 PMCID: PMC6875776 DOI: 10.1038/s41593-019-0476-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/23/2019] [Indexed: 11/08/2022]
Abstract
Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here we combine genetic tagging of nuclei and ribosomes with RNA sequencing, chromatin immunoprecipitation with sequencing, assay for transposase-accessible chromatin using sequencing and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different time points after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions and the formation of gene loops that bring together the transcription start site and transcription termination site of induced genes and may sustain the fast reloading of RNA polymerase complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.
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Affiliation(s)
- Jordi Fernandez-Albert
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - Michal Lipinski
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - María T Lopez-Cascales
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - M Jordan Rowley
- Department of Biology, Emory University, Atlanta, GA, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ana M Martin-Gonzalez
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
- Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Beatriz Del Blanco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | | | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain.
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46
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de Hoz L, Gierej D, Lioudyno V, Jaworski J, Blazejczyk M, Cruces-Solís H, Beroun A, Lebitko T, Nikolaev T, Knapska E, Nelken I, Kaczmarek L. Blocking c-Fos Expression Reveals the Role of Auditory Cortex Plasticity in Sound Frequency Discrimination Learning. Cereb Cortex 2019; 28:1645-1655. [PMID: 28334281 DOI: 10.1093/cercor/bhx060] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 01/03/2023] Open
Abstract
The behavioral changes that comprise operant learning are associated with plasticity in early sensory cortices as well as with modulation of gene expression, but the connection between the behavioral, electrophysiological, and molecular changes is only partially understood. We specifically manipulated c-Fos expression, a hallmark of learning-induced synaptic plasticity, in auditory cortex of adult mice using a novel approach based on RNA interference. Locally blocking c-Fos expression caused a specific behavioral deficit in a sound discrimination task, in parallel with decreased cortical experience-dependent plasticity, without affecting baseline excitability or basic auditory processing. Thus, c-Fos-dependent experience-dependent cortical plasticity is necessary for frequency discrimination in an operant behavioral task. Our results connect behavioral, molecular and physiological changes and demonstrate a role of c-Fos in experience-dependent plasticity and learning.
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Affiliation(s)
- Livia de Hoz
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Dorota Gierej
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.,Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Victoria Lioudyno
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Jacek Jaworski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Magda Blazejczyk
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Hugo Cruces-Solís
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.,International Max Planck Research School for Neurosciences, Göttingen Graduate School for Neurosciences and Molecular Biosciences, 37077 Göttingen, Germany
| | - Anna Beroun
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tomasz Lebitko
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.,Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tomasz Nikolaev
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ewelina Knapska
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Israel Nelken
- Edmond and Lily Safra Center for Brain Sciences and the Department of Neurobiology, Hebrew University, 9190401 Jerusalem, Israel
| | - Leszek Kaczmarek
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
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Yap EL, Greenberg ME. Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior. Neuron 2019; 100:330-348. [PMID: 30359600 DOI: 10.1016/j.neuron.2018.10.013] [Citation(s) in RCA: 322] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/02/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022]
Abstract
Gene transcription is the process by which the genetic codes of organisms are read and interpreted as a set of instructions for cells to divide, differentiate, migrate, and mature. As cells function in their respective niches, transcription further allows mature cells to interact dynamically with their external environment while reliably retaining fundamental information about past experiences. In this Review, we provide an overview of the field of activity-dependent transcription in the vertebrate brain and highlight contemporary work that ranges from studies of activity-dependent chromatin modifications to plasticity mechanisms underlying adaptive behaviors. We identify key gaps in knowledge and propose integrated approaches toward a deeper understanding of how activity-dependent transcription promotes the refinement and plasticity of neural circuits for cognitive function.
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Affiliation(s)
- Ee-Lynn Yap
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Michael E Greenberg
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.
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48
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Pruunsild P, Bading H. Shaping the human brain: evolutionary cis-regulatory plasticity drives changes in synaptic activity-controlled adaptive gene expression. Curr Opin Neurobiol 2019; 59:34-40. [PMID: 31102862 DOI: 10.1016/j.conb.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
Abstract
Neuronal activity-induced gene expression programs involved in synaptic structure- and plasticity-related functions are similar in mice and humans, yet bear distinct features. These include gains or losses of activity-responsiveness of certain genes and differences in gene induction profiles. Here, we discuss a possible origin of dissimilarities in activity-regulated transcription between species. We highlight that while synapse-to-nucleus signalling pathways are evolutionarily conserved, cis-regulatory plasticity has been driving species-specific remodelling of the activity-controlled enhancer landscape, thereby affecting gene regulation. In particular, evolutionary rearrangements of transcription factor binding site placements together with potential species-dependent developmental stage- and/or cell type-specific epigenetic and other trans-acting mechanisms are most likely at least in part accountable for between-species diversity in activity-regulated transcription. It is conceivable that cis-regulatory plasticity may have equipped the synaptic activity-driven adaptive gene program in human neurons with unique, species-specific qualities.
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Affiliation(s)
- Priit Pruunsild
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany.
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49
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Benatti C, Radighieri G, Alboni S, Blom JMC, Brunello N, Tascedda F. Modulation of neuroplasticity-related targets following stress-induced acute escape deficit. Behav Brain Res 2019; 364:140-148. [PMID: 30771367 DOI: 10.1016/j.bbr.2019.02.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/07/2019] [Indexed: 12/12/2022]
Abstract
Understanding resilience is a major challenge to improve current pharmacological therapies aimed at complementing psychological-based approaches of stress-related disorders. In particular, resilience is a multi-factorial construct where the complex network of molecular events that drive the process still needs to be resolved. Here, we exploit the acute escape deficit model, an animal model based on exposure to acute unavoidable stress followed by an escape test, to define vulnerable and resilient phenotypes in rats. Hippocampus and prefrontal cortex (PFC), two of the brain areas most involved in the stress response, were analysed for gene expression at two different time points (3 and 24 h) after the escape test. Total Brain-Derived Neurotrophic Factor (BDNF) was highly responsive in the PFC at 24-h after the escape test, while expression of BDNF transcript IV increased in the hippocampus of resistant animals 3 h post-test. Expression of memory enhancers like Neuronal PAS Domain Protein 4 (Npas4) and Activity-regulated cytoskeleton-associated protein (Arc) decreased in a time- and region-dependent fashion in both behavioural phenotypes. Also, the memory inhibitor Protein Phosphatase 1 (Ppp1ca) was increased in the hippocampus of resilient rats at 3 h post-test. Given the importance of neurotrophic factors and synaptic plasticity-related genes for the development of appropriate coping strategies, our data contribute to an additional step forward in the comprehension of the psychobiology of stress and resiliency.
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Affiliation(s)
- C Benatti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - G Radighieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - S Alboni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy
| | - J M C Blom
- Department of Education and Human Sciences, University of Modena and Reggio Emilia, viale Antonio Allegri 9, 42121, Reggio Emilia, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - N Brunello
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy
| | - F Tascedda
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy; Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy.
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50
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Scandaglia M, Barco A. Contribution of spurious transcription to intellectual disability disorders. J Med Genet 2019; 56:491-498. [PMID: 30745423 DOI: 10.1136/jmedgenet-2018-105668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/17/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
During the development of multicellular organisms, chromatin-modifying enzymes orchestrate the establishment of gene expression programmes that characterise each differentiated cell type. These enzymes also contribute to the maintenance of cell type-specific transcription profiles throughout life. But what happens when epigenomic regulation goes awry? Genomic screens in experimental models of intellectual disability disorders (IDDs) caused by mutations in epigenetic machinery-encoding genes have shown that transcriptional dysregulation constitutes a hallmark of these conditions. Here, we underscore the connections between a subset of chromatin-linked IDDs and spurious transcription in brain cells. We also propose that aberrant gene expression in neurons, including both the ectopic transcription of non-neuronal genes and the activation of cryptic promoters, may importantly contribute to the pathoaetiology of these disorders.
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Affiliation(s)
- Marilyn Scandaglia
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
| | - Angel Barco
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
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