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Bedja-Iacona L, Richard E, Marouillat S, Brulard C, Alouane T, Beltran S, Andres CR, Blasco H, Corcia P, Veyrat-Durebex C, Vourc’h P. Post-Translational Variants of Major Proteins in Amyotrophic Lateral Sclerosis Provide New Insights into the Pathophysiology of the Disease. Int J Mol Sci 2024; 25:8664. [PMID: 39201350 PMCID: PMC11354932 DOI: 10.3390/ijms25168664] [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: 06/30/2024] [Revised: 08/04/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Post-translational modifications (PTMs) affecting proteins during or after their synthesis play a crucial role in their localization and function. The modification of these PTMs under pathophysiological conditions, i.e., their appearance, disappearance, or variation in quantity caused by a pathological environment or a mutation, corresponds to post-translational variants (PTVs). These PTVs can be directly or indirectly involved in the pathophysiology of diseases. Here, we present the PTMs and PTVs of four major amyotrophic lateral sclerosis (ALS) proteins, SOD1, TDP-43, FUS, and TBK1. These modifications involve acetylation, phosphorylation, methylation, ubiquitination, SUMOylation, and enzymatic cleavage. We list the PTM positions known to be mutated in ALS patients and discuss the roles of PTVs in the pathophysiological processes of ALS. In-depth knowledge of the PTMs and PTVs of ALS proteins is needed to better understand their role in the disease. We believe it is also crucial for developing new therapies that may be more effective in ALS.
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Affiliation(s)
- Léa Bedja-Iacona
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | - Elodie Richard
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | - Sylviane Marouillat
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | | | | | - Stéphane Beltran
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Neurologie, CHRU de Tours, 37000 Tours, France
| | - Christian R. Andres
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Hélène Blasco
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Philippe Corcia
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Neurologie, CHRU de Tours, 37000 Tours, France
| | - Charlotte Veyrat-Durebex
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- UTTIL, CHRU de Tours, 37000 Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Patrick Vourc’h
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- UTTIL, CHRU de Tours, 37000 Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
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2
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Clayton EL, Huggon L, Cousin MA, Mizielinska S. Synaptopathy: presynaptic convergence in frontotemporal dementia and amyotrophic lateral sclerosis. Brain 2024; 147:2289-2307. [PMID: 38451707 PMCID: PMC11224618 DOI: 10.1093/brain/awae074] [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: 08/18/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are common forms of neurodegenerative disease that share overlapping genetics and pathologies. Crucially, no significantly disease-modifying treatments are available for either disease. Identifying the earliest changes that initiate neuronal dysfunction is important for designing effective intervention therapeutics. The genes mutated in genetic forms of frontotemporal dementia and amyotrophic lateral sclerosis have diverse cellular functions, and multiple disease mechanisms have been proposed for both. Identification of a convergent disease mechanism in frontotemporal dementia and amyotrophic lateral sclerosis would focus research for a targetable pathway, which could potentially effectively treat all forms of frontotemporal dementia and amyotrophic lateral sclerosis (both familial and sporadic). Synaptopathies are diseases resulting from physiological dysfunction of synapses, and define the earliest stages in multiple neuronal diseases, with synapse loss a key feature in dementia. At the presynapse, the process of synaptic vesicle recruitment, fusion and recycling is necessary for activity-dependent neurotransmitter release. The unique distal location of the presynaptic terminal means the tight spatio-temporal control of presynaptic homeostasis is dependent on efficient local protein translation and degradation. Recently, numerous publications have shown that mutations associated with frontotemporal dementia and amyotrophic lateral sclerosis present with synaptopathy characterized by presynaptic dysfunction. This review will describe the complex local signalling and membrane trafficking events that occur at the presynapse to facilitate neurotransmission and will summarize recent publications linking frontotemporal dementia/amyotrophic lateral sclerosis genetic mutations to presynaptic function. This evidence indicates that presynaptic synaptopathy is an early and convergent event in frontotemporal dementia and amyotrophic lateral sclerosis and illustrates the need for further research in this area, to identify potential therapeutic targets with the ability to impact this convergent pathomechanism.
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Affiliation(s)
- Emma L Clayton
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Laura Huggon
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
- Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Sarah Mizielinska
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
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3
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Chauhan W, Sudharshan SJ, Kafle S, Zennadi R. SnoRNAs: Exploring Their Implication in Human Diseases. Int J Mol Sci 2024; 25:7202. [PMID: 39000310 PMCID: PMC11240930 DOI: 10.3390/ijms25137202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) are earning increasing attention from research communities due to their critical role in the post-transcriptional modification of various RNAs. These snoRNAs, along with their associated proteins, are crucial in regulating the expression of a vast array of genes in different human diseases. Primarily, snoRNAs facilitate modifications such as 2'-O-methylation, N-4-acetylation, and pseudouridylation, which impact not only ribosomal RNA (rRNA) and their synthesis but also different RNAs. Functionally, snoRNAs bind with core proteins to form small nucleolar ribonucleoproteins (snoRNPs). These snoRNAs then direct the protein complex to specific sites on target RNA molecules where modifications are necessary for either standard cellular operations or the regulation of pathological mechanisms. At these targeted sites, the proteins coupled with snoRNPs perform the modification processes that are vital for controlling cellular functions. The unique characteristics of snoRNAs and their involvement in various non-metabolic and metabolic diseases highlight their potential as therapeutic targets. Moreover, the precise targeting capability of snoRNAs might be harnessed as a molecular tool to therapeutically address various disease conditions. This review delves into the role of snoRNAs in health and disease and explores the broad potential of these snoRNAs as therapeutic agents in human pathologies.
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Affiliation(s)
| | | | | | - Rahima Zennadi
- Department of Physiology, University of Tennessee Health Science Center, 71 S. Manassas St., Memphis, TN 38103, USA; (W.C.); (S.S.); (S.K.)
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4
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Fernández Comaduran M, Minotti S, Jacob-Tomas S, Rizwan J, Larochelle N, Robitaille R, Sephton CF, Vera M, Nalbantoglu JN, Durham HD. Impact of histone deacetylase inhibition and arimoclomol on heat shock protein expression and disease biomarkers in primary culture models of familial ALS. Cell Stress Chaperones 2024; 29:359-380. [PMID: 38570009 PMCID: PMC11015512 DOI: 10.1016/j.cstres.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Protein misfolding and mislocalization are common themes in neurodegenerative disorders, including motor neuron disease, and amyotrophic lateral sclerosis (ALS). Maintaining proteostasis is a crosscutting therapeutic target, including the upregulation of heat shock proteins (HSP) to increase chaperoning capacity. Motor neurons have a high threshold for upregulating stress-inducible HSPA1A, but constitutively express high levels of HSPA8. This study compared the expression of these HSPs in cultured motor neurons expressing three variants linked to familial ALS: TAR DNA binding protein 43 kDa (TDP-43)G348C, fused in sarcoma (FUS)R521G, or superoxide dismutase I (SOD1)G93A. All variants were poor inducers of Hspa1a, and reduced levels of Hspa8 mRNA and protein, indicating multiple compromises in chaperoning capacity. To promote HSP expression, cultures were treated with the putative HSP coinducer, arimoclomol, and class I histone deacetylase inhibitors, to promote active chromatin for transcription, and with the combination. Treatments had variable, often different effects on the expression of Hspa1a and Hspa8, depending on the ALS variant expressed, mRNA distribution (somata and dendrites), and biomarker of toxicity measured (histone acetylation, maintaining nuclear TDP-43 and the neuronal Brm/Brg-associated factor chromatin remodeling complex component Brg1, mitochondrial transport, FUS aggregation). Overall, histone deacetylase inhibition alone was effective on more measures than arimoclomol. As in the FUS model, arimoclomol failed to induce HSPA1A or preserve Hspa8 mRNA in the TDP-43 model, despite preserving nuclear TDP-43 and Brg1, indicating neuroprotective properties other than HSP induction. The data speak to the complexity of drug mechanisms against multiple biomarkers of ALS pathogenesis, as well as to the importance of HSPA8 for neuronal proteostasis in both somata and dendrites.
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Affiliation(s)
- Mario Fernández Comaduran
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Sandra Minotti
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Javeria Rizwan
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Nancy Larochelle
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Richard Robitaille
- Département de Neurosciences and Groupe de Recherche sur le Système Nerveux Central, Université de Montréal, and Centre Interdisciplinaire de Recherche sur le Cerveau et l'apprentissage, Montreal, Quebec, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Josephine N Nalbantoglu
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Heather D Durham
- Department of Neurology & Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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5
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Caggiano C, Morselli M, Qian X, Celona B, Thompson M, Wani S, Tosevska A, Taraszka K, Heuer G, Ngo S, Steyn F, Nestor P, Wallace L, McCombe P, Heggie S, Thorpe K, McElligott C, English G, Henders A, Henderson R, Lomen-Hoerth C, Wray N, McRae A, Pellegrini M, Garton F, Zaitlen N. Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.08.24305503. [PMID: 38645132 PMCID: PMC11030489 DOI: 10.1101/2024.04.08.24305503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.
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Affiliation(s)
- C Caggiano
- Department of Neurology, UCLA, Los Angeles, California
- Institute of Genomic Health, Icahn School of Medicine at Mt Sinai, New York, New York
| | - M Morselli
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - X Qian
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - B Celona
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - M Thompson
- Department of Neurology, UCLA, Los Angeles, California
- Systems and Synthetic Biology, Centre for Genomic Regulation, Barcelona, Spain
| | - S Wani
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - A Tosevska
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Vienna, Austria
| | - K Taraszka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - G Heuer
- Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, California
| | - S Ngo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - F Steyn
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - P Nestor
- Queensland Brain Institute, Unviversity of Queensland, Brisbane, Australia
- Mater Public Hospital, Brisbane, Australia
| | - L Wallace
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - P McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - S Heggie
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - K Thorpe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | | | - G English
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A Henders
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - R Henderson
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - C Lomen-Hoerth
- Department of Neurology, UCSF, San Francisco, California
| | - N Wray
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A McRae
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - M Pellegrini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - F Garton
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - N Zaitlen
- Department of Neurology, UCLA, Los Angeles, California
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California
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6
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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7
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Kodavati M, Wang H, Guo W, Mitra J, Hegde PM, Provasek V, Rao VHM, Vedula I, Zhang A, Mitra S, Tomkinson AE, Hamilton DJ, Van Den Bosch L, Hegde ML. FUS unveiled in mitochondrial DNA repair and targeted ligase-1 expression rescues repair-defects in FUS-linked motor neuron disease. Nat Commun 2024; 15:2156. [PMID: 38461154 PMCID: PMC10925063 DOI: 10.1038/s41467-024-45978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 02/08/2024] [Indexed: 03/11/2024] Open
Abstract
This study establishes the physiological role of Fused in Sarcoma (FUS) in mitochondrial DNA (mtDNA) repair and highlights its implications to the pathogenesis of FUS-associated neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Endogenous FUS interacts with and recruits mtDNA Ligase IIIα (mtLig3) to DNA damage sites within mitochondria, a relationship essential for maintaining mtDNA repair and integrity in healthy cells. Using ALS patient-derived FUS mutant cell lines, a transgenic mouse model, and human autopsy samples, we discovered that compromised FUS functionality hinders mtLig3's repair role, resulting in increased mtDNA damage and mutations. These alterations cause various manifestations of mitochondrial dysfunction, particularly under stress conditions relevant to disease pathology. Importantly, rectifying FUS mutations in patient-derived induced pluripotent cells (iPSCs) preserves mtDNA integrity. Similarly, targeted introduction of human DNA Ligase 1 restores repair mechanisms and mitochondrial activity in FUS mutant cells, suggesting a potential therapeutic approach. Our findings unveil FUS's critical role in mitochondrial health and mtDNA repair, offering valuable insights into the mechanisms underlying mitochondrial dysfunction in FUS-associated motor neuron disease.
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Affiliation(s)
- Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Haibo Wang
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Wenting Guo
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- INSERM, UMR-S1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence, Université de Strasbourg, CRBS, Strasbourg, France
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Pavana M Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Vincent Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
- College of Medicine, Texas A&M University, College Station, TX, USA
| | - Vikas H Maloji Rao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Indira Vedula
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
| | - Aijun Zhang
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Houston Methodist, Weill Cornell Medicine affiliate, Houston, TX, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, and Molecular Genetics and Microbiology and University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Dale J Hamilton
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Houston Methodist, Weill Cornell Medicine affiliate, Houston, TX, USA
| | - Ludo Van Den Bosch
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Neuroscience, Weill Cornell Medical College, New York, NY, USA.
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8
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Esteban-Hofer L, Emmanouilidis L, Yulikov M, Allain FHT, Jeschke G. Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate. Biophys J 2024; 123:538-554. [PMID: 38279531 PMCID: PMC10938082 DOI: 10.1016/j.bpj.2024.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/06/2023] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.
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Affiliation(s)
- Laura Esteban-Hofer
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Maxim Yulikov
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Gunnar Jeschke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.
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9
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Anilkumar AK, Vij P, Lopez S, Leslie SM, Doxtater K, Khan MM, Yallapu MM, Chauhan SC, Maestre GE, Tripathi MK. Long Non-Coding RNAs: New Insights in Neurodegenerative Diseases. Int J Mol Sci 2024; 25:2268. [PMID: 38396946 PMCID: PMC10889599 DOI: 10.3390/ijms25042268] [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: 01/03/2024] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of NDDs are related to mitochondrial dysfunction, oxidative stress, and inflammation, which further stimulate the progression of NDDs. Recently, long non-coding RNAs (lncRNAs) have attracted ample attention as critical mediators in the pathology of NDDs. However, there is a significant gap in understanding the biological function, molecular mechanisms, and potential importance of lncRNAs in NDDs. This review documents the current research on lncRNAs and their implications in NDDs. We further summarize the potential implication of lncRNAs to serve as novel therapeutic targets and biomarkers for patients with NDDs.
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Affiliation(s)
- Adithya K. Anilkumar
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Puneet Vij
- Department of Pharmaceutical Sciences, St. John’s University, Queens, NY 11439, USA
| | - Samantha Lopez
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Sophia M. Leslie
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Kyle Doxtater
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Murali M. Yallapu
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Gladys E. Maestre
- Department of Neurosciences, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78550, USA
- South Texas Alzheimer’s Disease Research Center, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX 78550, USA
| | - Manish K. Tripathi
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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10
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Schöpf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan GD, Carrero ZI, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Helm D, Schneider M, Nilsson A, Øra I, Imle R, Banito A, Russell RB, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions. Nat Commun 2024; 15:51. [PMID: 38168093 PMCID: PMC10761971 DOI: 10.1038/s41467-023-44360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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Affiliation(s)
- Julia Schöpf
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kwang-Seok Lee
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Gaurav D Diwan
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Zunamys I Carrero
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Faculty of Biology, TUD Dresden University of Technology, Dresden, Germany
| | - Tobias Hohl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Patricia Rudolph-Hähnel
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | | | - Anna Nilsson
- Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ana Banito
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
| | - Robert B Russell
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Barbara C Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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11
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Geisler MS, Kemp JP, Duronio RJ. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 2023; 14:2293604. [PMID: 38095604 PMCID: PMC10730174 DOI: 10.1080/19491034.2023.2293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology.
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Affiliation(s)
- Mark S. Geisler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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12
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Wang YL, Zhao WW, Shi J, Wan XB, Zheng J, Fan XJ. Liquid-liquid phase separation in DNA double-strand breaks repair. Cell Death Dis 2023; 14:746. [PMID: 37968256 PMCID: PMC10651886 DOI: 10.1038/s41419-023-06267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
DNA double-strand breaks (DSBs) are the fatal type of DNA damage mostly induced by exposure genome to ionizing radiation or genotoxic chemicals. DSBs are mainly repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). To repair DSBs, a large amount of DNA repair factors was observed to be concentrated at the end of DSBs in a specific spatiotemporal manner to form a repair center. Recently, this repair center was characterized as a condensate derived from liquid-liquid phase separation (LLPS) of key DSBs repair factors. LLPS has been found to be the mechanism of membraneless organelles formation and plays key roles in a variety of biological processes. In this review, the recent advances and mechanisms of LLPS in the formation of DSBs repair-related condensates are summarized.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
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13
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Singh D, Desai N, Shah V, Datta B. In Silico Identification of Potential Quadruplex Forming Sequences in LncRNAs of Cervical Cancer. Int J Mol Sci 2023; 24:12658. [PMID: 37628839 PMCID: PMC10454738 DOI: 10.3390/ijms241612658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as auxiliary regulators of gene expression influencing tumor microenvironment, metastasis and radio-resistance in cancer. The presence of lncRNA in extracellular fluids makes them promising diagnostic markers. LncRNAs deploy higher-order structures to facilitate a complex range of functions. Among such structures, G-quadruplexes (G4s) can be detected or targeted by small molecular probes to drive theranostic applications. The in vitro identification of G4 formation in lncRNAs can be a tedious and expensive proposition. Bioinformatics-driven strategies can provide comprehensive and economic alternatives in conjunction with suitable experimental validation. We propose a pipeline to identify G4-forming sequences, protein partners and biological functions associated with dysregulated lncRNAs in cervical cancer. We identified 17 lncRNA clusters which possess transcripts that can fold into a G4 structure. We confirmed in vitro G4 formation in the four biologically active isoforms of SNHG20, MEG3, CRNDE and LINP1 by Circular Dichroism spectroscopy and Thioflavin-T-assisted fluorescence spectroscopy and reverse-transcriptase stop assay. Gene expression data demonstrated that these four lncRNAs can be potential prognostic biomarkers of cervical cancer. Two approaches were employed for identifying G4 specific protein partners for these lncRNAs and FMR2 was a potential interacting partner for all four clusters. We report a detailed investigation of G4 formation in lncRNAs that are dysregulated in cervical cancer. LncRNAs MEG3, CRNDE, LINP1 and SNHG20 are shown to influence cervical cancer progression and we report G4 specific protein partners for these lncRNAs. The protein partners and G4s predicted in lncRNAs can be exploited for theranostic objectives.
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Affiliation(s)
- Deepshikha Singh
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India
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14
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Li M, Chen G, Zhang Z. Modeling the effects of phosphorylation on phase separation of the FUS low-complexity domain. Biophys J 2023; 122:2636-2645. [PMID: 37211763 PMCID: PMC10397571 DOI: 10.1016/j.bpj.2023.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023] Open
Abstract
Aggregation of the RNA-binding protein fused in sarcoma (FUS) is a hallmark of neurodegenerative diseases. Phosphorylation of Ser/Thr in the FUS low-complexity domain (FUS-LC) may regulate phase separation of FUS and prevent pathological aggregation in cells. However, many details of this process remain elusive to date. In this work, we systematically investigated the phosphorylation of FUS-LC and the underlying molecular mechanism by molecular dynamics (MD) simulations and free energy calculations. The results clearly show that phosphorylation can destroy the fibril core structure of FUS-LC by breaking interchain interactions, particularly contacts involving residues like Tyr, Ser, and Gln. Among the six phosphorylation sites, Ser61 and Ser84 may have more important effects on the stability of the fibril core. Our study reveals structural and dynamic details of FUS-LC phase separation modulated by phosphorylation.
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Affiliation(s)
- Mingwei Li
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Guanglin Chen
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Zhiyong Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, P.R. China; Department of Physics, University of Science and Technology of China, Hefei, Anhui, P.R. China.
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15
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Kumar MS, Stallworth KM, Murthy AC, Lim SM, Li N, Jain A, Munro JB, Fawzi NL, Lagier-Tourenne C, Bosco DA. Interactions between FUS and the C-terminal Domain of Nup62 are Sufficient for their Co-phase Separation into Amorphous Assemblies. J Mol Biol 2023; 435:167972. [PMID: 36690069 PMCID: PMC10329203 DOI: 10.1016/j.jmb.2023.167972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergistic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain of Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.
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Affiliation(s)
- Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA; Biochemistry and Molecular Biotechnology Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karly M Stallworth
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Su Min Lim
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nan Li
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA.
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16
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Jagtap YA, Kumar P, Kinger S, Dubey AR, Choudhary A, Gutti RK, Singh S, Jha HC, Poluri KM, Mishra A. Disturb mitochondrial associated proteostasis: Neurodegeneration and imperfect ageing. Front Cell Dev Biol 2023; 11:1146564. [PMID: 36968195 PMCID: PMC10036443 DOI: 10.3389/fcell.2023.1146564] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
The disturbance in mitochondrial functions and homeostasis are the major features of neuron degenerative conditions, like Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Alzheimer’s disease, along with protein misfolding. The aberrantly folded proteins are known to link with impaired mitochondrial pathways, further contributing to disease pathogenesis. Despite their central significance, the implications of mitochondrial homeostasis disruption on other organelles and cellular processes remain insufficiently explored. Here, we have reviewed the dysfunction in mitochondrial physiology, under neuron degenerating conditions. The disease misfolded proteins impact quality control mechanisms of mitochondria, such as fission, fusion, mitophagy, and proteasomal clearance, to the detriment of neuron. The adversely affected mitochondrial functional roles, like oxidative phosphorylation, calcium homeostasis, and biomolecule synthesis as well as its axes and contacts with endoplasmic reticulum and lysosomes are also discussed. Mitochondria sense and respond to multiple cytotoxic stress to make cell adapt and survive, though chronic dysfunction leads to cell death. Mitochondria and their proteins can be candidates for biomarkers and therapeutic targets. Investigation of internetworking between mitochondria and neurodegeneration proteins can enhance our holistic understanding of such conditions and help in designing more targeted therapies.
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Affiliation(s)
- Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sarika Singh
- Division of Neuroscience and Ageing Biology, Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
- *Correspondence: Amit Mishra,
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17
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Gawade K, Plewka P, Häfner SJ, Lund AH, Marchand V, Motorin Y, Szczesniak MW, Raczynska KD. FUS regulates a subset of snoRNA expression and modulates the level of rRNA modifications. Sci Rep 2023; 13:2974. [PMID: 36806717 PMCID: PMC9941101 DOI: 10.1038/s41598-023-30068-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this work, we show that FUS depletion results in the differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2'-O methylation (2'-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2'-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2'-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and progression.
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Affiliation(s)
- Kishor Gawade
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Patrycja Plewka
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Sophia J Häfner
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Virginie Marchand
- Université de Lorraine, UAR2008/US40 IBSLor CNRS-INSERM and UMR7365 IMoPA CNRS, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, UAR2008/US40 IBSLor CNRS-INSERM and UMR7365 IMoPA CNRS, Nancy, France
| | - Michal W Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Katarzyna D Raczynska
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland.
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland.
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18
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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19
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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20
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Chowdhury MN, Jin H. The RGG motif proteins: Interactions, functions, and regulations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1748. [PMID: 35661420 PMCID: PMC9718894 DOI: 10.1002/wrna.1748] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/31/2023]
Abstract
Proteins with motifs rich in arginines and glycines were discovered decades ago and are functionally involved in a staggering range of essential processes in the cell. Versatile, specific, yet adaptable molecular interactions enabled by the unique combination of arginine and glycine, combined with multiplicity of molecular recognition conferred by repeated di-, tri-, and multiple peptide motifs, allow RGG motif proteins to interact with a broad range of proteins and nucleic acids. Furthermore, posttranslational modifications at the arginines in the motif extend the RGG protein's capacity for a fine-tuned regulation. In this review, we focus on the biochemical properties of the RGG motif, its molecular interactions with RNAs and proteins, and roles of the posttranslational modification in modulating their interactions. We discuss current knowledge of the RGG motif proteins involved in mRNA transport and translation, highlight our merging understanding of their molecular functions in translational regulation and summarize areas of research in the future critical in understanding this important family of proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Mechanisms.
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Affiliation(s)
- Mashiat N. Chowdhury
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Corresponding author: Phone: (217)244-9493, Fax: (217)244-5858,
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21
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Chen QY, Wu P, Wen T, Qin X, Zhang R, Jia R, Jin J, Hu F, Xie X, Dang J. Association of cerebral spinal fluid copper imbalance in amyotrophic lateral sclerosis. Front Aging Neurosci 2022; 14:970711. [PMID: 36466599 PMCID: PMC9714432 DOI: 10.3389/fnagi.2022.970711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/28/2022] [Indexed: 10/24/2023] Open
Abstract
A plethora of environmental risk factors has been persistently implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), including metal/metalloids. This study aimed to examine potential associations between cerebral spinal fluid (CSF) metal/metalloids and ALS risks. CSF concentrations of copper (Cu), nickel (Ni), mercury (Hg), arsenic (As), manganese (Mn), and iron (Fe) in ALS (spinal- and bulbar-onset) patients and controls were measured using inductively coupled plasma mass spectrometry (ICP-MS). Results from this study revealed marked differences between control, spinal-onset, and bulbar-onset groups. We report that Cu levels were lower in the ALS and spinal-onset groups compared to the control group. Ni level were higher in the spinal-onset group compared to the control and bulbar-onset groups. In addition, associations between CSF metal/metalloid levels with disease severity, sex, and serum triglycerides were also examined to broach the potential relevance of neurotoxic metal/metalloids in ALS disease heterogeneity.
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Affiliation(s)
- Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, China
| | - Peng Wu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, China
| | - Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, China
| | - Xing Qin
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ronghua Zhang
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Rui Jia
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jiaoting Jin
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Fangfang Hu
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xiaoge Xie
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, China
| | - Jingxia Dang
- Department of Neurology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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22
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Murakami K, Ono K. Interactions of amyloid coaggregates with biomolecules and its relevance to neurodegeneration. FASEB J 2022; 36:e22493. [PMID: 35971743 DOI: 10.1096/fj.202200235r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloidogenic proteins is a pathological hallmark of various neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In these diseases, oligomeric intermediates or toxic aggregates of amyloids cause neuronal damage and degeneration. Despite the substantial effort made over recent decades to implement therapeutic interventions, these neurodegenerative diseases are not yet understood at the molecular level. In many cases, multiple disease-causing amyloids overlap in a sole pathological feature or a sole disease-causing amyloid represents multiple pathological features. Various amyloid pathologies can coexist in the same brain with or without clinical presentation and may even occur in individuals without disease. From sparse data, speculation has arisen regarding the coaggregation of amyloids with disparate amyloid species and other biomolecules, which are the same characteristics that make diagnostics and drug development challenging. However, advances in research related to biomolecular condensates and structural analysis have been used to overcome some of these challenges. Considering the development of these resources and techniques, herein we review the cross-seeding of amyloidosis, for example, involving the amyloids amyloid β, tau, α-synuclein, and human islet amyloid polypeptide, and their cross-inhibition by transthyretin and BRICHOS. The interplay of nucleic acid-binding proteins, such as prions, TAR DNA-binding protein 43, fused in sarcoma/translated in liposarcoma, and fragile X mental retardation polyglycine, with nucleic acids in the pathology of neurodegeneration are also described, and we thereby highlight the potential clinical applications in central nervous system therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenjiro Ono
- Department of Neurology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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23
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De Marco G, Lomartire A, Manera U, Canosa A, Grassano M, Casale F, Fuda G, Salamone P, Rinaudo MT, Colombatto S, Moglia C, Chiò A, Calvo A. Effects of intracellular calcium accumulation on proteins encoded by the major genes underlying amyotrophic lateral sclerosis. Sci Rep 2022; 12:395. [PMID: 35013445 PMCID: PMC8748718 DOI: 10.1038/s41598-021-04267-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
The aetiology of Amyotrophic Lateral Sclerosis (ALS) is still poorly understood. The discovery of genetic forms of ALS pointed out the mechanisms underlying this pathology, but also showed how complex these mechanisms are. Excitotoxicity is strongly suspected to play a role in ALS pathogenesis. Excitotoxicity is defined as neuron damage due to excessive intake of calcium ions (Ca2+) by the cell. This study aims to find a relationship between the proteins coded by the most relevant genes associated with ALS and intracellular Ca2+ accumulation. In detail, the profile of eight proteins (TDP-43, C9orf72, p62/sequestosome-1, matrin-3, VCP, FUS, SOD1 and profilin-1), was analysed in three different cell types induced to raise their cytoplasmic amount of Ca2+. Intracellular Ca2+ accumulation causes a decrease in the levels of TDP-43, C9orf72, matrin3, VCP, FUS, SOD1 and profilin-1 and an increase in those of p62/sequestosome-1. These events are associated with the proteolytic action of two proteases, calpains and caspases, as well as with the activation of autophagy. Interestingly, Ca2+ appears to both favour and hinder autophagy. Understanding how and why calpain-mediated proteolysis and autophagy, which are physiological processes, become pathological may elucidate the mechanisms responsible for ALS and help discover new therapeutic targets.
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Affiliation(s)
- Giovanni De Marco
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy. .,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy.
| | - Annarosa Lomartire
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy
| | - Umberto Manera
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy
| | - Antonio Canosa
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy.,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy
| | - Maurizio Grassano
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy
| | - Federico Casale
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy
| | - Giuseppe Fuda
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy
| | - Paolina Salamone
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy.,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy
| | - Maria Teresa Rinaudo
- Department of Oncology, University of Turin, via Michelangelo 27/b, 10126, Turin, Italy
| | - Sebastiano Colombatto
- Department of Oncology, University of Turin, via Michelangelo 27/b, 10126, Turin, Italy
| | - Cristina Moglia
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy.,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy
| | - Adriano Chiò
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy.,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy.,Neuroscience Institute of Turin (NIT), Via Verdi, 8, 10124, Turin, Italy.,Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, 00185, Rome, Italy
| | - Andrea Calvo
- Department of Neuroscience, ALS Centre, "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10126, Turin, Italy.,Neurology Unit 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Via Cherasco 15, 10126, Turin, Italy.,Neuroscience Institute of Turin (NIT), Via Verdi, 8, 10124, Turin, Italy
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24
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Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics 2021; 219:iyab145. [PMID: 34740247 PMCID: PMC8570788 DOI: 10.1093/genetics/iyab145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 01/22/2023] Open
Abstract
Many circular RNAs (circRNAs) are differentially expressed in different tissues or cell types, suggestive of specific factors that regulate their biogenesis. Here, taking advantage of available mutation strains of RNA-binding proteins (RBPs) in Caenorhabditis elegans, I performed a screening of circRNA regulation in 13 conserved RBPs. Among them, loss of FUST-1, the homolog of Fused in Sarcoma (FUS), caused downregulation of multiple circRNAs. By rescue experiments, I confirmed FUST-1 as a circRNA regulator. Through RNA sequencing using circRNA-enriched samples, circRNAs targets regulated by FUST-1 were identified globally, with hundreds of them significantly altered. Furthermore, I showed that FUST-1 regulates circRNA formation with only small to little effect on the cognate linear mRNAs. When recognizing circRNA pre-mRNAs, FUST-1 can affect both exon-skipping and circRNA in the same genes. Moreover, I identified an autoregulation loop in fust-1, where FUST-1, isoform a (FUST-1A) promotes the skipping of exon 5 of its own pre-mRNA, which produces FUST-1, isoform b (FUST-1B) with different N-terminal sequences. FUST-1A is the functional isoform in circRNA regulation. Although FUST-1B has the same functional domains as FUST-1A, it cannot regulate either exon-skipping or circRNA formation. This study provided an in vivo investigation of circRNA regulation, which will be helpful to understand the mechanisms that govern circRNA formation.
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Affiliation(s)
- Dong Cao
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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25
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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26
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A microfluidic approach to rescue ALS motor neuron degeneration using rapamycin. Sci Rep 2021; 11:18168. [PMID: 34518579 PMCID: PMC8438029 DOI: 10.1038/s41598-021-97405-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/17/2021] [Indexed: 01/27/2023] Open
Abstract
TAR DNA-binding protein-43 (TDP-43) is known to accumulate in ubiquitinated inclusions of amyotrophic lateral sclerosis affected motor neurons, resulting in motor neuron degeneration, loss of motor functions, and eventually death. Rapamycin, an mTOR inhibitor and a commonly used immunosuppressive drug, has been shown to increase the survivability of Amyotrophic Lateral Sclerosis (ALS) affected motor neurons. Here we present a transgenic, TDP-43-A315T, mouse model expressing an ALS phenotype and demonstrate the presence of ubiquitinated cytoplasmic TDP-43 aggregates with > 80% cell death by 28 days post differentiation in vitro. Embryonic stem cells from this mouse model were used to study the onset, progression, and therapeutic remediation of TDP-43 aggregates using a novel microfluidic rapamycin concentration gradient generator. Results using a microfluidic device show that ALS affected motor neuron survival can be increased by 40.44% in a rapamycin dosage range between 0.4-1.0 µM.
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27
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Arenas A, Chen J, Kuang L, Barnett KR, Kasarskis EJ, Gal J, Zhu H. Lysine acetylation regulates the RNA binding, subcellular localization and inclusion formation of FUS. Hum Mol Genet 2021; 29:2684-2697. [PMID: 32691043 DOI: 10.1093/hmg/ddaa159] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/17/2020] [Accepted: 07/11/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the preferential death of motor neurons. Approximately 10% of ALS cases are familial and 90% are sporadic. Fused in sarcoma (FUS) is a ubiquitously expressed RNA-binding protein implicated in familial ALS and frontotemporal dementia (FTD). The physiological function and pathological mechanism of FUS are not well understood, particularly whether post-translational modifications play a role in regulating FUS function. In this study, we discovered that FUS was acetylated at lysine-315/316 (K315/K316) and lysine-510 (K510) residues in two distinct domains. Located in the nuclear localization sequence, K510 acetylation disrupted the interaction between FUS and Transportin-1, resulting in the mislocalization of FUS in the cytoplasm and formation of stress granule-like inclusions. Located in the RNA recognition motif, K315/K316 acetylation reduced RNA binding to FUS and decreased the formation of cytoplasmic inclusions. Treatment with deacetylase inhibitors also significantly reduced the inclusion formation in cells expressing ALS mutation P525L. More interestingly, familial ALS patient fibroblasts showed higher levels of FUS K510 acetylation as compared with healthy controls. Lastly, CREB-binding protein/p300 acetylated FUS, whereas both sirtuins and histone deacetylases families of lysine deacetylases contributed to FUS deacetylation. These findings demonstrate that FUS acetylation regulates the RNA binding, subcellular localization and inclusion formation of FUS, implicating a potential role of acetylation in the pathophysiological process leading to FUS-mediated ALS/FTD.
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Affiliation(s)
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry
| | - Lisha Kuang
- Department of Molecular and Cellular Biochemistry
| | | | - Edward J Kasarskis
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Jozsef Gal
- Department of Molecular and Cellular Biochemistry
| | - Haining Zhu
- Department of Toxicology and Cancer Biology.,Department of Molecular and Cellular Biochemistry.,Lexington VA Medical Center, Research and Development, Lexington, KY 40502, USA
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28
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Lin YC, Kumar MS, Ramesh N, Anderson EN, Nguyen AT, Kim B, Cheung S, McDonough JA, Skarnes WC, Lopez-Gonzalez R, Landers JE, Fawzi NL, Mackenzie IR, Lee EB, Nickerson JA, Grunwald D, Pandey UB, Bosco DA. Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. Nat Neurosci 2021; 24:1077-1088. [PMID: 34059832 PMCID: PMC8832378 DOI: 10.1038/s41593-021-00859-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 02/05/2023]
Abstract
Nucleocytoplasmic transport (NCT) decline occurs with aging and neurodegeneration. Here, we investigated the NCT pathway in models of amyotrophic lateral sclerosis-fused in sarcoma (ALS-FUS). Expression of ALS-FUS led to a reduction in NCT and nucleoporin (Nup) density within the nuclear membrane of human neurons. FUS and Nups were found to interact independently of RNA in cells and to alter the phase-separation properties of each other in vitro. FUS-Nup interactions were not localized to nuclear pores, but were enriched in the nucleus of control neurons versus the cytoplasm of mutant neurons. Our data indicate that the effect of ALS-linked mutations on the cytoplasmic mislocalization of FUS, rather than on the physiochemical properties of the protein itself, underlie our reported NCT defects. An aberrant interaction between mutant FUS and Nups is underscored by studies in Drosophila, whereby reduced Nup expression rescued multiple toxic FUS-induced phenotypes, including abnormal nuclear membrane morphology in neurons.
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Affiliation(s)
- Yen-Chen Lin
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Nandini Ramesh
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, 15261, USA
| | - Eric N. Anderson
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Aivi T. Nguyen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Boram Kim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Cheung
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | | | | | - Rodrigo Lopez-Gonzalez
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Nicolas L. Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, 02912, USA
| | - Ian R.A. Mackenzie
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeffrey A. Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, 01605, USA
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Udai B. Pandey
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Daryl A. Bosco
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA,Lead Contact,To whom correspondence should be addressed: Daryl A. Bosco: Department of Neurology, University of Massachusetts Medical Center, Worcester, MA 01605; ; Tel. (774) 455-3745; Fax. (508) 856-6750
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ALS-linked FUS mutants affect the localization of U7 snRNP and replication-dependent histone gene expression in human cells. Sci Rep 2021; 11:11868. [PMID: 34088960 PMCID: PMC8178370 DOI: 10.1038/s41598-021-91453-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 05/18/2021] [Indexed: 11/24/2022] Open
Abstract
Genes encoding replication-dependent histones lack introns, and the mRNAs produced are a unique class of RNA polymerase II transcripts in eukaryotic cells that do not end in a polyadenylated tail. Mature mRNAs are thus formed by a single endonucleolytic cleavage that releases the pre-mRNA from the DNA and is the only processing event necessary. U7 snRNP is one of the key factors that determines the cleavage site within the 3ʹUTR of replication-dependent histone pre-mRNAs. We have previously showed that the FUS protein interacts with U7 snRNA/snRNP and regulates the expression of histone genes by stimulating transcription and 3ʹ end maturation. Mutations in the FUS gene first identified in patients with amyotrophic lateral sclerosis (ALS) lead to the accumulation of the FUS protein in cytoplasmic inclusions. Here, we report that mutations in FUS lead to disruption of the transcriptional activity of FUS and mislocalization of U7 snRNA/snRNP in cytoplasmic aggregates in cellular models and primary neurons. As a consequence, decreased transcriptional efficiency and aberrant 3ʹ end processing of histone pre-mRNAs were observed. This study highlights for the first time the deregulation of replication-dependent histone gene expression and its involvement in ALS.
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Xue YC, Ng CS, Mohamud Y, Fung G, Liu H, Bahreyni A, Zhang J, Luo H. FUS/TLS Suppresses Enterovirus Replication and Promotes Antiviral Innate Immune Responses. J Virol 2021; 95:e00304-21. [PMID: 33827951 PMCID: PMC8316056 DOI: 10.1128/jvi.00304-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
During viral infection, the dynamic virus-host relationship is constantly in play. Many cellular proteins, such as RNA-binding proteins (RBPs), have been shown to mediate antiviral responses during viral infection. Here, we report that the RBP FUS/TLS (fused in sarcoma/translocated in liposarcoma) acts as a host-restricting factor against infection with coxsackievirus B3 (CVB3). Mechanistically, we found that deletion of FUS leads to increased viral RNA transcription and enhanced internal ribosome entry site (IRES)-driven translation, with no apparent impact on viral RNA stability. We further demonstrated that FUS physically interacts with the viral genome, which may contribute to direct inhibition of viral RNA transcription/translation. Moreover, we identified a novel function for FUS in regulating host innate immune response. We show that in the absence of FUS, gene expression of type I interferons and proinflammatory cytokines elicited by viral or bacterial infection is significantly impaired. Emerging evidence suggests a role for stress granules (SGs) in antiviral innate immunity. We further reveal that knockout of FUS abolishes the ability to form SGs upon CVB3 infection or poly(I·C) treatment. Finally, we show that, to avoid FUS-mediated antiviral response and innate immunity, CVB3 infection results in cytoplasmic mislocalization and cleavage of FUS through the enzymatic activity of viral proteases. Together, our findings in this study identify FUS as a novel host antiviral factor which restricts CVB3 replication through direct inhibition of viral RNA transcription and protein translation and through regulation of host antiviral innate immunity.IMPORTANCE Enteroviruses are common human pathogens, including those that cause myocarditis (coxsackievirus B3 [CVB3]), poliomyelitis (poliovirus), and hand, foot, and mouth disease (enterovirus 71). Understanding the virus-host interaction is crucial for developing means of treating and preventing diseases caused by these pathogens. In this study, we explored the interplay between the host RNA-binding protein FUS/TLS and CVB3 and found that FUS/TLS restricts CVB3 replication through direct inhibition of viral RNA transcription/translation and through regulation of cellular antiviral innate immunity. To impede the antiviral role of FUS, CVB3 targets FUS for mislocalization and cleavage. Findings from this study provide novel insights into interactions between CVB3 and FUS, which may lead to novel therapeutic interventions against enterovirus-induced diseases.
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Affiliation(s)
- Yuan Chao Xue
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Seng Ng
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yasir Mohamud
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabriel Fung
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Huitao Liu
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amirhossein Bahreyni
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jingchun Zhang
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Honglin Luo
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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31
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Hernández-Candia CN, Pearce S, Tucker CL. A modular tool to query and inducibly disrupt biomolecular condensates. Nat Commun 2021; 12:1809. [PMID: 33753744 PMCID: PMC7985322 DOI: 10.1038/s41467-021-22096-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/01/2021] [Indexed: 01/29/2023] Open
Abstract
Dynamic membraneless compartments formed by protein condensates have multifunctional roles in cellular biology. Tools that inducibly trigger condensate formation have been useful for exploring their cellular function, however, there are few tools that provide inducible control over condensate disruption. To address this need we developed DisCo (Disassembly of Condensates), which relies on the use of chemical dimerizers to inducibly recruit a ligand to the condensate-forming protein, triggering condensate dissociation. We demonstrate use of DisCo to disrupt condensates of FUS, associated with amyotrophic lateral sclerosis, and to prevent formation of polyglutamine-containing huntingtin condensates, associated with Huntington's disease. In addition, we combined DisCo with a tool to induce condensates with light, CRY2olig, achieving bidirectional control of condensate formation and disassembly using orthogonal inputs of light and rapamycin. Our results demonstrate a method to manipulate condensate states that will have broad utility, enabling better understanding of the biological role of condensates in health and disease.
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Affiliation(s)
| | - Sarah Pearce
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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32
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Gonzalez A, Mannen T, Çağatay T, Fujiwara A, Matsumura H, Niesman AB, Brautigam CA, Chook YM, Yoshizawa T. Mechanism of karyopherin-β2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X). Sci Rep 2021; 11:3754. [PMID: 33580145 PMCID: PMC7881136 DOI: 10.1038/s41598-021-83196-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations in the RNA-binding protein FUS cause familial amyotropic lateral sclerosis (ALS). Several mutations that affect the proline-tyrosine nuclear localization signal (PY-NLS) of FUS cause severe juvenile ALS. FUS also undergoes liquid-liquid phase separation (LLPS) to accumulate in stress granules when cells are stressed. In unstressed cells, wild type FUS resides predominantly in the nucleus as it is imported by the importin Karyopherin-β2 (Kapβ2), which binds with high affinity to the C-terminal PY-NLS of FUS. Here, we analyze the interactions between two ALS-related variants FUS(P525L) and FUS(R495X) with importins, especially Kapβ2, since they are still partially localized to the nucleus despite their defective/missing PY-NLSs. The crystal structure of the Kapβ2·FUS(P525L)PY-NLS complex shows the mutant peptide making fewer contacts at the mutation site, explaining decreased affinity for Kapβ2. Biochemical analysis revealed that the truncated FUS(R495X) protein, although missing the PY-NLS, can still bind Kapβ2 and suppresses LLPS. FUS(R495X) uses its C-terminal tandem arginine-glycine-glycine regions, RGG2 and RGG3, to bind the PY-NLS binding site of Kapβ2 for nuclear localization in cells when arginine methylation is inhibited. These findings suggest the importance of the C-terminal RGG regions in nuclear import and LLPS regulation of ALS variants of FUS that carry defective PY-NLSs.
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Affiliation(s)
- Abner Gonzalez
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taro Mannen
- College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Tolga Çağatay
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ayano Fujiwara
- College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | | | - Ashley B Niesman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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33
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Arenas A, Kuang L, Zhang J, Kingren MS, Zhu H. FUS regulates autophagy by mediating the transcription of genes critical to the autophagosome formation. J Neurochem 2021; 157:752-763. [PMID: 33354770 DOI: 10.1111/jnc.15281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 12/17/2022]
Abstract
Fused in sarcoma (FUS) is a ubiquitously expressed RNA/DNA-binding protein that plays different roles in the cell. FUS pathology has been reported in neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Mutations in FUS have also been linked to a subset of familial ALS. FUS is mainly localized in the nucleus although it shuttles between the nucleus and the cytoplasm. ALS-linked mutations cause the accumulation of the FUS protein in cytoplasm where it forms stress granule-like inclusions. The protein- and RNA-containing inclusions are reported to be positive of autophagosome markers and degraded by the autophagy pathway. However, the role of FUS in the autophagy pathway remains to be better understood. Using immunoblot and confocal imaging techniques in this study, we found that FUS knockout (KO) cells showed a decreased basal autophagy level. Rapamycin and bafilomycin A1 treatment showed that FUS KO cells were not able to initiate autophagy as efficiently as wild-type cells, suggesting that the autophagosome formation is affected in the absence of FUS. Moreover, using immunoblot and quantitative PCR techniques, we found that the mRNA and protein levels of the genes critical in the initial steps of the autophagy pathway (FIP200, ATG16L1 and ATG12) were significantly lower in FUS KO cells. Re-expressing FUS in the KO cells restored the expression of FIP200 and ATG16L1. Our findings demonstrate a novel role of FUS in the autophagy pathway, that is, regulating the transcription of genes involved in early stages of autophagy such as the initiation and elongation of autophagosomes.
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Affiliation(s)
- Alexandra Arenas
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Lisha Kuang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Lexington VA Medical Center, Research and Development, Lexington, KY, USA
| | - Jiayu Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Meagan S Kingren
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Haining Zhu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA.,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Lexington VA Medical Center, Research and Development, Lexington, KY, USA
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Abd Raboh NM, Hakim SA, Abd El Atti RM. Implications of androgen receptor and FUS expression on tumor progression in urothelial carcinoma. Histol Histopathol 2020; 36:325-337. [PMID: 33354760 DOI: 10.14670/hh-18-295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Androgen receptor (AR) interact with many pathways involved in bladder cancer development and progression. FUS (fused in liposarcoma), a multifunctional protein essential for different cellular processes, has been demonstrated as a key link between androgen receptor signaling and cell-cycle progression in prostate cancer but has not been examined in urothelial carcinoma (UC) despite an intimate association between prostate and bladder carcinogenesis. AIM To examine the immunohistochemical expression of AR and FUS in urothelial carcinoma in relation to prognostic parameters and to extrapolate any possible link between the expression of both markers and tumor progression. STUDY DESIGN Retrospective study using immunohistochemical staining for AR and FUS on (88) cases of urothelial carcinoma. RESULTS AR shows statistically significant relations with late tumor stage, high tumor grade, and non-papillary tumor pattern. On the other hand, FUS expression correlates with early tumor stage, low tumor grade and papillary pattern. An inverse relation is found between AR and FUS expression (p=0.001). Cases with high AR IHC expression show statistically significant shorter OS, RFS and PFS compared to cases with low AR expression. Cases with high FUS IHC expression reveal statistically significant longer OS, RFS and PFS compared to cases with low FUS expression. CONCLUSION FUS expression is associated with favorable prognostic parameters of UC. A possible interaction is suggested between FUS and AR pathways involved in urothelial cancer progression. Manipulating FUS levels and androgen deprivation therapy can provide new promising targets for treatment trials.
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Affiliation(s)
| | - Sarah Adel Hakim
- Department of Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Johnson MA, Deng Q, Taylor G, McEachin ZT, Chan AWS, Root J, Bassell GJ, Kukar T. Divergent FUS phosphorylation in primate and mouse cells following double-strand DNA damage. Neurobiol Dis 2020; 146:105085. [PMID: 32950644 PMCID: PMC8064403 DOI: 10.1016/j.nbd.2020.105085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Fused in sarcoma (FUS) is a RNA/DNA protein involved in multiple nuclear and cytoplasmic functions including transcription, splicing, mRNA trafficking, and stress granule formation. To accomplish these many functions, FUS must shuttle between cellular compartments in a highly regulated manner. When shuttling is disrupted, FUS abnormally accumulates into cytoplasmic inclusions that can be toxic. Disrupted shuttling of FUS into the nucleus is a hallmark of ~10% of frontotemporal lobar degeneration (FTLD) cases, the neuropathology that underlies frontotemporal dementia (FTD). Multiple pathways are known to disrupt nuclear/cytoplasmic shuttling of FUS. In earlier work, we discovered that double-strand DNA breaks (DSBs) trigger DNA-dependent protein kinase (DNA-PK) to phosphorylate FUS (p-FUS) at N-terminal residues leading to the cytoplasmic accumulation of FUS. Therefore, DNA damage may contribute to the development of FTLD pathology with FUS inclusions. In the present study, we examined how DSBs effect FUS phosphorylation in various primate and mouse cellular models. All cell lines derived from human and non-human primates exhibit N-terminal FUS phosphorylation following calicheamicin γ1 (CLM) induced DSBs. In contrast, we were unable to detect FUS phosphorylation in mouse-derived primary neurons or immortalized cell lines regardless of CLM treatment, duration, or concentration. Despite DNA damage induced by CLM treatment, we find that mouse cells do not phosphorylate FUS, likely due to reduced levels and activity of DNA-PK compared to human cells. Taken together, our work reveals that mouse-derived cellular models regulate FUS in an anomalous manner compared to primate cells. This raises the possibility that mouse models may not fully recapitulate the pathogenic cascades that lead to FTLD with FUS pathology.
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Affiliation(s)
- Michelle A Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Qiudong Deng
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Georgia Taylor
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Zachary T McEachin
- Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America; Department of Cell Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Laboratory of Translational Cell Biology, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Anthony W S Chan
- Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America; Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA, United States of America; Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, 954 Gatewood Rd, NE, Atlanta, GA, United States of America
| | - Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Gary J Bassell
- Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America; Department of Cell Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Laboratory of Translational Cell Biology, Emory University, School of Medicine, Atlanta, GA, United States of America
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, GA, United States of America; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, GA, United States of America; Department of Neurology, Emory University, School of Medicine, Atlanta, GA, United States of America.
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Scarola M, Comisso E, Rosso M, Del Sal G, Schneider C, Schoeftner S, Benetti R. FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity. Commun Biol 2020; 3:632. [PMID: 33128015 PMCID: PMC7603346 DOI: 10.1038/s42003-020-01355-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 10/01/2020] [Indexed: 11/16/2022] Open
Abstract
The resurrection of pseudogenes during evolution produced lncRNAs with new biological function. Here we show that pseudogene-evolution created an Oct4 pseudogene lncRNA that is able to direct epigenetic silencing of the parental Oct4 gene via a 2-step, lncRNA dependent mechanism. The murine Oct4 pseudogene 4 (mOct4P4) lncRNA recruits the RNA binding protein FUS to allow the binding of the SUV39H1 HMTase to a defined mOct4P4 lncRNA sequence element. The mOct4P4-FUS-SUV39H1 silencing complex holds target site specificity for the parental Oct4 promoter and interference with individual components results in loss of Oct4 silencing. SUV39H1 and FUS do not bind parental Oct4 mRNA, confirming the acquisition of a new biological function by the mOct4P4 lncRNA. Importantly, all features of mOct4P4 function are recapitulated by the human hOCT4P3 pseudogene lncRNA, indicating evolutionary conservation. Our data highlight the biological relevance of rapidly evolving lncRNAs that infiltrate into central epigenetic regulatory circuits in vertebrate cells.
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Affiliation(s)
- Michele Scarola
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy
- Dipartimento di Area Medica (DAME), Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Elisa Comisso
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy
- Dipartimento di Area Medica (DAME), Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Massimo Rosso
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy
- Dipartimento di Science della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Giannino Del Sal
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy
- Dipartimento di Science della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Claudio Schneider
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy
- Dipartimento di Area Medica (DAME), Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Stefan Schoeftner
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy.
- Dipartimento di Science della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
| | - Roberta Benetti
- Laboratorio Nazionale-Consorzio Interuniversitario per le Biotecnologie, Laboratorio Nazionale (LNCIB), Padriciano 99, 34149, Trieste, Italy.
- Dipartimento di Area Medica (DAME), Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy.
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Mohanta A, Chakrabarti K. Dbr1 functions in mRNA processing, intron turnover and human diseases. Biochimie 2020; 180:134-142. [PMID: 33038423 DOI: 10.1016/j.biochi.2020.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/29/2022]
Abstract
Pre-mRNA processing and mRNA stability play direct roles in controlling protein abundance in a cell. Before the mRNA can be translated into a protein, the introns in the pre-mRNA transcripts need to be removed by splicing, such that exons can be ligated together and can code for a protein. In this process, the function of the RNA lariat debranching enzyme or Dbr1 provides a rate-limiting step in the intron turnover process and possibly regulating the production of translation competent mRNAs. Surprising new roles of Dbr1 are emerging in cellular metabolism which extends beyond intron turnover processes, ranging from splicing regulation to translational control. In this review, we highlight the importance of the Dbr1 enzyme, its structure and how anomalies in its function could relate to various human diseases.
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Affiliation(s)
- Arundhati Mohanta
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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38
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Sukhanova MV, Singatulina AS, Pastré D, Lavrik OI. Fused in Sarcoma (FUS) in DNA Repair: Tango with Poly(ADP-ribose) Polymerase 1 and Compartmentalisation of Damaged DNA. Int J Mol Sci 2020; 21:E7020. [PMID: 32987654 PMCID: PMC7582374 DOI: 10.3390/ijms21197020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022] Open
Abstract
The fused in sarcoma (FUS) protein combines prion-like properties with a multifunctional DNA/RNA-binding domain and has functions spanning the regulation of RNA metabolism, including transcription, pre-mRNA splicing, mRNA transport and translation. In addition to its roles in RNA metabolism, FUS is implicated in the maintenance of DNA integrity. In this review, we examine the participation of FUS in major DNA repair pathways, focusing on DNA repair associated with poly(ADP-ribosyl)ation events and on how the interaction of FUS with poly(ADP-ribose) may orchestrate transient compartmentalisation of DNA strand breaks. Unravelling how prion-like RNA-binding proteins control DNA repair pathways will deepen our understanding of the pathogenesis of some neurological diseases and cancer as well as provide the basis for the development of relevant innovative therapeutic technologies. This knowledge may also extend the range of applications of poly(ADP-ribose) polymerase inhibitors to the treatment of neurodegenerative diseases related to RNA-binding proteins in the cell, e.g., amyotrophic lateral sclerosis and frontotemporal lobar degeneration.
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Affiliation(s)
- Maria V. Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (A.S.S.); (O.I.L.)
| | - Anastasia S. Singatulina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (A.S.S.); (O.I.L.)
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U1204, Université Paris-Saclay, 91025 Evry, France;
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (A.S.S.); (O.I.L.)
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39
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Dash BP, Naumann M, Sterneckert J, Hermann A. Genome Wide Analysis Points towards Subtype-Specific Diseases in Different Genetic Forms of Amyotrophic Lateral Sclerosis. Int J Mol Sci 2020; 21:E6938. [PMID: 32967368 PMCID: PMC7555318 DOI: 10.3390/ijms21186938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
Amyotropic lateral sclerosis (ALS) is a lethally progressive and irreversible neurodegenerative disease marked by apparent death of motor neurons present in the spinal cord, brain stem and motor cortex. While more and more gene mutants being established for genetic ALS, the vast majority suffer from sporadic ALS (>90%). It has been challenging, thus, to model sporadic ALS which is one reason why the underlying pathophysiology remains elusive and has stalled the development of therapeutic strategies of this progressive motor neuron disease. To further unravel these pathological signaling pathways, human induced pluripotent stem cell (hiPSCs)-derived motor neurons (MNs) from FUS- and SOD1 ALS patients and healthy controls were systematically compared to independent published datasets. Here through this study we created a gene profile of ALS by analyzing the DEGs, the Kyoto encyclopedia of Genes and Genomes (KEGG) pathways, the interactome and the transcription factor profiles (TF) that would identify altered molecular/functional signatures and their interactions at both transcriptional (mRNAs) and translational levels (hub proteins and TFs). Our findings suggest that FUS and SOD1 may develop from dysregulation in several unique pathways and herpes simplex virus (HSV) infection was among the topmost predominant cellular pathways connected to FUS and not to SOD1. In contrast, SOD1 is mainly characterized by alterations in the metabolic pathways and alterations in the neuroactive-ligand-receptor interactions. This suggests that different genetic ALS forms are singular diseases rather than part of a common spectrum. This is important for patient stratification clearly pointing towards the need for individualized medicine approaches in ALS.
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Affiliation(s)
- Banaja P. Dash
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (B.P.D.); (M.N.)
| | - Marcel Naumann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (B.P.D.); (M.N.)
| | - Jared Sterneckert
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01069 Dresden, Germany;
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (B.P.D.); (M.N.)
- German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
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40
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Neumann M, Mackenzie IRA. Review: Neuropathology of non-tau frontotemporal lobar degeneration. Neuropathol Appl Neurobiol 2020; 45:19-40. [PMID: 30357887 DOI: 10.1111/nan.12526] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/29/2018] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia (FTD) is a heterogeneous clinical syndrome associated with frontotemporal lobar degeneration (FTLD) as a relatively consistent neuropathological hallmark feature. However, the discoveries in the past decade of many of the relevant pathological proteins aggregating in human FTD brains in addition to several new FTD causing gene mutations underlined that FTD is a diverse condition on the neuropathological and genetic basis. This resulted in a novel molecular classification of these conditions based on the predominant protein abnormality and allows most cases of FTD to be placed now into one of three broad molecular subgroups; FTLD with tau, TAR DNA-binding protein 43 or FET protein accumulation (FTLD-tau, FTLD-TDP and FTLD-FET respectively). This review will provide an overview of the molecular neuropathology of non-tau FTLD, insights into disease mechanisms gained from the study of human post mortem tissue as well as discussion of current controversies in the field.
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Affiliation(s)
- M Neumann
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, Germany.,Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - I R A Mackenzie
- Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, BC, Canada
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41
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Phenotypic Suppression of ALS/FTD-Associated Neurodegeneration Highlights Mechanisms of Dysfunction. J Neurosci 2020; 39:8217-8224. [PMID: 31619490 DOI: 10.1523/jneurosci.1159-19.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
A fundamental question regarding the etiology of amyotrophic lateral sclerosis (ALS) is whether the various gene mutations associated with the disease converge on a single molecular pathway or act through multiple pathways to trigger neurodegeneration. Notably, several of the genes and cellular processes implicated in ALS have also been linked to frontotemporal dementia (FTD), suggesting these two diseases share common origins with varied clinical presentations. Scientists are rapidly identifying ALS/FTD suppressors that act on conserved pathways from invertebrates to vertebrates to alleviate degeneration. The elucidation of such genetic modifiers provides insight into the molecular pathways underlying this rapidly progressing neurodegenerative disease, while also revealing new targets for therapeutic development.
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42
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Taiana E, Ronchetti D, Todoerti K, Nobili L, Tassone P, Amodio N, Neri A. LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems? Noncoding RNA 2020; 6:ncrna6030026. [PMID: 32630183 PMCID: PMC7549348 DOI: 10.3390/ncrna6030026] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 12/13/2022] Open
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
| | - Domenica Ronchetti
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Katia Todoerti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
| | - Lucia Nobili
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (P.T.); (N.A.)
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (D.R.); (L.N.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy;
- Correspondence: (E.T.); (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.)
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43
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Kodavati M, Wang H, Hegde ML. Altered Mitochondrial Dynamics in Motor Neuron Disease: An Emerging Perspective. Cells 2020; 9:cells9041065. [PMID: 32344665 PMCID: PMC7226538 DOI: 10.3390/cells9041065] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria plays privotal role in diverse pathways that regulate cellular function and survival, and have emerged as a prime focus in aging and age-associated motor neuron diseases (MNDs), such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Accumulating evidence suggests that many amyloidogenic proteins, including MND-associated RNA/DNA-binding proteins fused in sarcoma (FUS) and TAR DNA binding protein (TDP)-43, are strongly linked to mitochondrial dysfunction. Animal model and patient studies have highlighted changes in mitochondrial structure, plasticity, replication/copy number, mitochondrial DNA instability, and altered membrane potential in several subsets of MNDs, and these observations are consistent with the evidence of increased excitotoxicity, induction of reactive oxygen species, and activation of intrinsic apoptotic pathways. Studies in MND rodent models also indicate that mitochondrial abnormalities begin prior to the clinical and pathological onset of the disease, suggesting a causal role of mitochondrial dysfunction. Our recent studies, which demonstrated the involvement of specific defects in DNA break-ligation mediated by DNA ligase 3 (LIG3) in FUS-associated ALS, raised a key question of its potential implication in mitochondrial DNA transactions because LIG3 is essential for both mitochondrial DNA replication and repair. This question, as well as how wild-type and mutant MND-associated factors affect mitochondria, remain to be elucidated. These new investigation avenues into the mechanistic role of mitochondrial dysfunction in MNDs are critical to identify therapeutic targets to alleviate mitochondrial toxicity and its consequences. In this article, we critically review recent advances in our understanding of mitochondrial dysfunction in diverse subgroups of MNDs and discuss challenges and future directions.
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Affiliation(s)
- Manohar Kodavati
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
| | - Haibo Wang
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
| | - Muralidhar L. Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (M.K.); (H.W.)
- Department of Neurosurgery, Weill Medical College, New York, NY 10065, USA
- Correspondence:
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44
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Baron DM, Matheny T, Lin YC, Leszyk JD, Kenna K, Gall KV, Santos DP, Tischbein M, Funes S, Hayward LJ, Kiskinis E, Landers JE, Parker R, Shaffer SA, Bosco DA. Quantitative proteomics identifies proteins that resist translational repression and become dysregulated in ALS-FUS. Hum Mol Genet 2020; 28:2143-2160. [PMID: 30806671 DOI: 10.1093/hmg/ddz048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 12/13/2022] Open
Abstract
Aberrant translational repression is a feature of multiple neurodegenerative diseases. The association between disease-linked proteins and stress granules further implicates impaired stress responses in neurodegeneration. However, our knowledge of the proteins that evade translational repression is incomplete. It is also unclear whether disease-linked proteins influence the proteome under conditions of translational repression. To address these questions, a quantitative proteomics approach was used to identify proteins that evade stress-induced translational repression in arsenite-treated cells expressing either wild-type or amyotrophic lateral sclerosis (ALS)-linked mutant FUS. This study revealed hundreds of proteins that are actively synthesized during stress-induced translational repression, irrespective of FUS genotype. In addition to proteins involved in RNA- and protein-processing, proteins associated with neurodegenerative diseases such as ALS were also actively synthesized during stress. Protein synthesis under stress was largely unperturbed by mutant FUS, although several proteins were found to be differentially expressed between mutant and control cells. One protein in particular, COPBI, was downregulated in mutant FUS-expressing cells under stress. COPBI is the beta subunit of the coat protein I (COPI), which is involved in Golgi to endoplasmic reticulum (ER) retrograde transport. Further investigation revealed reduced levels of other COPI subunit proteins and defects in COPBI-relatedprocesses in cells expressing mutant FUS. Even in the absence of stress, COPBI localization was altered in primary and human stem cell-derived neurons expressing ALS-linked FUS variants. Our results suggest that Golgi to ER retrograde transport may be important under conditions of stress and is perturbed upon the expression of disease-linked proteins such as FUS.
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Affiliation(s)
- Desiree M Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tyler Matheny
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Yen-Chen Lin
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John D Leszyk
- Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Kevin Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Katherine V Gall
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - David P Santos
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Maeve Tischbein
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Salome Funes
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Hayward
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Pharmacology, Worcester, MA, USA
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45
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Wong CO, Venkatachalam K. Motor neurons from ALS patients with mutations in C9ORF72 and SOD1 exhibit distinct transcriptional landscapes. Hum Mol Genet 2020; 28:2799-2810. [PMID: 31107959 DOI: 10.1093/hmg/ddz104] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that culminates in paralysis and death. Here, we present our analyses of publicly available multiOMIC data sets generated using motor neurons from ALS patients and control cohorts. Functional annotation of differentially expressed genes in induced pluripotent stem cell (iPSC)-derived motor neurons generated from patients with mutations in C9ORF72 (C9-ALS) suggests elevated expression of genes that pertain to extracellular matrix (ECM) and cell adhesion, inflammation and TGFβ targets. On the other end of the continuum, we detected diminished expression of genes repressed by quiescence-promoting E2F4/DREAM complex. Proteins whose abundance was significantly altered in C9-ALS neurons faithfully recapitulated the transcriptional aberrations. Importantly, patterns of gene expression in spinal motor neurons dissected from C9-ALS or sporadic ALS patients were highly concordant with each other and with the C9-ALS iPSC neurons. In contrast, motor neurons from patients with mutations in SOD1 exhibited dramatically different signatures. Elevated expression of gene sets such as ECM and cell adhesion genes occurs in C9 and sporadic ALS but not SOD1-ALS. These analyses indicate that despite the similarities in outward manifestations, transcriptional and proteomic signatures in ALS motor neurons can vary significantly depending on the identity of the causal mutations.
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Affiliation(s)
- Ching-On Wong
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX 77030, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX 77030, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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46
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Kawaguchi T, Rollins MG, Moinpour M, Morera AA, Ebmeier CC, Old WM, Schwartz JC. Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage. J Proteome Res 2020; 19:360-370. [PMID: 31693373 PMCID: PMC6947635 DOI: 10.1021/acs.jproteome.9b00575] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Indexed: 12/13/2022]
Abstract
The RNA-binding proteins TDP-43 and FUS are tied as the third leading known genetic cause for amyotrophic lateral sclerosis (ALS), and TDP-43 proteopathies are found in nearly all ALS patients. Both the natural function and contribution to pathology for TDP-43 remain unclear. The intersection of functions between TDP-43 and FUS can focus attention for those natural functions mostly likely to be relevant to disease. Here, we compare the role played by TDP-43 and FUS, maintaining chromatin stability for dividing HEK293T cells. We also determine and compare the interactomes of TDP-43 and FUS, quantitating changes in those before and after DNA damage. Finally, selected interactions with known importance to DNA damage repair were validated by co-immunoprecipitation assays. This study uncovered TDP-43 and FUS binding to several factors important to DNA repair mechanisms that can be replication-dependent, -independent, or both. These results provide further evidence that TDP-43 has an important role in DNA stability and provide new ways that TDP-43 can bind to the machinery that guards DNA integrity in cells.
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Affiliation(s)
- Tetsuya Kawaguchi
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Matthew G. Rollins
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Mahta Moinpour
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Andres A. Morera
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher C. Ebmeier
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - William M. Old
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - Jacob C. Schwartz
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
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47
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Wang H, Rangaswamy S, Kodavati M, Mitra J, Guo W, Guerrero EN, Van Den Bosch L, Hegde ML. RT 2 PCR array screening reveals distinct perturbations in DNA damage response signaling in FUS-associated motor neuron disease. Mol Brain 2019; 12:103. [PMID: 31801573 PMCID: PMC6894127 DOI: 10.1186/s13041-019-0526-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/26/2019] [Indexed: 02/23/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a degenerative motor neuron disease that has been linked to defective DNA repair. Many familial ALS patients harbor autosomal dominant mutations in the gene encoding the RNA/DNA binding protein 'fused in sarcoma' (FUS) commonly inducing its cytoplasmic mislocalization. Recent reports from our group and others demonstrate a role of FUS in maintaining genome integrity and the DNA damage response (DDR). FUS interacts with many DDR proteins and may regulate their recruitment at damage sites. Given the role of FUS in RNA transactions, here we explore whether FUS also regulates the expression of DDR factors. We performed RT2 PCR arrays for DNA repair and DDR signaling pathways in CRISPR/Cas9 FUS knockout (KO) and shRNA mediated FUS knockdown (KD) cells, which revealed significant (> 2-fold) downregulation of BRCA1, DNA ligase 4, MSH complex and RAD23B. Importantly, similar perturbations in these factors were also consistent in motor neurons differentiated from an ALS patient-derived induced pluripotent stem cell (iPSC) line with a FUS-P525L mutation, as well as in postmortem spinal cord tissue of sporadic ALS patients with FUS pathology. BRCA1 depletion has been linked to neuronal DNA double-strand breaks (DSBs) accumulation and cognitive defects. The ubiquitin receptor RAD23 functions both in nucleotide excision repair and proteasomal protein clearance pathway and is thus linked to neurodegeneration. Together, our study suggests that the FUS pathology perturbs DDR signaling via both its direct role and the effect on the expression of DDR genes. This underscors an intricate connections between FUS, genome instability, and neurodegeneration.
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Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA.,Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Suganya Rangaswamy
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Manohar Kodavati
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA.,Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA.,Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Wenting Guo
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), 3000, Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Erika N Guerrero
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Ludo Van Den Bosch
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), 3000, Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA. .,Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Neurological Institute, Houston Methodist Hospital, Houston, TX, 77030, USA. .,Weill Medical College, New York, NY, 10065, USA.
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48
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Ding X, Sun F, Chen J, Chen L, Tobin-Miyaji Y, Xue S, Qiang W, Luo SZ. Amyloid-Forming Segment Induces Aggregation of FUS-LC Domain from Phase Separation Modulated by Site-Specific Phosphorylation. J Mol Biol 2019; 432:467-483. [PMID: 31805282 DOI: 10.1016/j.jmb.2019.11.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/28/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) forms physiological granules and pathological fibrils, which facilitate RNA functions and cause neurodegenerative diseases, respectively. Phosphorylation at Ser/Thr residues may regulate the functional assembly of FUS and prevent pathological aggregation in cells. However, the low-complexity nature of the FUS sequence makes it challenging to characterize how phosphorylation of specific sites within the core amyloid-forming segment affects aggregation. Taking advantage of the recently solved molecular structures of the fibrillar core of the FUS low-complexity (FUS-LC) domain, we systematically investigated the aggregation of repeated segments within the core. We identified a segment with a strong amyloid-forming tendency that induced the aggregation of FUS-LC domain in phase-separated liquid droplets and further seeded the aggregation of full-length FUS. The aggregation propensity and seeding ability of this amyloid-forming segment were modulated by site-specific phosphorylation. Solid-state nuclear magnetic resonance (NMR) spectroscopy and computational modeling implied that site-specific phosphorylation at Ser61 plays key roles in FUS assembly by disrupting both intra- and intermolecular interactions that maintain the amyloid core structure.
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Affiliation(s)
- Xiufang Ding
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuto Tobin-Miyaji
- Department of Chemistry, Binghamton University, State University of New York, Vestal, NY 13902, USA
| | - Song Xue
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Vestal, NY 13902, USA.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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Cobos SN, Bennett SA, Torrente MP. The impact of histone post-translational modifications in neurodegenerative diseases. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1982-1991. [PMID: 30352259 PMCID: PMC6475498 DOI: 10.1016/j.bbadis.2018.10.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/05/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023]
Abstract
Every year, neurodegenerative disorders take more than 5000 lives in the US alone. Cures have not yet been found for many of the multitude of neuropathies. The majority of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD) cases have no known genetic basis. Thus, it is evident that contemporary genetic approaches have failed to explain the etiology or etiologies of ALS/FTD and PD. Recent investigations have explored the potential role of epigenetic mechanisms in disease development. Epigenetics comprises heritable changes in gene utilization that are not derived from changes in the genome. A main epigenetic mechanism involves the post-translational modification of histones. Increased knowledge of the epigenomic landscape of neurodegenerative diseases would not only further our understanding of the disease pathologies, but also lead to the development of treatments able to halt their progress. Here, we review recent advances on the association of histone post-translational modifications with ALS, FTD, PD and several ataxias.
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Affiliation(s)
- Samantha N Cobos
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Seth A Bennett
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Mariana P Torrente
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York 10016, United States.
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50
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Wang H, Hegde ML. New Mechanisms of DNA Repair Defects in Fused in Sarcoma-Associated Neurodegeneration: Stage Set for DNA Repair-Based Therapeutics? J Exp Neurosci 2019; 13:1179069519856358. [PMID: 31217692 PMCID: PMC6558540 DOI: 10.1177/1179069519856358] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/21/2019] [Indexed: 11/25/2022] Open
Abstract
Genome damage and defective DNA repair are etiologically linked to several
neurodegenerative disorders, including fused in sarcoma (FUS)–associated
amyotrophic lateral sclerosis (ALS). However, the underlying mechanisms remain
enigmatic, which is a roadblock for exploiting genome repair-targeted therapies.
Our recent studies identified defects in DNA nick ligation and oxidative damage
repair caused by mutations in the RNA/DNA-binding protein FUS in familial ALS
patients. In healthy neurons, FUS protects the genome by facilitating
PARP1-dependent recruitment of XRCC1/DNA Ligase IIIα (LigIII) to oxidized genome
sites and activating LigIII via direct interaction. This is a critical step in
the repair of oxidative genome damage, a foremost challenge for postmitotic
neurons due to their high oxygen consumption. We discovered that mutant FUS
significantly inhibited the recruitment of XRCC1/LigIII to DNA strand breaks,
causing defects in DNA ligation during the repair of oxidative DNA damage, which
contributed to neurodegeneration. While the FUS loss of function was responsible
for the repair defects, increased oxidative genome damage due to mutant FUS
aggregation could exacerbate the phenomenon. We highlight how these new
molecular insights into previously undescribed DNA repair defect linked to
FUS-associated neurodegeneration could provide an important opportunity for
exploring DNA repair-based therapeutic avenues.
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Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Neurological Institute, Institute of Academic Medicine, Houston Methodist, Houston, TX, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Neurological Institute, Institute of Academic Medicine, Houston Methodist, Houston, TX, USA.,Weill Cornell Medicine, New York, NY, USA
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