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Necarsulmer JC, Simon JM, Evangelista BA, Chen Y, Tian X, Nafees S, Marquez AB, Jiang H, Wang P, Ajit D, Nikolova VD, Harper KM, Ezzell JA, Lin FC, Beltran AS, Moy SS, Cohen TJ. RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy. eLife 2023; 12:RP85921. [PMID: 37819053 PMCID: PMC10567115 DOI: 10.7554/elife.85921] [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] [Indexed: 10/13/2023] Open
Abstract
TDP-43 proteinopathies including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by aggregation and mislocalization of the nucleic acid-binding protein TDP-43 and subsequent neuronal dysfunction. Here, we developed endogenous models of sporadic TDP-43 proteinopathy based on the principle that disease-associated TDP-43 acetylation at lysine 145 (K145) alters TDP-43 conformation, impairs RNA-binding capacity, and induces downstream mis-regulation of target genes. Expression of acetylation-mimic TDP-43K145Q resulted in stress-induced nuclear TDP-43 foci and loss of TDP-43 function in primary mouse and human-induced pluripotent stem cell (hiPSC)-derived cortical neurons. Mice harboring the TDP-43K145Q mutation recapitulated key hallmarks of FTLD, including progressive TDP-43 phosphorylation and insolubility, TDP-43 mis-localization, transcriptomic and splicing alterations, and cognitive dysfunction. Our study supports a model in which TDP-43 acetylation drives neuronal dysfunction and cognitive decline through aberrant splicing and transcription of critical genes that regulate synaptic plasticity and stress response signaling. The neurodegenerative cascade initiated by TDP-43 acetylation recapitulates many aspects of human FTLD and provides a new paradigm to further interrogate TDP-43 proteinopathies.
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Affiliation(s)
- Julie C Necarsulmer
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Baggio A Evangelista
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Youjun Chen
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Xu Tian
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Sara Nafees
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Ariana B Marquez
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
| | - Huijun Jiang
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Ping Wang
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Deepa Ajit
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Viktoriya D Nikolova
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Kathryn M Harper
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - J Ashley Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, University of North CarolinaChapel HillUnited States
| | - Feng-Chang Lin
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Adriana S Beltran
- Department of Genetics, University of North CarolinaChapel HillUnited States
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
- Department of Pharmacology, University of North CarolinaChapel HillUnited States
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Todd J Cohen
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Department of Biochemistry and Biophysics, University of North CarolinaChapel HillUnited States
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2
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Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. Int J Mol Sci 2023; 24:13807. [PMID: 37762112 PMCID: PMC10530927 DOI: 10.3390/ijms241813807] [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: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
Since its initial involvement in numerous neurodegenerative pathologies in 2006, either as a principal actor or as a cofactor, new pathologies implicating transactive response (TAR) DNA-binding protein 43 (TDP-43) are regularly emerging also beyond the neuronal system. This reflects the fact that TDP-43 functions are particularly complex and broad in a great variety of human cells. In neurodegenerative diseases, this protein is often pathologically delocalized to the cytoplasm, where it irreversibly aggregates and is subjected to various post-translational modifications such as phosphorylation, polyubiquitination, and cleavage. Until a few years ago, the research emphasis has been focused particularly on the impacts of this aggregation and/or on its widely described role in complex RNA splicing, whether related to loss- or gain-of-function mechanisms. Interestingly, recent studies have strengthened the knowledge of TDP-43 activity at the chromatin level and its implication in the regulation of DNA transcription and stability. These discoveries have highlighted new features regarding its own transcriptional regulation and suggested additional mechanistic and disease models for the effects of TPD-43. In this review, we aim to give a comprehensive view of the potential epigenetic (de)regulations driven by (and driving) this multitask DNA/RNA-binding protein.
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Affiliation(s)
- Juliette Gimenez
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Alida Spalloni
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Sara Cappelli
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Francesca Ciaiola
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
- Department of Systems Medicine, University of Roma Tor Vergata, 00133 Rome, Italy
| | - Valerio Orlando
- KAUST Environmental Epigenetics Program, Biological Environmental Sciences and Engineering Division BESE, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Emanuele Buratti
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Patrizia Longone
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
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3
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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McMillan M, Gomez N, Hsieh C, Bekier M, Li X, Miguez R, Tank EMH, Barmada SJ. RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia. Mol Cell 2023; 83:219-236.e7. [PMID: 36634675 PMCID: PMC9899051 DOI: 10.1016/j.molcel.2022.12.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/14/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023]
Abstract
RNA methylation at adenosine N6 (m6A) is one of the most common RNA modifications, impacting RNA stability, transport, and translation. Previous studies uncovered RNA destabilization in amyotrophic lateral sclerosis (ALS) models in association with accumulation of the RNA-binding protein TDP43. Here, we show that TDP43 recognizes m6A RNA and that RNA methylation is critical for both TDP43 binding and autoregulation. We also observed extensive RNA hypermethylation in ALS spinal cord, corresponding to methylated TDP43 substrates. Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via single-cell CRISPR-Cas9 in primary neurons. The most promising modifier-the canonical m6A reader YTHDF2-accumulated within ALS spinal neurons, and its knockdown prolonged the survival of human neurons carrying ALS-associated mutations. Collectively, these data show that m6A modifications modulate RNA binding by TDP43 and that m6A is pivotal for TDP43-related neurodegeneration in ALS.
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Affiliation(s)
- Michael McMillan
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicolas Gomez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caroline Hsieh
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roberto Miguez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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5
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Paron F, Barattucci S, Cappelli S, Romano M, Berlingieri C, Stuani C, Laurents D, Mompeán M, Buratti E. Unravelling the toxic effects mediated by the neurodegenerative disease-associated S375G mutation of TDP-43 and its S375E phosphomimetic variant. J Biol Chem 2022; 298:102252. [PMID: 35835219 PMCID: PMC9364110 DOI: 10.1016/j.jbc.2022.102252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/05/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nucleic acid–binding protein found in the nucleus that accumulates in the cytoplasm under pathological conditions, leading to proteinopathies, such as frontotemporal dementia and ALS. An emerging area of TDP-43 research is represented by the study of its post-translational modifications, the way they are connected to disease-associated mutations, and what this means for pathological processes. Recently, we described a novel mutation in TDP-43 in an early onset ALS case that was affecting a potential phosphorylation site in position 375 (S375G). A preliminary characterization showed that both the S375G mutation and its phosphomimetic variant, S375E, displayed altered nuclear–cytoplasmic distribution and cellular toxicity. To better investigate these effects, here we established cell lines expressing inducible WT, S375G, and S375E TDP-43 variants. Interestingly, we found that these mutants do not seem to affect well-studied aspects of TDP-43, such as RNA splicing or autoregulation, or protein conformation, dynamics, or aggregation, although they do display dysmorphic nuclear shape and cell cycle alterations. In addition, RNA-Seq analysis of these cell lines showed that although the disease-associated S375G mutation and its phosphomimetic S375E variant regulate distinct sets of genes, they have a common target in mitochondrial apoptotic genes. Taken together, our data strongly support the growing evidence that alterations in TDP-43 post-translational modifications can play a potentially important role in disease pathogenesis and provide a further link between TDP-43 pathology and mitochondrial health.
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Affiliation(s)
- Francesca Paron
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Simone Barattucci
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Sara Cappelli
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Berlingieri
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Cristiana Stuani
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Douglas Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy.
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6
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Šušnjar U, Škrabar N, Brown AL, Abbassi Y, Phatnani H, Cortese A, Cereda C, Bugiardini E, Cardani R, Meola G, Ripolone M, Moggio M, Romano M, Secrier M, Fratta P, Buratti E. Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. Commun Biol 2022; 5:314. [PMID: 35383280 PMCID: PMC8983780 DOI: 10.1038/s42003-022-03253-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
TDP-43 (TAR DNA-binding protein 43) aggregation and redistribution are recognised as a hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. As TDP-43 inclusions have recently been described in the muscle of inclusion body myositis patients, this highlights the need to understand the role of TDP-43 beyond the central nervous system. Using RNA-seq, we directly compare TDP-43-mediated RNA processing in muscle (C2C12) and neuronal (NSC34) mouse cells. TDP-43 displays a cell-type-characteristic behaviour targeting unique transcripts in each cell-type, which is due to characteristic expression of RNA-binding proteins, that influence TDP-43's performance and define cell-type specific splicing. Among splicing events commonly dysregulated in both cell lines, we identify some that are TDP-43-dependent also in human cells. Inclusion levels of these alternative exons are altered in tissues of patients suffering from FTLD and IBM. We therefore propose that TDP-43 dysfunction contributes to disease development either in a common or a tissue-specific manner.
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Affiliation(s)
- Urša Šušnjar
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Neva Škrabar
- Tumour Virology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Generatio GmbH, Center for Animal, Genetics, Tübingen, Germany
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Yasmine Abbassi
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, USA
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- Department of Brain and Behaviour Sciences, University of Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Rosanna Cardani
- BioCor Biobank, UOC SMEL-1 of Clinical Pathology, IRCCS-Policlinico San Donato, San Donato Milanese, Italy
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- Department of Neurorehabilitation Sciences, Casa di Cura del Policlinico, Milan, Italy
| | - Michela Ripolone
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Moggio
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Emanuele Buratti
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
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Yang C, Qiao T, Yu J, Wang H, Guo Y, Salameh J, Metterville J, Parsi S, Yusuf I, Brown RH, Cai H, Xu Z. Low-level overexpression of wild type TDP-43 causes late-onset, progressive neurodegeneration and paralysis in mice. PLoS One 2022; 17:e0255710. [PMID: 35113871 PMCID: PMC8812852 DOI: 10.1371/journal.pone.0255710] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Modestly increased expression of transactive response DNA binding protein (TDP-43) gene have been reported in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neuromuscular diseases. However, whether this modest elevation triggers neurodegeneration is not known. Although high levels of TDP-43 overexpression have been modeled in mice and shown to cause early death, models with low-level overexpression that mimic the human condition have not been established. In this study, transgenic mice overexpressing wild type TDP-43 at less than 60% above the endogenous CNS levels were constructed, and their phenotypes analyzed by a variety of techniques, including biochemical, molecular, histological, behavioral techniques and electromyography. The TDP-43 transgene was expressed in neurons, astrocytes, and oligodendrocytes in the cortex and predominantly in astrocytes and oligodendrocytes in the spinal cord. The mice developed a reproducible progressive weakness ending in paralysis in mid-life. Detailed analysis showed ~30% loss of large pyramidal neurons in the layer V motor cortex; in the spinal cord, severe demyelination was accompanied by oligodendrocyte injury, protein aggregation, astrogliosis and microgliosis, and elevation of neuroinflammation. Surprisingly, there was no loss of lower motor neurons in the lumbar spinal cord despite the complete paralysis of the hindlimbs. However, denervation was detected at the neuromuscular junction. These results demonstrate that low-level TDP-43 overexpression can cause diverse aspects of ALS, including late-onset and progressive motor dysfunction, neuroinflammation, and neurodegeneration. Our findings suggest that persistent modest elevations in TDP-43 expression can lead to ALS and other neurological disorders involving TDP-43 proteinopathy. Because of the predictable and progressive clinical paralytic phenotype, this transgenic mouse model will be useful in preclinical trial of therapeutics targeting neurological disorders associated with elevated levels of TDP-43.
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Affiliation(s)
- Chunxing Yang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Tao Qiao
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jia Yu
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Hongyan Wang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Yansu Guo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Johnny Salameh
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jake Metterville
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sepideh Parsi
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Issa Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- RNA Therapeutic Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Neuroscience Program, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Huaibin Cai
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- RNA Therapeutic Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Neuroscience Program, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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8
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Amyotrophic lateral sclerosis: Correlations between fluid biomarkers of NfL, TDP-43, and tau, and clinical characteristics. PLoS One 2021; 16:e0260323. [PMID: 34843548 PMCID: PMC8629269 DOI: 10.1371/journal.pone.0260323] [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: 07/09/2021] [Accepted: 11/07/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES We previously reported the diagnostic and prognostic performance of neurofilament light chain (NfL), TAR DNA-binding protein 43 (TDP-43), and total tau (t-tau) in cerebrospinal fluid (CSF) and plasma as amyotrophic lateral sclerosis (ALS) biomarkers. The present study aimed to elucidate associations between clinical characteristics and the markers as well as mutual associations of the markers in ALS patients using the same dataset. METHODS NfL, TDP-43, and t-tau levels in CSF and plasma in 75 ALS patients were analyzed. The associations between those markers and clinical details were investigated by uni- and multivariate analyses. Correlations between the markers were analyzed univariately. RESULTS In multivariate analysis of CSF proteins, the disease progression rate (DPR) was positively correlated with NfL (β: 0.51, p = 0.007) and t-tau (β: 0.37, p = 0.03). Plasma NfL was correlated with age (β: 0.53, p = 0.005) and diagnostic grade (β: -0.42, p = 0.02) in multivariate analysis. Plasma TDP-43 was correlated negatively with split hand index (β: -0.48, p = 0.04) and positively with % vital capacity (β: 0.64, p = 0.03) in multivariate analysis. Regarding mutual biomarker analysis, a negative correlation between CSF-NfL and TDP-43 was identified (r: -0.36, p = 0.002). CONCLUSIONS Elevated NfL and t-tau levels in CSF may be biomarkers to predict rapid DPR from onset to sample collection. The negative relationship between CSF NfL and TDP-43 suggests that elevation of CSF TDP-43 in ALS is not a simple consequence of its release into CSF during neurodegeneration. The negative correlation between plasma TDP-43 and split hand index may support the pathophysiological association between plasma TDP-43 and ALS.
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9
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Sun H, Chen W, Chen L, Zheng W. Exploring the molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43 using molecular dynamics simulation and free energy calculation. J Comput Chem 2021; 42:1670-1680. [PMID: 34109652 DOI: 10.1002/jcc.26704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/15/2021] [Accepted: 05/23/2021] [Indexed: 11/12/2022]
Abstract
Transactivation response element RNA/DNA-binding protein 43 (TDP-43) is involved in the regulation of alternative splicing of human neurodegenerative disease-related genes through binding to long UG-rich RNA sequences. Mutations in TDP-43, most in the homeodomain, cause neurological disorders such as amyotrophic lateral sclerosis and fronto temporal lobar degeneration. Several mutants destabilize the structure and disrupt RNA-binding activity. The biological functions of these mutants have been characterized, but the structural basis behind the loss of RNA-binding activity is unclear. Focused on the specific TDP-43-ssRNA complex (PDB code 4BS2), we applied molecular dynamics simulations and the molecular mechanics Poisson-Boltzmann surface area free energy calculation to characterize and explore the structural and dynamic effects between ssRNA and TDP-43. The energetic analysis indicated that the intermolecular van der Waals interaction and nonpolar solvation energy play an important role in the binding process of TDP-43 and ssRNA. Compared with the wild-type TDP-43, the reduction of the polar or non-polar interaction between all the mutants F149A, D105A/S254A, R171A/D174A, F147L/F149L/F229L/F231L and ssRNA is the main reason for the reduction of its binding free energy. Decomposing energies suggested that the extensive interactions between TDP-43 and the nitrogenous bases of ssRNA are responsible for the specific ssRNA recognition by TDP-43. These results elucidated the TDP-43-ssRNA interaction comprehensively and further extended our understanding of the previous experimental data. The uncovering of TDP-43-ssRNA recognition mechanism will provide us useful insights and new chances for the development of anti-neurodegenerative drugs.
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Affiliation(s)
- Han Sun
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Wei Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
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10
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Chhangani D, Martín-Peña A, Rincon-Limas DE. Molecular, functional, and pathological aspects of TDP-43 fragmentation. iScience 2021; 24:102459. [PMID: 34013172 PMCID: PMC8113996 DOI: 10.1016/j.isci.2021.102459] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transactive response DNA binding protein 43 (TDP-43) is a DNA/RNA binding protein involved in transcriptional regulation and RNA processing. It is linked to sporadic and familial amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 is predominantly nuclear, but it translocates to the cytoplasm under pathological conditions. Cytoplasmic accumulation, phosphorylation, ubiquitination and truncation of TDP-43 are the main hallmarks of TDP-43 proteinopathies. Among these processes, the pathways leading to TDP-43 fragmentation remain poorly understood. We review here the molecular and biochemical properties of several TDP-43 fragments, the mechanisms and factors mediating their production, and their potential role in disease progression. We also address the presence of TDP-43 C-terminal fragments in several neurological disorders, including Alzheimer's disease, and highlight their respective implications. Finally, we discuss features of animal models expressing TDP-43 fragments as well as recent therapeutic strategies to approach TDP-43 truncation.
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Affiliation(s)
- Deepak Chhangani
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA
| | - Alfonso Martín-Peña
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA.,Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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11
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Buratti E. Trends in Understanding the Pathological Roles of TDP-43 and FUS Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1281:243-267. [PMID: 33433879 DOI: 10.1007/978-3-030-51140-1_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Following the discovery of TDP-43 and FUS involvement in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD), the major challenge in the field has been to understand their physiological functions, both in normal and disease conditions. The hope is that this knowledge will improve our understanding of disease and lead to the development of effective therapeutic options. Initially, the focus has been directed at characterizing the role of these proteins in the control of RNA metabolism, because the main function of TDP-43 and FUS is to bind coding and noncoding RNAs to regulate their life cycle within cells. As a result, we now have an in-depth picture of the alterations that occur in RNA metabolism following their aggregation in various ALS/FTLD models and, to a somewhat lesser extent, in patients' brains. In parallel, progress has been made with regard to understanding how aggregation of these proteins occurs in neurons, how it can spread in different brain regions, and how these changes affect various metabolic cellular pathways to result in neuronal death. The aim of this chapter will be to provide a general overview of the trending topics in TDP-43 and FUS investigations and to highlight what might represent the most promising avenues of research in the years to come.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
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12
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Hicks DA. TDP-43 and amyloid precursor protein processing: implications for Alzheimer's disease. Neural Regen Res 2021; 16:1402-1403. [PMID: 33318427 PMCID: PMC8284272 DOI: 10.4103/1673-5374.300983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- David A Hicks
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester; Current address: RBMOnline, Bourn Hall, Bourn, Cambridge, UK
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13
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François-Moutal L, Perez-Miller S, Scott DD, Miranda VG, Mollasalehi N, Khanna M. Structural Insights Into TDP-43 and Effects of Post-translational Modifications. Front Mol Neurosci 2019; 12:301. [PMID: 31920533 PMCID: PMC6934062 DOI: 10.3389/fnmol.2019.00301] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Transactive response DNA binding protein (TDP-43) is a key player in neurodegenerative diseases. In this review, we have gathered and presented structural information on the different regions of TDP-43 with high resolution structures available. A thorough understanding of TDP-43 structure, effect of modifications, aggregation and sites of localization is necessary as we develop therapeutic strategies targeting TDP-43 for neurodegenerative diseases. We discuss how different domains as well as post-translational modification may influence TDP-43 overall structure, aggregation and droplet formation. The primary aim of the review is to utilize structural insights as we develop an understanding of the deleterious behavior of TDP-43 and highlight locations of established and proposed post-translation modifications. TDP-43 structure and effect on localization is paralleled by many RNA-binding proteins and this review serves as an example of how structure may be modulated by numerous compounding elements.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - David D Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Victor G Miranda
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Niloufar Mollasalehi
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
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14
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Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. Nucleic Acids Res 2019; 47:5293-5306. [PMID: 30916337 PMCID: PMC6547761 DOI: 10.1093/nar/gkz193] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic analysis integrating three data sources, eCLIP assays for a large RBP panel, shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq, to identify novel such autoregulatory feedback loops. We show that RBPs frequently bind their own pre-mRNAs, their exons respond prominently to NMD pathway disruption, and that the responding exons are enriched with nearby eCLIP peaks. We confirm previously proposed models of autoregulation in SRSF7 and U2AF1 genes and present two novel models, in which (i) SFPQ binds its mRNA and promotes switching to an alternative distal 3'-UTR that is targeted by NMD, and (ii) RPS3 binding activates a poison 5'-splice site in its pre-mRNA that leads to a frame shift and degradation by NMD. We also suggest specific splicing events that could be implicated in autoregulatory feedback loops in RBM39, HNRNPM, and U2AF2 genes. The results are available through a UCSC Genome Browser track hub.
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Affiliation(s)
- Dmitri Pervouchine
- Skolkovo Institute of Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Yaroslav Popov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Andy Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Beatrice Borsari
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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15
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Spiller KJ, Khan T, Dominique MA, Restrepo CR, Cotton-Samuel D, Levitan M, Jafar-Nejad P, Zhang B, Soriano A, Rigo F, Trojanowski JQ, Lee VMY. Reduction of matrix metalloproteinase 9 (MMP-9) protects motor neurons from TDP-43-triggered death in rNLS8 mice. Neurobiol Dis 2018; 124:133-140. [PMID: 30458231 DOI: 10.1016/j.nbd.2018.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/10/2018] [Accepted: 11/16/2018] [Indexed: 12/13/2022] Open
Abstract
Therapeutic strategies are needed for the treatment of amyotrophic lateral sclerosis (ALS). One potential target is matrix metalloproteinase-9 (MMP-9), which is expressed only by fast motor neurons (MNs) that are selectively vulnerable to various ALS-relevant triggers. Previous studies have shown that reduction of MMP-9 function delayed motor dysfunction in a mouse model of familial ALS. However, given that the majority of ALS cases are sporadic, we propose preclinical testing in a mouse model which may be more clinically translatable: rNLS8 mice. In rNLS8 mice, neurodegeneration is triggered by the major pathological hallmark of ALS, TDP-43 mislocalization and aggregation. MMP-9 was targeted in 3 different ways in rNLS8 mice: by AAV9-mediated knockdown, using antisense oligonucleotide (ASO) technology, and by genetic modification. All 3 strategies preserved the motor unit during disease, as measured by MN counts, tibialis anterior (TA) muscle innervation, and physiological recordings from muscle. However, the strategies that reduced MMP-9 beyond the motor unit lead to premature deaths in a subset of rNLS8 mice. Therefore, selective targeting of MMP-9 in MNs could be beneficial in ALS, but side effects outside of the motor circuit may limit the most commonly used clinical targeting strategies.
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Affiliation(s)
- Krista J Spiller
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Tahiyana Khan
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Myrna A Dominique
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clark R Restrepo
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dejania Cotton-Samuel
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maya Levitan
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Bin Zhang
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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16
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Sun Y, Bao Y, Han W, Song F, Shen X, Zhao J, Zuo J, Saffen D, Chen W, Wang Z, You X, Wang Y. Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay. Nucleic Acids Res 2017; 45:8524-8540. [PMID: 28586478 PMCID: PMC5737846 DOI: 10.1093/nar/gkx508] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/27/2017] [Indexed: 12/15/2022] Open
Abstract
Mutations in the spliceosomal RNA binding protein RBM10 cause TARP syndrome and are frequently observed in lung adenocarcinoma (LUAD). We have previously shown that RBM10 enhances exon skipping of its target genes, including its paralog RBM5. Here, we report that RBM10 negatively regulates its own mRNA and protein expression and that of RBM5 by promoting alternative splicing-coupled nonsense-mediated mRNA decay (AS-NMD). Through computational analysis and experimental validation, we identified RBM10-promoted skipping of exon 6 or 12 in RBM10 and exon 6 or 16 in RBM5 as the underlying AS-NMD events. Importantly, we showed that LUAD-associated mutations affecting splice sites of RBM10 exons 6 or 12 abolished exon inclusion and correlated with reduced expression of RBM10 RNA. Together, our investigations have revealed novel molecular mechanisms underlying RBM10 autoregulation and cross-regulation of RBM5, thereby providing insights concerning the functions of RBM10 under various physiological and pathological conditions. Our combined computational and experimental approach should be useful for elucidating the role of AS-NMD in auto- and cross-regulation by other splicing regulators.
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Affiliation(s)
- Yue Sun
- School of Life Sciences, Fudan University, Shanghai 200438, China.,Institutes of Brain Science, Fudan University, Shanghai 200032, China.,Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenjian Han
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Fan Song
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xianfeng Shen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jiawei Zhao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ji Zuo
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - David Saffen
- Institutes of Brain Science, Fudan University, Shanghai 200032, China.,Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai 200032, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zefeng Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Xintian You
- Zuse Institute Berlin, Takustrasse 7, Berlin 14195, Germany
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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17
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Bhandare VV, Ramaswamy A. The proteinopathy of D169G and K263E mutants at the RNA Recognition Motif (RRM) domain of tar DNA-binding protein (tdp43) causing neurological disorders: A computational study. J Biomol Struct Dyn 2017; 36:1075-1093. [DOI: 10.1080/07391102.2017.1310670] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Amutha Ramaswamy
- Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India
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18
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Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet 2017; 13:e1006635. [PMID: 28301478 PMCID: PMC5354250 DOI: 10.1371/journal.pgen.1006635] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable neurodegenerative disorders that exist on a symptomological spectrum and share both genetic underpinnings and pathophysiological hallmarks. Functional abnormality of TAR DNA-binding protein 43 (TDP-43), an aggregation-prone RNA and DNA binding protein, is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases, but the cascade of events leading to cell death are not understood. We have expressed human TDP-43 (hTDP-43) in Drosophila neurons and glia, a model that recapitulates many of the characteristics of TDP-43-linked human disease including protein aggregation pathology, locomotor impairment, and premature death. We report that such expression of hTDP-43 impairs small interfering RNA (siRNA) silencing, which is the major post-transcriptional mechanism of retrotransposable element (RTE) control in somatic tissue. This is accompanied by de-repression of a panel of both LINE and LTR families of RTEs, with somewhat different elements being active in response to hTDP-43 expression in glia versus neurons. hTDP-43 expression in glia causes an early and severe loss of control of a specific RTE, the endogenous retrovirus (ERV) gypsy. We demonstrate that gypsy causes the degenerative phenotypes in these flies because we are able to rescue the toxicity of glial hTDP-43 either by genetically blocking expression of this RTE or by pharmacologically inhibiting RTE reverse transcriptase activity. Moreover, we provide evidence that activation of DNA damage-mediated programmed cell death underlies both neuronal and glial hTDP-43 toxicity, consistent with RTE-mediated effects in both cell types. Our findings suggest a novel mechanism in which RTE activity contributes to neurodegeneration in TDP-43-mediated diseases such as ALS and FTLD.
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Affiliation(s)
- Lisa Krug
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Nabanita Chatterjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | | | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Wen-Wei Liao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Kathleen Morrill
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Lisa Prazak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Biology, Farmingdale State College, Farmingdale, NY United States of America
| | - Nikolay Rozhkov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Delphine Theodorou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Josh Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, United States of America
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19
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Abstract
TDP-43 is a dimeric nuclear protein that plays a central role in RNA metabolism. In recent years, this protein has become a focal point of research in the amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) disease spectrum, as pathognomonic inclusions within affected neurons contain post-translationally modified TDP-43. A key question in TDP-43 research involves determining the mechanisms and triggers that cause TDP-43 to form pathological aggregates. This review gives a brief overview of the physiological and pathological roles of TDP-43 and focuses on the structural features of its protein domains and how they may contribute to normal protein function and to disease. A special emphasis is placed on the C-terminal prion-like region thought to be implicated in pathology, as it is where nearly all ALS/FTD-associated mutations reside. Recent structural studies of this domain revealed its crucial role in the formation of phase-separated liquid droplets through a partially populated α-helix. This new discovery provides further support for the theory that liquid droplets such as stress granules may be precursors to pathological aggregates, linking environmental effects such as stress to the potential etiology of the disease. The transition of TDP-43 among soluble, droplet, and aggregate phases and the implications of these transitions for pathological aggregation are summarized and discussed.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada
| | - Avijit Chakrabartty
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada.,Department of Biochemistry, University of Toronto , Toronto, Ontario M5G1L7, Canada
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20
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Alfieri JA, Silva PR, Igaz LM. Early Cognitive/Social Deficits and Late Motor Phenotype in Conditional Wild-Type TDP-43 Transgenic Mice. Front Aging Neurosci 2016; 8:310. [PMID: 28066234 PMCID: PMC5167738 DOI: 10.3389/fnagi.2016.00310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal Dementia (FTD) and amyotrophic lateral sclerosis (ALS) are two neurodegenerative diseases associated to mislocalization and aggregation of TAR DNA-binding protein 43 (TDP-43). To investigate in depth the behavioral phenotype associated with this proteinopathy, we used as a model transgenic (Tg) mice conditionally overexpressing human wild-type TDP 43 protein (hTDP-43-WT) in forebrain neurons. We previously characterized these mice at the neuropathological level and found progressive neurodegeneration and other features that evoke human TDP-43 proteinopathies of the FTD/ALS spectrum. In the present study we analyzed the behavior of mice at multiple domains, including motor, social and cognitive performance. Our results indicate that young hTDP-43-WT Tg mice (1 month after post-weaning transgene induction) present a normal motor phenotype compared to control littermates, as assessed by accelerated rotarod performance, spontaneous locomotor activity in the open field test and a mild degree of spasticity shown by a clasping phenotype. Analysis of social and cognitive behavior showed a rapid installment of deficits in social interaction, working memory (Y-maze test) and recognition memory (novel object recognition test) in the absence of overt motor abnormalities. To investigate if the motor phenotype worsen with age, we analyzed the behavior of mice after long-term (up to 12 months) transgene induction. Our results reveal a decreased performance on the rotarod test and in the hanging wire test, indicating a motor phenotype that was absent in younger mice. In addition, long-term hTDP-43-WT expression led to hyperlocomotion in the open field test. In sum, these results demonstrate a time-dependent emergence of a motor phenotype in older hTDP-43-WT Tg mice, recapitulating aspects of clinical FTD presentations with motor involvement in human patients, and providing a complementary animal model for studying TDP-43 proteinopathies.
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Affiliation(s)
- Julio A Alfieri
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires - CONICET Buenos Aires, Argentina
| | - Pablo R Silva
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires - CONICET Buenos Aires, Argentina
| | - Lionel M Igaz
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires - CONICET Buenos Aires, Argentina
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21
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Boeynaems S, Bogaert E, Van Damme P, Van Den Bosch L. Inside out: the role of nucleocytoplasmic transport in ALS and FTLD. Acta Neuropathol 2016; 132:159-173. [PMID: 27271576 PMCID: PMC4947127 DOI: 10.1007/s00401-016-1586-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/27/2016] [Accepted: 05/28/2016] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases are characterized by the presence of protein inclusions with a different protein content depending on the type of disease. Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are no exceptions to this common theme. In most ALS and FTLD cases, the predominant pathological species are RNA-binding proteins. Interestingly, these proteins are both depleted from their normal nuclear localization and aggregated in the cytoplasm. This key pathological feature has suggested a potential dual mechanism with both nuclear loss of function and cytoplasmic gain of function being at play. Yet, why and how this pathological cascade is initiated in most patients, and especially sporadic cases, is currently unresolved. Recent breakthroughs in C9orf72 ALS/FTLD disease models point at a pivotal role for the nuclear transport system in toxicity. To address whether defects in nuclear transport are indeed implicated in the disease, we reviewed two decades of ALS/FTLD literature and combined this with bioinformatic analyses. We find that both RNA-binding proteins and nuclear transport factors are key players in ALS/FTLD pathology. Moreover, our analyses suggest that disturbances in nucleocytoplasmic transport play a crucial initiating role in the disease, by bridging both nuclear loss and cytoplasmic gain of functions. These findings highlight this process as a novel and promising therapeutic target for ALS and FTLD.
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Affiliation(s)
- Steven Boeynaems
- />Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, 3000 Leuven, Belgium
- />Laboratory of Neurobiology, Vesalius Research Center, VIB, Campus Gasthuisberg O&N4, PB912, Herestraat 49, 3000 Leuven, Belgium
| | - Elke Bogaert
- />Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, 3000 Leuven, Belgium
- />Laboratory of Neurobiology, Vesalius Research Center, VIB, Campus Gasthuisberg O&N4, PB912, Herestraat 49, 3000 Leuven, Belgium
| | - Philip Van Damme
- />Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, 3000 Leuven, Belgium
- />Laboratory of Neurobiology, Vesalius Research Center, VIB, Campus Gasthuisberg O&N4, PB912, Herestraat 49, 3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- />Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, 3000 Leuven, Belgium
- />Laboratory of Neurobiology, Vesalius Research Center, VIB, Campus Gasthuisberg O&N4, PB912, Herestraat 49, 3000 Leuven, Belgium
- />Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
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22
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Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares M, Burge CB, Ravits J, Rigo F, Yeo GW. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nat Commun 2016; 7:12143. [PMID: 27378374 PMCID: PMC4935974 DOI: 10.1038/ncomms12143] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 06/03/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3' untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism.
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Affiliation(s)
- Katannya Kapeli
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Anthony Q Vu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Kasey R Hutt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Fernando J Martinez
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Ranjan Batra
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Neurosciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Peter Freese
- Department of Biology, MIT, Cambridge, Massachusetts 02142, USA
| | | | - Stephanie C Huelga
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Seung J Chun
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Tiffany Y Liang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Jeremy Chang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - John P Donohue
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | - Lily Shiue
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | - Jiayu Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Franca Cambi
- Department of Neurology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Edward Kasarskis
- Department of Neurology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Shawn Hoon
- Molecular Engineering Laboratory, A*STAR, Singapore 138673, Singapore
| | - Manuel Ares
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
| | | | - John Ravits
- Department of Neurosciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California 92010, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore.,Department of Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093, USA.,Molecular Engineering Laboratory, A*STAR, Singapore 138673, Singapore
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23
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Koyama A, Sugai A, Kato T, Ishihara T, Shiga A, Toyoshima Y, Koyama M, Konno T, Hirokawa S, Yokoseki A, Nishizawa M, Kakita A, Takahashi H, Onodera O. Increased cytoplasmic TARDBP mRNA in affected spinal motor neurons in ALS caused by abnormal autoregulation of TDP-43. Nucleic Acids Res 2016; 44:5820-36. [PMID: 27257061 PMCID: PMC4937342 DOI: 10.1093/nar/gkw499] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disorder. In motor neurons of ALS, TAR DNA binding protein-43 (TDP-43), a nuclear protein encoded by TARDBP, is absent from the nucleus and forms cytoplasmic inclusions. TDP-43 auto-regulates the amount by regulating the TARDBP mRNA, which has three polyadenylation signals (PASs) and three additional alternative introns within the last exon. However, it is still unclear how the autoregulatory mechanism works and how the status of autoregulation in ALS motor neurons without nuclear TDP-43 is. Here we show that TDP-43 inhibits the selection of the most proximal PAS and induces splicing of multiple alternative introns in TARDBP mRNA to decrease the amount of cytoplasmic TARDBP mRNA by nonsense-mediated mRNA decay. When TDP-43 is depleted, the TARDBP mRNA uses the most proximal PAS and is increased in the cytoplasm. Finally, we have demonstrated that in ALS motor neurons—especially neurons with mislocalized TDP-43—the amount of TARDBP mRNA is increased in the cytoplasm. Our observations indicate that nuclear TDP-43 contributes to the autoregulation and suggests that the absence of nuclear TDP-43 induces an abnormal autoregulation and increases the amount of TARDBP mRNA. The vicious cycle might accelerate the disease progression of ALS.
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Affiliation(s)
- Akihide Koyama
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan Center for Transdisciplinary Research, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Akihiro Sugai
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Taisuke Kato
- Department of Molecular Neuroscience, Resource Branch for Brain Disease Research, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Tomohiko Ishihara
- Department of Molecular Neuroscience, Resource Branch for Brain Disease Research, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Atsushi Shiga
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan Center for Transdisciplinary Research, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Yasuko Toyoshima
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Misaki Koyama
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Takuya Konno
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Sachiko Hirokawa
- Department of Molecular Neuroscience, Resource Branch for Brain Disease Research, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Akio Yokoseki
- Department of Molecular Neuroscience, Resource Branch for Brain Disease Research, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Masatoyo Nishizawa
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Center for Bioresource-based Research, Brain Research Institute, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Hitoshi Takahashi
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, 1-757 Asahimachi-dori, Chuo-ku, Niigata-City, Niigata 951-8585, Japan
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24
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Monahan Z, Shewmaker F, Pandey UB. Stress granules at the intersection of autophagy and ALS. Brain Res 2016; 1649:189-200. [PMID: 27181519 DOI: 10.1016/j.brainres.2016.05.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/06/2016] [Accepted: 05/12/2016] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, fatal disease caused by loss of upper and lower motor neurons. The majority of ALS cases are classified as sporadic (80-90%), with the remaining considered familial based on patient history. The last decade has seen a surge in the identification of ALS-causing genes - including TARDBP (TDP-43), FUS, MATR3 (Matrin-3), C9ORF72 and several others - providing important insights into the molecular pathways involved in pathogenesis. Most of the protein products of ALS-linked genes fall into two functional categories: RNA-binding/homeostasis and protein-quality control (i.e. autophagy and proteasome). The RNA-binding proteins tend to be aggregation-prone with low-complexity domains similar to the prion-forming domains of yeast. Many also incorporate into stress granules (SGs), which are cytoplasmic ribonucleoprotein complexes that form in response to cellular stress. Mutant forms of TDP-43 and FUS perturb SG dynamics, lengthening their cytoplasmic persistence. Recent evidence suggests that SGs are regulated by the autophagy pathway, suggesting a unifying connection between many of the ALS-linked genes. Persistent SGs may give rise to intractable aggregates that disrupt neuronal homeostasis, thus failure to clear SGs by autophagic processes may promote ALS pathogenesis. This article is part of a Special Issue entitled SI:Autophagy.
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Affiliation(s)
- Zachary Monahan
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Frank Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Udai Bhan Pandey
- Department of Pediatrics, Division of Child Neurology, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States; Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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25
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De Conti L, Akinyi MV, Mendoza-Maldonado R, Romano M, Baralle M, Buratti E. TDP-43 affects splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways. Nucleic Acids Res 2015; 43:8990-9005. [PMID: 26261209 PMCID: PMC4605304 DOI: 10.1093/nar/gkv814] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
In recent times, high-throughput screening analyses have broadly defined the RNA cellular targets of TDP-43, a nuclear factor involved in neurodegeneration. A common outcome of all these studies is that changing the expression levels of this protein can alter the expression of several hundred RNAs within cells. What still remains to be clarified is which changes represent direct cellular targets of TDP-43 or just secondary variations due to the general role played by this protein in RNA metabolism. Using an HTS-based splicing junction analysis we identified at least six bona fide splicing events that are consistent with being controlled by TDP-43. Validation of the data, both in neuronal and non-neuronal cell lines demonstrated that TDP-43 substantially alters the levels of isoform expression in four genes potentially important for neuropathology: MADD/IG20, STAG2, FNIP1 and BRD8. For MADD/IG20 and STAG2, these changes could also be confirmed at the protein level. These alterations were also observed in a cellular model that successfully mimics TDP-43 loss of function effects following its aggregation. Most importantly, our study demonstrates that cell cycle alterations induced by TDP-43 knockdown can be recovered by restoring the STAG2, an important component of the cohesin complex, normal splicing profile.
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Affiliation(s)
- Laura De Conti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Maureen V Akinyi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | | | - Maurizio Romano
- LNCIB-Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Laboratorio di Oncologia Molecolare, 34012 Trieste, Italy
| | - Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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26
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Smethurst P, Sidle KCL, Hardy J. Review: Prion-like mechanisms of transactive response DNA binding protein of 43 kDa (TDP-43) in amyotrophic lateral sclerosis (ALS). Neuropathol Appl Neurobiol 2015; 41:578-97. [PMID: 25487060 DOI: 10.1111/nan.12206] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/03/2014] [Indexed: 01/13/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal devastating neurodegenerative disorder which predominantly affects the motor neurons in the brain and spinal cord. The death of the motor neurons in ALS causes subsequent muscle atrophy, paralysis and eventual death. Clinical and biological evidence now demonstrates that ALS has many similarities to prion disease in terms of disease onset, phenotype variability and progressive spread. The pathognomonic ubiquitinated inclusions deposited in the neurons and glial cells in brains and spinal cords of patients with ALS and fronto-temporal lobar degeneration with ubiquitinated inclusions contain aggregated transactive response DNA binding protein of 43 kDa (TDP-43), and evidence now suggests that TDP-43 has cellular prion-like properties. The cellular mechanisms of prion protein misfolding and aggregation are thought to be responsible for the characteristics of prion disease. Therefore, there is a strong mechanistic basis for a prion-like behaviour of the TDP-43 protein being responsible for some characteristics of ALS. In this review, we compare the prion-like mechanisms of TDP-43 to the clinical and biological nature of ALS in order to investigate how this protein could be responsible for some of the characteristic properties of the disease.
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Affiliation(s)
- Phillip Smethurst
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square House, London, UK
| | | | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square House, London, UK
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27
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Lystad AH, Simonsen A. Assays to monitor aggrephagy. Methods 2015; 75:112-9. [DOI: 10.1016/j.ymeth.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022] Open
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28
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Sun Y, Arslan PE, Won A, Yip CM, Chakrabartty A. Binding of TDP-43 to the 3'UTR of its cognate mRNA enhances its solubility. Biochemistry 2014; 53:5885-94. [PMID: 25171271 DOI: 10.1021/bi500617x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
TAR DNA binding protein of 43 kDa (TDP-43) has been implicated in the pathogenesis of a broad range of neurodegenerative diseases termed TDP-43 proteinopathies, which encompass a spectrum of diseases ranging from amyotrophic lateral sclerosis to frontotemporal dementia. Pathologically misfolded and aggregated forms of TDP-43 are found in cytoplasmic inclusion bodies of affected neurons in these diseases. The mechanism by which TDP-43 misfolding causes disease is not well-understood. Current hypotheses postulate that the TDP-43 aggregation process plays a major role in pathogenesis. We amplify that hypothesis and suggest that binding of cognate ligands to TDP-43 can stabilize the native functional state of the protein and ameliorate aggregation. We expressed recombinant TDP-43 containing an N-terminal Venus yellow fluorescent protein tag in Escherichia coli and induced its aggregation by altering solvent salt concentrations and examined the extent to which various oligonucleotide molecules affect its aggregation in vitro using aggregation-induced turbidity assays. We show that vYFP-TDP-43 binding to its naturally occurring RNA target that comprises a sequence on the 3'UTR region of its mRNA improves its solubility, suggesting interplay among TDP-43 solubility, oligonucleotide binding, and TDP-43 autoregulation.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G 1L7, Canada
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29
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Nehls J, Koppensteiner H, Brack-Werner R, Floss T, Schindler M. HIV-1 replication in human immune cells is independent of TAR DNA binding protein 43 (TDP-43) expression. PLoS One 2014; 9:e105478. [PMID: 25127017 PMCID: PMC4134290 DOI: 10.1371/journal.pone.0105478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022] Open
Abstract
The TAR DNA binding protein (TDP-43) was originally identified as a host cell factor binding to the HIV-1 LTR and thereby suppressing HIV-1 transcription and gene expression (Ou et al., J.Virol. 1995, 69(6):3584). TDP-43 is a global regulator of transcription, can influence RNA metabolism in many different ways and is ubiquitously expressed. Thus, TDP-43 could be a major factor restricting HIV-1 replication at the level of LTR transcription and gene expression. These facts prompted us to revisit the role of TDP-43 for HIV-1 replication. We utilized established HIV-1 cell culture systems as well as primary cell models and performed a comprehensive analysis of TDP-43 function and investigated its putative impact on HIV-1 gene expression. In HIV-1 infected cells TDP-43 was neither degraded nor sequestered from the nucleus. Furthermore, TDP-43 overexpression as well as siRNA mediated knockdown did not affect HIV-1 gene expression and virus production in T cells and macrophages. In summary, our experiments argue against a restricting role of TDP-43 during HIV-1 replication in immune cells.
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Affiliation(s)
- Julia Nehls
- Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Herwig Koppensteiner
- Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Floss
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schindler
- Institute of Virology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, Tübingen, Germany
- * E-mail:
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30
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Therrien M, Parker JA. Worming forward: amyotrophic lateral sclerosis toxicity mechanisms and genetic interactions in Caenorhabditis elegans. Front Genet 2014; 5:85. [PMID: 24860590 PMCID: PMC4029022 DOI: 10.3389/fgene.2014.00085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/30/2014] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases share pathogenic mechanisms at the cellular level including protein misfolding, excitotoxicity and altered RNA homeostasis among others. Recent advances have shown that the genetic causes underlying these pathologies overlap, hinting at the existence of a genetic network for neurodegeneration. This is perhaps best illustrated by the recent discoveries of causative mutations for amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Once thought to be distinct entities, it is now recognized that these diseases exist along a genetic spectrum. With this wealth of discoveries comes the need to develop new genetic models of ALS and FTD to investigate not only pathogenic mechanisms linked to causative mutations, but to uncover potential genetic interactions that may point to new therapeutic targets. Given the conservation of many disease genes across evolution, Caenorhabditis elegans is an ideal system to investigate genetic interactions amongst these genes. Here we review the use of C. elegans to model ALS and investigate a putative genetic network for ALS/FTD that may extend to other neurological disorders.
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Affiliation(s)
- Martine Therrien
- Départment de Pathologie et Biologie Cellulaire, CRCHUM-Centre Hospitalier de l'Université de Montréal, Université de Montréal Montréal, QC, Canada
| | - J Alex Parker
- Départment de Pathologie et Biologie Cellulaire, Départment de Neurosciences, CRCHUM-Centre Hospitalier de l'Université de Montréal, Université de Montréal Montréal, QC, Canada
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31
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Stribl C, Samara A, Trümbach D, Peis R, Neumann M, Fuchs H, Gailus-Durner V, Hrabě de Angelis M, Rathkolb B, Wolf E, Beckers J, Horsch M, Neff F, Kremmer E, Koob S, Reichert AS, Hans W, Rozman J, Klingenspor M, Aichler M, Walch AK, Becker L, Klopstock T, Glasl L, Hölter SM, Wurst W, Floss T. Mitochondrial dysfunction and decrease in body weight of a transgenic knock-in mouse model for TDP-43. J Biol Chem 2014; 289:10769-10784. [PMID: 24515116 DOI: 10.1074/jbc.m113.515940] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The majority of amyotrophic lateral sclerosis (ALS) cases as well as many patients suffering from frontotemporal lobar dementia (FTLD) with ubiquitinated inclusion bodies show TDP-43 pathology, the protein encoded by the TAR DNA-binding protein (Tardbp) gene. We used recombinase-mediated cassette exchange to introduce an ALS patient cDNA into the mouse Tdp-43 locus. Expression levels of human A315T TDP-43 protein were 300% elevated in heterozygotes, whereas the endogenous mouse Tdp-43 was decreased to 20% of wild type levels as a result of disturbed feedback regulation. Heterozygous TDP-43(A315TKi) mutants lost 10% of their body weight and developed insoluble TDP-43 protein starting as early as 3 months after birth, a pathology that was exacerbated with age. We analyzed the splicing patterns of known Tdp-43 target genes as well as genome-wide gene expression levels in different tissues that indicated mitochondrial dysfunction. In heterozygous mutant animals, we observed a relative decrease in expression of Parkin (Park2) and the fatty acid transporter CD36 along with an increase in fatty acids, HDL cholesterol, and glucose in the blood. As seen in transmission electron microscopy, neuronal cells in motor cortices of TDP-43(A315TKi) animals had abnormal neuronal mitochondrial cristae formation. Motor neurons were reduced to 90%, but only slight motoric impairment was detected. The observed phenotype was interpreted as a predisease model, which might be valuable for the identification of further environmental or genetic triggers of neurodegeneration.
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Affiliation(s)
- Carola Stribl
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Aladin Samara
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Dietrich Trümbach
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Regina Peis
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Manuela Neumann
- Institute of Neuropathology, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Technische Universität München, c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Vertigo and Balance Disorders, Ludwig-Maximilians-Universität, Ziemssenstrasse 1a, 80336 Munich, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Eckhard Wolf
- Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Technische Universität München, c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Marion Horsch
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Frauke Neff
- Institute of Pathology, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Elisabeth Kremmer
- Helmholtz Institut für Molekulare Immunologie (IMI), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sebastian Koob
- Buchmann Institute for Molecular Life Sciences, Mitochondrial Biology, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany; Mitochondriale Biologie, Zentrum für Molekulare Medizin, Goethe Universität Frankfurt am Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Andreas S Reichert
- Buchmann Institute for Molecular Life Sciences, Mitochondrial Biology, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany; Mitochondriale Biologie, Zentrum für Molekulare Medizin, Goethe Universität Frankfurt am Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Mitochondriale Biologie, Zentrum für Molekulare Medizin, Goethe Universität Frankfurt am Main, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Wolfgang Hans
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Nutritional Medicine, Else Kröner Fresenius Center and ZIEL Research Center for Nutrition and Food Science, Technische Universität München, Gregor-Mendel-Strasse 2, 85350 Freising-Weihenstephan, Germany
| | - Jan Rozman
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Nutritional Medicine, Else Kröner Fresenius Center and ZIEL Research Center for Nutrition and Food Science, Technische Universität München, Gregor-Mendel-Strasse 2, 85350 Freising-Weihenstephan, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Else Kröner Fresenius Center and ZIEL Research Center for Nutrition and Food Science, Technische Universität München, Gregor-Mendel-Strasse 2, 85350 Freising-Weihenstephan, Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology, Institute of Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Axel Karl Walch
- Research Unit Analytical Pathology, Institute of Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-Universität, Ziemssenstrasse 1a, 80336 Munich, Germany
| | - Thomas Klopstock
- Research Unit Analytical Pathology, Institute of Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-Universität, Ziemssenstrasse 1a, 80336 Munich, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Site Munich, Schillerstrasse 44, D-80336 Munich, Germany
| | - Lisa Glasl
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Sabine M Hölter
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technische Universität München, c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technische Universität München, c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Site Munich, Schillerstrasse 44, D-80336 Munich, Germany; Max-Planck-Institute of Psychiatry, Kraepelinstrasse 2-10, 80804 München, Germany
| | - Thomas Floss
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technische Universität München, c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany.
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Disease-associated mutations of TDP-43 promote turnover of the protein through the proteasomal pathway. Mol Neurobiol 2014; 50:1049-58. [PMID: 24477737 DOI: 10.1007/s12035-014-8644-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 01/13/2014] [Indexed: 12/12/2022]
Abstract
TAR DNA-binding protein (TDP-43) is a major component of most ubiquitin-positive neuronal and glial inclusions of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). A number of missense mutations in the TARDBP gene have been identified in patients with familial and sporadic ALS, as well as familial FTLD with ALS. In the diseased states, TDP-43 proteins exhibit characteristic alterations, including truncation, abnormal phosphorylation, and altered subcellular distribution. However, the mechanisms by which TDP-43 mutations induce neurodegeneration remain unclear at present. In the current study, we analyzed protein turnover and subcellular distribution of wild-type TDP-43 and two disease-associated mutants (G298S and A382T) in human neuroblastoma SH-SY5Y cells stably expressing TDP-43 with a C-terminal tag. Cycloheximide chase experiments revealed more rapid turnover of TDP-43 mutant proteins than their wild-type counterpart. The decrease in the TDP-43 level after cycloheximide treatment was partially recovered upon co-treatment with the proteasome inhibitor, epoxomicin, but not the lysosomotropic agent, chloroquine, suggesting involvement of the proteasomal pathway in TDP-43 degradation. Analysis of the subcellular distribution of TDP-43 revealed predominant localization in the nuclear fraction, whereas the relative level in the cytoplasm remained unaltered in cells expressing either mutant protein, compared with wild-type protein. Our results suggest that higher turnover of disease-associated mutant TDP-43 proteins through the ubiquitin proteasome system is pathogenetically relevant and highlight the significance of proteolysis in the pathogenetic mechanism of TDP-43 proteinopathy.
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Ricketts T, McGoldrick P, Fratta P, de Oliveira HM, Kent R, Phatak V, Brandner S, Blanco G, Greensmith L, Acevedo-Arozena A, Fisher EMC. A nonsense mutation in mouse Tardbp affects TDP43 alternative splicing activity and causes limb-clasping and body tone defects. PLoS One 2014; 9:e85962. [PMID: 24465814 PMCID: PMC3897576 DOI: 10.1371/journal.pone.0085962] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 12/03/2013] [Indexed: 12/11/2022] Open
Abstract
Mutations in TARDBP, encoding Tar DNA binding protein-43 (TDP43), cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Attempts to model TDP43 dysfunction in mice have used knockouts or transgenic overexpressors, which have revealed the difficulties of manipulating TDP43, whose level is tightly controlled by auto-regulation. In a complementary approach, to create useful mouse models for the dissection of TDP43 function and pathology, we have identified a nonsense mutation in the endogenous mouse Tardbp gene through screening an N-ethyl-N-nitrosourea (ENU) mutant mouse archive. The mutation is predicted to cause a Q101X truncation in TDP43. We have characterised Tardbp(Q101X) mice to investigate this mutation in perturbing TDP43 biology at endogenous expression levels. We found the Tardbp(Q101X) mutation is homozygous embryonic lethal, highlighting the importance of TDP43 in early development. Heterozygotes (Tardbp(+/Q101X) ) have abnormal levels of mutant transcript, but we find no evidence of the truncated protein and mice have similar full-length TDP43 protein levels as wildtype littermates. Nevertheless, Tardbp(+/Q101X) mice have abnormal alternative splicing of downstream gene targets, and limb-clasp and body tone phenotypes. Thus the nonsense mutation in Tardbp causes a mild loss-of-function phenotype and behavioural assessment suggests underlying neurological abnormalities. Due to the role of TDP43 in ALS, we investigated potential interactions with another known causative gene, mutant superoxide dismutase 1 (SOD1). Tardbp(+/Q101X) mice were crossed with the SOD1(G93Adl) transgenic mouse model of ALS. Behavioural and physiological assessment did not reveal modifying effects on the progression of ALS-like symptoms in the double mutant progeny from this cross. In summary, the Tardbp(Q101X) mutant mice are a useful tool for the dissection of TDP43 protein regulation, effects on splicing, embryonic development and neuromuscular phenotypes. These mice are freely available to the community.
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Affiliation(s)
- Thomas Ricketts
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Philip McGoldrick
- Sobell Department of Motor Neuroscience and Movement Disorders and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Pietro Fratta
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | | | - Rosie Kent
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
| | - Vinaya Phatak
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
| | - Sebastian Brandner
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Gonzalo Blanco
- Biology Department, University of York, York, United Kingdom
| | - Linda Greensmith
- Sobell Department of Motor Neuroscience and Movement Disorders and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
| | - Abraham Acevedo-Arozena
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
| | - Elizabeth M. C. Fisher
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire, United Kingdom
- Department of Neurodegenerative Diseases and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
- * E-mail: (LG); (AA-A); (EF)
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Bembich S, Herzog JS, De Conti L, Stuani C, Avendaño-Vázquez SE, Buratti E, Baralle M, Baralle FE. Predominance of spliceosomal complex formation over polyadenylation site selection in TDP-43 autoregulation. Nucleic Acids Res 2013; 42:3362-71. [PMID: 24369426 PMCID: PMC3950720 DOI: 10.1093/nar/gkt1343] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
TDP-43 is a nuclear protein involved in many aspects of RNA metabolism. To ensure cellular viability, its expression levels within cells must be tightly regulated. We have previously demonstrated that TDP-43 autoregulation occurs through the activation of a normally silent intron in its 3′-UTR sequence that results in the use of alternative polyadenylation sites. In this work, we analyse which is the dominant event in autoregulation: the recognition of the splice sites of 3′-UTR intron 7 or the intrinsic quality of the alternative polyadenylation sites. A panel of minigene constructs was tested for autoregulation functionality, protein production and subcellular messenger RNA localization. Our data clearly indicate that constitutive spliceosome complex formation across intron 7 does not lead to high protein production but, on the contrary, to lower TDP-43 messenger RNA and protein levels. This is due to altered nucleocytoplasmic distribution of the RNA that is mostly retained in the nucleus and degraded. This study provides a novel in-depth characterization of how RNA binding proteins can autoregulate their own levels within cells, an essential regulatory process in maintaining cellular viability.
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Affiliation(s)
- Sara Bembich
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
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Janssens J, Van Broeckhoven C. Pathological mechanisms underlying TDP-43 driven neurodegeneration in FTLD-ALS spectrum disorders. Hum Mol Genet 2013; 22:R77-87. [PMID: 23900071 PMCID: PMC3782069 DOI: 10.1093/hmg/ddt349] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 07/07/2013] [Accepted: 07/21/2013] [Indexed: 01/09/2023] Open
Abstract
Aggregation of misfolded TAR DNA-binding protein 43 (TDP-43) is a striking hallmark of neurodegenerative processes that are observed in several neurological disorders, and in particular in most patients diagnosed with frontotemporal lobar degeneration (FTLD) or amyotrophic lateral sclerosis (ALS). A direct causal link with TDP-43 brain proteinopathy was provided by the identification of pathogenic mutations in TARDBP, the gene encoding TDP-43, in ALS families. However, TDP-43 proteinopathy has also been observed in carriers of mutations in several other genes associated with both ALS and FTLD demonstrating a key role for TDP-43 in neurodegeneration. To date, and despite substantial research into the biology of TDP-43, its functioning in normal brain and in neurodegeneration processes remains largely elusive. Nonetheless, breakthroughs using cellular and animal models have provided valuable insights into ALS and FTLD pathogenesis. Accumulating evidence has redirected the research focus towards a major role for impaired RNA metabolism and protein homeostasis. At the same time, the concept that toxic TDP-43 protein aggregates promote neurodegeneration is losing its credibility. This review aims at highlighting and discussing the current knowledge on TDP-43 driven pathomechanisms leading to neurodegeneration as observed in TDP-43 proteinopathies. Based on the complexity of the associated neurological diseases, a clear understanding of the essential pathological modifications will be crucial for further therapeutic interventions.
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Affiliation(s)
- Jonathan Janssens
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
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Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG. Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. Nucleic Acids Res 2013; 41:9987-98. [PMID: 24003031 PMCID: PMC3905859 DOI: 10.1093/nar/gkt794] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson’s disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis.
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Affiliation(s)
- Andreas Zanzoni
- Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Abstract
Dysfunctions at the level of RNA processing have recently been shown to play a fundamental role in the pathogenesis of many neurodegenerative diseases. Several proteins responsible for these dysfunctions (TDP-43, FUS/TLS, and hnRNP A/Bs) belong to the nuclear class of heterogeneous ribonucleoproteins (hnRNPs) that predominantly function as general regulators of both coding and noncoding RNA metabolism. The discovery of the importance of these factors in mediating neuronal death has represented a major paradigmatic shift in our understanding of neurodegenerative processes. As a result, these discoveries have also opened the way toward novel biomolecular screening approaches in our search for therapeutic options. One of the major hurdles in this search is represented by the correct identification of the most promising targets to be prioritized. These may include aberrant aggregation processes, protein-protein interactions, RNA-protein interactions, or specific cellular pathways altered by disease. In this review, we discuss these four major options together with their various advantages and drawbacks.
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Affiliation(s)
- Maurizio Romano
- 1Department of Life Sciences, University of Trieste, Trieste, Italy
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Bhardwaj A, Myers MP, Buratti E, Baralle FE. Characterizing TDP-43 interaction with its RNA targets. Nucleic Acids Res 2013; 41:5062-74. [PMID: 23519609 PMCID: PMC3643599 DOI: 10.1093/nar/gkt189] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the most important functional features of nuclear factor TDP-43 is its ability to bind UG-repeats with high efficiency. Several cross-linking and immunoprecipitation (CLIP) and RNA immunoprecipitation-sequencing (RIP-seq) analyses have indicated that TDP-43 in vivo can also specifically bind loosely conserved UG/GU-rich repeats interspersed by other nucleotides. These sequences are predominantly localized within long introns and in the 3′UTR of various genes. Most importantly, some of these sequences have been found to exist in the 3′UTR region of TDP-43 itself. In the TDP-43 3′UTR context, the presence of these UG-like sequences is essential for TDP-43 to autoregulate its own levels through a negative feedback loop. In this work, we have compared the binding of TDP-43 with these types of sequences as opposed to perfect UG-stretches. We show that the binding affinity to the UG-like sequences has a dissociation constant (Kd) of ∼110 nM compared with a Kd of 8 nM for straight UGs, and have mapped the region of contact between protein and RNA. In addition, our results indicate that the local concentration of UG dinucleotides in the CLIP sequences is one of the major factors influencing the interaction of these RNA sequences with TDP-43.
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Affiliation(s)
- Amit Bhardwaj
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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Fallini C, Bassell GJ, Rossoll W. The ALS disease protein TDP-43 is actively transported in motor neuron axons and regulates axon outgrowth. Hum Mol Genet 2012; 21:3703-18. [PMID: 22641816 DOI: 10.1093/hmg/dds205] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease specifically affecting cortical and spinal motor neurons. Cytoplasmic inclusions containing hyperphosphorylated and ubiquitinated TDP-43 are a pathological hallmark of ALS, and mutations in the gene encoding TDP-43 have been directly linked to the development of the disease. TDP-43 is a ubiquitous DNA/RNA-binding protein with a nuclear role in pre-mRNA splicing. However, the selective vulnerability and axonal degeneration of motor neurons in ALS pose the question of whether TDP-43 may have an additional role in the regulation of the cytoplasmic and axonal fate of mRNAs, processes important for neuron function. To investigate this possibility, we have characterized TDP-43 localization and dynamics in primary cultured motor neurons. Using a combination of cell imaging and biochemical techniques, we demonstrate that TDP-43 is localized and actively transported in live motor neuron axons, and that it co-localizes with well-studied axonal mRNA-binding proteins. Expression of the TDP-43 C-terminal fragment led to the formation of hyperphosphorylated and ubiquitinated inclusions in motor neuron cell bodies and neurites, and these inclusions specifically sequestered the mRNA-binding protein HuD. Additionally, we showed that overexpression of full-length or mutant TDP-43 in motor neurons caused a severe impairment in axon outgrowth, which was dependent on the C-terminal protein-interacting domain of TDP-43. Taken together, our results suggest a role of TDP-43 in the regulation of axonal growth, and suggest that impairment in the post-transcriptional regulation of mRNAs in the cytoplasm of motor neurons may be a major factor in the development of ALS.
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Affiliation(s)
- Claudia Fallini
- Department of Cell Biology and Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
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40
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Buratti E, Baralle FE. TDP-43: gumming up neurons through protein-protein and protein-RNA interactions. Trends Biochem Sci 2012; 37:237-47. [PMID: 22534659 DOI: 10.1016/j.tibs.2012.03.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/02/2012] [Accepted: 03/08/2012] [Indexed: 12/11/2022]
Abstract
Since the discovery that 43 kDa TAR DNA binding protein (TDP-43) is involved in neurodegeneration, studies of this protein have focused on the global effects of TDP-43 expression modulation on cell metabolism and survival. The major difficulty with these global searches, which can yield hundreds to thousands of variations in gene expression level and/or mRNA isoforms, is our limited ability to separate specific TDP-43 effects from secondary dysregulations occurring at the gene expression and various mRNA processing steps. In this review, we focus on two biochemical properties of TDP-43: its ability to bind RNA and its protein-protein interactions. In particular, we overview how these two properties may affect potentially very important processes for the pathology, from the autoregulation of TDP-43 to aggregation in the cytoplasmic/nuclear compartments.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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