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Decker L, Menge S, Freischmidt A. Cryptic exon inclusion in TDP-43 proteinopathies: opportunities and challenges. Neural Regen Res 2025; 20:2003-2004. [PMID: 39254559 DOI: 10.4103/nrr.nrr-d-24-00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/24/2024] [Indexed: 09/11/2024] Open
Affiliation(s)
- Lorena Decker
- Department of Neurology, Ulm University, Ulm, Germany
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2
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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [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: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Vassallu F, Igaz LM. TDP-43 nuclear condensation and neurodegenerative proteinopathies. Trends Neurosci 2024:S0166-2236(24)00175-9. [PMID: 39327159 DOI: 10.1016/j.tins.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024]
Abstract
RNA-binding proteins (RBPs) can undergo phase separation and form condensates, processes that, in turn, can be critical for their functionality. In a recent study, Huang, Ellis, and colleagues show that cellular stress can trigger transient alterations in nuclear TAR DNA-binding protein 43 (TDP-43), leading to changes crucial for proper neuronal function. These findings have implications for understanding neurological TDP-43 proteinopathies.
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Affiliation(s)
- Florencia Vassallu
- 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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4
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Plessis-Belair J, Ravano K, Han E, Janniello A, Molina C, Sher RB. NEMF mutations in mice illustrate how Importin-β specific nuclear transport defects recapitulate neurodegenerative disease hallmarks. PLoS Genet 2024; 20:e1011411. [PMID: 39312574 DOI: 10.1371/journal.pgen.1011411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
Pathological disruption of Nucleocytoplasmic Transport (NCT), such as the mis-localization of nuclear pore complex proteins (Nups), nuclear transport receptors, Ran-GTPase, and RanGAP1, are seen in both animal models and in familial and sporadic forms of amyotrophic lateral sclerosis (ALS), frontal temporal dementia and frontal temporal lobar degeneration (FTD\FTLD), and Alzheimer's and Alzheimer's Related Dementias (AD/ADRD). However, the question of whether these alterations represent a primary cause, or a downstream consequence of disease is unclear, and what upstream factors may account for these defects are unknown. Here, we report four key findings that shed light on the upstream causal role of Importin-β-specific nuclear transport defects in disease onset. First, taking advantage of two novel mouse models of NEMF neurodegeneration (NemfR86S and NemfR487G) that recapitulate many cellular and biochemical aspects of neurodegenerative diseases, we find an Importin-β-specific nuclear import block. Second, we observe cytoplasmic mis-localization and aggregation of multiple proteins implicated in the pathogenesis of ALS/FTD and AD/ADRD, including TDP43, Importin-β, RanGap1, and Ran. These findings are further supported by a pathological interaction between Importin-β and the mutant NEMFR86S protein in cytoplasmic accumulations. Third, we identify similar transcriptional dysregulation in key genes associated with neurodegenerative disease. Lastly, we show that even transient pharmaceutical inhibition of Importin-β in both mouse and human neuronal and non-neuronal cells induces key proteinopathies and transcriptional alterations seen in our mouse models and in neurodegeneration. Our convergent results between mouse and human neuronal and non-neuronal cellular biology provide mechanistic evidence that many of the mis-localized proteins and dysregulated transcriptional events seen in multiple neurodegenerative diseases may in fact arise primarily from a primary upstream defect in Importin- β nuclear import. These findings have critical implications for investigating how sporadic forms of neurodegeneration may arise from presently unidentified genetic and environmental perturbations in Importin-β function.
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Affiliation(s)
- Jonathan Plessis-Belair
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathryn Ravano
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
| | - Ellen Han
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
| | - Aubrey Janniello
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
| | - Catalina Molina
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
| | - Roger B Sher
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, United States of America
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5
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Yang J, Li Y, Li H, Zhang H, Guo H, Zheng X, Yu XF, Wei W. HIV-1 Vpu induces neurotoxicity by promoting Caspase 3-dependent cleavage of TDP-43. EMBO Rep 2024:10.1038/s44319-024-00238-y. [PMID: 39242776 DOI: 10.1038/s44319-024-00238-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/09/2024] Open
Abstract
Despite the efficacy of highly active antiretroviral therapy in controlling the incidence and mortality of AIDS, effective interventions for HIV-1-induced neurological damage and cognitive impairment remain elusive. In this study, we found that HIV-1 infection can induce proteolytic cleavage and aberrant aggregation of TAR DNA-binding protein 43 (TDP-43), a pathological protein associated with various severe neurological disorders. The HIV-1 accessory protein Vpu was found to be responsible for the cleavage of TDP-43, as ectopic expression of Vpu alone was sufficient to induce TDP-43 cleavage, whereas HIV-1 lacking Vpu failed to cleave TDP-43. Mechanistically, the cleavage of TDP-43 at Asp89 by HIV-1 relies on Vpu-mediated activation of Caspase 3, and pharmacological inhibition of Caspase 3 activity effectively suppressed the HIV-1-induced aggregation and neurotoxicity of TDP-43. Overall, these results suggest that TDP-43 is a conserved host target of HIV-1 Vpu and provide evidence for the involvement of TDP-43 dysregulation in the neural pathogenesis of HIV-1.
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Affiliation(s)
- Jiaxin Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Huili Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Haichen Zhang
- Department of Neurology and Neuroscience Center, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Haoran Guo
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Xiangyu Zheng
- Department of Neurology and Neuroscience Center, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Wei
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China.
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, 130021, Changchun, Jilin, China.
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6
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Thornburg-Suresh EJC, Summers DW. Microtubules, Membranes, and Movement: New Roles for Stathmin-2 in Axon Integrity. J Neurosci Res 2024; 102:e25382. [PMID: 39253877 PMCID: PMC11407747 DOI: 10.1002/jnr.25382] [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: 05/07/2024] [Revised: 08/06/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024]
Abstract
Neurons establish functional connections responsible for how we perceive and react to the world around us. Communication from a neuron to its target cell occurs through a long projection called an axon. Axon distances can exceed 1 m in length in humans and require a dynamic microtubule cytoskeleton for growth during development and maintenance in adulthood. Stathmins are microtubule-associated proteins that function as relays between kinase signaling and microtubule polymerization. In this review, we describe the prolific role of Stathmins in microtubule homeostasis with an emphasis on emerging roles for Stathmin-2 (Stmn2) in axon integrity and neurodegeneration. Stmn2 levels are altered in Amyotrophic Lateral Sclerosis and loss of Stmn2 provokes motor and sensory neuropathies. There is growing potential for employing Stmn2 as a disease biomarker or even a therapeutic target. Meeting this potential requires a mechanistic understanding of emerging complexity in Stmn2 function. In particular, Stmn2 palmitoylation has a surprising contribution to axon maintenance through undefined mechanisms linking membrane association, tubulin interaction, and axon transport. Exploring these connections will reveal new insight on neuronal cell biology and novel opportunities for disease intervention.
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Affiliation(s)
| | - Daniel W Summers
- Department of Biology, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
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7
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Sun H, Yang B, Li Q, Zhu X, Song E, Liu C, Song Y, Jiang G. Polystyrene nanoparticles trigger aberrant condensation of TDP-43 and amyotrophic lateral sclerosis-like symptoms. NATURE NANOTECHNOLOGY 2024; 19:1354-1365. [PMID: 38849544 DOI: 10.1038/s41565-024-01683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/23/2024] [Indexed: 06/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the dysfunction and progressive death of cerebral and spinal motor neurons. Preliminary epidemiological research has hinted at a relationship between environmental risks and the escalation of ALS, but the underlying reasons remain mostly mysterious. Here we show that nanosize polystyrene plastics (PS) induce ALS-like symptoms and illustrate the related molecular mechanism. When exposed to PS, cells endure internal oxidative stress, which leads to the aggregation of TAR DNA-binding protein 43 kDa (TDP-43), triggering ALS-like characteristics. In addition, the oxidized heat shock protein 70 fails to escort TDP-43 back to the nucleus. The cytoplasmic accumulation of TDP-43 facilitates the formation of a complex between PS and TDP-43, enhancing the condensation and solidification of TDP-43. These findings are corroborated through in silico and in vivo assays. Altogether, our work illustrates a unique toxicological mechanism induced by nanoparticles and provides insights into the connection between environmental pollution and neurodegenerative disorders.
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Affiliation(s)
- Hang Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Bingwei Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Qiong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Xiaokang Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Erqun Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yang Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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8
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Phipps AJ, Dwyer S, Collins JM, Kabir F, Atkinson RAK, Chowdhury MA, Matthews L, Dixit D, Terry RS, Smith J, Gueven N, Bennett W, Cook AL, King AE, Perry S. HDAC6 inhibition as a mechanism to prevent neurodegeneration in the mSOD1 G93A mouse model of ALS. Heliyon 2024; 10:e34587. [PMID: 39130445 PMCID: PMC11315133 DOI: 10.1016/j.heliyon.2024.e34587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/13/2024] Open
Abstract
The loss of upper and lower motor neurons, and their axons is central to the loss of motor function and death in amyotrophic lateral sclerosis (ALS). Due to the diverse range of genetic and environmental factors that contribute to the pathogenesis of ALS, there have been difficulties in developing effective therapies for ALS. One emerging dichotomy is that protection of the neuronal cell soma does not prevent axonal vulnerability and degeneration, suggesting the need for targeted therapeutics to prevent axon degeneration. Post-translational modifications of protein acetylation can alter the function, stability and half-life of individual proteins, and can be enzymatically modified by histone acetyltransferases (HATs) and histone deacetyltransferases (HDACs), which add, or remove acetyl groups, respectively. Maintenance of post-translational microtubule acetylation has been suggested as a mechanism to stabilize axons, prevent axonal loss and neurodegeneration in ALS. This study used an orally dosed potent HDAC6 inhibitor, ACY-738, prevent deacetylation and stabilize microtubules in the mSOD1G93A mouse model of ALS. Co-treatment with riluzole was performed to determine any effects or drug interactions and potentially enhance preclinical research translation. This study shows ACY-738 treatment increased acetylation of microtubules in the spinal cord of mSOD1G93A mice, reduced lower motor neuron degeneration in female mice, ameliorated reduction in peripheral nerve axon puncta size, but did not prevent overt motor function decline. The current study also shows peripheral nerve axon puncta size to be partially restored after treatment with riluzole and highlights the importance of co-treatment to measure the potential effects of therapeutics in ALS.
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Affiliation(s)
- Andrew J. Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Samuel Dwyer
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Jessica M. Collins
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Fariha Kabir
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Rachel AK. Atkinson
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Md Anisuzzaman Chowdhury
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Lyzette Matthews
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Deepika Dixit
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Rhiannon S. Terry
- School of Natural Sciences (Chemistry), College of Sciences and Engineering, University of Tasmania, Australia
| | - Jason Smith
- School of Natural Sciences (Chemistry), College of Sciences and Engineering, University of Tasmania, Australia
| | - Nuri Gueven
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Australia
| | - William Bennett
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Australia
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Tilliole P, Fix S, Godin JD. hnRNPs: roles in neurodevelopment and implication for brain disorders. Front Mol Neurosci 2024; 17:1411639. [PMID: 39086926 PMCID: PMC11288931 DOI: 10.3389/fnmol.2024.1411639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a family of multifunctional RNA-binding proteins able to process nuclear pre-mRNAs into mature mRNAs and regulate gene expression in multiple ways. They comprise at least 20 different members in mammals, named from A (HNRNP A1) to U (HNRNP U). Many of these proteins are components of the spliceosome complex and can modulate alternative splicing in a tissue-specific manner. Notably, while genes encoding hnRNPs exhibit ubiquitous expression, increasing evidence associate these proteins to various neurodevelopmental and neurodegenerative disorders, such as intellectual disability, epilepsy, microcephaly, amyotrophic lateral sclerosis, or dementias, highlighting their crucial role in the central nervous system. This review explores the evolution of the hnRNPs family, highlighting the emergence of numerous new members within this family, and sheds light on their implications for brain development.
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Affiliation(s)
- Pierre Tilliole
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Simon Fix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Juliette D. Godin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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10
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Xie L, Merjane J, Bergmann CA, Xu J, Hurtle B, Donnelly CJ. CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603231. [PMID: 39026766 PMCID: PMC11257528 DOI: 10.1101/2024.07.12.603231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Given the mounting evidence implicating TDP-43 dysfunction in several neurodegenerative diseases, there is a pressing need to establish accessible tools to sense and quantify TDP-43 loss-of-function (LOF). These tools are crucial for assessing potential disease contributors and exploring therapeutic candidates in TDP-43 proteinopathies. Here, we develop a sensitive and accurate real-time sensor for TDP-43 LOF: the CUTS (CFTR UNC13A TDP-43 Loss-of-Function) system. This system combines previously reported cryptic exons regulated by TDP-43 with a reporter, enabling the tracking of TDP-43 LOF through live microscopy and RNA/protein-based assays. We demonstrate CUTS' effectiveness in detecting LOF caused by TDP-43 mislocalization and RNA binding dysfunction, and pathological aggregation. Our results highlight the sensitivity and accuracy of the CUTS system in detecting and quantifying TDP-43 LOF, opening avenues to explore unknown TDP-43 interactions that regulate its function. In addition, by replacing the fluorescent tag in the CUTS system with the coding sequence for TDP-43, we show significant recovery of its function under TDP-43 LOF conditions, highlighting CUTS' potential for self-regulating gene therapy applications. In summary, CUTS represents a versatile platform for evaluating TDP-43 LOF in real-time and advancing gene-replacement therapies in neurodegenerative diseases associated with TDP-43 dysfunction.
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Affiliation(s)
- Longxin Xie
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, China
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jessica Merjane
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cristian A Bergmann
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jiazhen Xu
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Interdisciplinary Biomedical Graduate Program Cellular and Molecular Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan Hurtle
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher J Donnelly
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- LiveLikeLou Center for ALS Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Interdisciplinary Biomedical Graduate Program Cellular and Molecular Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Institute for Neurodegeneration, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Protein Conformational Diseases, University of Pittsburgh, Pittsburgh, PA, USA
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11
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Keuss MJ, Harley P, Ryadnov E, Jackson RE, Zanovello M, Wilkins OG, Barattucci S, Mehta PR, Oliveira MG, Parkes JE, Sinha A, Correa-Sánchez AF, Oliver PL, Fisher EM, Schiavo G, Shah M, Burrone J, Fratta P. Loss of TDP-43 induces synaptic dysfunction that is rescued by UNC13A splice-switching ASOs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599684. [PMID: 38979232 PMCID: PMC11230273 DOI: 10.1101/2024.06.20.599684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
TDP-43 loss of function induces multiple splicing changes, including a cryptic exon in the amyotrophic lateral sclerosis and fronto-temporal lobar degeneration risk gene UNC13A, leading to nonsense-mediated decay of UNC13A transcripts and loss of protein. UNC13A is an active zone protein with an integral role in coordinating pre-synaptic function. Here, we show TDP-43 depletion induces a severe reduction in synaptic transmission, leading to an asynchronous pattern of network activity. We demonstrate that these deficits are largely driven by a single cryptic exon in UNC13A. Antisense oligonucleotides targeting the UNC13A cryptic exon robustly rescue UNC13A protein levels and restore normal synaptic function, providing a potential new therapeutic approach for ALS and other TDP-43-related disorders.
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Affiliation(s)
- Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Rachel E. Jackson
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Marcio G. Oliveira
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | | | - Aparna Sinha
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | | | - Peter L. Oliver
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Giampietro Schiavo
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- UK Dementia Research Institute at University College London; London, WC1N 3BG, UK
| | - Mala Shah
- Department of Pharmacology, School of Pharmacy, University College London; London, WC1N 4AX, UK
| | - Juan Burrone
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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12
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Carmen-Orozco RP, Tsao W, Ye Y, Sinha IR, Chang K, Trinh VT, Chung W, Bowden K, Troncoso JC, Blackshaw S, Hayes LR, Sun S, Wong PC, Ling JP. Elevated nuclear TDP-43 induces constitutive exon skipping. Mol Neurodegener 2024; 19:45. [PMID: 38853250 PMCID: PMC11163724 DOI: 10.1186/s13024-024-00732-w] [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: 06/30/2023] [Accepted: 05/20/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Cytoplasmic inclusions and loss of nuclear TDP-43 are key pathological features found in several neurodegenerative disorders, suggesting both gain- and loss-of-function mechanisms of disease. To study gain-of-function, TDP-43 overexpression has been used to generate in vitro and in vivo model systems. METHODS We analyzed RNA-seq datasets from mouse and human neurons overexpressing TDP-43 to explore species specific splicing patterns. We explored the dynamics between TDP-43 levels and exon repression in vitro. Furthermore we analyzed human brain samples and publicly available RNA datasets to explore the relationship between exon repression and disease. RESULTS Our study shows that excessive levels of nuclear TDP-43 protein lead to constitutive exon skipping that is largely species-specific. Furthermore, while aberrant exon skipping is detected in some human brains, it is not correlated with disease, unlike the incorporation of cryptic exons that occurs after loss of TDP-43. CONCLUSIONS Our findings emphasize the need for caution in interpreting TDP-43 overexpression data and stress the importance of controlling for exon skipping when generating models of TDP-43 proteinopathy.
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Affiliation(s)
- Rogger P Carmen-Orozco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Tsao
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Irika R Sinha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Vickie T Trinh
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Chung
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kyra Bowden
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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13
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Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594552. [PMID: 38798341 PMCID: PMC11118483 DOI: 10.1101/2024.05.16.594552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.
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Affiliation(s)
- Vincent E Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Suganya Rangaswamy
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Issa O Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Vikas H Malojirao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Gavin W Britz
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neurosurgery and Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ralph M Garruto
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
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14
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Cheng X, Jiang G, Zhou X, Wang J, Zhao Z, Zhang J, Ni T. The landscape and clinical relevance of intronic polyadenylation in human cancers. J Genet Genomics 2024:S1673-8527(24)00099-7. [PMID: 38740258 DOI: 10.1016/j.jgg.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Intronic polyadenylation (IPA) is an RNA 3' end processing event which has been reported to play important roles in cancer development. However, the comprehensive landscape of IPA events across various cancer types is lacking. Here, we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas (TCGA) project. We totally identify 21,835 IPA events, almost half of which are ubiquitously expressed. We identify 2761 unique dynamically changed IPA events across cancer types. Furthermore, we observe 8855 non-redundant clinically relevant IPA events, which could potentially be used as prognostic indicators. Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response. Finally, we develop a user-friendly data portal, IPACancer Atlas (http://www.tingni-lab.com/Pancan_IPA/), to search and explore IPAs in cancer.
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Affiliation(s)
- Xiaomeng Cheng
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guanghui Jiang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolan Zhou
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China; MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiayu Zhang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China.
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15
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Genge A, Wainwright S, Vande Velde C. Amyotrophic lateral sclerosis: exploring pathophysiology in the context of treatment. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:225-236. [PMID: 38001557 DOI: 10.1080/21678421.2023.2278503] [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: 08/02/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex, neurodegenerative disorder in which alterations in structural, physiological, and metabolic parameters act synergistically. Over the last decade there has been a considerable focus on developing drugs to slow the progression of the disease. Despite this, only four disease-modifying therapies are approved in North America. Although additional research is required for a thorough understanding of ALS, we have accumulated a large amount of knowledge that could be better integrated into future clinical trials to accelerate drug development and provide patients with improved treatment options. It is likely that future, successful ALS treatments will take a multi-pronged therapeutic approach, targeting different pathways, akin to personalized medicine in oncology. In this review, we discuss the link between ALS pathophysiology and treatments, looking at the therapeutic failures as learning opportunities that can help us refine and optimize drug development.
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Affiliation(s)
- Angela Genge
- Clinical Research Unit Director, ALS Clinic, Montreal, Quebec, Canada
| | - Steven Wainwright
- Amylyx Pharmaceuticals, Inc, Vancouver, British Columbia, Canada, and
| | - Christine Vande Velde
- CHUM Research Center, Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada
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16
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Cantara S, Simoncelli G, Ricci C. Antisense Oligonucleotides (ASOs) in Motor Neuron Diseases: A Road to Cure in Light and Shade. Int J Mol Sci 2024; 25:4809. [PMID: 38732027 PMCID: PMC11083842 DOI: 10.3390/ijms25094809] [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: 02/28/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are short oligodeoxynucleotides designed to bind to specific regions of target mRNA. ASOs can modulate pre-mRNA splicing, increase levels of functional proteins, and decrease levels of toxic proteins. ASOs are being developed for the treatment of motor neuron diseases (MNDs), including spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and spinal and bulbar muscular atrophy (SBMA). The biggest success has been the ASO known as nusinersen, the first effective therapy for SMA, able to improve symptoms and slow disease progression. Another success is tofersen, an ASO designed to treat ALS patients with SOD1 gene mutations. Both ASOs have been approved by the FDA and EMA. On the other hand, ASO treatment in ALS patients with the C9orf72 gene mutation did not show any improvement in disease progression. The aim of this review is to provide an up-to-date overview of ASO research in MNDs, from preclinical studies to clinical trials and, where available, regulatory approval. We highlight the successes and failures, underline the strengths and limitations of the current ASO research, and suggest possible approaches that could lead to more effective treatments.
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Affiliation(s)
- Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy;
| | - Giorgia Simoncelli
- Unit of Neurology and Clinical Neurophysiology, Department of Neurological and Motor Sciences, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy;
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy;
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17
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Trink Y, Urbach A, Dekel B, Hohenstein P, Goldberger J, Kalisky T. Characterization of Alternative Splicing in High-Risk Wilms' Tumors. Int J Mol Sci 2024; 25:4520. [PMID: 38674106 PMCID: PMC11050615 DOI: 10.3390/ijms25084520] [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: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The significant heterogeneity of Wilms' tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms' tumors using a publicly available RNAseq dataset of high-risk Wilms' tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or "archetypes", resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the epithelial-to-mesenchymal transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms' tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.
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Affiliation(s)
- Yaron Trink
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute and Division of Pediatric Nephrology, Edmond and Lily Safra Children’s Hospital, Sheba Tel-HaShomer Medical Centre, Ramat Gan 5262000, Israel
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Jacob Goldberger
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Tomer Kalisky
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
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18
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Chen T, Chen Z, Wu P, Luo J, Liu Q, Yang H, Peng C, Zhang G, Lin H, Ji Z. The Interaction between ADK and SCG10 Regulate the Repair of Nerve Damage. Neuroscience 2024; 544:75-87. [PMID: 38423163 DOI: 10.1016/j.neuroscience.2024.02.023] [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: 07/24/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
The cytoskeleton must be remodeled during neurite outgrowth, and Superior Cervical Ganglion 10 (SCG10) plays a critical role in this process by depolymerizing Microtubules (MTs), conferring highly dynamic properties to the MTs. However, the precise mechanism of action of SCG10 in the repair of injured neurons remains largely uncertain. Using transcriptomic identification, we discovered that SCG10 expression was downregulated in neurons after Spinal Cord Injury (SCI). Additionally, through mass spectrometry identification, immunoprecipitation, and pull-down assays, we established that SCG10 could interact with Adenosine Kinase (ADK). Furthermore, we developed an excitotoxicity-induced neural injury model and discovered that ADK suppressed injured neurite re-growth, whereas, through overexpression and small molecule interference experiments, SCG10 enhanced it. Moreover, we discovered ADK to be the upstream of SCG10. More importantly, the application of the ADK inhibitor called 5-Iodotubercidin (5-ITu) was found to significantly enhance the recovery of motor function in mice with SCI. Consequently, our findings suggest that ADK plays a negative regulatory role in the repair of injured neurons. Herein, we propose a molecular interaction model of the SCG10-ADK axis to regulate neuronal recovery.
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Affiliation(s)
- Tianjun Chen
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Zhiwan Chen
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Ping Wu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Jianxian Luo
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Qiuling Liu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Hua Yang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Cheng Peng
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Guowei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Hongsheng Lin
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Zhisheng Ji
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China.
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19
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Liu Y, Yan D, Yang L, Chen X, Hu C, Chen M. Stathmin 2 is a potential treatment target for TDP-43 proteinopathy in amyotrophic lateral sclerosis. Transl Neurodegener 2024; 13:20. [PMID: 38600555 PMCID: PMC11007978 DOI: 10.1186/s40035-024-00413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Affiliation(s)
- Yunqing Liu
- Key Laboratory of Brain, Cognition and Education Sciences, South China Normal University, Ministry of Education, Guangzhou, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Dejun Yan
- Key Laboratory of Brain, Cognition and Education Sciences, South China Normal University, Ministry of Education, Guangzhou, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Lin Yang
- Department of Anesthesiology, the Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, China
- Rehabilitation Medicine Institute of Panyu District, Guangzhou, 511499, China
| | - Xian Chen
- Key Laboratory of Brain, Cognition and Education Sciences, South China Normal University, Ministry of Education, Guangzhou, China
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Chun Hu
- Key Laboratory of Brain, Cognition and Education Sciences, South China Normal University, Ministry of Education, Guangzhou, China.
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China.
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
| | - Meilan Chen
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
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20
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Cheng F, Chapman T, Zhang S, Morsch M, Chung R, Lee A, Rayner SL. Understanding age-related pathologic changes in TDP-43 functions and the consequence on RNA splicing and signalling in health and disease. Ageing Res Rev 2024; 96:102246. [PMID: 38401571 DOI: 10.1016/j.arr.2024.102246] [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: 10/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
TAR DNA binding protein-43 (TDP-43) is a key component in RNA splicing which plays a crucial role in the aging process. In neurodegenerative diseases such as amyotrophic lateral sclerosis, frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, TDP-43 can be mutated, mislocalised out of the nucleus of neurons and glial cells and form cytoplasmic inclusions. These TDP-43 alterations can lead to its RNA splicing dysregulation and contribute to mis-splicing of various types of RNA, such as mRNA, microRNA, and circular RNA. These changes can result in the generation of an altered transcriptome and proteome within cells, ultimately changing the diversity and quantity of gene products. In this review, we summarise the findings of novel atypical RNAs resulting from TDP-43 dysfunction and their potential as biomarkers or targets for therapeutic development.
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Affiliation(s)
- Flora Cheng
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
| | - Tyler Chapman
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Selina Zhang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Marco Morsch
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Roger Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
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21
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Sinha IR, Sandal PS, Burns GD, Mallika AP, Irwin KE, Cruz ALF, Wang V, Rodríguez JL, Wong PC, Ling JP. Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587011. [PMID: 38585725 PMCID: PMC10996699 DOI: 10.1101/2024.03.27.587011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.
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Affiliation(s)
- Irika R Sinha
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Parker S Sandal
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Grace D Burns
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Katherine E Irwin
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Anna Lourdes F Cruz
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vania Wang
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Philip C Wong
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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22
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Krus KL, Benitez AM, Strickland A, Milbrandt J, Bloom AJ, DiAntonio A. Reduced STMN2 and pathogenic TDP-43, two hallmarks of ALS, synergize to accelerate motor decline in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585052. [PMID: 38562780 PMCID: PMC10983882 DOI: 10.1101/2024.03.19.585052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pathological TDP-43 loss from the nucleus and cytoplasmic aggregation occurs in almost all cases of ALS and half of frontotemporal dementia patients. Stathmin2 (Stmn2) is a key target of TDP-43 regulation and aberrantly spliced Stmn2 mRNA is found in patients with ALS, frontotemporal dementia, and Alzheimer's Disease. STMN2 participates in the axon injury response and its depletion in vivo partially replicates ALS-like symptoms including progressive motor deficits and distal NMJ denervation. The interaction between STMN2 loss and TDP-43 dysfunction has not been studied in mice because TDP-43 regulates human but not murine Stmn2 splicing. Therefore, we generated trans-heterozygous mice that lack one functional copy of Stmn2 and express one mutant TDP-43Q331K knock-in allele to investigate whether reduced STMN2 function exacerbates TDP-43-dependent pathology. Indeed, we observe synergy between these two alleles, resulting in an early onset, progressive motor deficit. Surprisingly, this behavioral defect is not accompanied by detectable neuropathology in the brain, spinal cord, peripheral nerves or at neuromuscular junctions (NMJs). However, the trans-heterozygous mice exhibit abnormal mitochondrial morphology in their distal axons and NMJs. As both STMN2 and TDP-43 affect mitochondrial dynamics, and neuronal mitochondrial dysfunction is a cardinal feature of many neurodegenerative diseases, this abnormality likely contributes to the observed motor deficit. These findings demonstrate that partial loss of STMN2 significantly exacerbates TDP-43-associated phenotypes, suggesting that STMN2 restoration could ameliorate TDP-43 related disease before the onset of degeneration.
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Affiliation(s)
- Kelsey L. Krus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Ana Morales Benitez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Amy Strickland
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - A. Joseph Bloom
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
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23
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Spence H, Waldron FM, Saleeb RS, Brown AL, Rifai OM, Gilodi M, Read F, Roberts K, Milne G, Wilkinson D, O'Shaughnessy J, Pastore A, Fratta P, Shneider N, Tartaglia GG, Zacco E, Horrocks MH, Gregory JM. RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS. Acta Neuropathol 2024; 147:50. [PMID: 38443601 PMCID: PMC10914926 DOI: 10.1007/s00401-024-02705-1] [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: 11/28/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
TDP-43 is an aggregation-prone protein which accumulates in the hallmark pathological inclusions of amyotrophic lateral sclerosis (ALS). However, the analysis of deeply phenotyped human post-mortem samples has shown that TDP-43 aggregation, revealed by standard antibody methods, correlates poorly with symptom manifestation. Recent identification of cryptic-splicing events, such as the detection of Stathmin-2 (STMN-2) cryptic exons, are providing evidence implicating TDP-43 loss-of-function as a potential driving pathomechanism but the temporal nature of TDP-43 loss and its relation to the disease process and clinical phenotype is not known. To address these outstanding questions, we used a novel RNA aptamer, TDP-43APT, to detect TDP-43 pathology and used single molecule in situ hybridization to sensitively reveal TDP-43 loss-of-function and applied these in a deeply phenotyped human post-mortem tissue cohort. We demonstrate that TDP-43APT identifies pathological TDP-43, detecting aggregation events that cannot be detected by classical antibody stains. We show that nuclear TDP-43 pathology is an early event, occurring prior to cytoplasmic accumulation and is associated with loss-of-function measured by coincident STMN-2 cryptic splicing pathology. Crucially, we show that these pathological features of TDP-43 loss-of-function precede the clinical inflection point and are not required for region specific clinical manifestation. Furthermore, we demonstrate that gain-of-function in the form of extensive cytoplasmic accumulation, but not loss-of-function, is the primary molecular correlate of clinical manifestation. Taken together, our findings demonstrate implications for early diagnostics as the presence of STMN-2 cryptic exons and early TDP-43 aggregation events could be detected prior to symptom onset, holding promise for early intervention in ALS.
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Affiliation(s)
- Holly Spence
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Fergal M Waldron
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Rebecca S Saleeb
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Olivia M Rifai
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Martina Gilodi
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Fiona Read
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kristine Roberts
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK
| | - Gillian Milne
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Debbie Wilkinson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Judi O'Shaughnessy
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | | | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Neil Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | | | - Elsa Zacco
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Jenna M Gregory
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK.
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24
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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25
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Sun Z, Zhang B, Peng Y. Development of novel treatments for amyotrophic lateral sclerosis. Metab Brain Dis 2024; 39:467-482. [PMID: 38078970 DOI: 10.1007/s11011-023-01334-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/01/2023] [Indexed: 03/22/2024]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that causes paralysis whose etiology and pathogenesis have not been fully elucidated. Presently it is incurable and rapidly progressive with a survival of 2-5 years from onset, and no treatments could cure it. Therefore, it is urgent to identify which therapeutic target(s) are more promising to develop treatments that could effectively treat ALS. So far, more than 90 novel treatments for ALS patients have been registered on ClinicalTrials.gov, of which 23 are in clinical trials, 12 have been terminated and the rest suspended. This review will systematically summarize the possible targets of these novel treatments under development or failing based on published literature and information released by sponsors, so as to provide basis and support for subsequent drug research and development.
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Affiliation(s)
- Zhuo Sun
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- Department of Pharmacy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Bo Zhang
- Department of Pharmacy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, 100730, China.
| | - Ying Peng
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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26
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Van Daele SH, Masrori P, Van Damme P, Van Den Bosch L. The sense of antisense therapies in ALS. Trends Mol Med 2024; 30:252-262. [PMID: 38216448 DOI: 10.1016/j.molmed.2023.12.003] [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: 10/05/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/14/2024]
Abstract
Treatment of patients with amyotrophic lateral sclerosis (ALS) has entered a new era now that encouraging results about antisense oligonucleotides (ASOs) are becoming available and a first ASO therapy for ALS has been approved by the FDA. Moreover, there is hope not only that ALS can be stopped but also that symptoms can be reversed. Until now, degrading ASOs seemed to be successful mostly for rarer forms of familial ALS. However, the first attempts to correct mis-splicing events in sporadic ALS are underway, as well as a clinical trial examining interference with a genetic modifier. In this review, we discuss the current status of using ASOs in ALS and the possibilities and pitfalls of this therapeutic strategy.
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Affiliation(s)
- Sien H Van Daele
- KU Leuven - University of Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), Leuven, Belgium; Laboratory of Neurobiology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Pegah Masrori
- KU Leuven - University of Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), Leuven, Belgium; Laboratory of Neurobiology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), Leuven, Belgium; Laboratory of Neurobiology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium.
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), Leuven, Belgium; Laboratory of Neurobiology, VIB Center for Brain & Disease Research, Leuven, Belgium.
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27
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Irwin KE, Jasin P, Braunstein KE, Sinha IR, Garret MA, Bowden KD, Chang K, Troncoso JC, Moghekar A, Oh ES, Raitcheva D, Bartlett D, Miller T, Berry JD, Traynor BJ, Ling JP, Wong PC. A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS-FTD. Nat Med 2024; 30:382-393. [PMID: 38278991 PMCID: PMC10878965 DOI: 10.1038/s41591-023-02788-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects loss of function of TDP-43, and thus detection of proteins containing cryptic exon-encoded neoepitopes in cerebrospinal fluid (CSF) or blood could reveal the earliest stages of TDP-43 dysregulation in patients. Here we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in ALS-FTD, including in presymptomatic C9orf72 mutation carriers. Cryptic hepatoma-derived growth factor-like protein 2 (HDGFL2) accumulates in CSF at significantly higher levels in familial ALS-FTD and sporadic ALS compared with controls and is elevated earlier than neurofilament light and phosphorylated neurofilament heavy chain protein levels in familial disease. Cryptic HDGFL2 can also be detected in blood of individuals with ALS-FTD, including in presymptomatic C9orf72 mutation carriers, and accumulates at levels highly correlated with those in CSF. Our findings indicate that loss of TDP-43 cryptic splicing repression occurs early in disease progression, even presymptomatically, and that detection of the HDGFL2 cryptic neoepitope serves as a potential diagnostic biomarker for ALS, which should facilitate patient recruitment and measurement of target engagement in clinical trials.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Pei Jasin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | - Irika R Sinha
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Mark A Garret
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Kyra D Bowden
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Esther S Oh
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | | | - Timothy Miller
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- National Institute of Neurological Disorders, National Institutes of Health, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA.
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28
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Mohan S, Hakami MA, Dailah HG, Khalid A, Najmi A, Zoghebi K, Halawi MA. Bridging autoimmunity and epigenetics: The influence of lncRNA MALAT1. Pathol Res Pract 2024; 254:155041. [PMID: 38199135 DOI: 10.1016/j.prp.2023.155041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024]
Abstract
Autoimmune disorders represent a heterogeneous spectrum of conditions defined by an immune system's atypical reactivity against endogenous constituents. In the complex anatomy of autoimmune pathogenesis, lncRNAs have appeared as pivotal arbiters orchestrating the mechanisms of ailment initiation, immune cascades, and transcriptional modulation. One such lncRNA, MALAT1, has garnered attention for its potential association with the aetiology of several autoimmune diseases. MALAT1 has been shown to influence a wide spectrum of cellular processes, which include cell multiplication and specialization, as well as apoptosis and inflammation. In autoimmune diseases, MALAT1 exhibits both disease-specific and shared patterns of dysregulation, often correlating with disease severity. The molecular mechanisms underlying MALAT1's impact on autoimmune disorders include epigenetic modifications, alternative splicing, and modulation of gene expression networks. Additionally, MALAT1's intricate interactions with microRNAs, other lncRNAs, and protein-coding genes further underscore its role in immune regulation and autoimmune disease progression. Understanding the contribution of MALAT1 in autoimmune pathogenesis across different diseases could offer valuable insights into shared pathways, thereby clearing a path for the creation of innovative and enhanced therapeutic approaches to address these complex disorders. This review aims to elucidate the complex role of MALAT1 in autoimmune disorders, encompassing rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease (Crohn's disease and ulcerative colitis), type 1 diabetes, systemic lupus erythematosus, and psoriasis. Furthermore, it discusses the potential of MALAT1 as a diagnostic biomarker, therapeutic target, and prognostic indicator.
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Affiliation(s)
- Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; School of Health Sciences, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India; Center for Global health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia.
| | - Hamad Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Maryam A Halawi
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
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29
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Bryce-Smith S, Brown AL, Mehta PR, Mattedi F, Mikheenko A, Barattucci S, Zanovello M, Dattilo D, Yome M, Hill SE, Qi YA, Wilkins OG, Sun K, Ryadnov E, Wan Y, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Ward M, Secrier M, Fratta P. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576625. [PMID: 38313254 PMCID: PMC10836071 DOI: 10.1101/2024.01.22.576625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Francesca Mattedi
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dario Dattilo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Yome
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E. Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yue A. Qi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Kai Sun
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Yixuan Wan
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Jose Norberto S. Vargas
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicol Birsa
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
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30
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Zeng Y, Lovchykova A, Akiyama T, Liu C, Guo C, Jawahar VM, Sianto O, Calliari A, Prudencio M, Dickson DW, Petrucelli L, Gitler AD. TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575730. [PMID: 38328059 PMCID: PMC10849503 DOI: 10.1101/2024.01.22.575730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B) and providing evidence that alternative polyadenylation is a new facet of TDP-43 pathology.
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Affiliation(s)
- Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Caiwei Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vidhya Maheswari Jawahar
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Odilia Sianto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Calliari
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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31
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Arnold FJ, Cui Y, Michels S, Colwin MR, Stockford C, Ye W, Tam OH, Menon S, Situ WG, Ehsani KCK, Howard S, Hammell MG, Li W, La Spada AR. TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in ALS/FTD and related disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576709. [PMID: 38328178 PMCID: PMC10849549 DOI: 10.1101/2024.01.22.576709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Nuclear clearance and cytoplasmic aggregation of the RNA-binding protein TDP-43 are observed in many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and fronto- temporal dementia (FTD). Although TDP-43 dysregulation of splicing has emerged as a key event in these diseases, TDP-43 can also regulate polyadenylation; yet, this has not been adequately studied. Here, we applied the dynamic analysis of polyadenylation from RNA-seq (DaPars) tool to ALS/FTD transcriptome datasets, and report extensive alternative polyadenylation (APA) upon TDP-43 alteration in ALS/FTD cell models and postmortem ALS/FTD neuronal nuclei. Importantly, many identified APA genes highlight pathways implicated in ALS/FTD pathogenesis. To determine the functional significance of APA elicited by TDP-43 nuclear depletion, we examined microtubule affinity regulating kinase 3 (MARK3). Nuclear loss of TDP-43 yielded increased expression of MARK3 transcripts with longer 3'UTRs, resulting in greater transcript stability and elevated MARK3 protein levels, which promotes increased neuronal tau S262 phosphorylation. Our findings define changes in polyadenylation site selection as a previously unrecognized feature of TDP-43-driven disease pathology in ALS/FTD and highlight a potentially novel mechanistic link between TDP-43 dysfunction and tau regulation.
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32
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Shen Y, Ali M, Timsina J, Wang C, Do A, Western D, Liu M, Gorijala P, Budde J, Liu H, Gordon B, McDade E, Morris JC, Llibre-Guerra JJ, Bateman RJ, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Goate A, Renton AE, Surace EI, Johnson ECB, Levey AI, Alvarez I, Levin J, Ringman JM, Allegri RF, Seyfried N, Day GS, Wu Q, Fernández MV, Ibanez L, Sung YJ, Cruchaga C. Systematic proteomics in Autosomal dominant Alzheimer's disease reveals decades-early changes of CSF proteins in neuronal death, and immune pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301242. [PMID: 38260583 PMCID: PMC10802763 DOI: 10.1101/2024.01.12.24301242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background To date, there is no high throughput proteomic study in the context of Autosomal Dominant Alzheimer's disease (ADAD). Here, we aimed to characterize early CSF proteome changes in ADAD and leverage them as potential biomarkers for disease monitoring and therapeutic strategies. Methods We utilized Somascan® 7K assay to quantify protein levels in the CSF from 291 mutation carriers (MCs) and 185 non-carriers (NCs). We employed a multi-layer regression model to identify proteins with different pseudo-trajectories between MCs and NCs. We replicated the results using publicly available ADAD datasets as well as proteomic data from sporadic Alzheimer's disease (sAD). To biologically contextualize the results, we performed network and pathway enrichment analyses. Machine learning was applied to create and validate predictive models. Findings We identified 125 proteins with significantly different pseudo-trajectories between MCs and NCs. Twelve proteins showed changes even before the traditional AD biomarkers (Aβ42, tau, ptau). These 125 proteins belong to three different modules that are associated with age at onset: 1) early stage module associated with stress response, glutamate metabolism, and mitochondria damage; 2) the middle stage module, enriched in neuronal death and apoptosis; and 3) the presymptomatic stage module was characterized by changes in microglia, and cell-to-cell communication processes, indicating an attempt of rebuilding and establishing new connections to maintain functionality. Machine learning identified a subset of nine proteins that can differentiate MCs from NCs better than traditional AD biomarkers (AUC>0.89). Interpretation Our findings comprehensively described early proteomic changes associated with ADAD and captured specific biological processes that happen in the early phases of the disease, fifteen to five years before clinical onset. We identified a small subset of proteins with the potentials to become therapy-monitoring biomarkers of ADAD MCs. Funding Proteomic data generation was supported by NIH: RF1AG044546.
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33
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Zhu L, Deng F, Bai D, Hou J, Jia Q, Zhang C, Ou K, Li S, Li XJ, Yin P. Loss of TDP-43 mediates severe neurotoxicity by suppressing PJA1 gene transcription in the monkey brain. Cell Mol Life Sci 2024; 81:16. [PMID: 38194085 PMCID: PMC11072099 DOI: 10.1007/s00018-023-05066-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
The nuclear loss and cytoplasmic accumulation of TDP-43 (TAR DNA/RNA binding protein 43) are pathological hallmarks of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previously, we reported that the primate-specific cleavage of TDP-43 accounts for its cytoplasmic mislocalization in patients' brains. This prompted us to investigate further whether and how the loss of nuclear TDP-43 mediates neuropathology in primate brain. In this study, we report that TDP-43 knockdown at the similar effectiveness, induces more damage to neuronal cells in the monkey brain than rodent mouse. Importantly, the loss of TDP-43 suppresses the E3 ubiquitin ligase PJA1 expression in the monkey brain at transcriptional level, but yields an opposite upregulation of PJA1 in the mouse brain. This distinct effect is due to the species-dependent binding of nuclear TDP-43 to the unique promoter sequences of the PJA1 genes. Further analyses reveal that the reduction of PJA1 accelerates neurotoxicity, whereas overexpressing PJA1 diminishes neuronal cell death by the TDP-43 knockdown in vivo. Our findings not only uncover a novel primate-specific neurotoxic contribution to the loss of function theory of TDP-43 proteinopathy, but also underscore a potential therapeutic approach of PJA1 to the loss of nuclear TDP-43.
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Affiliation(s)
- Longhong Zhu
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Fuyu Deng
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Dazhang Bai
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, 637000, China
- Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, 637000, China
| | - Junqi Hou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Qingqing Jia
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Chen Zhang
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Kaili Ou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
| | - Peng Yin
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
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34
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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35
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López-Erauskin J, Bravo-Hernandez M, Presa M, Baughn MW, Melamed Z, Beccari MS, Agra de Almeida Quadros AR, Arnold-Garcia O, Zuberi A, Ling K, Platoshyn O, Niño-Jara E, Ndayambaje IS, McAlonis-Downes M, Cabrera L, Artates JW, Ryan J, Hermann A, Ravits J, Bennett CF, Jafar-Nejad P, Rigo F, Marsala M, Lutz CM, Cleveland DW, Lagier-Tourenne C. Stathmin-2 loss leads to neurofilament-dependent axonal collapse driving motor and sensory denervation. Nat Neurosci 2024; 27:34-47. [PMID: 37996528 PMCID: PMC10842032 DOI: 10.1038/s41593-023-01496-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/16/2023] [Indexed: 11/25/2023]
Abstract
The mRNA transcript of the human STMN2 gene, encoding for stathmin-2 protein (also called SCG10), is profoundly impacted by TAR DNA-binding protein 43 (TDP-43) loss of function. The latter is a hallmark of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Using a combination of approaches, including transient antisense oligonucleotide-mediated suppression, sustained shRNA-induced depletion in aging mice, and germline deletion, we show that stathmin-2 has an important role in the establishment and maintenance of neurofilament-dependent axoplasmic organization that is critical for preserving the caliber and conduction velocity of myelinated large-diameter axons. Persistent stathmin-2 loss in adult mice results in pathologies found in ALS, including reduced interneurofilament spacing, axonal caliber collapse that drives tearing within outer myelin layers, diminished conduction velocity, progressive motor and sensory deficits, and muscle denervation. These findings reinforce restoration of stathmin-2 as an attractive therapeutic approach for ALS and other TDP-43-dependent neurodegenerative diseases.
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Affiliation(s)
- Jone López-Erauskin
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Mariana Bravo-Hernandez
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | | | - Michael W Baughn
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melinda S Beccari
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ana Rita Agra de Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olatz Arnold-Garcia
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | | | - Karen Ling
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Oleksandr Platoshyn
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Elkin Niño-Jara
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa McAlonis-Downes
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Larissa Cabrera
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Jonathan W Artates
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Anita Hermann
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Martin Marsala
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Don W Cleveland
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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36
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Dogan EO, Bouley J, Zhong J, Harkins AL, Keeler AM, Bosco DA, Brown RH, Henninger N. Genetic ablation of Sarm1 attenuates expression and mislocalization of phosphorylated TDP-43 after mouse repetitive traumatic brain injury. Acta Neuropathol Commun 2023; 11:206. [PMID: 38124145 PMCID: PMC10731794 DOI: 10.1186/s40478-023-01709-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Traumatic brain injury (TBI), particularly when moderate-to-severe and repetitive, is a strong environmental risk factor for several progressive neurodegenerative disorders. Mislocalization and deposition of transactive response DNA binding protein 43 (TDP-43) has been reported in both TBI and TBI-associated neurodegenerative diseases. It has been hypothesized that axonal pathology, an early event after TBI, may promote TDP-43 dysregulation and serve as a trigger for neurodegenerative processes. We sought to determine whether blocking the prodegenerative Sarm1 (sterile alpha and TIR motif containing 1) axon death pathway attenuates TDP-43 pathology after TBI. We subjected 111 male Sarm1 wild type, hemizygous, and knockout mice to moderate-to-severe repetitive TBI (rTBI) using a previously established injury paradigm. We conducted serial neurological assessments followed by histological analyses (NeuN, MBP, Iba-1, GFAP, pTDP-43, and AT8) at 1 month after rTBI. Genetic ablation of the Sarm1 gene attenuated the expression and mislocalization of phosphorylated TDP-43 (pTDP-43) and accumulation of pTau. In addition, Sarm1 knockout mice had significantly improved cortical neuronal and axonal integrity, functional deficits, and improved overall survival after rTBI. In contrast, removal of one Sarm1 allele delayed, but did not prevent, neurological deficits and neuroaxonal loss. Nevertheless, Sarm1 haploinsufficient mice showed significantly less microgliosis, pTDP-43 pathology, and pTau accumulation when compared to wild type mice. These data indicate that the Sarm1-mediated prodegenerative pathway contributes to pathogenesis in rTBI including the pathological accumulation of pTDP-43. This suggests that anti-Sarm1 therapeutics are a viable approach for preserving neurological function after moderate-to-severe rTBI.
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Affiliation(s)
- Elif O Dogan
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - James Bouley
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Jianjun Zhong
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ashley L Harkins
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Allison M Keeler
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Nils Henninger
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA.
- Department of Psychiatry, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA.
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37
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Rothstein JD, Warlick C, Coyne AN. Highly variable molecular signatures of TDP-43 loss of function are associated with nuclear pore complex injury in a population study of sporadic ALS patient iPSNs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571299. [PMID: 38168312 PMCID: PMC10760028 DOI: 10.1101/2023.12.12.571299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The nuclear depletion and cytoplasmic aggregation of the RNA binding protein TDP-43 is widely considered a pathological hallmark of Amyotrophic Lateral Sclerosis (ALS) and related neurodegenerative diseases. Recent studies have artificially reduced TDP-43 in wildtype human neurons to replicate loss of function associated events. Although this prior work has defined a number of gene expression and mRNA splicing changes that occur in a TDP-43 dependent manner, it is unclear how these alterations relate to authentic ALS where TDP-43 is not depleted from the cell but miscompartmentalized to variable extents. Here, in this population study, we generate ~30,000 qRT-PCR data points spanning 20 genes in induced pluripotent stem cell (iPSC) derived neurons (iPSNs) from >150 control, C9orf72 ALS/FTD, and sALS patients to examine molecular signatures of TDP-43 dysfunction. This data set defines a time dependent and variable profile of individual molecular hallmarks of TDP-43 loss of function within and amongst individual patient lines. Importantly, nearly identical changes are observed in postmortem CNS tissues obtained from a subset of patients whose iPSNs were examined. Notably, these studies provide evidence that induction of nuclear pore complex (NPC) injury via reduction of the transmembrane Nup POM121 in wildtype iPSNs is sufficient to phenocopy disease associated signatured of TDP-43 loss of function thereby directly linking NPC integrity to TDP-43 loss of function. Therapeutically, we demonstrate that the expression of all mRNA species associated with TDP-43 loss of function can be restored in sALS iPSNs via two independent methods to repair NPC injury. Collectively, this data 1) represents a substantial resource for the community to examine TDP-43 loss of function events in authentic sALS patient iPSNs, 2) demonstrates that patient derived iPSNs can accurately reflect actual TDP-43 associated alterations in patient brain, and 3) that targeting NPC injury events can be preclinically and reliably accomplished in an iPSN based platform of a sporadic disease.
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Affiliation(s)
- Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | - Caroline Warlick
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | - Alyssa N. Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205
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38
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [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: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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39
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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.
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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
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40
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Okano H, Morimoto S, Kato C, Nakahara J, Takahashi S. Induced pluripotent stem cells-based disease modeling, drug screening, clinical trials, and reverse translational research for amyotrophic lateral sclerosis. J Neurochem 2023; 167:603-614. [PMID: 37952981 DOI: 10.1111/jnc.16005] [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: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023]
Abstract
It has been more than 10 years since the hopes for disease modeling and drug discovery using induced pluripotent stem cell (iPSC) technology boomed. Recently, clinical trials have been conducted with drugs identified using this technology, and some promising results have been reported. For amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease, several groups have identified candidate drugs, ezogabine (retigabine), bosutinib, and ropinirole, using iPSCs-based drug discovery, and clinical trials using these drugs have been conducted, yielding interesting results. In our previous study, an iPSCs-based drug repurposing approach was utilized to show the potential of ropinirole hydrochloride (ROPI) in reducing ALS-specific pathological phenotypes. Recently, a phase 1/2a trial was conducted to investigate the effects of ropinirole on ALS further. This double-blind, randomized, placebo-controlled study confirmed the safety and tolerability of and provided evidence of its ability to delay disease progression and prolong the time to respiratory failure in ALS patients. Furthermore, in the reverse translational research, in vitro characterization of patient-derived iPSCs-motor neurons (MNs) mimicked the therapeutic effects of ROPI in vivo, suggesting the potential application of this technology to the precision medicine of ALS. Interestingly, RNA-seq data showed that ROPI treatment suppressed the sterol regulatory element-binding protein 2-dependent cholesterol biosynthesis pathway. Therefore, this pathway may be involved in the therapeutic effect of ROPI on ALS. The possibility that this pathway may be involved in the therapeutic effect of ALS was demonstrated. Finally, new future strategies for ALS using iPSCs technology will be discussed in this paper.
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Affiliation(s)
- Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Satoru Morimoto
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Chris Kato
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Jin Nakahara
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Shinichi Takahashi
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
- Department of Neurology and Stroke, Saitama Medical University International Medical Center, Saitama, Japan
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41
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Wilkins OG, Chien MZ, Wlaschin JJ, Pisliakova M, Thompson D, Digby H, Simkin RL, Diaz JA, Mehta PR, Keuss MJ, Zanovello M, Brown AL, Harley P, Darbey A, Karda R, Fisher EM, Cunningham TJ, Le Pichon CE, Ule J, Fratta P. Creation of de novo cryptic splicing for ALS/FTD precision medicine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.565967. [PMID: 38014203 PMCID: PMC10680699 DOI: 10.1101/2023.11.15.565967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe "TDP-REG", a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOF in vitro and in vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate the UNC13A cryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals.
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Affiliation(s)
- Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Max Z.Y.J. Chien
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Josette J. Wlaschin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Maria Pisliakova
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Holly Digby
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Rebecca L. Simkin
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Juan Antinao Diaz
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Annalucia Darbey
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Rajvinder Karda
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Tom J. Cunningham
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Claire E. Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Jernej Ule
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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42
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Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, England WE, Singha M, Stocksdale JT, Jang KH, Jung S, McKnight JI, Ho LN, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565004. [PMID: 37961595 PMCID: PMC10635028 DOI: 10.1101/2023.10.31.565004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene encoding huntingtin. Prior reports have established a correlation between CAG expanded HTT and altered gene expression. However, the mechanisms leading to disruption of RNA processing in HD remain unclear. Here, our analysis of the reported HTT protein interactome identifies interactions with known RNA-binding proteins (RBPs). Total, long-read sequencing and targeted RASL-seq of RNAs from cortex and striatum of the HD mouse model R6/2 reveals increased exon skipping which is confirmed in Q150 and Q175 knock-in mice and in HD human brain. We identify the RBP TDP-43 and the N6-methyladenosine (m6A) writer protein methyltransferase 3 (METTL3) to be upstream regulators of exon skipping in HD. Along with this novel mechanistic insight, we observe decreased nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 in HD mice and human brain. In addition, TDP-43 co-localizes with HTT in human HD brain forming novel nuclear aggregate-like bodies distinct from mutant HTT inclusions or previously observed TDP-43 pathologies. Binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a novel mechanism underlying alternative splicing/unannotated exon usage in HD and highlights the critical nature of TDP-43 function across multiple neurodegenerative diseases.
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43
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Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. Nucleic Acids Res 2023; 51:9610-9628. [PMID: 37587694 PMCID: PMC10570059 DOI: 10.1093/nar/gkad665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Gene expression is a multistep process and crosstalk among regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant gene expression coordination, we performed a systematic reverse-genetic interaction screen in C. elegans, combining RNA binding protein (RBP) and transcription factor (TF) mutants to generate over 100 RBP;TF double mutants. We identified many unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no effect on the health of the organism. However, fust-1;ceh-14 and tdp-1;ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-Seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. A skipped exon in the polyglutamine-repeat protein pqn-41 is aberrantly included in tdp-1 mutants, and genetically forcing this exon to be skipped in tdp-1;ceh-14 double mutants rescues their fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility and a shared molecular role in exon inhibition.
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Affiliation(s)
- Morgan Taylor
- Southern Methodist University, Dallas, TX 75205, USA
| | - Olivia Marx
- Southern Methodist University, Dallas, TX 75205, USA
| | - Adam Norris
- Southern Methodist University, Dallas, TX 75205, USA
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44
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Gittings LM, Alsop EB, Antone J, Singer M, Whitsett TG, Sattler R, Van Keuren-Jensen K. Cryptic exon detection and transcriptomic changes revealed in single-nuclei RNA sequencing of C9ORF72 patients spanning the ALS-FTD spectrum. Acta Neuropathol 2023; 146:433-450. [PMID: 37466726 PMCID: PMC10412668 DOI: 10.1007/s00401-023-02599-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023]
Abstract
The C9ORF72-linked diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by the nuclear depletion and cytoplasmic accumulation of TAR DNA-binding protein 43 (TDP-43). Recent studies have shown that the loss of TDP-43 function leads to the inclusion of cryptic exons (CE) in several RNA transcript targets of TDP-43. Here, we show for the first time the detection of CEs in a single-nuclei RNA sequencing (snRNA-seq) dataset obtained from frontal and occipital cortices of C9ORF72 patients that phenotypically span the ALS-FTD disease spectrum. We assessed each cellular cluster for detection of recently described TDP-43-induced CEs. Transcripts containing CEs in the genes STMN2 and KALRN were detected in the frontal cortex of all C9ORF72 disease groups with the highest frequency in excitatory neurons in the C9ORF72-FTD group. Within the excitatory neurons, the cluster with the highest proportion of cells containing a CE had transcriptomic similarities to von Economo neurons, which are known to be vulnerable to TDP-43 pathology and selectively lost in C9ORF72-FTD. Differential gene expression and pathway analysis of CE-containing neurons revealed multiple dysregulated metabolic processes. Our findings reveal novel insights into the transcriptomic changes of neurons vulnerable to TDP-43 pathology.
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Affiliation(s)
- Lauren M Gittings
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Eric B Alsop
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Jerry Antone
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Mo Singer
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Timothy G Whitsett
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA
| | - Rita Sattler
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.
| | - Kendall Van Keuren-Jensen
- Neurogenomics Division, Translational Genomics Research Institute, part of City of Hope, Phoenix, AZ, USA.
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45
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Lu J, Li Z, Gitler AD, Lu B. Drugging "undruggable" neurodegenerative disease targets with small molecules. Sci Bull (Beijing) 2023; 68:1715-1718. [PMID: 37468412 DOI: 10.1016/j.scib.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Affiliation(s)
- Junmei Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, New Cornerstone Science Laboratory, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhaoyang Li
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, New Cornerstone Science Laboratory, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Aaron D Gitler
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, New Cornerstone Science Laboratory, School of Life Sciences, Fudan University, Shanghai 200438, China.
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46
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Estades Ayuso V, Pickles S, Todd T, Yue M, Jansen-West K, Song Y, González Bejarano J, Rawlinson B, DeTure M, Graff-Radford NR, Boeve BF, Knopman DS, Petersen RC, Dickson DW, Josephs KA, Petrucelli L, Prudencio M. TDP-43-regulated cryptic RNAs accumulate in Alzheimer's disease brains. Mol Neurodegener 2023; 18:57. [PMID: 37605276 PMCID: PMC10441763 DOI: 10.1186/s13024-023-00646-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Inclusions of TAR DNA-binding protein 43 kDa (TDP-43) has been designated limbic-predominant, age-related TDP-43 encephalopathy (LATE), with or without co-occurrence of Alzheimer's disease (AD). Approximately, 30-70% AD cases present TDP-43 proteinopathy (AD-TDP), and a greater disease severity compared to AD patients without TDP-43 pathology. However, it remains unclear to what extent TDP-43 dysfunction is involved in AD pathogenesis. METHODS To investigate whether TDP-43 dysfunction is a prominent feature in AD-TDP cases, we evaluated whether non-conserved cryptic exons, which serve as a marker of TDP-43 dysfunction in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP), accumulate in AD-TDP brains. We assessed a cohort of 192 post-mortem brains from three different brain regions: amygdala, hippocampus, and frontal cortex. Following RNA and protein extraction, qRT-PCR and immunoassays were performed to quantify the accumulation of cryptic RNA targets and phosphorylated TDP-43 pathology, respectively. RESULTS We detected the accumulation of misspliced cryptic or skiptic RNAs of STMN2, KCNQ2, UNC13A, CAMK2B, and SYT7 in the amygdala and hippocampus of AD-TDP cases. The topographic distribution of cryptic RNA accumulation mimicked that of phosphorylated TDP-43, regardless of TDP-43 subtype classification. Further, cryptic RNAs efficiently discriminated AD-TDP cases from controls. CONCLUSIONS Overall, our results indicate that cryptic RNAs may represent an intriguing new therapeutic and diagnostic target in AD, and that methods aimed at detecting and measuring these species in patient biofluids could be used as a reliable tool to assess TDP-43 pathology in AD. Our work also raises the possibility that TDP-43 dysfunction and related changes in cryptic splicing could represent a common molecular mechanism shared between AD-TDP and FTLD-TDP.
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Affiliation(s)
- Virginia Estades Ayuso
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Tiffany Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Yuping Song
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | | | | | | | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.
- Department of Research, Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.
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47
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Pickles S, Zanetti Alepuz D, Koike Y, Yue M, Tong J, Liu P, Zhou Y, Jansen-West K, Daughrity LM, Song Y, DeTure M, Oskarsson B, Graff-Radford NR, Boeve BF, Petersen RC, Josephs KA, Dickson DW, Ward ME, Dong L, Prudencio M, Cook CN, Petrucelli L. CRISPR interference to evaluate modifiers of C9ORF72-mediated toxicity in FTD. Front Cell Dev Biol 2023; 11:1251551. [PMID: 37614226 PMCID: PMC10443592 DOI: 10.3389/fcell.2023.1251551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023] Open
Abstract
Treatments for neurodegenerative disease, including Frontotemporal dementia (FTD) and Amyotrophic lateral sclerosis (ALS), remain rather limited, underscoring the need for greater mechanistic insight and disease-relevant models. Our ability to develop novel disease models of genetic risk factors, disease modifiers, and other FTD/ALS-relevant targets is impeded by the significant amount of time and capital required to develop conventional knockout and transgenic mice. To overcome these limitations, we have generated a novel CRISPRi interference (CRISPRi) knockin mouse. CRISPRi uses a catalytically dead form of Cas9, fused to a transcriptional repressor to knockdown protein expression, following the introduction of single guide RNA against the gene of interest. To validate the utility of this model we have selected the TAR DNA binding protein (TDP-43) splicing target, stathmin-2 (STMN2). STMN2 RNA is downregulated in FTD/ALS due to loss of TDP-43 activity and STMN2 loss is suggested to play a role in ALS pathogenesis. The involvement of STMN2 loss of function in FTD has yet to be determined. We find that STMN2 protein levels in familial FTD cases are significantly reduced compared to controls, supporting that STMN2 depletion may be involved in the pathogenesis of FTD. Here, we provide proof-of-concept that we can simultaneously knock down Stmn2 and express the expanded repeat in the Chromosome 9 open reading frame 72 (C9ORF72) gene, successfully replicating features of C9-associated pathology. Of interest, depletion of Stmn2 had no effect on expression or deposition of dipeptide repeat proteins (DPRs), but significantly decreased the number of phosphorylated Tdp-43 (pTdp-43) inclusions. We submit that our novel CRISPRi mouse provides a versatile and rapid method to silence gene expression in vivo and propose this model will be useful to understand gene function in isolation or in the context of other neurodegenerative disease models.
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Affiliation(s)
- Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | | | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Jimei Tong
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Pinghu Liu
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yugui Zhou
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | | | - Yuping Song
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, United States
| | | | - Bradley F. Boeve
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | | | - Keith A. Josephs
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
- Department of Neurology, Mayo Clinic, Jacksonville, FL, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | - Casey N. Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
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48
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Rojas F, Aguilar R, Almeida S, Fritz E, Corvalán D, Ampuero E, Abarzúa S, Garcés P, Amaro A, Diaz I, Arredondo C, Cortes N, Sanchez M, Mercado C, Varela-Nallar L, Gao FB, Montecino M, van Zundert B. Mature iPSC-derived astrocytes of an ALS/FTD patient carrying the TDP43 A90V mutation display a mild reactive state and release polyP toxic to motoneurons. Front Cell Dev Biol 2023; 11:1226604. [PMID: 37645251 PMCID: PMC10461635 DOI: 10.3389/fcell.2023.1226604] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
Astrocytes play a critical role in the maintenance of a healthy central nervous system and astrocyte dysfunction has been implicated in various neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). There is compelling evidence that mouse and human ALS and ALS/FTD astrocytes can reduce the number of healthy wild-type motoneurons (MNs) in co-cultures or after treatment with astrocyte conditioned media (ACM), independently of their genotype. A growing number of studies have shown that soluble toxic factor(s) in the ACM cause non-cell autonomous MN death, including our recent identification of inorganic polyphosphate (polyP) that is excessively released from mouse primary astrocytes (SOD1, TARDBP, and C9ORF72) and human induced pluripotent stem cells (iPSC)-derived astrocytes (TARDBP) to kill MNs. However, others have reported that astrocytes carrying mutant TDP43 do not produce detectable MN toxicity. This controversy is likely to arise from the findings that human iPSC-derived astrocytes exhibit a rather immature and/or reactive phenotype in a number of studies. Here, we have succeeded in generating a highly homogenous population of functional quiescent mature astrocytes from control subject iPSCs. Using identical conditions, we also generated mature astrocytes from an ALS/FTD patient carrying the TDP43A90V mutation. These mutant TDP43 patient-derived astrocytes exhibit key pathological hallmarks, including enhanced cytoplasmic TDP-43 and polyP levels. Additionally, mutant TDP43 astrocytes displayed a mild reactive signature and an aberrant function as they were unable to promote synaptogenesis of hippocampal neurons. The polyP-dependent neurotoxic nature of the TDP43A90V mutation was further confirmed as neutralization of polyP in ACM derived from mutant TDP43 astrocytes prevented MN death. Our results establish that human astrocytes carrying the TDP43A90V mutation exhibit a cell-autonomous pathological signature, hence providing an experimental model to decipher the molecular mechanisms underlying the generation of the neurotoxic phenotype.
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Affiliation(s)
- Fabiola Rojas
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Aguilar
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School (UMMS), Worcester, MA, United States
| | - Elsa Fritz
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Daniela Corvalán
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Estibaliz Ampuero
- Department of Biology, Faculty of Chemistry and Biology, Universidad de Santiago, Santiago, Chile
| | - Sebastián Abarzúa
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Polett Garcés
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Armando Amaro
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Iván Diaz
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Cristian Arredondo
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Nicole Cortes
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Mario Sanchez
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Constanza Mercado
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Lorena Varela-Nallar
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School (UMMS), Worcester, MA, United States
| | - Martin Montecino
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
- Millennium Institute Center for Genome Regulation CRG, Santiago, Chile
| | - Brigitte van Zundert
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile
- Department of Neurology, University of Massachusetts Chan Medical School (UMMS), Worcester, MA, United States
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49
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Onda-Ohto A, Hasegawa-Ogawa M, Matsuno H, Shiraishi T, Bono K, Hiraki H, Kanegae Y, Iguchi Y, Okano HJ. Specific vulnerability of iPSC-derived motor neurons with TDP-43 gene mutation to oxidative stress. Mol Brain 2023; 16:62. [PMID: 37496071 PMCID: PMC10369818 DOI: 10.1186/s13041-023-01050-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a disease that affects motor neurons and has a poor prognosis. We focused on TAR DNA-binding protein 43 kDa (TDP-43), which is a common component of neuronal inclusions in many ALS patients. To analyze the contribution of TDP-43 mutations to ALS in human cells, we first introduced TDP-43 mutations into healthy human iPSCs using CRISPR/Cas9 gene editing technology, induced the differentiation of these cells into motor and sensory neurons, and analyzed factors that are assumed to be altered in or associated with ALS (cell morphology, TDP-43 localization and aggregate formation, cell death, TDP-43 splicing function, etc.). We aimed to clarify the pathological alterations caused solely by TDP-43 mutation, i.e., the changes in human iPSC-derived neurons with TDP-43 mutation compared with those with the same genetic background except TDP-43 mutation. Oxidative stress induced by hydrogen peroxide administration caused the death of TDP-43 mutant-expressing motor neurons but not in sensory neurons, indicating the specific vulnerability of human iPSC-derived motor neurons with TDP-43 mutation to oxidative stress. In our model, we observed aggregate formation in a small fraction of TDP-43 mutant-expressing motor neurons, suggesting that aggregate formation seems to be related to ALS pathology but not the direct cause of cell death. This study provides basic knowledge for elucidating the pathogenesis of ALS and developing treatments for the disease.
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Affiliation(s)
- Asako Onda-Ohto
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Minami Hasegawa-Ogawa
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Hiromasa Matsuno
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Tomotaka Shiraishi
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Keiko Bono
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Hiromi Hiraki
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Yumi Kanegae
- Core Research Facilities, Research Center for Medical Sciences, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Yasuyuki Iguchi
- Department of Neurology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Hirotaka James Okano
- Division of Regenerative Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.
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50
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Menge S, Decker L, Freischmidt A. Restoring expression of Stathmin-2: a novel strategy to treat TDP-43 proteinopathies. Signal Transduct Target Ther 2023; 8:266. [PMID: 37433765 DOI: 10.1038/s41392-023-01533-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 07/13/2023] Open
Affiliation(s)
- Sonja Menge
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Lorena Decker
- Department of Neurology, Ulm University, 89081, Ulm, Germany
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