1
|
Scherer NM, Maurel C, Graus M, McAlary L, Richter G, Radford RW, Hogan A, Don E, Lee A, Yerbury J, Francois M, Chung R, Morsch M. RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo. Nucleic Acids Res 2024; 52:5301-5319. [PMID: 38381071 PMCID: PMC11109982 DOI: 10.1093/nar/gkae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Insoluble cytoplasmic aggregate formation of the RNA-binding protein TDP-43 is a major hallmark of neurodegenerative diseases including Amyotrophic Lateral Sclerosis. TDP-43 localizes predominantly in the nucleus, arranging itself into dynamic condensates through liquid-liquid phase separation (LLPS). Mutations and post-translational modifications can alter the condensation properties of TDP-43, contributing to the transition of liquid-like biomolecular condensates into solid-like aggregates. However, to date it has been a challenge to study the dynamics of this process in vivo. We demonstrate through live imaging that human TDP-43 undergoes nuclear condensation in spinal motor neurons in a living animal. RNA-binding deficiencies as well as post-translational modifications can lead to aberrant condensation and altered TDP-43 compartmentalization. Single-molecule tracking revealed an altered mobility profile for RNA-binding deficient TDP-43. Overall, these results provide a critically needed in vivo characterization of TDP-43 condensation, demonstrate phase separation as an important regulatory mechanism of TDP-43 accessibility, and identify a molecular mechanism of how functional TDP-43 can be regulated.
Collapse
Affiliation(s)
- Natalie M Scherer
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Cindy Maurel
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Matthew S Graus
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Grant Richter
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Rowan A W Radford
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Alison Hogan
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily K Don
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Justin Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Mathias Francois
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Roger S Chung
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Marco Morsch
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
2
|
Demongin C, Tranier S, Joshi V, Ceschi L, Desforges B, Pastré D, Hamon L. RNA and the RNA-binding protein FUS act in concert to prevent TDP-43 spatial segregation. J Biol Chem 2024; 300:105716. [PMID: 38311174 PMCID: PMC10912363 DOI: 10.1016/j.jbc.2024.105716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
FUS and TDP-43 are two self-adhesive aggregation-prone mRNA-binding proteins whose pathological mutations have been linked to neurodegeneration. While TDP-43 and FUS form reversible mRNA-rich compartments in the nucleus, pathological mutations promote their respective cytoplasmic aggregation in neurons with no apparent link between the two proteins except their intertwined function in mRNA processing. By combining analyses in cellular context and at high resolution in vitro, we unraveled that TDP-43 is specifically recruited in FUS assemblies to form TDP-43-rich subcompartments but without reciprocity. The presence of mRNA provides an additional scaffold to promote the mixing between TDP-43 and FUS. Accordingly, we also found that the pathological truncated form of TDP-43, TDP-25, which has an impaired RNA-binding ability, no longer mixes with FUS. Together, these results suggest that the binding of FUS along nascent mRNAs enables TDP-43, which is highly aggregation-prone, to mix with FUS phase to form mRNA-rich subcompartments. A functional link between FUS and TDP-43 may explain their common implication in amyotrophic lateral sclerosis.
Collapse
Affiliation(s)
- Clément Demongin
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Léa Ceschi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | | | - David Pastré
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France.
| |
Collapse
|
3
|
García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
Collapse
Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
| |
Collapse
|
4
|
Zeballos C MA, Moore HJ, Smith TJ, Powell JE, Ahsan NS, Zhang S, Gaj T. Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins. Nat Commun 2023; 14:6492. [PMID: 37838698 PMCID: PMC10576788 DOI: 10.1038/s41467-023-42147-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
The TDP-43 proteinopathies, which include amyotrophic lateral sclerosis and frontotemporal dementia, are a devastating group of neurodegenerative disorders that are characterized by the mislocalization and aggregation of TDP-43. Here we demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene silencing agents that includes the Cas13 family of enzymes and Cas7-11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. In addition to inhibiting the aggregation and transit of TDP-43 to stress granules, we find that the in vivo delivery of an ataxin-2-targeting Cas13 system to a mouse model of TDP-43 proteinopathy improved functional deficits, extended survival, and reduced the severity of neuropathological hallmarks. Further, we benchmark RNA-targeting CRISPR platforms against ataxin-2 and find that high-fidelity forms of Cas13 possess improved transcriptome-wide specificity compared to Cas7-11 and a first-generation effector. Our results demonstrate the potential of CRISPR technology for TDP-43 proteinopathies.
Collapse
Affiliation(s)
- M Alejandra Zeballos C
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hayden J Moore
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tyler J Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jackson E Powell
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Najah S Ahsan
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sijia Zhang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|