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Samardak K, Bâcle J, Moriel-Carretero M. Behind the stoNE wall: A fervent activity for nuclear lipids. Biochimie 2024:S0300-9084(24)00179-2. [PMID: 39111564 DOI: 10.1016/j.biochi.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/27/2024]
Abstract
The four main types of biomolecules are nucleic acids, proteins, carbohydrates and lipids. The knowledge about their respective interactions is as important as the individual understanding of each of them. However, while, for example, the interaction of proteins with the other three groups is extensively studied, that of nucleic acids and lipids is, in comparison, very poorly explored. An iconic paradigm of physical (and likely functional) proximity between DNA and lipids is the case of the genomic DNA in eukaryotes: enclosed within the nucleus by two concentric lipid bilayers, the wealth of implications of this interaction, for example in genome stability, remains underassessed. Nuclear lipid-related phenotypes have been observed for 50 years, yet in most cases kept as mere anecdotical descriptions. In this review, we will bring together the evidence connecting lipids with both the nuclear envelope and the nucleoplasm, and will make critical analyses of these descriptions. Our exploration establishes a scenario in which lipids irrefutably play a role in nuclear homeostasis.
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Affiliation(s)
- Kseniya Samardak
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France.
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2
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Liu L, Wu J, Zhang C, Cao T, Lu Y, He Z, Li Z. Inhibition of endoplasmic reticulum stress attenuates morphine protracted abstinence-induced anxiety-like behaviors in the male mice. Brain Res 2024; 1835:148930. [PMID: 38604556 DOI: 10.1016/j.brainres.2024.148930] [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: 01/19/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
The anxiety caused by morphine protracted abstinence is considered to be an important factor contributes to drug-seeking and relapse. Endoplasmic reticulum (ER) stress plays important roles in many kinds of mental disorders including drug addiction and anxiety, but it is unclear whether ER stress is involved in anxiety-like behaviors induced by morphine withdrawal. In this study, by using behavioral test, western blot, immunofluorescence, electron transmission microscope, we found that: (1) Inhibition of endoplasmic reticulum stress by 4-Phenylbutyric acid (4-PBA) could attenuate anxiety-like behaviors induced by morphine withdrawal. (2) The endoplasmic reticulum stress-related proteins in the lateral habenula (LHb) but not in the nucleus accumbens (NAc), ventral pallidum (VP), basolateral amygdala (BLA) and CA1 of hippocampus was upregulated by morphine withdrawal, upregulation of endoplasmic reticulum stress-related proteins in the lateral habenula induced by morphine withdrawal was inhibited by 4-PBA. (3) Endoplasmic reticulum stress-related protein CHOP and eIF2α were expressed in neurons but not in microglia in the LHb. (4) Morphine withdrawal induced neuronal morphological change in the LHb, which was attenuated by 4-PBA.
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Affiliation(s)
- Lu Liu
- College of Basic Medical Science, China Three Gorges University, Yichang, China; Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, China
| | - Jie Wu
- College of Basic Medical Science, China Three Gorges University, Yichang, China; Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, China
| | - Changlin Zhang
- College of Basic Medical Science, China Three Gorges University, Yichang, China; Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, China; Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Tong Cao
- Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yongli Lu
- College of Basic Medical Science, China Three Gorges University, Yichang, China; Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, China
| | - Zhi He
- Department of Pharmacology, College of Medicine, Jiaxing University, Jiaxing 314001, China.
| | - Zicheng Li
- College of Basic Medical Science, China Three Gorges University, Yichang, China; Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, China.
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3
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Bueno C, García-Bernal D, Martínez S, Blanquer M, Moraleda JM. The nuclei of human adult stem cells can move within the cell and generate cellular protrusions to contact other cells. Stem Cell Res Ther 2024; 15:32. [PMID: 38321563 PMCID: PMC10848534 DOI: 10.1186/s13287-024-03638-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND The neuronal transdifferentiation of adult bone marrow cells (BMCs) is still considered an artifact based on an alternative explanation of experimental results supporting this phenomenon obtained over decades. However, recent studies have shown that following neural induction, BMCs enter an intermediate cellular state before adopting neural-like morphologies by active neurite extension and that binucleated BMCs can be formed independent of any cell fusion events. These findings provide evidence to reject the idea that BMC neural transdifferentiation is merely an experimental artifact. Therefore, understanding the intermediate states that cells pass through during transdifferentiation is crucial given their potential application in regenerative medicine and disease modelling. METHODS In this study, we examined the functional significance of the variety of morphologies and positioning that cell nuclei of human bone marrow-derived mesenchymal stem cells (hBM-MSCs) can adopt during neural-like differentiation using live-cell nuclear fluorescence labelling, time-lapse microscopy, and confocal microscopy analysis. RESULTS Here, we showed that after neural induction, hBM-MSCs enter an intermediate cellular state in which the nuclei are able to move within the cells, switching shapes and positioning and even generating cellular protrusions as they attempt to contact the cells around them. These findings suggest that changes in nuclear positioning occur because human cell nuclei somehow sense their environment. In addition, we showed the process of direct interactions between cell nuclei, which opens the possibility of a new level of intercellular interaction. CONCLUSIONS The present study advances the understanding of the intermediate stage through which hBM-MSCs pass during neural transdifferentiation, which may be crucial to understanding the mechanisms of these cell conversion processes and eventually harness them for use in regenerative medicine. Importantly, our study provides for the first time evidence that the nuclei of hBM-MSC-derived intermediate cells somehow sense their environment, generating cellular protrusions to contact other cells. In summary, human mesenchymal stromal cells could not only help to increase our understanding of the mechanisms underlying cellular plasticity but also facilitate the exact significance of nuclear positioning in cellular function and in tissue physiology.
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Affiliation(s)
- Carlos Bueno
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain.
| | - David García-Bernal
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Murcia, 30100, Murcia, Spain
| | - Salvador Martínez
- Instituto de Neurociencias de Alicante (UMH-CSIC), Universidad Miguel Hernandez, 03550, San Juan, Alicante, Spain
- Center of Biomedical Network Research on Mental Health (CIBERSAM), ISCIII, 28029, Madrid, Spain
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010, Alicante, Spain
| | - Miguel Blanquer
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
| | - José M Moraleda
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
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4
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Faber T, McConville JT, Lamprecht A. Focused ion beam-scanning electron microscopy provides novel insights of drug delivery phenomena. J Control Release 2024; 366:312-327. [PMID: 38161031 DOI: 10.1016/j.jconrel.2023.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Scanning electron microscopy (SEM) has long been a standard tool for morphological analyses, providing sub micrometer resolution of pharmaceutical formulations. However, analysis of internal morphologies of such formulations can often be biased due to the introduction of artifacts that originate from sample preparation. A recent advancement in SEM, is the focused ion beam scanning electron microscopy (FIB-SEM). This technique uses a focused ion beam (FIB) to remove material with nanometer precision, to provide virtually sample-independent access to sub-surface structures. The FIB can be combined with SEM imaging capabilities within the same instrumentation. As a powerful analytical tool, electron microscopy and FIB-milling are performed sequentially to produce high-resolution 3D models of structural peculiarities of diverse drug delivery systems or their behavior in a biological environment, i.e. intracellular or -tissue distribution. This review paper briefly describes the technical background of the method, outlines a wide array of potential uses within the drug delivery field, and focuses on intracellular transport where high-resolution images are an essential tool for mechanistical insights.
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Affiliation(s)
- Thilo Faber
- Department of Pharmaceutics, Institute of Pharmacy, University of Bonn, Bonn, Germany
| | - Jason T McConville
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, USA
| | - Alf Lamprecht
- Department of Pharmaceutics, Institute of Pharmacy, University of Bonn, Bonn, Germany; Université de Franche-Comté, INSERM UMR1098 Right, Besançon, France.
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5
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Frey T, Murakami T, Maki K, Kawaue T, Tani N, Sugai A, Nakazawa N, Ishiguro K, Adachi T, Kengaku M, Ohki K, Gotoh Y, Kishi Y. Age-associated reduction of nuclear shape dynamics in excitatory neurons of the visual cortex. Aging Cell 2023; 22:e13925. [PMID: 37476844 PMCID: PMC10497821 DOI: 10.1111/acel.13925] [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: 01/10/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
Neurons decline in their functionality over time, and age-related neuronal alterations are associated with phenotypes of neurodegenerative diseases. In nonneural tissues, an infolded nuclear shape has been proposed as a hallmark of aged cells and neurons with infolded nuclei have also been reported to be associated with neuronal activity. Here, we performed time-lapse imaging in the visual cortex of Nex-Cre;SUN1-GFP mice. Nuclear infolding was observed within 10 min of stimulation in young nuclei, while the aged nuclei were already infolded pre-stimulation and showed reduced dynamics of the morphology. In young nuclei, the depletion of the stimuli restored the nucleus to a spherical shape and reduced the dynamic behavior, suggesting that nuclear infolding is a reversible process. We also found the aged nucleus to be stiffer than the young one, further relating to the age-associated loss of nuclear shape dynamics. We reveal temporal changes in the nuclear shape upon external stimulation and observe that these morphological dynamics decrease with age.
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Affiliation(s)
- Tanita Frey
- Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
- New York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Tomonari Murakami
- Graduate School of MedicineThe University of TokyoTokyoJapan
- Institute for AI and Beyond, The University of TokyoTokyoJapan
| | - Koichiro Maki
- Institute for Life and Medical Sciences, Kyoto UniversityKyotoJapan
| | - Takumi Kawaue
- Institute for Integrated Cell‐Material Sciences, Institute for Advanced Study, Kyoto UniversityKyotoJapan
| | - Naoki Tani
- Liaison Laboratory Research Promotion CenterIMEG, Kumamoto UniversityKumamotoJapan
| | - Ayaka Sugai
- Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
- Institute for Quantitative Biosciences, The University of TokyoTokyoJapan
| | - Naotaka Nakazawa
- Institute for Integrated Cell‐Material Sciences, Institute for Advanced Study, Kyoto UniversityKyotoJapan
- Department of Energy and Materials, Faculty of Science and EngineeringKindai UniversityOsakaJapan
| | - Kei‐ichiro Ishiguro
- Department of Chromosome BiologyInstitute of Molecular Embryology and Genetics (IMEG), Kumamoto UniversityKumamotoJapan
| | - Taiji Adachi
- Institute for Life and Medical Sciences, Kyoto UniversityKyotoJapan
| | - Mineko Kengaku
- Institute for Integrated Cell‐Material Sciences, Institute for Advanced Study, Kyoto UniversityKyotoJapan
| | - Kenichi Ohki
- Graduate School of MedicineThe University of TokyoTokyoJapan
- Institute for AI and Beyond, The University of TokyoTokyoJapan
- International Research Center for Neurointelligence (WPI‐IRCN), The University of TokyoTokyoJapan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
- International Research Center for Neurointelligence (WPI‐IRCN), The University of TokyoTokyoJapan
| | - Yusuke Kishi
- Graduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
- Institute for Quantitative Biosciences, The University of TokyoTokyoJapan
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6
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Coscarella IL, Landim-Vieira M, Rastegarpouyani H, Chase PB, Irianto J, Pinto JR. Nucleus Mechanosensing in Cardiomyocytes. Int J Mol Sci 2023; 24:13341. [PMID: 37686151 PMCID: PMC10487505 DOI: 10.3390/ijms241713341] [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: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Cardiac muscle contraction is distinct from the contraction of other muscle types. The heart continuously undergoes contraction-relaxation cycles throughout an animal's lifespan. It must respond to constantly varying physical and energetic burdens over the short term on a beat-to-beat basis and relies on different mechanisms over the long term. Muscle contractility is based on actin and myosin interactions that are regulated by cytoplasmic calcium ions. Genetic variants of sarcomeric proteins can lead to the pathophysiological development of cardiac dysfunction. The sarcomere is physically connected to other cytoskeletal components. Actin filaments, microtubules and desmin proteins are responsible for these interactions. Therefore, mechanical as well as biochemical signals from sarcomeric contractions are transmitted to and sensed by other parts of the cardiomyocyte, particularly the nucleus which can respond to these stimuli. Proteins anchored to the nuclear envelope display a broad response which remodels the structure of the nucleus. In this review, we examine the central aspects of mechanotransduction in the cardiomyocyte where the transmission of mechanical signals to the nucleus can result in changes in gene expression and nucleus morphology. The correlation of nucleus sensing and dysfunction of sarcomeric proteins may assist the understanding of a wide range of functional responses in the progress of cardiomyopathic diseases.
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Affiliation(s)
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hosna Rastegarpouyani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Prescott Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
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7
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Bâcle J, Groizard L, Kumanski S, Moriel-Carretero M. Nuclear envelope-remodeling events as models to assess the potential role of membranes on genome stability. FEBS Lett 2023; 597:1946-1956. [PMID: 37339935 DOI: 10.1002/1873-3468.14688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope (NE) encloses the genetic material and functions in chromatin organization and stability. In Saccharomyces cerevisiae, the NE is bound to the ribosomal DNA (rDNA), highly repeated and transcribed, thus prone to genetic instability. While tethering limits instability, it simultaneously triggers notable NE remodeling. We posit here that NE remodeling may contribute to genome integrity maintenance. The NE importance in genome expression, structure, and integrity is well recognized, yet studies mostly focus on peripheral proteins and nuclear pores, not on the membrane itself. We recently characterized a NE invagination drastically obliterating the rDNA, which we propose here as a model to probe if and how membranes play an active role in genome stability preservation.
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Affiliation(s)
- Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Léa Groizard
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Centre National de la Recherche Scientifique, Université de Montpellier, France
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8
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Das S, Ramanan N. Region-specific heterogeneity in neuronal nuclear morphology in young, aged and in Alzheimer's disease mouse brains. Front Cell Dev Biol 2023; 11:1032504. [PMID: 36819109 PMCID: PMC9929567 DOI: 10.3389/fcell.2023.1032504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Neurons in the mammalian brain exhibit enormous structural and functional diversity across different brain regions. Compared to our understanding of the morphological diversity of neurons, very little is known about the heterogeneity of neuronal nuclear morphology and how nuclear size changes in aging and diseased brains. Here, we report that the neuronal cell nucleus displays differences in area, perimeter, and circularity across different anatomical regions in the mouse brain. The pyramidal neurons of the hippocampal CA3 region exhibited the largest area whereas the striatal neuronal nuclei were the smallest. These nuclear size parameters also exhibited dichotomous changes with age across brain regions-while the neocortical and striatal neurons showed a decrease in nuclear area and perimeter, the CA3 neurons showed an increase with age. The nucleus of parvalbumin- and calbindin-positive interneurons had comparable morphological features but exhibited differences between brain regions. In the context of activity-dependent transcription in response to a novel environment, there was a decrease in nuclear size and circularity in c-Fos expressing neurons in the somatosensory cortex and hippocampal CA1 and CA3. In an APP/PS1 mutant mouse model of Alzheimer's disease (AD), the neuronal nuclear morphology varies with plaque size and with increasing distance from the plaque. The neuronal nuclear morphology in the immediate vicinity of the plaque was independent of the plaque size and the morphology tends to change away from the plaque. These changes in the neuronal nuclear size and shape at different ages and in AD may be attributed to changes in transcriptional activity. This study provides a detailed report on the differences that exist between neurons in nuclear morphology and can serve as a basis for future studies.
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Bueno C, Blanquer M, García-Bernal D, Martínez S, Moraleda JM. Binucleated human bone marrow-derived mesenchymal cells can be formed during neural-like differentiation with independence of any cell fusion events. Sci Rep 2022; 12:20615. [PMID: 36450873 PMCID: PMC9712539 DOI: 10.1038/s41598-022-24996-8] [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: 07/30/2022] [Accepted: 11/23/2022] [Indexed: 12/09/2022] Open
Abstract
Although it has been reported that bone marrow-derived cells (BMDCs) can transdifferentiate into neural cells, the findings are considered unlikely. It has been argued that the rapid neural transdifferentiation of BMDCs reported in culture studies is actually due to cytotoxic changes induced by the media. While transplantation studies indicated that BMDCs can form new neurons, it remains unclear whether the underlying mechanism is transdifferentiation or BMDCs-derived cell fusion with the existing neuronal cells. Cell fusion has been put forward to explain the presence of gene-marked binucleated neurons after gene-marked BMDCs transplantation. In the present study, we demostrated that human BMDCs can rapidly adopt a neural-like morphology through active neurite extension and binucleated human BMDCs can form with independence of any cell fusion events. We also showed that BMDCs neural-like differentiation involves the formation of intermediate cells which can then redifferentiate into neural-like cells, redifferentiate back to the mesenchymal fate or even repeatedly switch lineages without cell division. Furthermore, we have discovered that nuclei from intermediate cells rapidly move within the cell, adopting different morphologies and even forming binucleated cells. Therefore, our results provide a stronger basis for rejecting the idea that BMDCs neural transdifferentiation is merely an artefact.
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Affiliation(s)
- Carlos Bueno
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
| | - Miguel Blanquer
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
| | - David García-Bernal
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain ,grid.10586.3a0000 0001 2287 8496Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
| | - Salvador Martínez
- grid.26811.3c0000 0001 0586 4893Instituto de Neurociencias de Alicante (UMH-CSIC), Universidad Miguel Hernandez, 03550 San Juan, Alicante, Spain
| | - José M. Moraleda
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
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10
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Mehrotra S, Pierce ML, Dravid SM, Murray TF. Stimulation of Neurite Outgrowth in Cerebrocortical Neurons by Sodium Channel Activator Brevetoxin-2 Requires Both N-Methyl-D-aspartate Receptor 2B (GluN2B) and p21 Protein (Cdc42/Rac)-Activated Kinase 1 (PAK1). Mar Drugs 2022; 20:559. [PMID: 36135748 PMCID: PMC9504648 DOI: 10.3390/md20090559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 12/05/2022] Open
Abstract
N-methyl-D-aspartate (NMDA) receptors play a critical role in activity-dependent dendritic arborization, spinogenesis, and synapse formation by stimulating calcium-dependent signaling pathways. Previously, we have shown that brevetoxin 2 (PbTx-2), a voltage-gated sodium channel (VGSC) activator, produces a concentration-dependent increase in intracellular sodium [Na+]I and increases NMDA receptor (NMDAR) open probabilities and NMDA-induced calcium (Ca2+) influxes. The objective of this study is to elucidate the downstream signaling mechanisms by which the sodium channel activator PbTx-2 influences neuronal morphology in murine cerebrocortical neurons. PbTx-2 and NMDA triggered distinct Ca2+-influx pathways, both of which involved the NMDA receptor 2B (GluN2B). PbTx-2-induced neurite outgrowth in day in vitro 1 (DIV-1) neurons required the small Rho GTPase Rac1 and was inhibited by both a PAK1 inhibitor and a PAK1 siRNA. PbTx-2 exposure increased the phosphorylation of PAK1 at Thr-212. At DIV-5, PbTx-2 induced increases in dendritic protrusion density, p-cofilin levels, and F-actin throughout the dendritic arbor and soma. Moreover, PbTx-2 increased miniature excitatory post-synaptic currents (mEPSCs). These data suggest that the stimulation of neurite outgrowth, spinogenesis, and synapse formation produced by PbTx-2 are mediated by GluN2B and PAK1 signaling.
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Affiliation(s)
- Suneet Mehrotra
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
- Omeros, Seattle, WA 98119, USA
| | - Marsha L. Pierce
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Shashank M. Dravid
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Thomas F. Murray
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA
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11
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Kamikawa Y, Saito A, Imaizumi K. Impact of Nuclear Envelope Stress on Physiological and Pathological Processes in Central Nervous System. Neurochem Res 2022; 47:2478-2487. [PMID: 35486254 DOI: 10.1007/s11064-022-03608-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 01/10/2023]
Abstract
The nuclear envelope (NE) separates genomic DNA from the cytoplasm and provides the molecular platforms for nucleocytoplasmic transport, higher-order chromatin organization, and physical links between the nucleus and cytoskeleton. Recent studies have shown that the NE is often damaged by various stresses termed "NE stress", leading to critical cellular dysfunction. Accumulating evidence has revealed the crucial roles of NE stress in the pathology of a broad spectrum of diseases. In the central nervous system (CNS), NE dysfunction impairs neural development and is associated with several neurological disorders, such as Alzheimer's disease and autosomal dominant leukodystrophy. In this review, the structure and functions of the NE are summarized, and the concepts of NE stress and NE stress responses are introduced. Additionally, the significant roles of the NE in the development of CNS and the mechanistic connections between NE stress and neurological disorders are described.
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Affiliation(s)
- Yasunao Kamikawa
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
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12
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [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] [Indexed: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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13
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Sun D, Weng J, Dong Y, Jiang Y. Three-dimensional genome organization in the central nervous system, implications for neuropsychological disorders. J Genet Genomics 2021; 48:1045-1056. [PMID: 34426099 DOI: 10.1016/j.jgg.2021.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Chromosomes in eukaryotic cell nuclei are highly compacted and finely organized into hierarchical three-dimensional (3D) configuration. In recent years, scientists have gained deeper understandings of 3D genome structures and revealed novel evidence linking 3D genome organization to various important cell events on the molecular level. Most importantly, alteration of 3D genome architecture has emerged as an intriguing higher order mechanism that connects disease-related genetic variants in multiple heterogenous and polygenic neuropsychological disorders, delivering novel insights into the etiology. In this review, we provide a brief overview of the hierarchical structures of 3D genome and two proposed regulatory models, loop extrusion and phase separation. We then focus on recent Hi-C data in the central nervous system and discuss 3D genome alterations during normal brain development and in mature neurons. Most importantly, we make a comprehensive review on current knowledge and discuss the role of 3D genome in multiple neuropsychological disorders, including schizophrenia, repeat expansion disorders, 22q11 deletion syndrome, and others.
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Affiliation(s)
- Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, MOE Frontier Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, MOE Frontier Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuhao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, MOE Frontier Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, MOE Frontier Center for Brain Science, Fudan University, Shanghai, 200032, China.
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14
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Differentiation of human adult-derived stem cells towards a neural lineage involves a dedifferentiation event prior to differentiation to neural phenotypes. Sci Rep 2021; 11:12034. [PMID: 34103613 PMCID: PMC8187441 DOI: 10.1038/s41598-021-91566-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
Although it has been reported that mesenchymal stem cells isolated from adult tissues can be induced to overcome their mesenchymal fate and transdifferentiate into neural cells, the findings and their interpretation have been challenged. The main argument against this process is that the cells rapidly adopt neuron-like morphologies through retraction of the cytoplasm rather than active neurite extension. In this study, we examined the sequence of biological events during neural differentiation of human periodontal ligament-derived stem cells (hPDLSCs), human bone marrow-derived stem cells (hBMSCs) and human dental pulp-derived stem cells (hDPSCs) by time-lapse microscopy. We have demonstrated that hPDLSCs, hBMSCs and hDPSCs can directly differentiate into neuron-like cells without passing through a mitotic stage and that they shrink dramatically and change their morphology to that of neuron-like cells through active neurite extension. Furthermore, we observed micronuclei movement and transient cell nuclei lobulation concurrent to in vitro neurogenesis from hBMSCs and hDPSCs. Our results demonstrate that the differentiation of hPDLSCs, hBMSCs and hDPSCs towards a neural lineage occurs through a dedifferentiation step followed by differentiation to neural phenotypes, and therefore we definitively confirm that the rapid acquisition of the neural phenotype is via a differentiation trait.
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15
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Peter M, Aschauer DF, Rose R, Sinning A, Grössl F, Kargl D, Kraitsy K, Burkard TR, Luhmann HJ, Haubensak W, Rumpel S. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation. PLoS One 2021; 16:e0244038. [PMID: 33951054 PMCID: PMC8099114 DOI: 10.1371/journal.pone.0244038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominik F. Aschauer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Renata Rose
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Anne Sinning
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Florian Grössl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Klaus Kraitsy
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Preclinical Phenotyping, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Thomas R. Burkard
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heiko J. Luhmann
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Wulf Haubensak
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
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16
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Mozolewski P, Jeziorek M, Schuster CM, Bading H, Frost B, Dobrowolski R. The role of nuclear Ca2+ in maintaining neuronal homeostasis and brain health. J Cell Sci 2021; 134:jcs254904. [PMID: 33912918 PMCID: PMC8084578 DOI: 10.1242/jcs.254904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nuclear Ca2+ has emerged as one of the most potent mediators of the dialogue between neuronal synapses and the nucleus that regulates heterochromatin states, transcription factor activity, nuclear morphology and neuronal gene expression induced by synaptic activity. Recent studies underline the importance of nuclear Ca2+ signaling in long-lasting, activity-induced adaptation and maintenance of proper brain function. Diverse forms of neuroadaptation require transient nuclear Ca2+ signaling and cyclic AMP-responsive element-binding protein (CREB1, referred to here as CREB) as its prime target, which works as a tunable switch to drive and modulate specific gene expression profiles associated with memory, pain, addiction and neuroprotection. Furthermore, a reduction of nuclear Ca2+ levels has been shown to be neurotoxic and a causal factor driving the progression of neurodegenerative disorders, as well as affecting neuronal autophagy. Because of its central role in the brain, deficits in nuclear Ca2+ signaling may underlie a continuous loss of neuroprotection in the aging brain, contributing to the pathophysiology of Alzheimer's disease. In this Review, we discuss the principles of the 'nuclear calcium hypothesis' in the context of human brain function and its role in controlling diverse forms of neuroadaptation and neuroprotection. Furthermore, we present the most relevant and promising perspectives for future studies.
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Affiliation(s)
- Pawel Mozolewski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Maciej Jeziorek
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Christoph M. Schuster
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, INF 345 and INF 366, 69120 Heidelberg, Germany
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, INF 345 and INF 366, 69120 Heidelberg, Germany
| | - Bess Frost
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
| | - Radek Dobrowolski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
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17
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Suthakar K, Ryugo DK. Projections from the ventral nucleus of the lateral lemniscus to the cochlea in the mouse. J Comp Neurol 2021; 529:2995-3012. [PMID: 33754334 DOI: 10.1002/cne.25143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 02/01/2023]
Abstract
Auditory efferents originate in the central auditory system and project to the cochlea. Although the specific anatomy of the olivocochlear (OC) efferents can vary between species, two types of auditory efferents have been identified based upon the general location of their cell bodies and their distinctly different axon terminations in the organ of Corti. In the mouse, the relatively small somata of the lateral (LOC) efferents reside in the lateral superior olive (LSO), have unmyelinated axons, and terminate around ipsilateral inner hair cells (IHCs), primarily against the afferent processes of type I auditory nerve fibers. In contrast, the larger somata of the medial (MOC) efferents are distributed in the ventral nucleus of the trapezoid body (VNTB), have myelinated axons, and terminate bilaterally against the base of multiple outer hair cells (OHCs). Using in vivo retrograde cell body marking, anterograde axon tracing, immunohistochemistry, and electron microscopy, we have identified a group of efferent neurons in mouse, whose cell bodies reside in the ventral nucleus of the lateral lemniscus (VNLL). By virtue of their location, we call them dorsal efferent (DE) neurons. Labeled DE cells were immuno-negative for tyrosine hydroxylase, glycine, and GABA, but immuno-positive for choline acetyltransferase. Morphologically, DEs resembled LOC efferents by their small somata, unmyelinated axons, and ipsilateral projection to IHCs. These three classes of efferent neurons all project axons directly to the cochlea and exhibit cholinergic staining characteristics. The challenge is to discover the contributions of this new population of neurons to auditory efferent function.
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Affiliation(s)
- Kirupa Suthakar
- Hearing Research, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, New South Wales, Australia
| | - David K Ryugo
- Hearing Research, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, New South Wales, Australia.,Department of Otolaryngology, Head, Neck & Skull Base Surgery, St. Vincent's Hospital, Sydney, New South Wales, Australia.,The Johns Hopkins University School of Medicine, Otolaryngology-HNS, Baltimore, Maryland, USA
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18
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Burrus CJ, McKinstry SU, Kim N, Ozlu MI, Santoki AV, Fang FY, Ma A, Karadeniz YB, Worthington AK, Dragatsis I, Zeitlin S, Yin HH, Eroglu C. Striatal Projection Neurons Require Huntingtin for Synaptic Connectivity and Survival. Cell Rep 2021; 30:642-657.e6. [PMID: 31968243 DOI: 10.1016/j.celrep.2019.12.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 11/07/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022] Open
Abstract
Huntington's disease (HD) is caused by an autosomal dominant polyglutamine expansion mutation of Huntingtin (HTT). HD patients suffer from progressive motor, cognitive, and psychiatric impairments, along with significant degeneration of the striatal projection neurons (SPNs) of the striatum. HD is widely accepted to be caused by a toxic gain-of-function of mutant HTT. However, whether loss of HTT function, because of dominant-negative effects of the mutant protein, plays a role in HD and whether HTT is required for SPN health and function are not known. Here, we delete Htt from specific subpopulations of SPNs using the Cre-Lox system and find that SPNs require HTT for motor regulation, synaptic development, cell health, and survival during aging. Our results suggest that loss of HTT function in SPNs could play a critical role in HD pathogenesis.
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Affiliation(s)
- Caley J Burrus
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Spencer U McKinstry
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Namsoo Kim
- Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - M Ilcim Ozlu
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Aditya V Santoki
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Francia Y Fang
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Annie Ma
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yonca B Karadeniz
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Atesh K Worthington
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ioannis Dragatsis
- Department of Physiology, The University of Tennessee, Health Science Center, Memphis, TN 38163, USA
| | - Scott Zeitlin
- Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Henry H Yin
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA; Duke Institute for Brain Sciences, Durham, NC 27710, USA
| | - Cagla Eroglu
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences, Durham, NC 27710, USA; Regeneration Next Initiative, Duke University, Durham, NC 27710, USA.
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19
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Nahirney PC, Tremblay ME. Brain Ultrastructure: Putting the Pieces Together. Front Cell Dev Biol 2021; 9:629503. [PMID: 33681208 PMCID: PMC7930431 DOI: 10.3389/fcell.2021.629503] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Unraveling the fine structure of the brain is important to provide a better understanding of its normal and abnormal functioning. Application of high-resolution electron microscopic techniques gives us an unprecedented opportunity to discern details of the brain parenchyma at nanoscale resolution, although identifying different cell types and their unique features in two-dimensional, or three-dimensional images, remains a challenge even to experts in the field. This article provides insights into how to identify the different cell types in the central nervous system, based on nuclear and cytoplasmic features, amongst other unique characteristics. From the basic distinction between neurons and their supporting cells, the glia, to differences in their subcellular compartments, organelles and their interactions, ultrastructural analyses can provide unique insights into the changes in brain function during aging and disease conditions, such as stroke, neurodegeneration, infection and trauma. Brain parenchyma is composed of a dense mixture of neuronal and glial cell bodies, together with their intertwined processes. Intracellular components that vary between cells, and can become altered with aging or disease, relate to the cytoplasmic and nucleoplasmic density, nuclear heterochromatin pattern, mitochondria, endoplasmic reticulum and Golgi complex, lysosomes, neurosecretory vesicles, and cytoskeletal elements (actin, intermediate filaments, and microtubules). Applying immunolabeling techniques to visualize membrane-bound or intracellular proteins in neurons and glial cells gives an even better appreciation of the subtle differences unique to these cells across contexts of health and disease. Together, our observations reveal how simple ultrastructural features can be used to identify specific changes in cell types, their health status, and functional relationships in the brain.
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20
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Feurle P, Abentung A, Cera I, Wahl N, Ablinger C, Bucher M, Stefan E, Sprenger S, Teis D, Fischer A, Laighneach A, Whitton L, Morris DW, Apostolova G, Dechant G. SATB2-LEMD2 interaction links nuclear shape plasticity to regulation of cognition-related genes. EMBO J 2021; 40:e103701. [PMID: 33319920 PMCID: PMC7849313 DOI: 10.15252/embj.2019103701] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
SATB2 is a schizophrenia risk gene and is genetically associated with human intelligence. How it affects cognition at molecular level is currently unknown. Here, we show that interactions between SATB2, a chromosomal scaffolding protein, and the inner nuclear membrane protein LEMD2 orchestrate the response of pyramidal neurons to neuronal activation. Exposure to novel environment in vivo causes changes in nuclear shape of CA1 hippocampal neurons via a SATB2-dependent mechanism. The activity-driven plasticity of the nuclear envelope requires not only SATB2, but also its protein interactor LEMD2 and the ESCRT-III/VPS4 membrane-remodeling complex. Furthermore, LEMD2 depletion in cortical neurons, similar to SATB2 ablation, affects neuronal activity-dependent regulation of multiple rapid and delayed primary response genes. In human genetic data, LEMD2-regulated genes are enriched for de novo mutations reported in intellectual disability and schizophrenia and are, like SATB2-regulated genes, enriched for common variants associated with schizophrenia and cognitive function. Hence, interactions between SATB2 and the inner nuclear membrane protein LEMD2 influence gene expression programs in pyramidal neurons that are linked to cognitive ability and psychiatric disorder etiology.
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Affiliation(s)
- Patrick Feurle
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Andreas Abentung
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Isabella Cera
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Nico Wahl
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Cornelia Ablinger
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Michael Bucher
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Simon Sprenger
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - Andre Fischer
- Department of Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GoettingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical CenterGoettingenGermany
| | - Aodán Laighneach
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Laura Whitton
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Derek W Morris
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Galina Apostolova
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Georg Dechant
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
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21
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Samer S, Raman R, Laube G, Kreutz MR, Karpova A. The nuclear lamina is a hub for the nuclear function of Jacob. Mol Brain 2021; 14:9. [PMID: 33436037 PMCID: PMC7802242 DOI: 10.1186/s13041-020-00722-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/26/2020] [Indexed: 12/23/2022] Open
Abstract
Jacob is a synapto-nuclear messenger protein that couples NMDAR activity to CREB-dependent gene expression. In this study, we investigated the nuclear distribution of Jacob and report a prominent targeting to the nuclear envelope that requires NMDAR activity and nuclear import. Immunogold electron microscopy and proximity ligation assay combined with STED imaging revealed preferential association of Jacob with the inner nuclear membrane where it directly binds to LaminB1, an intermediate filament and core component of the inner nuclear membrane (INM). The association with the INM is transient; it involves a functional nuclear export signal in Jacob and a canonical CRM1-RanGTP-dependent export mechanism that defines the residing time of the protein at the INM. Taken together, the data suggest a stepwise redistribution of Jacob within the nucleus following nuclear import and prior to nuclear export.
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Affiliation(s)
- Sebastian Samer
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Rajeev Raman
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Gregor Laube
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto Von Guericke University, 39106, Magdeburg, Germany.
- Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
| | - Anna Karpova
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto Von Guericke University, 39106, Magdeburg, Germany.
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22
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Regulation and dysregulation of spatial chromatin structure in the central nervous system. Anat Sci Int 2021; 96:179-186. [PMID: 33392926 DOI: 10.1007/s12565-020-00567-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Chromatin exists as a non-linear, "three-dimensional" structure in the nuclear space. The dynamic alteration of the chromatin structure leads to transcriptional changes during the formation of the neuronal network. Several studies providing evidence for the link between the dysregulation of spatial chromatin architecture and developmental disorders have accumulated. Therefore, we studied and reviewed the regulation and dysregulation of 3D genome organization in the central nervous system, with a special focus on the cohesin complex that is crucial for the formation of the chromatin loop structure. This review summarizes the function and mechanisms of spatial chromatin architecture during the development of the central nervous system. We discuss the link between the disturbances in the 3D chromatin structure and the diseases of the central nervous system. Finally, we discuss how the knowledge of 3D genome organization may lead to further advances in diagnosis and therapy for the diseases of the central nervous system.
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23
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Abstract
Unraveling the fine structure of the brain is important to provide a better understanding of its normal and abnormal functioning. Application of high-resolution electron microscopic techniques gives us an unprecedented opportunity to discern details of the brain parenchyma at nanoscale resolution, although identifying different cell types and their unique features in two-dimensional, or three-dimensional images, remains a challenge even to experts in the field. This article provides insights into how to identify the different cell types in the central nervous system, based on nuclear and cytoplasmic features, amongst other unique characteristics. From the basic distinction between neurons and their supporting cells, the glia, to differences in their subcellular compartments, organelles and their interactions, ultrastructural analyses can provide unique insights into the changes in brain function during aging and disease conditions, such as stroke, neurodegeneration, infection and trauma. Brain parenchyma is composed of a dense mixture of neuronal and glial cell bodies, together with their intertwined processes. Intracellular components that vary between cells, and can become altered with aging or disease, relate to the cytoplasmic and nucleoplasmic density, nuclear heterochromatin pattern, mitochondria, endoplasmic reticulum and Golgi complex, lysosomes, neurosecretory vesicles, and cytoskeletal elements (actin, intermediate filaments, and microtubules). Applying immunolabeling techniques to visualize membrane-bound or intracellular proteins in neurons and glial cells gives an even better appreciation of the subtle differences unique to these cells across contexts of health and disease. Together, our observations reveal how simple ultrastructural features can be used to identify specific changes in cell types, their health status, and functional relationships in the brain.
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Affiliation(s)
- Patrick C Nahirney
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Eve Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
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24
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Affiliation(s)
- Carlos Bueno
- Instituto de Neurociencias de Alicante (UMH-CSIC), San Juan, Alicante, Spain
| | - Salvador Martínez
- Instituto de Neurociencias de Alicante (UMH-CSIC), San Juan, Alicante, Spain
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25
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Abstract
The brain is a complex organ operating on multiple scales. From molecular events that inform electrical and biochemical cellular responses, the brain interconnects processes all the way up to the massive network size of billions of brain cells. This strongly coupled, nonlinear, system has been subject to research that has turned increasingly multidisciplinary. The seminal work of Hodgkin and Huxley in the 1950s made use of experimental data to derive a coherent physical model of electrical signaling in neurons, which can be solved using mathematical and computational methods, thus bringing together neuroscience, physics, mathematics, and computer science. Over the last decades numerous projects have been dedicated to modeling and simulation of specific parts of molecular dynamics, neuronal signaling, and neural network behavior. Simulators have been developed around a specific objective and scale, in order to cope with the underlying computational complexity. Often times a dimension reduction approach allows larger scale simulations, this however has the inherent drawback of losing insight into structure-function interplay at the cellular level. This paper gives an overview of the project NeuroBox that has the objective of integrating multiple brain scales and associated physical models into one unified framework. NeuroBox hosts geometry and anatomical reconstruction methods, such that detailed three-dimensional domains can be integrated into numerical simulations of models based on partial differential equations. The project further focusses on deriving numerical methods for handling complex computational domains, and to couple multiple spatial dimensions. The latter allows the user to specify in which parts of the biological problem high-dimensional representations are necessary and where low-dimensional approximations are acceptable. NeuroBox offers workflow user interfaces that are automatically generated with VRL-Studio and can be controlled by non-experts. The project further uses uG4 as the numerical backend, and therefore accesses highly advanced discretization methods as well as hierarchical and scalable numerical solvers for very large neurobiological problems.
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Evans AM. On a Magical Mystery Tour with 8-Bromo-Cyclic ADP-Ribose: From All-or-None Block to Nanojunctions and the Cell-Wide Web. Molecules 2020; 25:E4768. [PMID: 33081414 PMCID: PMC7587525 DOI: 10.3390/molecules25204768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
A plethora of cellular functions are controlled by calcium signals, that are greatly coordinated by calcium release from intracellular stores, the principal component of which is the sarco/endooplasmic reticulum (S/ER). In 1997 it was generally accepted that activation of various G protein-coupled receptors facilitated inositol-1,4,5-trisphosphate (IP3) production, activation of IP3 receptors and thus calcium release from S/ER. Adding to this, it was evident that S/ER resident ryanodine receptors (RyRs) could support two opposing cellular functions by delivering either highly localised calcium signals, such as calcium sparks, or by carrying propagating, global calcium waves. Coincidentally, it was reported that RyRs in mammalian cardiac myocytes might be regulated by a novel calcium mobilising messenger, cyclic adenosine diphosphate-ribose (cADPR), that had recently been discovered by HC Lee in sea urchin eggs. A reputedly selective and competitive cADPR antagonist, 8-bromo-cADPR, had been developed and was made available to us. We used 8-bromo-cADPR to further explore our observation that S/ER calcium release via RyRs could mediate two opposing functions, namely pulmonary artery dilation and constriction, in a manner seemingly independent of IP3Rs or calcium influx pathways. Importantly, the work of others had shown that, unlike skeletal and cardiac muscles, smooth muscles might express all three RyR subtypes. If this were the case in our experimental system and cADPR played a role, then 8-bromo-cADPR would surely block one of the opposing RyR-dependent functions identified, or the other, but certainly not both. The latter seemingly implausible scenario was confirmed. How could this be, do cells hold multiple, segregated SR stores that incorporate different RyR subtypes in receipt of spatially segregated signals carried by cADPR? The pharmacological profile of 8-bromo-cADPR action supported not only this, but also indicated that intracellular calcium signals were delivered across intracellular junctions formed by the S/ER. Not just one, at least two. This article retraces the steps along this journey, from the curious pharmacological profile of 8-bromo-cADPR to the discovery of the cell-wide web, a diverse network of cytoplasmic nanocourses demarcated by S/ER nanojunctions, which direct site-specific calcium flux and may thus coordinate the full panoply of cellular processes.
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Grants
- 01/A/S/07453 Biotechnology and Biological Sciences Research Council
- WT046374 , WT056423, WT070772, WT074434, WT081195AIA, WT212923, WT093147 Wellcome Trust
- PG/10/95/28657 British Heart Foundation
- FS/03/033/15432, FS/05/050, PG/05/128/19884, RG/12/14/29885, PG/10/95/28657 British Heart Foundation
- RG/12/14/29885 British Heart Foundation
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Affiliation(s)
- A Mark Evans
- Centre for Discovery Brain Sciences and Cardiovascular Science, Edinburgh Medical School, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
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27
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López AJ, Hecking JK, White AO. The Emerging Role of ATP-Dependent Chromatin Remodeling in Memory and Substance Use Disorders. Int J Mol Sci 2020; 21:E6816. [PMID: 32957495 PMCID: PMC7555352 DOI: 10.3390/ijms21186816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Long-term memory formation requires coordinated regulation of gene expression and persistent changes in cell function. For decades, research has implicated histone modifications in regulating chromatin compaction necessary for experience-dependent changes to gene expression and cell function during memory formation. Recent evidence suggests that another epigenetic mechanism, ATP-dependent chromatin remodeling, works in concert with the histone-modifying enzymes to produce large-scale changes to chromatin structure. This review examines how histone-modifying enzymes and chromatin remodelers restructure chromatin to facilitate memory formation. We highlight the emerging evidence implicating ATP-dependent chromatin remodeling as an essential mechanism that mediates activity-dependent gene expression, plasticity, and cell function in developing and adult brains. Finally, we discuss how studies that target chromatin remodelers have expanded our understanding of the role that these complexes play in substance use disorders.
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Affiliation(s)
- Alberto J. López
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Julia K. Hecking
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
| | - André O. White
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
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28
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Chen X, Xie C, Tian W, Sun L, Wang Z, Hawes S, Chang L, Kung J, Ding J, Chen S, Le W, Cai H. Parkinson's disease-related Leucine-rich repeat kinase 2 modulates nuclear morphology and genomic stability in striatal projection neurons during aging. Mol Neurodegener 2020; 15:12. [PMID: 32075681 PMCID: PMC7031993 DOI: 10.1186/s13024-020-00360-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Multiple missense mutations in Leucine-rich repeat kinase 2 (LRRK2) are associated with familial forms of late onset Parkinson's disease (PD), the most common age-related movement disorder. The dysfunction of dopamine transmission contributes to PD-related motor symptoms. Interestingly, LRRK2 is more abundant in the dopaminoceptive striatal spiny projection neurons (SPNs) compared to the dopamine-producing nigrostriatal dopaminergic neurons. Aging is the most important risk factor for PD and other neurodegenerative diseases. However, whether LRRK2 modulates the aging of SPNs remains to be determined. METHODS We conducted RNA-sequencing (RNA-seq) analyses of striatal tissues isolated from Lrrk2 knockout (Lrrk2-/-) and control (Lrrk2+/+) mice at 2 and 12 months of age. We examined SPN nuclear DNA damage and epigenetic modifications; SPN nuclear, cell body and dendritic morphology; and the locomotion and motor skill learning of Lrrk2+/+ and Lrrk2-/- mice from 2 to 24 months of age. Considering the strength of cell cultures for future mechanistic studies, we also performed preliminary studies in primary cultured SPNs derived from the Lrrk2+/+ and Lrrk2-/- mice as well as the PD-related Lrrk2 G2019S and R1441C mutant mice. RESULTS Lrrk2-deficiency accelerated nuclear hypertrophy and induced dendritic atrophy, soma hypertrophy and nuclear invagination in SPNs during aging. Additionally, increased nuclear DNA damage and abnormal histone methylations were also observed in aged Lrrk2-/- striatal neurons, together with alterations of molecular pathways involved in regulating neuronal excitability, genome stability and protein homeostasis. Furthermore, both the PD-related Lrrk2 G2019S mutant and LRRK2 kinase inhibitors caused nuclear hypertrophy, while the Lrrk2 R1441C mutant and γ-Aminobutyric acid type A receptor (GABA-AR) inhibitors promoted nuclear invagination in the cultured SPNs. On the other hand, inhibition of neuron excitability prevented the formation of nuclear invagination in the cultured Lrrk2-/- and R1441C SPNs. CONCLUSIONS Our findings support an important physiological function of LRRK2 in maintaining nuclear structure integrity and genomic stability during the normal aging process, suggesting that PD-related LRRK2 mutations may cause the deterioration of neuronal structures through accelerating the aging process.
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Affiliation(s)
- Xi Chen
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
- Clinical Research Center on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, 116011 People’s Republic of China
| | - Chengsong Xie
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Wotu Tian
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
- Department of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 20025 China
| | - Lixin Sun
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Zheng Wang
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Sarah Hawes
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Lisa Chang
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Justin Kung
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Shengdi Chen
- Department of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 20025 China
| | - Weidong Le
- Clinical Research Center on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, 116011 People’s Republic of China
| | - Huaibin Cai
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building 35, Room 1A112, MSC 3707, 35 Convent Drive, Bethesda, MD 20892–3707 USA
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29
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Bas-Orth C, Koch M, Lau D, Buchthal B, Bading H. A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling. Mol Brain 2020; 13:3. [PMID: 31924235 PMCID: PMC6954508 DOI: 10.1186/s13041-020-0546-0] [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: 10/15/2019] [Accepted: 01/05/2020] [Indexed: 12/27/2022] Open
Abstract
The cellular consequences of N-Methyl-D-Aspartate receptor (NMDAR) stimulation depend on the receptors' subcellular localization. Synaptic NMDARs promote plasticity and survival whereas extrasynaptic NMDARs mediate excitotoxicity and contribute to cell death in neurodegenerative diseases. The mechanisms that couple activation of extrasynaptic NMDARs to cell death remain incompletely understood. We here show that activation of extrasynaptic NMDARs by bath application of NMDA or L-glutamate leads to the upregulation of a group of 19 microRNAs in cultured mouse hippocampal neurons. In contrast, none of these microRNAs is induced upon stimulation of synaptic activity. Increased microRNA expression depends on the pri-miRNA processing enzyme Drosha, but not on de novo gene transcription. These findings suggest that toxic NMDAR signaling involves changes in the expression levels of particular microRNAs.
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Affiliation(s)
- Carlos Bas-Orth
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, 69120, Heidelberg, Germany. .,Department of Medical Cell Biology, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
| | - Mirja Koch
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - David Lau
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Bettina Buchthal
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, 69120, Heidelberg, Germany
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30
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Bueno C, Martínez-Morga M, Martínez S. Non-proliferative neurogenesis in human periodontal ligament stem cells. Sci Rep 2019; 9:18038. [PMID: 31792338 PMCID: PMC6888846 DOI: 10.1038/s41598-019-54745-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the sequence of events from undifferentiated stem cells to neuron is not only important for the basic knowledge of stem cell biology, but also for therapeutic applications. In this study we examined the sequence of biological events during neural differentiation of human periodontal ligament stem cells (hPDLSCs). Here, we show that hPDLSCs-derived neural-like cells display a sequence of morphologic development highly similar to those reported before in primary neuronal cultures derived from rodent brains. We observed that cell proliferation is not present through neurogenesis from hPDLSCs. Futhermore, we may have discovered micronuclei movement and transient cell nuclei lobulation coincident to in vitro neurogenesis. Morphological analysis also reveals that neurogenic niches in the adult mouse brain contain cells with nuclear shapes highly similar to those observed during in vitro neurogenesis from hPDLSCs. Our results provide additional evidence that it is possible to differentiate hPDLSCs to neuron-like cells and suggest the possibility that the sequence of events from stem cell to neuron does not necessarily requires cell division from stem cell.
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Affiliation(s)
- Carlos Bueno
- Instituto de Neurociencias de Alicante (UMH-CSIC), San Juan, Alicante, 03550, Spain.
| | - Marta Martínez-Morga
- Department of Human Anatomy and Institute of Biomedical Research (IMIB), University of Murcia, Faculty of Medicine, Murcia, 30800, Spain
| | - Salvador Martínez
- Instituto de Neurociencias de Alicante (UMH-CSIC), San Juan, Alicante, 03550, Spain
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31
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Gopal S, Chiappini C, Armstrong JPK, Chen Q, Serio A, Hsu CC, Meinert C, Klein TJ, Hutmacher DW, Rothery S, Stevens MM. Immunogold FIB-SEM: Combining Volumetric Ultrastructure Visualization with 3D Biomolecular Analysis to Dissect Cell-Environment Interactions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1900488. [PMID: 31197896 PMCID: PMC6778054 DOI: 10.1002/adma.201900488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/20/2019] [Indexed: 05/03/2023]
Abstract
Volumetric imaging techniques capable of correlating structural and functional information with nanoscale resolution are necessary to broaden the insight into cellular processes within complex biological systems. The recent emergence of focused ion beam scanning electron microscopy (FIB-SEM) has provided unparalleled insight through the volumetric investigation of ultrastructure; however, it does not provide biomolecular information at equivalent resolution. Here, immunogold FIB-SEM, which combines antigen labeling with in situ FIB-SEM imaging, is developed in order to spatially map ultrastructural and biomolecular information simultaneously. This method is applied to investigate two different cell-material systems: the localization of histone epigenetic modifications in neural stem cells cultured on microstructured substrates and the distribution of nuclear pore complexes in myoblasts differentiated on a soft hydrogel surface. Immunogold FIB-SEM offers the potential for broad applicability to correlate structure and function with nanoscale resolution when addressing questions across cell biology, biomaterials, and regenerative medicine.
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Affiliation(s)
- Sahana Gopal
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Ciro Chiappini
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - James P K Armstrong
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Qu Chen
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Andrea Serio
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Chia-Chen Hsu
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Christoph Meinert
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Travis J Klein
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
- Australian Research Council Industrial Transformation Training Centre, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Dietmar W Hutmacher
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
- Australian Research Council Industrial Transformation Training Centre, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Stephen Rothery
- Facility for Light Microscopy, Imperial College London, London, SW7 2AZ, UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
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32
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Duan J, Navarro-Dorado J, Clark JH, Kinnear NP, Meinke P, Schirmer EC, Evans AM. The cell-wide web coordinates cellular processes by directing site-specific Ca 2+ flux across cytoplasmic nanocourses. Nat Commun 2019; 10:2299. [PMID: 31127110 PMCID: PMC6534574 DOI: 10.1038/s41467-019-10055-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/10/2019] [Indexed: 02/01/2023] Open
Abstract
Ca2+ coordinates diverse cellular processes, yet how function-specific signals arise is enigmatic. We describe a cell-wide network of distinct cytoplasmic nanocourses with the nucleus at its centre, demarcated by sarcoplasmic reticulum (SR) junctions (≤400 nm across) that restrict Ca2+ diffusion and by nanocourse-specific Ca2+-pumps that facilitate signal segregation. Ryanodine receptor subtype 1 (RyR1) supports relaxation of arterial myocytes by unloading Ca2+ into peripheral nanocourses delimited by plasmalemma-SR junctions, fed by sarco/endoplasmic reticulum Ca2+ ATPase 2b (SERCA2b). Conversely, stimulus-specified increases in Ca2+ flux through RyR2/3 clusters selects for rapid propagation of Ca2+ signals throughout deeper extraperinuclear nanocourses and thus myocyte contraction. Nuclear envelope invaginations incorporating SERCA1 in their outer nuclear membranes demarcate further diverse networks of cytoplasmic nanocourses that receive Ca2+ signals through discrete RyR1 clusters, impacting gene expression through epigenetic marks segregated by their associated invaginations. Critically, this circuit is not hardwired and remodels for different outputs during cell proliferation. Although calcium signals are known to be critical for many cellular processes, how signaling elicits specific functions remains unclear. In visually striking work, Duan et al. reveal that networks of cytoplasmic nanocourses orchestrate cell activity by directing site-specific calcium signals.
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Affiliation(s)
- Jingxian Duan
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jorge Navarro-Dorado
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jill H Clark
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Nicholas P Kinnear
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Peter Meinke
- Wellcome Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - A Mark Evans
- Centres for Discovery Brain Sciences and Cardiovascular Sciences, College of Medicine and Veterinary Medicine, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK.
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33
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Brookes E, Riccio A. Location, location, location: nuclear structure regulates gene expression in neurons. Curr Opin Neurobiol 2019; 59:16-25. [PMID: 31005709 DOI: 10.1016/j.conb.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/27/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
Genome architecture plays a critical role in regulating the expression of genes that are essential for nervous system development. During neuronal differentiation, spatially and temporally regulated transcription allows neuronal migration, the growth of dendrites and axons, and at later stages, synaptic formation and the establishment of neuronal circuitry. Genome topology and relocation of gene loci within the nucleus are now regarded as key factors that contribute to transcriptional regulation. Here, we review recent work supporting the hypothesis that the dynamic organization of chromatin within the nucleus impacts gene activation in response to extrinsic signalling and during neuronal differentiation. The consequences of disruption of the genome architecture on neuronal health will be also discussed.
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Affiliation(s)
- Emily Brookes
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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34
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Kishi Y, Gotoh Y. Regulation of Chromatin Structure During Neural Development. Front Neurosci 2018; 12:874. [PMID: 30618540 PMCID: PMC6297780 DOI: 10.3389/fnins.2018.00874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
The regulation of genome architecture is a key determinant of gene transcription patterns and neural development. Advances in methodologies based on chromatin conformation capture (3C) have shed light on the genome-wide organization of chromatin in developmental processes. Here, we review recent discoveries regarding the regulation of three-dimensional (3D) chromatin conformation, including promoter-enhancer looping, and the dynamics of large chromatin domains such as topologically associated domains (TADs) and A/B compartments. We conclude with perspectives on how these conformational changes govern neural development and may go awry in disease states.
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Affiliation(s)
- Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
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35
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Breit M, Kessler M, Stepniewski M, Vlachos A, Queisser G. Spine-to-Dendrite Calcium Modeling Discloses Relevance for Precise Positioning of Ryanodine Receptor-Containing Spine Endoplasmic Reticulum. Sci Rep 2018; 8:15624. [PMID: 30353066 PMCID: PMC6199256 DOI: 10.1038/s41598-018-33343-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/18/2018] [Indexed: 12/15/2022] Open
Abstract
The endoplasmic reticulum (ER) forms a complex endomembrane network that reaches into the cellular compartments of a neuron, including dendritic spines. Recent work discloses that the spine ER is a dynamic structure that enters and leaves spines. While evidence exists that ER Ca2+ release is involved in synaptic plasticity, the role of spine ER morphology remains unknown. Combining a new 3D spine generator with 3D Ca2+ modeling, we addressed the relevance of ER positioning on spine-to-dendrite Ca2+ signaling. Our simulations, which account for Ca2+ exchange on the plasma membrane and ER, show that spine ER needs to be present in distinct morphological conformations in order to overcome a barrier between the spine and dendritic shaft. We demonstrate that RyR-carrying spine ER promotes spine-to-dendrite Ca2+ signals in a position-dependent manner. Our simulations indicate that RyR-carrying ER can initiate time-delayed Ca2+ reverberation, depending on the precise position of the spine ER. Upon spine growth, structural reorganization of the ER restores spine-to-dendrite Ca2+ communication, while maintaining aspects of Ca2+ homeostasis in the spine head. Our work emphasizes the relevance of precise positioning of RyR-containing spine ER in regulating the strength and timing of spine Ca2+ signaling, which could play an important role in tuning spine-to-dendrite Ca2+ communication and homeostasis.
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Affiliation(s)
- Markus Breit
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Marcus Kessler
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Martin Stepniewski
- Goethe Center for Scientific Computing, Computational Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany. .,Bernstein Center Freiburg, University of Freiburg, Freiburg, 79104, Germany.
| | - Gillian Queisser
- Department of Mathematics, Temple University, Philadelphia, USA.
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36
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Sellers KJ, Watson IA, Gresz RE, Raval P, Srivastava DP. Cyto-nuclear shuttling of afadin is required for rapid estradiol-mediated modifications of histone H3. Neuropharmacology 2018; 143:153-162. [PMID: 30268521 PMCID: PMC6277849 DOI: 10.1016/j.neuropharm.2018.09.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/18/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022]
Abstract
Estrogens have been shown to rapidly regulate local signalling at synapses and within the nucleus. The result of these signalling events is to rapidly modulate synapse structure and function, as well as epigenetic mechanisms including histone modifications. Ultimately these mechanisms are thought to contribute to long-lasting changes in neural circuitry, and thus influence cognitive functions such as learning and memory. However, the mechanisms by which estrogen-mediated local synaptic and nuclear signalling events are coordinated are not well understood. In this study we have found that the scaffold protein afadin, (also known as AF-6), undergoes a bi-directional trafficking to both synaptic and nuclear compartment in response to acute 17β-estradiol (estradiol) treatment, in mixed sex neuronal cultures derived from fetal cortex. Interestingly, nuclear accumulation of afadin was coincidental with an increase in the phosphorylation of histone H3 at serine 10 (H3S10p). This epigenetic modification is associated with the remodeling of chromatin into an open euchromatin state, allowing for transcriptional activation and related learning and memory processes. Critically, the cyto-nuclear trafficking of afadin was required for estradiol-dependent H3S10p. We further determined that nuclear accumulation of afadin is sufficient to induce phosphorylation of the mitogentic kinases ERK1/2 (pERK1/2) within the nucleus. Moreover, nuclear pERK1/2 was required for estradiol-dependent H3S10p. Taken together, we propose a model whereby estradiol induces the bi-directional trafficking of afadin to synaptic and nuclear sub-compartments. Within the nucleus, afadin is required for increased pERK1/2 which in turn is required for H3S10p. Therefore this represents a mechanism through which estrogens may be able to coordinate both synaptic and nucleosomal events within the same neuronal population. 17β-estradiol targets afadin to membrane and nuclear subcompartments. Histone H3 is rapidly phosphorylated by 17β-estradiol. Histone H3 phosphorylation by 17β-estradiol requires afadin nuclear accumulation. 17β-estradiol-mediated ERK1/2 activation is required for histone H3 phosphorylation.
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Affiliation(s)
- Katherine J Sellers
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Iain A Watson
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Rahel E Gresz
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Pooja Raval
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK.
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System: Development, Function, and Neurodevelopmental Diseases. Front Genet 2018; 9:308. [PMID: 30127803 PMCID: PMC6087739 DOI: 10.3389/fgene.2018.00308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022] Open
Abstract
Decades of study have shown that epigenetic regulation plays an important role in neural development and function. Several layers of epigenetic mechanisms control functions of the eukaryotic cell nucleus, a well-organized subcellular organelle with distinct compartments: chromatin, its related architectural proteins, and nuclear bodies. As these components function together in the epigenetic regulation of cellular development and functions, they are collectively termed nuclear architecture. In the nervous system, dynamic rearrangement of nuclear architecture correlates with alteration of transcription programs. During maturation and upon depolarization, neurons undergo a reorganization of nuclear architecture that alters gene expression programs. As such changes allow for specialized functions, including learning and memory, nuclear architecture is distinct among cell types. Studying nuclear architecture of neurons may uncover cell-division-independent mechanisms of global and local changes to nuclear architecture. We herein review recent research concerning nuclear architecture in the nervous system and will discuss its importance to the development, maturation, function, and diseases of the nervous system.
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Affiliation(s)
- Kenji Ito
- Department of Pediatrics, Graduate School of Medicine, Gunma University, Maebashi, Japan.,Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takumi Takizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, Maebashi, Japan
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Tao-Cheng JH. Stimulation-induced structural changes at the nucleus, endoplasmic reticulum and mitochondria of hippocampal neurons. Mol Brain 2018; 11:44. [PMID: 30049284 PMCID: PMC6062868 DOI: 10.1186/s13041-018-0387-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
Neurons exhibit stimulation-induced ultrastructural changes such as increase of thickness and curvature of the postsynaptic density, decrease in contact area between subsurface cistern and plasma membrane, and formation of CaMKII clusters and synaptic spinules. These structural characteristics help in identifying the activity state of the neuron and should be taken into consideration when interpreting ultrastructural features of the neurons. Here in organotypic hippocampal slice cultures where experimental conditions can be easily manipulated, two additional features are documented in forebrain neurons as reliable benchmarks for stimulation-induced structural changes: (1) The neuronal nucleus showed conspicuous clustering of dark chromatin, and (2) the endoplasmic reticulum formed stacks with a uniform gap of ~ 13 nm filled with dark materials. Both structural changes progressed with time and were reversible upon returning the slice cultures to control medium. These stimulation-induced structural changes were also verified in dissociated hippocampal neuronal cultures and perfusion-fixed brains. In hippocampal slice cultures, the neuronal chromatin clustering was detectable within 30 s of depolarization with high K+ (90 mM) or treatment with NMDA (50 μM). In contrast, the formation of ER cisternal stacks did not become apparent for another 30 s. Importantly, in dissociated neuronal cultures, when the extracellular calcium was chelated by EGTA, treatment with high K+ no longer induced these changes. These results indicate that the stimulation-induced chromatin clustering and formation of ER stacks in neurons are calcium-dependent. Additionally, mitochondria in neuronal somas of tissue culture samples consistently became swollen upon stimulation. However, swollen mitochondria were also present in some neurons of control samples, but could be eliminated by blocking basal activity or calcium influx. This calcium-dependent structural change of mitochondria is specific to neurons. These structural changes may bring insights to the neuron’s response to intracellular calcium rise upon stimulation.
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Affiliation(s)
- Jung-Hwa Tao-Cheng
- NINDS Electron Microscopy Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
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Breit M, Queisser G. What Is Required for Neuronal Calcium Waves? A Numerical Parameter Study. JOURNAL OF MATHEMATICAL NEUROSCIENCE 2018; 8:9. [PMID: 30006849 PMCID: PMC6045568 DOI: 10.1186/s13408-018-0064-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/15/2018] [Indexed: 06/03/2023]
Abstract
Neuronal calcium signals propagating by simple diffusion and reaction with mobile and stationary buffers are limited to cellular microdomains. The distance intracellular calcium signals can travel may be significantly increased by means of calcium-induced calcium release from internal calcium stores, notably the endoplasmic reticulum. The organelle, which can be thought of as a cell-within-a-cell, is able to sequester large amounts of cytosolic calcium ions via SERCA pumps and selectively release them into the cytosol through ryanodine receptor channels leading to the formation of calcium waves. In this study, we set out to investigate the basic properties of such dendritic calcium waves and how they depend on the three parameters dendrite radius, ER radius and ryanodine receptor density in the endoplasmic membrane. We demonstrate that there are stable and abortive regimes for calcium waves, depending on the above morphological and physiological parameters. In stable regimes, calcium waves can travel across long dendritic distances, similar to electrical action potentials. We further observe that abortive regimes exist, which could be relevant for spike-timing dependent plasticity, as travel distances and wave velocities vary with changing intracellular architecture. For some of these regimes, analytic functions could be derived that fit the simulation data. In parameter spaces, that are non-trivially influenced by the three-dimensional calcium concentration profile, we were not able to derive such a functional description, demonstrating the mathematical requirement to model and simulate biochemical signaling in three-dimensional space.
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Affiliation(s)
- Markus Breit
- G-CSC, Goethe University Frankfurt, Frankfurt am Main, Germany
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Mörschel K, Breit M, Queisser G. Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph. Neuroinformatics 2018; 15:247-269. [PMID: 28447297 DOI: 10.1007/s12021-017-9329-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.
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Affiliation(s)
- Konstantin Mörschel
- Goethe Center for Scientific Computing, Goethe University Frankfurt, Kettenhofweg 139, 60325, Frankfurt am Main, Germany
| | - Markus Breit
- Goethe Center for Scientific Computing, Goethe University Frankfurt, Kettenhofweg 139, 60325, Frankfurt am Main, Germany
| | - Gillian Queisser
- Department of Mathematics, Temple University, 1805 N Broad Street, Philadelphia, PA, 19122-6094, USA.
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Abstract
Neurons are dynamic cells that respond and adapt to stimuli throughout their long postmitotic lives. The structural and functional plasticity of neurons requires the regulated transcription of new gene products, and dysregulation of transcription in either the developing or adult brain impairs cognition. We discuss how mechanisms of chromatin regulation help to orchestrate the transcriptional programs that underlie the maturation of developing neurons and the plasticity of adult neurons. We review how chromatin regulation acts locally to modulate the expression of specific genes and more broadly to coordinate gene expression programs during transitions between cellular states. These data highlight the importance of epigenetic transcriptional mechanisms in postmitotic neurons. We suggest areas where emerging methods may advance understanding in the future.
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Affiliation(s)
- David A Gallegos
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Urann Chan
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Liang-Fu Chen
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne E West
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface. Viruses 2018; 10:v10010028. [PMID: 29316722 PMCID: PMC5795441 DOI: 10.3390/v10010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.
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Baluška F, Mancuso S. Plant Cognition and Behavior: From Environmental Awareness to Synaptic Circuits Navigating Root Apices. MEMORY AND LEARNING IN PLANTS 2018. [DOI: 10.1007/978-3-319-75596-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Freifeld L, Odstrcil I, Förster D, Ramirez A, Gagnon JA, Randlett O, Costa EK, Asano S, Celiker OT, Gao R, Martin-Alarcon DA, Reginato P, Dick C, Chen L, Schoppik D, Engert F, Baier H, Boyden ES. Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proc Natl Acad Sci U S A 2017; 114:E10799-E10808. [PMID: 29162696 PMCID: PMC5740639 DOI: 10.1073/pnas.1706281114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Expansion microscopy (ExM) allows scalable imaging of preserved 3D biological specimens with nanoscale resolution on fast diffraction-limited microscopes. Here, we explore the utility of ExM in the larval and embryonic zebrafish, an important model organism for the study of neuroscience and development. Regarding neuroscience, we found that ExM enabled the tracing of fine processes of radial glia, which are not resolvable with diffraction-limited microscopy. ExM further resolved putative synaptic connections, as well as molecular differences between densely packed synapses. Finally, ExM could resolve subsynaptic protein organization, such as ring-like structures composed of glycine receptors. Regarding development, we used ExM to characterize the shapes of nuclear invaginations and channels, and to visualize cytoskeletal proteins nearby. We detected nuclear invagination channels at late prophase and telophase, potentially suggesting roles for such channels in cell division. Thus, ExM of the larval and embryonic zebrafish may enable systematic studies of how molecular components are configured in multiple contexts of interest to neuroscience and developmental biology.
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Affiliation(s)
- Limor Freifeld
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139
| | - Iris Odstrcil
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Dominique Förster
- Department Genes-Circuits-Behavior, Max Planck Institute of Neurobiology, Martinsried 82152, Germany
| | - Alyson Ramirez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Owen Randlett
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Emma K Costa
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139
| | - Shoh Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139
| | - Orhan T Celiker
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139
| | | | - Paul Reginato
- Department of Biological Engineering, MIT, Cambridge, MA 02139
- Department of Genetics, Harvard Medical School, Cambridge, MA 02138
| | - Cortni Dick
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139
| | - Linlin Chen
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139
- Neuroscience Program, Wellesley College, Wellesley, MA 02481
| | - David Schoppik
- Department of Otolaryngology, New York University School of Medicine, New York, NY 10016
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016
- Neuroscience Institute, New York University School of Medicine, New York NY 10016
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Herwig Baier
- Department Genes-Circuits-Behavior, Max Planck Institute of Neurobiology, Martinsried 82152, Germany
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139;
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139
- Center for Neurobiological Engineering, MIT, Cambridge, MA 02139
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45
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Fujita Y, Yamashita T. Spatial organization of genome architecture in neuronal development and disease. Neurochem Int 2017; 119:49-56. [PMID: 28757389 DOI: 10.1016/j.neuint.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/19/2017] [Accepted: 06/26/2017] [Indexed: 01/19/2023]
Abstract
Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains. Furthermore, they form chromatin domains that are arranged into chromosome territories in the three-dimensional space of the cell nucleus. Recent studies have shown that the spatial organization of the genome is essential for normal brain development and function. Activity-dependent alterations in the spatial organization of the genome can regulate transcriptional activity related to neuronal plasticity. Disruptions in the higher-order chromatin architecture have been implicated in neuropsychiatric disorders, such as cognitive dysfunction and anxiety. Here, we discuss the growing interest in the role of genome organization in brain development and neurological disorders.
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Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Cebrián-Silla A, Alfaro-Cervelló C, Herranz-Pérez V, Kaneko N, Park DH, Sawamoto K, Alvarez-Buylla A, Lim DA, García-Verdugo JM. Unique Organization of the Nuclear Envelope in the Post-natal Quiescent Neural Stem Cells. Stem Cell Reports 2017. [PMID: 28648897 PMCID: PMC5511107 DOI: 10.1016/j.stemcr.2017.05.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Neural stem cells (B1 astrocytes; NSCs) in the adult ventricular-subventricular-zone (V-SVZ) originate in the embryo. Surprisingly, recent work has shown that B1 cells remain largely quiescent. They are reactivated postnatally to function as primary progenitors for neurons destined for the olfactory bulb and some corpus callosum oligodendrocytes. The cellular and molecular properties of quiescent B1 cells remain unknown. Here we found that a subpopulation of B1 cells has a unique nuclear envelope invagination specialization similar to envelope-limited chromatin sheets (ELCS), reported in certain lymphocytes and some cancer cells. Using molecular markers, [3H]thymidine birth-dating, and Ara-C, we found that B1 cells with ELCS correspond to quiescent NSCs. ELCS begin forming in embryonic radial glia cells and represent a specific nuclear compartment containing particular epigenetic modifications and telomeres. These results reveal a unique nuclear compartment in quiescent NSCs, which is useful for identifying these primary progenitors and study their gene regulation. A subpopulation of V-SVZ B cells presents nuclear ELCS ELCS appear in RGCs at E14.5 and remain in a subpopulation of B cells postnatally Type B cells with ELCS exhibit characteristics of quiescent NSCs ELCS present characteristic chromatin modifications
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Affiliation(s)
- Arantxa Cebrián-Silla
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain
| | - Clara Alfaro-Cervelló
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Vicente Herranz-Pérez
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain; Predepartamental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Naoko Kaneko
- Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Dae Hwi Park
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan; Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Arturo Alvarez-Buylla
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain; Multiple Sclerosis and Neuroregeneration Mixed Unit, IIS Hospital La Fe, 46026 Valencia, Spain.
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Fernández‐Nogales M, Santos‐Galindo M, Merchán‐Rubira J, Hoozemans JJM, Rábano A, Ferrer I, Avila J, Hernández F, Lucas JJ. Tau-positive nuclear indentations in P301S tauopathy mice. Brain Pathol 2017; 27:314-322. [PMID: 27338164 PMCID: PMC8029483 DOI: 10.1111/bpa.12407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022] Open
Abstract
Increased incidence of neuronal nuclear indentations is a well-known feature of the striatum of Huntington's disease (HD) brains and, in Alzheimer's disease (AD), neuronal nuclear indentations have recently been reported to correlate with neurotoxicity caused by improper cytoskeletal/nucleoskeletal coupling. Initial detection of rod-shaped tau immunostaining in nuclei of cortical and striatal neurons of HD brains and in hippocampal neurons of early Braak stage AD led us to coin the term "tau nuclear rods (TNRs)." Although TNRs traverse nuclear space, they in fact occupy narrow cytoplasmic extensions that fill indentations of the nuclear envelope and we will here refer to this histological hallmark as Tau-immunopositive nuclear indentations (TNIs). We reasoned that TNI formation is likely secondary to tau alterations as TNI detection in HD correlates with an increase in total tau, particularly of the isoforms with four tubulin binding repeats (4R-tau). Here we analyze transgenic mice that overexpress human 4R-tau with a frontotemporal lobar degeneration-tau point mutation (P301S mice) to explore whether tau alteration is sufficient for TNI formation. Immunohistochemistry with various tau antibodies, immunoelectron microscopy and double tau-immunofluorescence/DAPI-nuclear counterstaining confirmed that excess 4R-tau in P301S mice is sufficient for the detection of abundant TNIs that fill nuclear indentations. Interestingly, this does not correlate with an increase in the number of nuclear indentations, thus suggesting that excess total tau or an isoform imbalance in favor of 4R-tau facilitates tau detection inside preexisting nuclear indentations but does not induce formation of the latter. In summary, here we demonstrate that tau alteration is sufficient for TNI detection and our results suggest that the neuropathological finding of TNIs becomes a possible indicator of increased total tau and/or increased 4R/3R-tau ratio in the affected neurons apart from being an efficient way to monitor pathology-associated nuclear indentations.
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Affiliation(s)
- Marta Fernández‐Nogales
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
| | - María Santos‐Galindo
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
| | - Jesús Merchán‐Rubira
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
| | - Jeroen J. M. Hoozemans
- Department of PathologyVU University Medical Center, Neuroscience Campus Amsterdam1007 MB Amsterdamthe Netherlands
| | - Alberto Rábano
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
- Departamento de Neuropatología y Banco de TejidosFundación CIENMadridSpain
| | - Isidro Ferrer
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
- Institute of Neuropathology; IDIBELL‐University Hospital BellvitgeUniversity of Barcelona; Hospitalet de LlobregatBarcelona08908Spain
| | - Jesús Avila
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
| | - Félix Hernández
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
| | - José J. Lucas
- Center for Molecular Biology “Severo Ochoa” (CBMSO) CSIC/UAM28049MadridSpain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos IIISpain
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Gigante CM, Dibattista M, Dong FN, Zheng X, Yue S, Young SG, Reisert J, Zheng Y, Zhao H. Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation. Nat Commun 2017; 8:15098. [PMID: 28425486 PMCID: PMC5411488 DOI: 10.1038/ncomms15098] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/28/2017] [Indexed: 01/29/2023] Open
Abstract
B-type lamins are major constituents of the nuclear lamina in all metazoan cells, yet have specific roles in the development of certain cell types. Although they are speculated to regulate gene expression in developmental contexts, a direct link between B-type lamins and developmental gene expression in an in vivo system is currently lacking. Here, we identify lamin B1 as a key regulator of gene expression required for the formation of functional olfactory sensory neurons. By using targeted knockout in olfactory epithelial stem cells in adult mice, we show that lamin B1 deficient neurons exhibit attenuated response to odour stimulation. This deficit can be explained by decreased expression of genes involved in mature neuron function, along with increased expression of genes atypical of the olfactory lineage. These results support that the broadly expressed lamin B1 regulates expression of a subset of genes involved in the differentiation of a specific cell type.
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Affiliation(s)
- Crystal M. Gigante
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Michele Dibattista
- Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104, USA
- Department of Basic Medical Sciences, Neuroscience and Sensory Organs, University of Bari ‘A. Moro', Bari 70121, Italy
| | - Frederick N. Dong
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Sibiao Yue
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Stephen G. Young
- Department of Medicine, Molecular Biology Institute and Department of Human Genetics, University of California, Los Angeles, California 90095, USA
| | - Johannes Reisert
- Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104, USA
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Haiqing Zhao
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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49
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Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. Skelet Muscle 2017; 7:5. [PMID: 28381300 PMCID: PMC5382473 DOI: 10.1186/s13395-017-0122-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/16/2017] [Indexed: 12/21/2022] Open
Abstract
Background The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development. Methods In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC. Results We observed significant local and global developmental changes despite high levels of correlation between the myotubes and myoblast genomes. Notably, the genes that exhibited the greatest variation in transcript levels between the different developmental stages were predominately within the euchromatic compartment. There was significant re-structuring and changes in the expression of replication-dependent histone variants within the HIST1 locus. Finally, treating terminally differentiated myotubes with AraC resulted in additional changes to the transcriptome and 3D genome organization of sets of genes that were all involved in pyroptosis. Conclusions Collectively, our results provide evidence for muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism. Electronic supplementary material The online version of this article (doi:10.1186/s13395-017-0122-1) contains supplementary material, which is available to authorized users.
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Blüthgen N, van Bentum M, Merz B, Kuhl D, Hermey G. Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo. Sci Rep 2017; 7:45101. [PMID: 28349920 PMCID: PMC5368636 DOI: 10.1038/srep45101] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
Activity-dependent alteration of the transcriptional program is central for shaping neuronal connectivity. Constitutively expressed transcription factors orchestrate the initial response to neuronal stimulation and serve as substrates for second messenger-regulated kinase signalling cascades. The mitogen-activated protein kinase ERK conveys signalling from the synapse to the nucleus but its genetic signature following neuronal activity has not been revealed. The goal of the present study was to identify ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus. We used generalized seizures combined with the pharmacological intervention of MEK activation as an in vivo model to determine the complete transcriptional program initiated by ERK after neuronal activity. Our survey demonstrates that the induction of a large number of activity-regulated genes, including Arc/Arg3.1, Arl5b, Gadd45b, Homer1, Inhba and Zwint, is indeed dependent on ERK phosphorylation. In contrast, expression of a small group of genes, including Npas4, Arl4d, Errfi1, and Rgs2, is only partially dependent or completely independent (Ppp1r15a) of this signalling pathway. Among the identified transcripts are long non-coding (lnc) RNAs and induction of LincPint and splice variants of NEAT1 are ERK dependent. Our survey provides a comprehensive analysis of the transcriptomic response conveyed by ERK signalling in the hippocampus.
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Affiliation(s)
- Nils Blüthgen
- Institute for Theoretical Biology and Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Mirjam van Bentum
- Institute for Theoretical Biology and Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Barbara Merz
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Dietmar Kuhl
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Guido Hermey
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
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