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Michel JC, Grivette MMB, Harshfield AT, Huynh L, Komons AP, Loomis B, McKinnis K, Miller BT, Nguyen EQ, Huang TW, Lauf S, Michel ES, Michel ME, Kissinger JS, Marsh AJ, Crow WE, Kaye LE, Lasseigne AM, Lukowicz-Bedford RM, Farnsworth DR, Martin EA, Miller AC. Electrical synapse structure requires distinct isoforms of a postsynaptic scaffold. PLoS Genet 2023; 19:e1011045. [PMID: 38011265 PMCID: PMC10703405 DOI: 10.1371/journal.pgen.1011045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/07/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
Electrical synapses are neuronal gap junction (GJ) channels associated with a macromolecular complex called the electrical synapse density (ESD), which regulates development and dynamically modifies electrical transmission. However, the proteomic makeup and molecular mechanisms utilized by the ESD that direct electrical synapse formation are not well understood. Using the Mauthner cell of zebrafish as a model, we previously found that the intracellular scaffolding protein ZO1b is a member of the ESD, localizing postsynaptically, where it is required for GJ channel localization, electrical communication, neural network function, and behavior. Here, we show that the complexity of the ESD is further diversified by the genomic structure of the ZO1b gene locus. The ZO1b gene is alternatively initiated at three transcriptional start sites resulting in isoforms with unique N-termini that we call ZO1b-Alpha, -Beta, and -Gamma. We demonstrate that ZO1b-Beta and ZO1b-Gamma are broadly expressed throughout the nervous system and localize to electrical synapses. By contrast, ZO1b-Alpha is expressed mainly non-neuronally and is not found at synapses. We generate mutants in all individual isoforms, as well as double mutant combinations in cis on individual chromosomes, and find that ZO1b-Beta is necessary and sufficient for robust GJ channel localization. ZO1b-Gamma, despite its localization to the synapse, plays an auxiliary role in channel localization. This study expands the notion of molecular complexity at the ESD, revealing that an individual genomic locus can contribute distinct isoforms to the macromolecular complex at electrical synapses. Further, independent scaffold isoforms have differential contributions to developmental assembly of the interneuronal GJ channels. We propose that ESD molecular complexity arises both from the diversity of unique genes and from distinct isoforms encoded by single genes. Overall, ESD proteomic diversity is expected to have critical impacts on the development, structure, function, and plasticity of electrical transmission.
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Affiliation(s)
- Jennifer Carlisle Michel
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Margaret M. B. Grivette
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Amber T. Harshfield
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Lisa Huynh
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Ava P. Komons
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Bradley Loomis
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kaitlan McKinnis
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Brennen T. Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Ethan Q. Nguyen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Tiffany W. Huang
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Sophia Lauf
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Elias S. Michel
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Mia E. Michel
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Jane S. Kissinger
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Audrey J. Marsh
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - William E. Crow
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Lila E. Kaye
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Abagael M. Lasseigne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Rachel M. Lukowicz-Bedford
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Dylan R. Farnsworth
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - E. Anne Martin
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Adam C. Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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Keating SS, Bademosi AT, San Gil R, Walker AK. Aggregation-prone TDP-43 sequesters and drives pathological transitions of free nuclear TDP-43. Cell Mol Life Sci 2023; 80:95. [PMID: 36930291 PMCID: PMC10023653 DOI: 10.1007/s00018-023-04739-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
Aggregation of the RNA-binding protein, TDP-43, is the unifying hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43-related neurodegeneration involves multiple changes to normal physiological TDP-43, which undergoes nuclear depletion, cytoplasmic mislocalisation, post-translational modification, and aberrant liquid-liquid phase separation, preceding inclusion formation. Along with toxic cytoplasmic aggregation, concurrent depletion and dysfunction of normal nuclear TDP-43 in cells with TDP-43 pathology is likely a key potentiator of neurodegeneration, but is not well understood. To define processes driving TDP-43 dysfunction, we used CRISPR/Cas9-mediated fluorescent tagging to investigate how disease-associated stressors and pathological TDP-43 alter abundance, localisation, self-assembly, aggregation, solubility, and mobility dynamics of normal nuclear TDP-43 over time in live cells. Oxidative stress stimulated liquid-liquid phase separation of endogenous TDP-43 into droplet-like puncta, or spherical shell-like anisosomes. Further, nuclear RNA-binding-ablated or acetylation-mimicking TDP-43 readily sequestered and depleted free normal nuclear TDP-43 into dynamic anisosomes, in which recruited endogenous TDP-43 proteins remained soluble and highly mobile. Large, phosphorylated inclusions formed by nuclear or cytoplasmic aggregation-prone TDP-43 mutants also caused sequestration, but rendered endogenous TDP-43 immobile and insoluble, indicating pathological transition. These findings suggest that RNA-binding deficiency and post-translational modifications including acetylation exacerbate TDP-43 aggregation and dysfunction by driving sequestration, mislocalisation, and depletion of normal nuclear TDP-43 in neurodegenerative diseases.
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Affiliation(s)
- Sean S Keating
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Adekunle T Bademosi
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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3
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Erkamp NA, Sneideris T, Ausserwöger H, Qian D, Qamar S, Nixon-Abell J, St George-Hyslop P, Schmit JD, Weitz DA, Knowles TPJ. Spatially non-uniform condensates emerge from dynamically arrested phase separation. Nat Commun 2023; 14:684. [PMID: 36755024 PMCID: PMC9908939 DOI: 10.1038/s41467-023-36059-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
The formation of biomolecular condensates through phase separation from proteins and nucleic acids is emerging as a spatial organisational principle used broadly by living cells. Many such biomolecular condensates are not, however, homogeneous fluids, but possess an internal structure consisting of distinct sub-compartments with different compositions. Notably, condensates can contain compartments that are depleted in the biopolymers that make up the condensate. Here, we show that such double-emulsion condensates emerge via dynamically arrested phase transitions. The combination of a change in composition coupled with a slow response to this change can lead to the nucleation of biopolymer-poor droplets within the polymer-rich condensate phase. Our findings demonstrate that condensates with a complex internal architecture can arise from kinetic, rather than purely thermodynamic driving forces, and provide more generally an avenue to understand and control the internal structure of condensates in vitro and in vivo.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Jonathon Nixon-Abell
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine (Division of Neurology), University of Toronto and University Health Network, Toronto, Ontario, M5S 3H2, Canada
- Department of Neurology, Columbia University, 630 West 168th St, New York, NY, 10032, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - David A Weitz
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA, 02138, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK.
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Yu H, Lu S, Gasior K, Singh D, Vazquez-Sanchez S, Tapia O, Toprani D, Beccari MS, Yates JR, Da Cruz S, Newby JM, Lafarga M, Gladfelter AS, Villa E, Cleveland DW. HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 2021; 371:science.abb4309. [PMID: 33335017 PMCID: PMC8286096 DOI: 10.1126/science.abb4309] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/05/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022]
Abstract
The RNA binding protein TDP-43 forms intranuclear or cytoplasmic aggregates in age-related neurodegenerative diseases. In this study, we found that RNA binding-deficient TDP-43 (produced by neurodegeneration-causing mutations or posttranslational acetylation in its RNA recognition motifs) drove TDP-43 demixing into intranuclear liquid spherical shells with liquid cores. These droplets, which we named "anisosomes", have shells that exhibit birefringence, thus indicating liquid crystal formation. Guided by mathematical modeling, we identified the primary components of the liquid core to be HSP70 family chaperones, whose adenosine triphosphate (ATP)-dependent activity maintained the liquidity of shells and cores. In vivo proteasome inhibition within neurons, to mimic aging-related reduction of proteasome activity, induced TDP-43-containing anisosomes. These structures converted to aggregates when ATP levels were reduced. Thus, acetylation, HSP70, and proteasome activities regulate TDP-43 phase separation and conversion into a gel or solid phase.
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Affiliation(s)
- Haiyang Yu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
| | - Shan Lu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
| | - Kelsey Gasior
- University of North Carolina Chapel Hill, Department of Biology, Chapel Hill, North Carolina, USA, University of North Carolina Chapel Hill, Department of Mathematics, Chapel Hill, North Carolina, USA
| | - Digvijay Singh
- Division of Biological Sciences, University of California, San Diego, San Diego, California, USA
| | - Sonia Vazquez-Sanchez
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
| | - Olga Tapia
- “Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas” (CIBERNED), Madrid, Spain., “Instituto de Investigación Sanitaria Valdecilla” (IDIVAL), Santander, Spain
| | - Divek Toprani
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
| | - Melinda S. Beccari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA, Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, USA
| | - John R. Yates
- Departments of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, USA
| | - Sandrine Da Cruz
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jay M. Newby
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2G1
| | - Miguel Lafarga
- “Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas” (CIBERNED), Madrid, Spain., “Instituto de Investigación Sanitaria Valdecilla” (IDIVAL), Santander, Spain, Department of Anatomy and Cell Biology, University of Cantabria, Santander, Spain
| | - Amy S. Gladfelter
- University of North Carolina Chapel Hill, Department of Biology, Chapel Hill, North Carolina, USA, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, San Diego, California, USA
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA, Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, USA,Corresponding authors: ,
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5
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Puente-Bedia A, Berciano MT, Tapia O, Martínez-Cué C, Lafarga M, Rueda N. Nuclear Reorganization in Hippocampal Granule Cell Neurons from a Mouse Model of Down Syndrome: Changes in Chromatin Configuration, Nucleoli and Cajal Bodies. Int J Mol Sci 2021; 22:ijms22031259. [PMID: 33514010 PMCID: PMC7865916 DOI: 10.3390/ijms22031259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Down syndrome (DS) or trisomy of chromosome 21 (Hsa21) is characterized by impaired hippocampal-dependent learning and memory. These alterations are due to defective neurogenesis and to neuromorphological and functional anomalies of numerous neuronal populations, including hippocampal granular cells (GCs). It has been proposed that the additional gene dose in trisomic cells induces modifications in nuclear compartments and on the chromatin landscape, which could contribute to some DS phenotypes. The Ts65Dn (TS) mouse model of DS carries a triplication of 92 genes orthologous to those found in Hsa21, and shares many phenotypes with DS individuals, including cognitive and neuromorphological alterations. Considering its essential role in hippocampal memory formation, we investigated whether the triplication of this set of Hsa21 orthologous genes in TS mice modifies the nuclear architecture of their GCs. Our results show that the TS mouse presents alterations in the nuclear architecture of its GCs, affecting nuclear compartments involved in transcription and pre-rRNA and pre-mRNA processing. In particular, the GCs of the TS mouse show alterations in the nucleolar fusion pattern and the molecular assembly of Cajal bodies (CBs). Furthermore, hippocampal GCs of TS mice present an epigenetic dysregulation of chromatin that results in an increased heterochromatinization and reduced global transcriptional activity. These nuclear alterations could play an important role in the neuromorphological and/or functional alterations of the hippocampal GCs implicated in the cognitive dysfunction characteristic of TS mice.
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Affiliation(s)
- Alba Puente-Bedia
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - María T. Berciano
- Department of Molecular Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain;
| | - Olga Tapia
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and Universidad Europea del Atlántico, 39011 Santander, Spain;
| | - Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology, “Red sobre Enfermedades Neurodegenerativas (CIBERNED)” and University of Cantabria-IDIVAL, 39011 Santander, Spain
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain; (A.P.-B.); (C.M.-C.)
- Correspondence: (M.L.); (N.R.); Tel.: +34-942201966 (N.R.); Fax: +34-942201903 (N.R.)
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6
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Pankivskyi S, Pastré D, Steiner E, Joshi V, Rynditch A, Hamon L. ITSN1 regulates SAM68 solubility through SH3 domain interactions with SAM68 proline-rich motifs. Cell Mol Life Sci 2020; 78:1745-1763. [PMID: 32780150 PMCID: PMC7904728 DOI: 10.1007/s00018-020-03610-y] [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: 03/26/2020] [Revised: 06/03/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023]
Abstract
SAM68 is an mRNA-binding protein involved in mRNA processing in the nucleus that forms membraneless compartments called SAM68 Nuclear Bodies (SNBs). We found that intersectin 1 (ITSN1), a multidomain scaffold protein harboring five soluble SH3 domains, interacts with SAM68 proline-rich motifs (PRMs) surrounded by self-adhesive low complexity domains. While SAM68 is poorly soluble in vitro, the interaction of ITSN1 SH3 domains and mRNA with SAM68 enhances its solubility. In HeLa cells, the interaction between the first ITSN1 SH3 domain (SH3A) and P0, the N-terminal PRM of SAM68, induces the dissociation of SNBs. In addition, we reveal the ability of another SH3 domain (SH3D) of ITSN1 to bind to mRNAs. ITSN1 and mRNA may thus act in concert to promote SAM68 solubilization, consistent with the absence of mRNA in SNBs in cells. Together, these results support the notion of a specific chaperoning of PRM-rich SAM68 within nuclear ribonucleoprotein complexes by ITSN1 that may regulate the processing of a fraction of nuclear mRNAs, notably SAM68-controlled splicing events related to higher neuronal functions or cancer progression. This observation may also serve as a putative model of the interaction between other PRM-rich RBPs and signaling proteins harboring SH3 domains.
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Affiliation(s)
- S Pankivskyi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.,Institute of Molecular Biology and Genetics, The National Academy of Sciences, 150 Zabolotnogo Street, Kyiv, 03680, Ukraine
| | - D Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - E Steiner
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - V Joshi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - A Rynditch
- Institute of Molecular Biology and Genetics, The National Academy of Sciences, 150 Zabolotnogo Street, Kyiv, 03680, Ukraine.
| | - L Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.
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Nusinersen ameliorates motor function and prevents motoneuron Cajal body disassembly and abnormal poly(A) RNA distribution in a SMA mouse model. Sci Rep 2020; 10:10738. [PMID: 32612161 PMCID: PMC7330045 DOI: 10.1038/s41598-020-67569-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/08/2020] [Indexed: 11/09/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a devastating autosomal recessive neuromuscular disease characterized by degeneration of spinal cord alpha motor neurons (αMNs). SMA is caused by the homozygous deletion or mutation of the survival motor neuron 1 (SMN1) gene, resulting in reduced expression of SMN protein, which leads to αMN degeneration and muscle atrophy. The majority of transcripts of a second gene (SMN2) generate an alternative spliced isoform that lacks exon 7 and produces a truncated nonfunctional form of SMN. A major function of SMN is the biogenesis of spliceosomal snRNPs, which are essential components of the pre-mRNA splicing machinery, the spliceosome. In recent years, new potential therapies have been developed to increase SMN levels, including treatment with antisense oligonucleotides (ASOs). The ASO-nusinersen (Spinraza) promotes the inclusion of exon 7 in SMN2 transcripts and notably enhances the production of full-length SMN in mouse models of SMA. In this work, we used the intracerebroventricular injection of nusinersen in the SMN∆7 mouse model of SMA to evaluate the effects of this ASO on the behavior of Cajal bodies (CBs), nuclear structures involved in spliceosomal snRNP biogenesis, and the cellular distribution of polyadenylated mRNAs in αMNs. The administration of nusinersen at postnatal day (P) 1 normalized SMN expression in the spinal cord but not in skeletal muscle, rescued the growth curve and improved motor behavior at P12 (late symptomatic stage). Importantly, this ASO recovered the number of canonical CBs in MNs, significantly reduced the abnormal accumulation of polyadenylated RNAs in nuclear granules, and normalized the expression of the pre-mRNAs encoding chondrolectin and choline acetyltransferase, two key factors for αMN homeostasis. We propose that the splicing modulatory function of nusinersen in SMA αMN is mediated by the rescue of CB biogenesis, resulting in enhanced polyadenylated pre-mRNA transcription and splicing and nuclear export of mature mRNAs for translation. Our results support that the selective restoration of SMN expression in the spinal cord has a beneficial impact not only on αMNs but also on skeletal myofibers. However, the rescue of SMN expression in muscle appears to be necessary for the complete recovery of motor function.
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Zhang X, Wu K, Huang Y, Xu L, Li X, Zhang N. Promoter Hypermethylation of CHODL Contributes to Carcinogenesis and Indicates Poor Survival in Patients with Early-stage Colorectal Cancer. J Cancer 2020; 11:2874-2886. [PMID: 32226505 PMCID: PMC7086254 DOI: 10.7150/jca.38815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/01/2019] [Indexed: 12/26/2022] Open
Abstract
Aims: Aberrant hypermethylation of CpG islands is an important hallmark of colorectal cancer (CRC). We previously utilized methyl-DNA immunoprecipitation assays to identify a novel methylated gene, chondrolectin (CHODL), preferentially methylated in human CRC. In this study, we examined the epigenetic inactivation, biological effects and prognostic significance of CHODL in CRC. Main methods: The methylation status of CHODL in CRC was evaluated by bisulfite genomic sequencing (BGS). The functions of CHODL in CRC were determined by proliferation, apoptosis, cell migration and invasion assays. The impact and underlying mechanisms of CHODL in CRC were characterized by western blot and RNA-Seq analyses. The association between CHODL and CRC clinical features was examined using The Cancer Genome Atlas (TCGA) database and immunohistochemical staining. Key findings: CHODL was downregulated in 10 CRC cell lines and CRC tissues, and promoter hypermethylation contributed to its inactivation. Ectopic expression of CHODL inhibited colony formation, suppressed cell viability, induced apoptosis, and restrained cell migration and invasion in vitro and in vivo. Furthermore, high CHODL expression in CRC was a predictor of improved survival, though CHODL hypermethylation was a poor prognostic factor for CRC patients, especially those with early-stage CRC. Significance: CHODL promoter hypermethylation silences CHODL expression in CRC, and CHODL suppresses CRC tumorigenesis. CHODL methylation and expression levels can be used as potential markers to evaluate the prognosis of CRC patients.
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Affiliation(s)
- Xinyue Zhang
- Department Of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080.,Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080
| | - Kaiming Wu
- Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080
| | - Yuhua Huang
- Department Of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China, 510080
| | - Lixia Xu
- Department Of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080
| | - Xiaoxing Li
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080
| | - Ning Zhang
- Department Of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 510080
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9
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Latonen L. Phase-to-Phase With Nucleoli - Stress Responses, Protein Aggregation and Novel Roles of RNA. Front Cell Neurosci 2019; 13:151. [PMID: 31080406 PMCID: PMC6497782 DOI: 10.3389/fncel.2019.00151] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022] Open
Abstract
Protein- and RNA-containing foci and aggregates are a hallmark of many age- and mutation-related neurodegenerative diseases. This article focuses on the role the nucleolus has as a hub in macromolecule regulation in the mammalian nucleus. The nucleolus has a well-established role in ribosome biogenesis and functions in several types of cellular stress responses. In addition to known reactions to DNA damaging and transcription inhibiting stresses, there is an emerging role of the nucleolus especially in responses to proteotoxic stress such as heat shock and inhibition of proteasome function. The nucleolus serves as an active regulatory site for detention of extranucleolar proteins. This takes place in nucleolar cavities and manifests in protein and RNA collections referred to as intranucleolar bodies (INBs), nucleolar aggresomes or amyloid bodies (A-bodies), depending on stress type, severity of accumulation, and material propensities of the macromolecular collections. These indicate a relevance of nucleolar function and regulation in neurodegeneration-related cellular events, but also provide surprising connections with cancer-related pathways. Yet, the molecular mechanisms governing these processes remain largely undefined. In this article, the nucleolus as the site of protein and RNA accumulation and as a possible protective organelle for nuclear proteins during stress is viewed. In addition, recent evidence of liquid-liquid phase separation (LLPS) and liquid-solid phase transition in the formation of nucleoli and its stress responses, respectively, are discussed, along with the increasingly indicated role and open questions for noncoding RNA species in these events.
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Affiliation(s)
- Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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