1
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Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [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: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
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Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
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2
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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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3
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Garcia-Montojo M, Fathi S, Rastegar C, Simula ER, Doucet-O'Hare T, Cheng YHH, Abrams RPM, Pasternack N, Malik N, Bachani M, Disanza B, Maric D, Lee MH, Wang H, Santamaria U, Li W, Sampson K, Lorenzo JR, Sanchez IE, Mezghrani A, Li Y, Sechi LA, Pineda S, Heiman M, Kellis M, Steiner J, Nath A. TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression. Nat Commun 2024; 15:4163. [PMID: 38755145 PMCID: PMC11099023 DOI: 10.1038/s41467-024-48488-7] [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: 02/04/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) proteinopathy in brain cells is the hallmark of amyotrophic lateral sclerosis (ALS) but its cause remains elusive. Asparaginase-like-1 protein (ASRGL1) cleaves isoaspartates, which alter protein folding and susceptibility to proteolysis. ASRGL1 gene harbors a copy of the human endogenous retrovirus HML-2, whose overexpression contributes to ALS pathogenesis. Here we show that ASRGL1 expression was diminished in ALS brain samples by RNA sequencing, immunohistochemistry, and western blotting. TDP-43 and ASRGL1 colocalized in neurons but, in the absence of ASRGL1, TDP-43 aggregated in the cytoplasm. TDP-43 was found to be prone to isoaspartate formation and a substrate for ASRGL1. ASRGL1 silencing triggered accumulation of misfolded, fragmented, phosphorylated and mislocalized TDP-43 in cultured neurons and motor cortex of female mice. Overexpression of ASRGL1 restored neuronal viability. Overexpression of HML-2 led to ASRGL1 silencing. Loss of ASRGL1 leading to TDP-43 aggregation may be a critical mechanism in ALS pathophysiology.
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Affiliation(s)
- Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Saeed Fathi
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cyrus Rastegar
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elena Rita Simula
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | - Tara Doucet-O'Hare
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Y H Hank Cheng
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rachel P M Abrams
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nasir Malik
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Muzna Bachani
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brianna Disanza
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Myoung-Hwa Lee
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Herui Wang
- Neuro-Oncology Branch, National Cancer Institute (NIH), Bethesda, MD, USA
| | - Ulisses Santamaria
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kevon Sampson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Juan Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Ignacio E Sanchez
- Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alexandre Mezghrani
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Centre de Biologie Structurale, Centre national de la recherche scientifique (CNRS), Montpellier, France
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Leonardo Antonio Sechi
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph Steiner
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA.
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Shao H, Huang J, Wang H, Wang G, Yang X, Cheng M, Sun C, Zou L, Yang Q, Zhang D, Liu Z, Jiang X, Shi L, Shi P, Han B, Jiao B. Fused in sarcoma (FUS) inhibits milk production efficiency in mammals. Nat Commun 2024; 15:3953. [PMID: 38729967 PMCID: PMC11087553 DOI: 10.1038/s41467-024-48428-5] [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: 08/25/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Efficient milk production in mammals confers evolutionary advantages by facilitating the transmission of energy from mother to offspring. However, the regulatory mechanism responsible for the gradual establishment of milk production efficiency in mammals, from marsupials to eutherians, remains elusive. Here, we find that mammary gland of the marsupial sugar glider contained milk components during adolescence, and that mammary gland development is less dynamically cyclic compared to that in placental mammals. Furthermore, fused in sarcoma (FUS) is found to be partially responsible for this establishment of low efficiency. In mouse model, FUS inhibit mammary epithelial cell differentiation through the cyclin-dependent kinase inhibitor p57Kip2, leading to lactation failure and pup starvation. Clinically, FUS levels are negatively correlated with milk production in lactating women. Overall, our results shed light on FUS as a negative regulator of milk production, providing a potential mechanism for the establishment of milk production from marsupial to eutherian mammals.
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Affiliation(s)
- Haili Shao
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jipeng Huang
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hui Wang
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guolei Wang
- Department of Obstetrics, Weifang People's Hospital, Weifang, Shandong, 261042, China
| | - Xu Yang
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Mei Cheng
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Changjie Sun
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Li Zou
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Qin Yang
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Dandan Zhang
- Luoyang Maternal and Child Health Hospital, Luoyang, Henan, 471000, China
| | - Zhen Liu
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xuelong Jiang
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lei Shi
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Peng Shi
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650203, China
| | - Baowei Han
- Luoyang Maternal and Child Health Hospital, Luoyang, Henan, 471000, China.
| | - Baowei Jiao
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650203, China.
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5
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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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6
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Li X, Pura J, Allen A, Owzar K, Lu J, Harms M, Xie J. DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree. Genet Epidemiol 2024; 48:42-55. [PMID: 38014869 PMCID: PMC10842871 DOI: 10.1002/gepi.22542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNamic Aggregation TEsting (DYNATE). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with a controlled weighted false discovery rate. DYNATE's main advantage lies in its strong ability to identify short genomic regions highly enriched for disease-associated RVs. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared with existing methods. We applied DYNATE to an amyotrophic lateral sclerosis study and identified a new gene, EPG5, harboring possibly pathogenic mutations.
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Affiliation(s)
- Xuechan Li
- Novartis Pharmaceuticals Corporation, Basel, Switzerland
| | | | - Andrew Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Jianfeng Lu
- Department of Mathematics, Duke University, Durham, North Carolina, USA
| | - Matthew Harms
- Department of Neurology, Columbia University, Broadway, New York, USA
| | - Jichun Xie
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
- Department of Mathematics, Duke University, Durham, North Carolina, USA
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7
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Perlegos AE, Durkin J, Belfer SJ, Rodriguez A, Shcherbakova O, Park K, Luong J, Bonini NM, Kayser MS. TDP-43 impairs sleep in Drosophila through Ataxin-2-dependent metabolic disturbance. SCIENCE ADVANCES 2024; 10:eadj4457. [PMID: 38198547 PMCID: PMC10780954 DOI: 10.1126/sciadv.adj4457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia are associated with substantial sleep disruption, which may accelerate cognitive decline and brain degeneration. Here, we define a role for trans-activation response element (TAR) DNA binding protein 43 (TDP-43), a protein associated with human neurodegenerative disease, in regulating sleep using Drosophila. Expression of TDP-43 severely disrupts sleep, and the sleep deficit is rescued by Atx2 knockdown. Brain RNA sequencing revealed that Atx2 RNA interference regulates transcripts enriched for small-molecule metabolic signaling in TDP-43 brains. Focusing on these Atx2-regulated genes, we identified suppressors of the TDP-43 sleep phenotype enriched for metabolism pathways. Knockdown of Atx2 or treatment with rapamycin attenuated the sleep phenotype and mitigated the disruption of small-molecule glycogen metabolism caused by TDP-43. Our findings provide a connection between toxicity of TDP-43 and sleep disturbances and highlight key aspects of metabolism that interplay with TDP-43 toxicity upon Atx2 rescue.
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Affiliation(s)
- Alexandra E. Perlegos
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jaclyn Durkin
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- National Institute of Neurological Disorders & Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel J. Belfer
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anyara Rodriguez
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oksana Shcherbakova
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen Park
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenny Luong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy M. Bonini
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew S. Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Chronobiology Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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De Marchi F, Venkatesan S, Saraceno M, Mazzini L, Grossini E. Acetyl-L-carnitine and Amyotrophic Lateral Sclerosis: Current Evidence and Potential use. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:588-601. [PMID: 36998125 DOI: 10.2174/1871527322666230330083757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND The management of neurodegenerative diseases can be frustrating for clinicians, given the limited progress of conventional medicine in this context. AIM For this reason, a more comprehensive, integrative approach is urgently needed. Among various emerging focuses for intervention, the modulation of central nervous system energetics, oxidative stress, and inflammation is becoming more and more promising. METHODS In particular, electrons leakage involved in the mitochondrial energetics can generate reactive oxygen-free radical-related mitochondrial dysfunction that would contribute to the etiopathology of many disorders, such as Alzheimer's and other dementias, Parkinson's disease, multiple sclerosis, stroke, and amyotrophic lateral sclerosis (ALS). RESULTS In this context, using agents, like acetyl L-carnitine (ALCAR), provides mitochondrial support, reduces oxidative stress, and improves synaptic transmission. CONCLUSION This narrative review aims to update the existing literature on ALCAR molecular profile, tolerability, and translational clinical potential use in neurodegeneration, focusing on ALS.
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Affiliation(s)
- Fabiola De Marchi
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Sakthipriyan Venkatesan
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale 28100, Novara, Italy
| | - Massimo Saraceno
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Letizia Mazzini
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Elena Grossini
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale 28100, Novara, Italy
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9
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Yuan Y, Bailey JM, Rivera-Lopez GM, Atchison WD. Preferential potentiation of AMPA-mediated currents in brainstem hypoglossal motoneurons by subchronic exposure of mice expressing the human superoxide dismutase 1 G93A gene mutation to neurotoxicant methylmercury in vivo. Neurotoxicology 2024; 100:72-84. [PMID: 38065418 PMCID: PMC10877233 DOI: 10.1016/j.neuro.2023.12.002] [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: 05/12/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
The exact causes of Amyotrophic lateral sclerosis (ALS), a progressive and fatal neurological disorder due to loss of upper and/or lower motoneurons, remain elusive. Gene-environment interactions are believed to be an important factor in the development of ALS. We previously showed that in vivo exposure of mice overexpressing the human superoxide dismutase 1 (hSOD1) gene mutation (hSOD1G93A; G93A), a mouse model for ALS, to environmental neurotoxicant methylmercury (MeHg) accelerated the onset of ALS-like phenotype. Here we examined the time-course of effects of MeHg on AMPA receptor (AMPAR)-mediated currents in hypoglossal motoneurons in brainstem slices prepared from G93A, hSOD1wild-type (hWT) and non-carrier WT mice following in vivo exposure to MeHg. Mice were exposed daily to 3 ppm (approximately 0.7 mg/kg/day) MeHg via drinking water beginning at postnatal day 28 (P28) and continued until P47, 64 or 84, then acute brainstem slices were prepared, and spontaneous excitatory postsynaptic currents (sEPSCs) or AMPA-evoked currents were examined using whole cell patch-clamp recording technique. Brainstem slices of untreated littermates were prepared at the same time points to serve as control. MeHg exposure had no significant effect on either sEPSCs or AMPA-evoked currents in slices from hWT or WT mice during any of those exposure time periods under our experimental conditions. MeHg also did not cause any significant effect on sEPSCs or AMPA-currents in G93A hypoglossal motoneurons at P47 and P64. However, at P84, MeHg significantly increased amplitudes of both sEPSCs and AMPA-evoked currents in hypoglossal motineurons from G93A mice (p < 0.05), but not the sEPSC frequency, suggesting a postsynaptic action on AMPARs. MeHg exposure did not cause any significant effect on GABAergic spontaneous inhibitory postsynaptic currents (sIPSCs). Therefore, MeHg exposure in vivo caused differential effects on AMPARs in hypoglossal motoneurons from mice with different genetic backgrounds. MeHg appears to preferentially stimulate the AMPAR-mediated currents in G93A hypoglossal motoneurons in an exposure time-dependent manner, which may contribute to the AMPAR-mediated motoneuron excitotoxicity, thereby facilitating development of ALS-like phenotype.
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Affiliation(s)
- Yukun Yuan
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA.
| | - Jordan M Bailey
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
| | - Gretchen M Rivera-Lopez
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
| | - William D Atchison
- Department of Pharmacology/Toxicology, Michigan State University, Life Sciences Building, 1355 Bogue Street, East Lansing, MI 48824-1317, USA
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10
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Ocharán-Mercado A, Loaeza-Loaeza J, Castro-Coronel Y, Acosta-Saavedra LC, Hernández-Kelly LC, Hernández-Sotelo D, Ortega A. RNA-Binding Proteins: A Role in Neurotoxicity? Neurotox Res 2023; 41:681-697. [PMID: 37776476 PMCID: PMC10682104 DOI: 10.1007/s12640-023-00669-w] [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: 03/15/2023] [Revised: 03/15/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.
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Affiliation(s)
- Andrea Ocharán-Mercado
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Jaqueline Loaeza-Loaeza
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Yaneth Castro-Coronel
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Leonor C Acosta-Saavedra
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Luisa C Hernández-Kelly
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México.
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11
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Candelise N, Caissutti D, Zenuni H, Nesci V, Scaricamazza S, Salvatori I, Spinello Z, Mattei V, Garofalo T, Ferri A, Valle C, Misasi R. Different Chronic Stress Paradigms Converge on Endogenous TDP43 Cleavage and Aggregation. Mol Neurobiol 2023; 60:6346-6361. [PMID: 37450246 PMCID: PMC10533643 DOI: 10.1007/s12035-023-03455-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] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023]
Abstract
The TAR-DNA binding protein (TDP43) is a nuclear protein whose cytoplasmic inclusions are hallmarks of Amyotrophic Lateral Sclerosis (ALS). Acute stress in cells causes TDP43 mobilization to the cytoplasm and its aggregation through different routes. Although acute stress elicits a strong phenotype, is far from recapitulating the years-long aggregation process. We applied different chronic stress protocols and described TDP43 aggregation in a human neuroblastoma cell line by combining solubility assays, thioflavin-based microscopy and flow cytometry. This approach allowed us to detect, for the first time to our knowledge in vitro, the formation of 25 kDa C-terminal fragment of TDP43, a pathogenic hallmark of ALS. Our results indicate that chronic stress, compared to the more common acute stress paradigm, better recapitulates the cell biology of TDP43 proteinopathies. Moreover, we optimized a protocol for the detection of bona fide prions in living cells, suggesting that TDP43 may form amyloids as a stress response.
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Affiliation(s)
- Niccolò Candelise
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
| | - Daniela Caissutti
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Henri Zenuni
- Department of Systems Medicine, Tor Vergata" University of Rome, 00133, Rome, Italy
| | - Valentina Nesci
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
- Department of Systems Medicine, Tor Vergata" University of Rome, 00133, Rome, Italy
| | | | - Illari Salvatori
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
| | - Zaira Spinello
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100, Rieti, Italy
| | - Tina Garofalo
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Alberto Ferri
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale Delle Ricerche (CNR), 00185, Rome, Italy
| | - Cristiana Valle
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy.
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale Delle Ricerche (CNR), 00185, Rome, Italy.
| | - Roberta Misasi
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy.
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12
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Sung W, Kim JA, Kim YS, Park J, Oh KW, Sung JJ, Ki CS, Kim YE, Kim SH. An analysis of variants in TARDBP in the Korean population with amyotrophic lateral sclerosis: comparison with previous data. Sci Rep 2023; 13:18805. [PMID: 37914747 PMCID: PMC10620191 DOI: 10.1038/s41598-023-45593-3] [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: 07/22/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
The TARDBP gene variant is a known major cause of amyotrophic lateral sclerosis (ALS), with limited reports of Korean patients with ALS harboring the variants in TARDBP. This large cohort study introduces four ALS patients who share the p.M337V variant of the TARDBP, allowing for an investigation of clinical characteristics and prognosis by analyzing previously reported cases with the same variant. From November 2014 to August 2022, participants were recruited from two tertiary hospitals in Seoul, Korea. Clinical characteristics of patients diagnosed with ALS carrying the variant in TARDBP were evaluated. Previous articles demonstrating subjects' characteristics were reviewed. Four patients were identified with the pathogenic missense variant (c.1009A>G; p.M337V) in the TARDBP. The mean age of onset was 55 years old, and none of the patients showed severe cognitive impairment. Sixty-three patients carrying the p.M337V variant in TARDBP from this study and previous reports delineated young age of onset (51.6 years), high frequency of bulbar onset patients (61.9%), and low comorbidity of frontotemporal dementia. This study reveals the presence of pathogenic variant of TARDBP in Korea and emphasizes the importance of genetic screening of the TARDBP gene, in diagnosing ALS and evaluating prognosis among familial and simplex ALS patients in Korea.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jin-Ah Kim
- Department of Translational Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yong Sung Kim
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jung-Joon Sung
- Department of Translational Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea.
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13
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Helmold BR, Pauss KE, Ozdinler PH. TDP-43 protein interactome informs about perturbed canonical pathways and may help develop personalized medicine approaches for patients with TDP-43 pathology. Drug Discov Today 2023; 28:103769. [PMID: 37714405 PMCID: PMC10872580 DOI: 10.1016/j.drudis.2023.103769] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/22/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Transactive response DNA binding protein of 43 kDa (TDP-43) pathology is a common proteinopathy observed among a broad spectrum of patients with neurodegenerative disease, regardless of the mutation. This suggests that protein-protein interactions of TDP-43 with other proteins may in part be responsible for the pathology. To gain better insights, we investigated TDP-43-binding proteins in each domain and correlated these interactions with canonical pathways. These investigations revealed key cellular events that are involved and are important at each domain and suggested previously identified compounds to modulate key aspects of these canonical pathways. Our approach proposes that personalized medicine approaches, which focus on perturbed cellular mechanisms would be feasible in the near future.
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Affiliation(s)
- Benjamin R Helmold
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Kate E Pauss
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - P Hande Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA; Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60611, USA; Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Feinberg School of Medicine, Les Turner ALS Center at Northwestern University, Chicago, IL 60611, USA.
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14
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Genin EC, Abou-Ali M, Paquis-Flucklinger V. Mitochondria, a Key Target in Amyotrophic Lateral Sclerosis Pathogenesis. Genes (Basel) 2023; 14:1981. [PMID: 38002924 PMCID: PMC10671245 DOI: 10.3390/genes14111981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondrial dysfunction occurs in numerous neurodegenerative diseases, particularly amyotrophic lateral sclerosis (ALS), where it contributes to motor neuron (MN) death. Of all the factors involved in ALS, mitochondria have been considered as a major player, as secondary mitochondrial dysfunction has been found in various models and patients. Abnormal mitochondrial morphology, defects in mitochondrial dynamics, altered activities of respiratory chain enzymes and increased production of reactive oxygen species have been described. Moreover, the identification of CHCHD10 variants in ALS patients was the first genetic evidence that a mitochondrial defect may be a primary cause of MN damage and directly links mitochondrial dysfunction to the pathogenesis of ALS. In this review, we focus on the role of mitochondria in ALS and highlight the pathogenic variants of ALS genes associated with impaired mitochondrial functions. The multiple pathways demonstrated in ALS pathogenesis suggest that all converge to a common endpoint leading to MN loss. This may explain the disappointing results obtained with treatments targeting a single pathological process. Fighting against mitochondrial dysfunction appears to be a promising avenue for developing combined therapies in the future.
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Affiliation(s)
- Emmanuelle C. Genin
- Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d’Azur, Inserm U1081, CNRS UMR7284, Centre Hospitalier Universitaire (CHU) de Nice, 06200 Nice, France; (M.A.-A.); (V.P.-F.)
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15
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Zeballos C MA, Moore HJ, Smith TJ, Powell JE, Ahsan NS, Zhang S, Gaj T. Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins. Nat Commun 2023; 14:6492. [PMID: 37838698 PMCID: PMC10576788 DOI: 10.1038/s41467-023-42147-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
The TDP-43 proteinopathies, which include amyotrophic lateral sclerosis and frontotemporal dementia, are a devastating group of neurodegenerative disorders that are characterized by the mislocalization and aggregation of TDP-43. Here we demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene silencing agents that includes the Cas13 family of enzymes and Cas7-11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. In addition to inhibiting the aggregation and transit of TDP-43 to stress granules, we find that the in vivo delivery of an ataxin-2-targeting Cas13 system to a mouse model of TDP-43 proteinopathy improved functional deficits, extended survival, and reduced the severity of neuropathological hallmarks. Further, we benchmark RNA-targeting CRISPR platforms against ataxin-2 and find that high-fidelity forms of Cas13 possess improved transcriptome-wide specificity compared to Cas7-11 and a first-generation effector. Our results demonstrate the potential of CRISPR technology for TDP-43 proteinopathies.
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Affiliation(s)
- M Alejandra Zeballos C
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hayden J Moore
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tyler J Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jackson E Powell
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Najah S Ahsan
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sijia Zhang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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16
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Necarsulmer JC, Simon JM, Evangelista BA, Chen Y, Tian X, Nafees S, Marquez AB, Jiang H, Wang P, Ajit D, Nikolova VD, Harper KM, Ezzell JA, Lin FC, Beltran AS, Moy SS, Cohen TJ. RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy. eLife 2023; 12:RP85921. [PMID: 37819053 PMCID: PMC10567115 DOI: 10.7554/elife.85921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
TDP-43 proteinopathies including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by aggregation and mislocalization of the nucleic acid-binding protein TDP-43 and subsequent neuronal dysfunction. Here, we developed endogenous models of sporadic TDP-43 proteinopathy based on the principle that disease-associated TDP-43 acetylation at lysine 145 (K145) alters TDP-43 conformation, impairs RNA-binding capacity, and induces downstream mis-regulation of target genes. Expression of acetylation-mimic TDP-43K145Q resulted in stress-induced nuclear TDP-43 foci and loss of TDP-43 function in primary mouse and human-induced pluripotent stem cell (hiPSC)-derived cortical neurons. Mice harboring the TDP-43K145Q mutation recapitulated key hallmarks of FTLD, including progressive TDP-43 phosphorylation and insolubility, TDP-43 mis-localization, transcriptomic and splicing alterations, and cognitive dysfunction. Our study supports a model in which TDP-43 acetylation drives neuronal dysfunction and cognitive decline through aberrant splicing and transcription of critical genes that regulate synaptic plasticity and stress response signaling. The neurodegenerative cascade initiated by TDP-43 acetylation recapitulates many aspects of human FTLD and provides a new paradigm to further interrogate TDP-43 proteinopathies.
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Affiliation(s)
- Julie C Necarsulmer
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Baggio A Evangelista
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Youjun Chen
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Xu Tian
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Sara Nafees
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Ariana B Marquez
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
| | - Huijun Jiang
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Ping Wang
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Deepa Ajit
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Viktoriya D Nikolova
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Kathryn M Harper
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - J Ashley Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, University of North CarolinaChapel HillUnited States
| | - Feng-Chang Lin
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Adriana S Beltran
- Department of Genetics, University of North CarolinaChapel HillUnited States
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
- Department of Pharmacology, University of North CarolinaChapel HillUnited States
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Todd J Cohen
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Department of Biochemistry and Biophysics, University of North CarolinaChapel HillUnited States
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17
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Zeballos C MA, Moore HJ, Smith TJ, Powell JE, Ahsan NS, Zhang S, Gaj T. Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536072. [PMID: 37066174 PMCID: PMC10104115 DOI: 10.1101/2023.04.07.536072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The TDP-43 proteinopathies, which include amyotrophic lateral sclerosis and frontotemporal dementia, are a devastating group of neurodegenerative disorders that are characterized by the mislocalization and aggregation of TDP-43. Here we demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene silencing agents that includes the Cas13 family of enzymes and Cas7-11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. In addition to inhibiting the aggregation and transit of TDP-43 to stress granules, we find that the in vivo delivery of an ataxin-2-targeting Cas13 system to a mouse model of TDP-43 proteinopathy improved functional deficits, extended survival, and reduced the severity of neuropathological hallmarks. Further, we benchmark RNA-targeting CRISPR platforms against ataxin-2 and find that high-fidelity forms of Cas13 possess improved transcriptome-wide specificity compared to Cas7-11 and a first-generation effector. Our results demonstrate the potential of CRISPR technology for TDP-43 proteinopathies.
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Affiliation(s)
- M. Alejandra Zeballos C
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Hayden J. Moore
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler J. Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Jackson E. Powell
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Najah S. Ahsan
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sijia Zhang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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18
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Bagyinszky E, Hulme J, An SSA. Studies of Genetic and Proteomic Risk Factors of Amyotrophic Lateral Sclerosis Inspire Biomarker Development and Gene Therapy. Cells 2023; 12:1948. [PMID: 37566027 PMCID: PMC10417729 DOI: 10.3390/cells12151948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5-10% of ALS cases are associated with positive family history (familial ALS or fALS), whilst the remainder are sporadic (sporadic ALS, sALS). At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 (SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially "at risk" individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.
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Affiliation(s)
- Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - John Hulme
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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19
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Worrall D, Ayoubi R, Fotouhi M, Southern K, McPherson PS, Laflamme C. The identification of high-performing antibodies for TDP-43 for use in Western Blot, immunoprecipitation and immunofluorescence. F1000Res 2023; 12:277. [PMID: 37359785 PMCID: PMC10285334 DOI: 10.12688/f1000research.131852.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA binding protein playing a critical role in the regulation of transcription, splicing and RNA stability. Mutations in TARDBP leading to aggregation, are suspected to be a characteristic feature of various neurogenerative diseases. The lack of well-characterized anti- TDP-43 antibodies acts as a barrier to establish reproducible TDP-43 research. In this study, we characterized eighteen TDP-43 commercial antibodies for Western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many well-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.
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Affiliation(s)
- Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | | | - ABIF Consortium
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
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20
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Worrall D, Ayoubi R, Fotouhi M, Southern K, McPherson PS, Laflamme C. The identification of high-performing antibodies for TDP-43 for use in Western Blot, immunoprecipitation and immunofluorescence. F1000Res 2023; 12:277. [PMID: 37359785 PMCID: PMC10285334 DOI: 10.12688/f1000research.131852.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/29/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA binding protein playing a critical role in the regulation of transcription, splicing and RNA stability. Mutations in TARDBP leading to aggregation, are suspected to be a characteristic feature of various neurogenerative diseases. The lack of well-characterized anti- TDP-43 antibodies acts as a barrier to establish reproducible TDP-43 research. In this study, we characterized eighteen TDP-43 commercial antibodies for Western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many well-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.
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Affiliation(s)
- Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | | | - ABIF Consortium
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
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21
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Evangelista BA, Cahalan SR, Ragusa JV, Mordant A, Necarsulmer JC, Perna RJ, Ajit T, White K, Barker NK, Tian X, Cohen S, Meeker R, Herring LE, Cohen TJ. Tandem detergent-extraction and immunoprecipitation of proteinopathy: Scalable enrichment of ALS-associated TDP-43 aggregates. iScience 2023; 26:106645. [PMID: 37182104 PMCID: PMC10173608 DOI: 10.1016/j.isci.2023.106645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Transactive response DNA-binding protein of 43 kDa (TDP-43) is a highly conserved, ubiquitously expressed nucleic acid-binding protein that regulates DNA/RNA metabolism. Genetics and neuropathology studies have linked TDP-43 to several neuromuscular and neurological disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Under pathological conditions, TDP-43 mislocalizes to the cytoplasm where it forms insoluble, hyper-phosphorylated aggregates during disease progression. Here, we optimized a scalable in vitro immuno-purification strategy referred to as tandem detergent-extraction and immunoprecipitation of proteinopathy (TDiP) to isolate TDP-43 aggregates that recapitulate those identified in postmortem ALS tissue. Moreover, we demonstrate that these purified aggregates can be utilized in biochemical, proteomics, and live-cell assays. This platform offers a rapid, accessible, and streamlined approach to study ALS disease mechanisms, while overcoming many limitations that have hampered TDP-43 disease modeling and therapeutic drug discovery efforts.
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Affiliation(s)
- Baggio A. Evangelista
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon R. Cahalan
- Medical Student Training in Aging Research, Center for Aging and Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joey V. Ragusa
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angie Mordant
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie C. Necarsulmer
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert J. Perna
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tejazaditya Ajit
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristen White
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie K. Barker
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xu Tian
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rick Meeker
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura E. Herring
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Todd J. Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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22
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Carmen-Orozco RP, Tsao W, Ye Y, Sinha IR, Chang K, Trinh V, Chung W, Bowden K, Troncoso JC, Blackshaw S, Hayes LR, Sun S, Wong PC, Ling JP. Elevated nuclear TDP-43 induces constitutive exon skipping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540291. [PMID: 37215013 PMCID: PMC10197708 DOI: 10.1101/2023.05.11.540291] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
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. 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. 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. Understanding the subtle aspects of TDP-43 toxicity within different subcellular locations is essential for the development of therapies targeting neurodegenerative disease.
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Affiliation(s)
- Rogger P Carmen-Orozco
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - William Tsao
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Yingzhi Ye
- Department of Physiology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Irika R Sinha
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Koping Chang
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Vickie Trinh
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - William Chung
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Kyra Bowden
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Juan C Troncoso
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Seth Blackshaw
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Ophthalmology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neurology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Lindsey R Hayes
- Department of Neurology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Shuying Sun
- Department of Physiology Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Philip C Wong
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
- Department of Neuroscience Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Jonathan P Ling
- Department of Pathology Johns Hopkins School of Medicine, Baltimore, MD 21205
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23
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Ishiguro A, Ishihama A. ALS-linked TDP-43 mutations interfere with the recruitment of RNA recognition motifs to G-quadruplex RNA. Sci Rep 2023; 13:5982. [PMID: 37046025 PMCID: PMC10097714 DOI: 10.1038/s41598-023-33172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023] Open
Abstract
TDP-43 is a major pathological protein in sporadic and familial amyotrophic lateral sclerosis (ALS) and mediates mRNA fate. TDP-43 dysfunction leads to causes progressive degeneration of motor neurons, the details of which remain elusive. Elucidation of the molecular mechanisms of RNA binding could enhance our understanding of this devastating disease. We observed the involvement of the glycine-rich (GR) region of TDP-43 in the initial recognition and binding of G-quadruplex (G4)-RNA in conjunction with its RNA recognition motifs (RRM). We performed a molecular dissection of these intramolecular RNA-binding modules in this study. We confirmed that the ALS-linked mutations in the GR region lead to alteration in the G4 structure. In contrast, amino acid substitutions in the GR region alter the protein structure but do not void the interaction with G4-RNA. Based on these observations, we concluded that the structural distortion of G4 caused by these mutations interferes with RRM recruitment and leads to TDP-43 dysfunction. This intramolecular organization between RRM and GR regions modulates the overall G4-binding properties.
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Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Midori-cho 3-11-15, Koganei, Tokyo, 184-0003, Japan.
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Midori-cho 3-11-15, Koganei, Tokyo, 184-0003, Japan
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24
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Liu X, Li X, Qiao Q, Li F, Wei G. ALS-Linked A315T and A315E Mutations Enhance β-Barrel Formation of the TDP-43 307-319 Hexamer: A REST2 Simulation Study. ACS Chem Neurosci 2023; 14:1310-1320. [PMID: 36888995 DOI: 10.1021/acschemneuro.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Pathogenic mutations of transactivation response element DNA-binding protein 43 (TDP-43) are closely linked with amyotrophic lateral sclerosis (ALS). It was recently reported that two ALS-linked familial mutants A315T and A315E of TDP-43307-319 peptides can self-assemble into oligomers including tetramers, hexamers, and octamers, among which hexamers were suggested to form the β-barrel structure. However, due to the transient nature of oligomers, their conformational properties and the atomic mechanisms underlying the β-barrel formation remain largely elusive. Herein, we investigated the hexameric conformational distributions of the wild-type (WT) TDP-43307-319 fragment and its A315T and A315E mutants by performing all-atom explicit-solvent replica exchange with solute tempering 2 simulations. Our simulations reveal that each peptide can self-assemble into diverse conformations including ordered β-barrels, bilayer β-sheets and/or monolayer β-sheets, and disordered complexes. A315T and A315E mutants display higher propensity to form β-barrel structures than the WT, which provides atomic explanation for their enhanced neurotoxicity reported previously. Detailed interaction analysis shows that A315T and A315E mutations increase inter-molecular interactions. Also, the β-barrel structures formed by the three different peptides are stabilized by distinct inter-peptide side-chain hydrogen bonding, hydrophobic, and aromatic stacking interactions. This study demonstrates the enhanced β-barrel formation of the TDP-43307-319 hexamer by the pathogenic A315T and A315E mutations and reveals the underlying molecular determinants, which may be helpful for in-depth understanding of the ALS-mutation-induced neurotoxicity of TDP-43 protein.
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Affiliation(s)
- Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
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25
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Ni J, Ren Y, Su T, Zhou J, Fu C, Lu Y, Li D, Zhao J, Li Y, Zhang Y, Fang Y, Liu N, Geng Y, Chen Y. Loss of TDP-43 function underlies hippocampal and cortical synaptic deficits in TDP-43 proteinopathies. Mol Psychiatry 2023; 28:931-945. [PMID: 34697451 DOI: 10.1038/s41380-021-01346-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
TDP-43 proteinopathy is linked to neurodegenerative diseases that feature synaptic loss in the cortex and hippocampus, although it remains unclear how TDP-43 regulates mature synapses. We report that, in adult mouse hippocampus, TDP-43 knockdown, but not overexpression, induces robust structural and functional damage to excitatory synapses, supporting a role for TDP-43 in maintaining mature synapses. Dendritic spine loss induced by TDP-43 knockdown is rescued by wild-type TDP-43, but not ALS/FTLD-associated mutants, suggesting a common TDP-43 functional deficiency in neurodegenerative diseases. Interestingly, M337V and A90V mutants also display dominant negative activities against WT TDP-43, partially explaining why M337V transgenic mice develop hippocampal degeneration similar to that in excitatory neuronal TDP-43 knockout mice, and why A90V mutation is associated with Alzheimer's disease. Further analyses reveal that a TDP-43 knockdown-induced reduction in GluN2A contributes to synaptic loss. Our results show that loss of TDP-43 function underlies hippocampal and cortical synaptic degeneration in TDP-43 proteinopathies.
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Affiliation(s)
- Jiangxia Ni
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yongfei Ren
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tonghui Su
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jia Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chaoying Fu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
| | - Yi Lu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - De'an Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jing Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yunxia Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China
| | - Yang Geng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China.
| | - Yelin Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd. Pudong New District, Shanghai, 201210, China.
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26
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Kumar R, Malik Z, Singh M, Rachana R, Mani S, Ponnusamy K, Haider S. Amyotrophic Lateral Sclerosis Risk Genes and Suppressor. Curr Gene Ther 2023; 23:148-162. [PMID: 36366843 DOI: 10.2174/1566523223666221108113330] [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: 04/11/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to death by progressive paralysis and respiratory failure within 2-4 years of onset. About 90-95% of ALS cases are sporadic (sALS), and 5-10% are inherited through family (fALS). Though the mechanisms of the disease are still poorly understood, so far, approximately 40 genes have been reported as ALS causative genes. The mutations in some crucial genes, like SOD1, C9ORF72, FUS, and TDP-43, are majorly associated with ALS, resulting in ROS-associated oxidative stress, excitotoxicity, protein aggregation, altered RNA processing, axonal and vesicular trafficking dysregulation, and mitochondrial dysfunction. Recent studies show that dysfunctional cellular pathways get restored as a result of the repair of a single pathway in ALS. In this review article, our aim is to identify putative targets for therapeutic development and the importance of a single suppressor to reduce multiple symptoms by focusing on important mutations and the phenotypic suppressors of dysfunctional cellular pathways in crucial genes as reported by other studies.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Zubbair Malik
- School of Computational and Integrative Science, Jawaharlal Nehru University, New Delhi-110067, India
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - R Rachana
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
| | | | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Sec-62, Noida, Uttar Pradesh, India
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27
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Therapeutic Effect of Rapamycin on TDP-43-Related Pathogenesis in Ischemic Stroke. Int J Mol Sci 2022; 24:ijms24010676. [PMID: 36614118 PMCID: PMC9820757 DOI: 10.3390/ijms24010676] [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: 10/28/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023] Open
Abstract
Stroke is a major cause of death and disability across the world, and its detrimental impact should not be underestimated. Therapies are available and effective for ischemic stroke (e.g., thrombolytic recanalization and mechanical thrombectomy); however, there are limitations to therapeutic interventions. Recanalization therapy has developed dramatically, while the use of adjunct neuroprotective agents as complementary therapies remains deficient. Pathological TAR DNA-binding protein (TDP-43) has been identified as a major component of insoluble aggregates in numerous neurodegenerative pathologies, including ALS, FTLD and Alzheimer's disease. Here, we show that increased pathological TDP-43 fractions accompanied by impaired mitochondrial function and increased gliosis were observed in an ischemic stroke rat model, suggesting a pathological role of TDP-43 in ischemic stroke. In ischemic rats administered rapamycin, the insoluble TDP-43 fraction was significantly decreased in the ischemic cortex region, accompanied by a recovery of mitochondrial function, the attenuation of cellular apoptosis, a reduction in infarct areas and improvements in motor defects. Accordingly, our results suggest that rapamycin provides neuroprotective benefits not only by ameliorating pathological TDP-43 levels, but also by reversing mitochondrial function and attenuating cell apoptosis in ischemic stroke.
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28
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Nirwal S, Saravanan P, Bajpai A, Meshram VD, Raju G, Deeksha W, Prabusankar G, Patel BK. In Vitro Interaction of a C-Terminal Fragment of TDP-43 Protein with Human Serum Albumin Modulates Its Aggregation. J Phys Chem B 2022; 126:9137-9151. [PMID: 36326054 DOI: 10.1021/acs.jpcb.2c04469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An increased level of naturally occurring anti-TDP-43 antibodies was observed in the serum and cerebrospinal fluid (CSF) of amyotrophic lateral sclerosis patients. Human serum albumin (HSA), the most abundant protein in blood plasma and CSF, is found to interact with pathological proteins like Aβ and α-synuclein. Therefore, we examined the effect on the in vitro aggregation of a C-terminal fragment of TDP-43 in the presence of HSA. We found that the lag phase in TDP-432C aggregation is abrogated in the presence of HSA, but there is an overall decreased aggregation as examined by thioflavin-T fluorescence spectroscopy and microscopy. An early onset of TDP-432C oligomer formation in the presence of HSA was observed using atomic force microscopy and transmission electron microscopy. Also, a known chemical inhibitor of TDP-432Caggregation, AIM4, abolishes the HSA-induced early formation of TDP-432C oligomers. Notably, the aggregates of TDP-432C formed in the presence of HSA are more stable against sarkosyl detergent. Using affinity copurification, we observed that HSA can bind to TDP-432C, and biolayer interferometry further supported their physical interaction and suggested the binding affinity to be in sub-micromolar range. Taken together, the data support that HSA can interact with TDP-432C in vitro and affect its aggregation.
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Affiliation(s)
- Sadhana Nirwal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Preethi Saravanan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Akarsh Bajpai
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Vini D Meshram
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Gembali Raju
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi Sangareddy, Telangana 502284, India
| | - Waghela Deeksha
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Ganesan Prabusankar
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi Sangareddy, Telangana 502284, India
| | - Basant K Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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29
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Tran NN, Lee BH. Functional implication of ubiquitinating and deubiquitinating mechanisms in TDP-43 proteinopathies. Front Cell Dev Biol 2022; 10:931968. [PMID: 36158183 PMCID: PMC9500471 DOI: 10.3389/fcell.2022.931968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease in which motor neurons in spinal cord and motor cortex are progressively lost. About 15% cases of ALS also develop the frontotemporal dementia (FTD), in which the frontotemporal lobar degeneration (FTLD) occurs in the frontal and temporal lobes of the brain. Among the pathologic commonalities in ALS and FTD is ubiquitin-positive cytoplasmic aggregation of TDP-43 that may reflect both its loss-of-function and gain-of-toxicity from proteostasis impairment. Deep understanding of how protein quality control mechanisms regulate TDP-43 proteinopathies still remains elusive. Recently, a growing body of evidence indicates that ubiquitinating and deubiquitinating pathways are critically engaged in the fate decision of aberrant or pathological TDP-43 proteins. E3 ubiquitin ligases coupled with deubiquitinating enzymes may influence the TDP-43-associated proteotoxicity through diverse events, such as protein stability, translocation, and stress granule or inclusion formation. In this article, we recapitulate our current understanding of how ubiquitinating and deubiquitinating mechanisms can modulate TDP-43 protein quality and its pathogenic nature, thus shedding light on developing targeted therapies for ALS and FTD by harnessing protein degradation machinery.
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Affiliation(s)
- Non-Nuoc Tran
- Department of New Biology, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Byung-Hoon Lee
- Department of New Biology, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
- Department of New Biology Research Center (NBRC), Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
- *Correspondence: Byung-Hoon Lee,
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30
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Xu F, Huang S, Li XY, Lin J, Feng X, Xie S, Wang Z, Li X, Zhu J, Lai H, Xu Y, Huang X, Yao X, Wang C. Identification of TARDBP Gly298Ser as a founder mutation for amyotrophic lateral sclerosis in Southern China. BMC Med Genomics 2022; 15:173. [PMID: 35932023 PMCID: PMC9356425 DOI: 10.1186/s12920-022-01327-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/30/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by predominant impairment of upper and lower motor neurons. Over 50 TARDBP mutations have been reported in both familial (FALS) and sporadic ALS (SALS). Some mutations in TARDBP, e.g. A382T and G294V, have genetic founder effects in certain geographic regions. However, such prevalence and founder effect have not been reported in Chinese. METHODS Whole-exome sequencing (WES) was performed in 16 Chinese FALS patients, followed by Sanger sequencing for the TARDBP p.Gly298Ser mutation (G298S) in 798 SALS patients and 1,325 controls. Haplotype analysis using microsatellites flanking TARDBP was conducted in the G298S-carrying patients and noncarriers. The geographic distribution and phenotypic correlation of the TARDBP mutations reported worldwide were reviewed. RESULTS WES detected the TARDBP G298S mutation in 8 FALS patients, and Sanger sequencing found additional 8 SALS cases, but no controls, carrying this mutation. All the 16 cases came from Southern China, and 7 of these patients shared the 117-286-257-145-246-270 allele for the D1S2736-D1S1151-D1S2667-D1S489-D1S434-D1S2697 markers, which was not found in the 92 non-carrier patients (0/92) (p < 0.0001) and 65 age-matched and neurologically normal individuals (0/65) (p < 0.0001). The A382T and G298S mutations were prevalent in Europeans and Eastern Asians, respectively. Additionally, carriers for the M337V mutation are dominated by bulbar onset with a long survival, whereas those for G298S are dominated by limb onset with a short survival. CONCLUSIONS Some prevalent TARDBP mutations are distributed in a geographic pattern and related to clinical profiles. TARDBP G298S mutation is a founder mutation in the Southern Chinese ALS population.
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Affiliation(s)
- Fanxi Xu
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China
| | - Sen Huang
- Department of Neurology, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xu-Ying Li
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China.,Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jianing Lin
- Department of Neurology, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xiuli Feng
- National Human Genome Center in Beijing, Beijing, China
| | - Shu Xie
- National Human Genome Center in Beijing, Beijing, China
| | - Zhanjun Wang
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China
| | - Xian Li
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China
| | - Junge Zhu
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China
| | - Hong Lai
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China
| | - Yanming Xu
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
| | - Xusheng Huang
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoli Yao
- Department of Neurology, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Chaodong Wang
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, No.45 Changchun Street, Beijing, 100053, China.
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31
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Liu X, Lao Z, Li X, Dong X, Wei G. ALS-associated A315E and A315pT variants exhibit distinct mechanisms in inducing irreversible aggregation of TDP-43 312-317 peptides. Phys Chem Chem Phys 2022; 24:16263-16273. [PMID: 35758309 DOI: 10.1039/d2cp01625g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is intensively associated with insoluble aggregates formed by transactivation response element DNA-binding protein 43 (TDP-43) in the cytoplasm of neuron cells. A recent experimental study reported that two ALS-linked familial variants, A315E and A315pT (pT, phosphorylated threonine), can induce irreversible aggregation of the TDP-43 312NFGAFS317 segment (TDP-43312-317). However, the underlying molecular mechanism remains largely elusive. Here, we investigated the early aggregation process of the wild type (WT) 312NFGAFS317 segment and its A315E and A315pT variants by performing multiple microsecond all-atom molecular dynamics simulations. Our simulations show that the two variants display lower fluidity than WT, consistent with their decreased labilities observed in previous denaturation assay experiments. Despite each of the two variants carrying one negative charge, unexpectedly, we find that both A315E mutation and A315pT phosphorylation enhance intermolecular interactions and result in the formation of more compact oligomers. Compared to WT, A315E oligomers possess low β-sheet content but a compact hydrophobic core, while A315pT oligomers have high β-sheet content and large β-sheets. Side chain hydrogen-bonding and hydrophobic interactions as well as N312-E315 salt bridges contribute most to the increased aggregation propensity of the A315E mutant. By contrast, main chain and side chain hydrogen-bonding interactions, side chain hydrophobic and aromatic interactions, are crucial to the enhanced aggregation capability of the A315pT variant. These results indicate that glutamate mutation and phosphorylation at position 315 induce the irreversible aggregation of TDP-43312-317 peptides through differential mechanisms, which remind us that we should be careful in the investigation of the phosphorylation effect on protein aggregation by using phosphomimetic substitutions. This study provides mechanistic insights into the A315E/A315pT-induced irreversible aggregation of TDP-43312-317, which may be helpful for the in-depth understanding of ALS-mutation/phosphorylation-associated liquid-to-solid phase transition of TDP-43 protein aggregates.
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Affiliation(s)
- Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
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32
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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33
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Smukowski SN, Maioli H, Latimer CS, Bird TD, Jayadev S, Valdmanis PN. Progress in Amyotrophic Lateral Sclerosis Gene Discovery: Reflecting on Classic Approaches and Leveraging Emerging Technologies. Neurol Genet 2022; 8:e669. [PMID: 35620141 PMCID: PMC9128037 DOI: 10.1212/nxg.0000000000000669] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/14/2022] [Indexed: 11/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most prominent motor neuron disease in humans. Its etiology consists of progressive motor neuron degeneration resulting in a rapid decline in motor function starting in the limbs or bulbar muscles and eventually fatally impairing central organs most typically resulting in loss of respiration. Pathogenic variants in 4 main genes, SOD1, TARDBP, FUS, and C9orf72, have been well characterized as causative for more than a decade now. However, these only account for a small fraction of all ALS cases. In this review, we highlight many additional variants that appear to be causative or confer increased risk for ALS, and we reflect on the technologies that have led to these discoveries. Next, we call attention to new challenges and opportunities for ALS and suggest next steps to increase our understanding of ALS genetics. Finally, we conclude with a synopsis of gene therapy paradigms and how increased understanding of ALS genetics can lead us to developing effective treatments. Ultimately, a consolidated update of the field can provide a launching point for researchers and clinicians to improve our search for ALS-related genes, defining pathogenic mechanisms, form diagnostics, and develop therapies.
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Affiliation(s)
- Samuel N Smukowski
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
| | - Heather Maioli
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
| | - Caitlin S Latimer
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
| | - Thomas D Bird
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
| | - Suman Jayadev
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
| | - Paul N Valdmanis
- Division of Medical Genetics (S.N.S., T.D.B., S.J., P.N.V.), University of Washington School of Medicine; Department of Laboratory Medicine and Pathology (H.M., C.S.L.), University of Washington; Northwest Mental Illness Research (C.M.), Education and Clinical Centers, VA Puget Sound Health Care System; Department of Neurology (T.D.B., S.J.), University of Washington; and Geriatric Research Education and Clinical Center (T.B.), VA Puget Sound Health Care System, Seattle, WA
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34
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Krause LJ, Herrera MG, Winklhofer KF. The Role of Ubiquitin in Regulating Stress Granule Dynamics. Front Physiol 2022; 13:910759. [PMID: 35694405 PMCID: PMC9174786 DOI: 10.3389/fphys.2022.910759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Stress granules (SGs) are dynamic, reversible biomolecular condensates, which assemble in the cytoplasm of eukaryotic cells under various stress conditions. Formation of SGs typically occurs upon stress-induced translational arrest and polysome disassembly. The increase in cytoplasmic mRNAs triggers the formation of a protein-RNA network that undergoes liquid-liquid phase separation when a critical interaction threshold has been reached. This adaptive stress response allows a transient shutdown of several cellular processes until the stress is removed. During the recovery from stress, SGs disassemble to re-establish cellular activities. Persistent stress and disease-related mutations in SG components favor the formation of aberrant SGs that are impaired in disassembly and prone to aggregation. Recently, posttranslational modifications of SG components have been identified as major regulators of SG dynamics. Here, we summarize new insights into the role of ubiquitination in affecting SG dynamics and clearance and discuss implications for neurodegenerative diseases linked to aberrant SG formation.
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Affiliation(s)
- Laura J. Krause
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Maria G. Herrera
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F. Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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35
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Rosenberg GM, Murray KA, Salwinski L, Hughes MP, Abskharon R, Eisenberg DS. Bioinformatic identification of previously unrecognized amyloidogenic proteins. J Biol Chem 2022; 298:101920. [PMID: 35405097 PMCID: PMC9108986 DOI: 10.1016/j.jbc.2022.101920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022] Open
Abstract
Low-complexity domains (LCDs) of proteins have been shown to self-associate, and pathogenic mutations within these domains often drive the proteins into amyloid aggregation associated with disease. These domains may be especially susceptible to amyloidogenic mutations because they are commonly intrinsically disordered and function in self-association. The question therefore arises whether a search for pathogenic mutations in LCDs of the human proteome can lead to identification of other proteins associated with amyloid disease. Here, we take a computational approach to identify documented pathogenic mutations within LCDs that may favor amyloid formation. Using this approach, we identify numerous known amyloidogenic mutations, including several such mutations within proteins previously unidentified as amyloidogenic. Among the latter group, we focus on two mutations within the TRK-fused gene protein (TFG), known to play roles in protein secretion and innate immunity, which are associated with two different peripheral neuropathies. We show that both mutations increase the propensity of TFG to form amyloid fibrils. We therefore conclude that TFG is a novel amyloid protein and propose that the diseases associated with its mutant forms may be amyloidoses.
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Affiliation(s)
- Gregory M Rosenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Kevin A Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Lukasz Salwinski
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA; Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA.
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36
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Kim HJ, Mohassel P, Donkervoort S, Guo L, O'Donovan K, Coughlin M, Lornage X, Foulds N, Hammans SR, Foley AR, Fare CM, Ford AF, Ogasawara M, Sato A, Iida A, Munot P, Ambegaonkar G, Phadke R, O'Donovan DG, Buchert R, Grimmel M, Töpf A, Zaharieva IT, Brady L, Hu Y, Lloyd TE, Klein A, Steinlin M, Kuster A, Mercier S, Marcorelles P, Péréon Y, Fleurence E, Manzur A, Ennis S, Upstill-Goddard R, Bello L, Bertolin C, Pegoraro E, Salviati L, French CE, Shatillo A, Raymond FL, Haack TB, Quijano-Roy S, Böhm J, Nelson I, Stojkovic T, Evangelista T, Straub V, Romero NB, Laporte J, Muntoni F, Nishino I, Tarnopolsky MA, Shorter J, Bönnemann CG, Taylor JP. Heterozygous frameshift variants in HNRNPA2B1 cause early-onset oculopharyngeal muscular dystrophy. Nat Commun 2022; 13:2306. [PMID: 35484142 PMCID: PMC9050844 DOI: 10.1038/s41467-022-30015-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 03/25/2022] [Indexed: 01/05/2023] Open
Abstract
Missense variants in RNA-binding proteins (RBPs) underlie a spectrum of disease phenotypes, including amyotrophic lateral sclerosis, frontotemporal dementia, and inclusion body myopathy. Here, we present ten independent families with a severe, progressive muscular dystrophy, reminiscent of oculopharyngeal muscular dystrophy (OPMD) but of much earlier onset, caused by heterozygous frameshift variants in the RBP hnRNPA2/B1. All disease-causing frameshift mutations abolish the native stop codon and extend the reading frame, creating novel transcripts that escape nonsense-mediated decay and are translated to produce hnRNPA2/B1 protein with the same neomorphic C-terminal sequence. In contrast to previously reported disease-causing missense variants in HNRNPA2B1, these frameshift variants do not increase the propensity of hnRNPA2 protein to fibrillize. Rather, the frameshift variants have reduced affinity for the nuclear import receptor karyopherin β2, resulting in cytoplasmic accumulation of hnRNPA2 protein in cells and in animal models that recapitulate the human pathology. Thus, we expand the phenotypes associated with HNRNPA2B1 to include an early-onset form of OPMD caused by frameshift variants that alter its nucleocytoplasmic transport dynamics. Missense variants in RNA-binding proteins underlie many diseases. Here the authors report an oculopharyngeal muscular dystrophy caused by heterozygous frameshift mutations in HNRNPA2B1 that alter its nucleocytoplasmic transport dynamics and result in cytoplasmic accumulation of hnRNPA2 protein.
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Affiliation(s)
- Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Payam Mohassel
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Lin Guo
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Kevin O'Donovan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Xaviere Lornage
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Princess Anne Hospital, Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, England
| | - Simon R Hammans
- Wessex Neurological Centre, University Hospital Southampton, Southampton, UK
| | - A Reghan Foley
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Charlotte M Fare
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Alice F Ford
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, NCNP, Kodaira, Tokyo, Japan
| | - Aki Sato
- Department of Neurology, Niigata City General Hospital, Niigata, Japan
| | | | - Pinki Munot
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Gautam Ambegaonkar
- Department of Paediatric Neurology, Cambridge University Hospital NHS Trust, Addenbrookes Hospital, Cambridge, CB2 0QQ, UK
| | - Rahul Phadke
- Division of Neuropathology, University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, UK and Division of Neuropathology, UCL Institute of Neurology, Dubowitz Neuromuscular Centre, London, UK
| | - Dominic G O'Donovan
- Department of Histopathology Box 235, Level 5 John Bonnett Clinical Laboratories Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Irina T Zaharieva
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Lauren Brady
- Division of Neuromuscular & Neurometabolic Disorders, Department of Pediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Ying Hu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrea Klein
- Division of Neuropaediatrics, Development and Rehabilitation, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Pediatric Neurology, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Maja Steinlin
- Division of Neuropaediatrics, Development and Rehabilitation, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alice Kuster
- Department of Neurometabolism, University Hospital of Nantes, Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence des Maladies Neuromusculaires AOC, 44000, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Pascale Marcorelles
- Service d'anatomopathologie, CHU Brest and EA 4685 LIEN, Université de Bretagne Occidentale, Brest, France
| | - Yann Péréon
- CHU de Nantes, Centre de Référence des Maladies Neuromusculaires, Filnemus, Euro-NMD, Hôtel-Dieu, Nantes, France
| | - Emmanuelle Fleurence
- Etablissement de Santé pour Enfants et Adolescents de la région Nantaise, Nantes, France
| | - Adnan Manzur
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rosanna Upstill-Goddard
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Luca Bello
- Department of Neurosciences, DNS, University of Padova, Padova, Italy
| | - Cinzia Bertolin
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Elena Pegoraro
- Department of Neurosciences, DNS, University of Padova, Padova, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women and Children's Health, CIR-Myo Myology Center, University of Padova, IRP Città della Speranza, Padova, Italy
| | | | - Andriy Shatillo
- Institute of Neurology, Psychiatry and Narcology of NAMS of Ukraine, Kharkiv, Ukraine
| | - F Lucy Raymond
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susana Quijano-Roy
- Neuromuscular Unit, Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches, France
| | - Johann Böhm
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Isabelle Nelson
- Sorbonne Université, INSERM, Centre of Research in Myology, UMRS974, Paris, France
| | - Tanya Stojkovic
- APHP, Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Norma B Romero
- APHP, Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France.,Unité de Morphologie Neuromusculaire, Institut de Myologie, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jocelyn Laporte
- Département Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U1258, Centre National de la Recherche Scientifique UMR7104, Université de Strasbourg, Illkirch, France
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, NCNP, Kodaira, Tokyo, Japan
| | - Mark A Tarnopolsky
- Division of Neuromuscular & Neurometabolic Disorders, Department of Pediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - James Shorter
- Department of Biochemistry & Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, United States. .,Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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37
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Roy R, Das G, Kuttanda IA, Bhatter N, Rajyaguru PI. Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly. Nat Commun 2022; 13:2077. [PMID: 35440550 PMCID: PMC9019020 DOI: 10.1038/s41467-022-29715-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/21/2022] [Indexed: 01/12/2023] Open
Abstract
P-bodies are conserved mRNP complexes that are implicated in determining mRNA fate by affecting translation and mRNA decay. In this report, we identify RGG-motif containing translation repressor protein Sbp1 as a disassembly factor of P-bodies since disassembly of P-bodies is defective in Δsbp1. RGG-motif is necessary and sufficient to rescue the PB disassembly defect in Δsbp1. Binding studies using purified proteins revealed that Sbp1 physically interacts with Edc3 and Sbp1-Edc3 interaction competes with Edc3-Edc3 interaction. Purified Edc3 forms assemblies, promoted by the presence of RNA and NADH and the addition of purified Sbp1, but not the RGG-deletion mutant, leads to significantly decreased Edc3 assemblies. We further note that the aggregates of human EWSR1 protein, implicated in neurodegeneration, are more persistent in the absence of Sbp1 and overexpression of EWSR1 in Δsbp1 leads to a growth defect. Taken together, our observations suggest a role of Sbp1 in disassembly, which could apply to disease-relevant heterologous protein-aggregates.
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Affiliation(s)
- Raju Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Gitartha Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Nupur Bhatter
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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38
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Koehler LC, Grese ZR, Bastos ACS, Mamede LD, Heyduk T, Ayala YM. TDP-43 Oligomerization and Phase Separation Properties Are Necessary for Autoregulation. Front Neurosci 2022; 16:818655. [PMID: 35495061 PMCID: PMC9048411 DOI: 10.3389/fnins.2022.818655] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
Loss of TDP-43 protein homeostasis and dysfunction, in particular TDP-43 aggregation, are tied to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 is an RNA binding protein tightly controlling its own expression levels through a negative feedback loop, involving TDP-43 recruitment to the 3′ untranslated region of its own transcript. Aberrant TDP-43 expression caused by autoregulation defects are linked to TDP-43 pathology. Therefore, interactions between TDP-43 and its own transcript are crucial to prevent TDP-43 aggregation and loss of function. However, the mechanisms that mediate this interaction remain ill-defined. We find that a central RNA sequence in the 3′ UTR, which mediates TDP-43 autoregulation, increases the liquid properties of TDP-43 phase separation. Furthermore, binding to this RNA sequence induces TDP-43 condensation in human cell lysates, suggesting that this interaction promotes TDP-43 self-assembly into dynamic ribonucleoprotein granules. In agreement with these findings, our experiments show that TDP-43 oligomerization and phase separation, mediated by the amino and carboxy-terminal domains, respectively, are essential for TDP-43 autoregulation. According to our additional observations, CLIP34-associated phase separation and autoregulation may be efficiently controlled by phosphorylation of the N-terminal domain. Importantly, we find that specific ALS-associated TDP-43 mutations, mainly M337V, and a shortened TDP-43 isoform recently tied to motor neuron toxicity in ALS, disrupt the liquid properties of TDP-43-RNA condensates as well as autoregulatory function. In addition, we find that M337V decreases the cellular clearance of TDP-43 and other RNA binding proteins associated with ALS/FTD. These observations suggest that loss of liquid properties in M337V condensates strongly affects protein homeostasis. Together, this work provides evidence for the central role of TDP-43 oligomerization and liquid-liquid phase separation linked to RNA binding in autoregulation. These mechanisms may be impaired by TDP-43 disease variants and controlled by specific cellular signaling.
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39
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Arkov AL. Looking at the Pretty "Phase" of Membraneless Organelles: A View From Drosophila Glia. Front Cell Dev Biol 2022; 10:801953. [PMID: 35198559 PMCID: PMC8859445 DOI: 10.3389/fcell.2022.801953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Membraneless granules assemble in different cell types and cellular loci and are the focus of intense research due to their fundamental importance for cellular organization. These dynamic organelles are commonly assembled from RNA and protein components and exhibit soft matter characteristics of molecular condensates currently characterized with biophysical approaches and super-resolution microscopy imaging. In addition, research on the molecular mechanisms of the RNA-protein granules assembly provided insights into the formation of abnormal granules and molecular aggregates, which takes place during many neurodegenerative disorders including Parkinson's diseases (PD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). While these disorders are associated with formation of abnormal granules, membraneless organelles are normally assembled in neurons and contribute to translational control and affect stability of neuronal RNAs. More recently, a new subtype of membraneless granules was identified in Drosophila glia (glial granules). Interestingly, glial granules were found to contain proteins which are the principal components of the membraneless granules in germ cells (germ granules), indicating some similarity in the functional assembly of these structures in glia and germline. This mini review highlights recent research on glial granules in the context of other membraneless organelles, including their assembly mechanisms and potential functions in the nervous system.
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Affiliation(s)
- Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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40
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Gilodi M, Lisi S, F. Dudás E, Fantini M, Puglisi R, Louka A, Marcatili P, Cattaneo A, Pastore A. Selection and Modelling of a New Single-Domain Intrabody Against TDP-43. Front Mol Biosci 2022; 8:773234. [PMID: 35237655 PMCID: PMC8884700 DOI: 10.3389/fmolb.2021.773234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated to deteriorating motor and cognitive functions, and short survival. The disease is caused by neuronal death which results in progressive muscle wasting and weakness, ultimately leading to lethal respiratory failure. The misbehaviour of a specific protein, TDP-43, which aggregates and becomes toxic in ALS patient’s neurons, is supposed to be one of the causes. TDP-43 is a DNA/RNA-binding protein involved in several functions related to nucleic acid metabolism. Sequestration of TDP-43 aggregates is a possible therapeutic strategy that could alleviate or block pathology. Here, we describe the selection and characterization of a new intracellular antibody (intrabody) against TDP-43 from a llama nanobody library. The structure of the selected intrabody was predicted in silico and the model was used to suggest mutations that enabled to improve its expression yield, facilitating its experimental validation. We showed how coupling experimental methodologies with in silico design may allow us to obtain an antibody able to recognize the RNA binding regions of TDP-43. Our findings illustrate a strategy for the mitigation of TDP-43 proteinopathy in ALS and provide a potential new tool for diagnostics.
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Affiliation(s)
- Martina Gilodi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Erika F. Dudás
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Rita Puglisi
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Alexandra Louka
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
| | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
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41
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Versluys L, Ervilha Pereira P, Schuermans N, De Paepe B, De Bleecker JL, Bogaert E, Dermaut B. Expanding the TDP-43 Proteinopathy Pathway From Neurons to Muscle: Physiological and Pathophysiological Functions. Front Neurosci 2022; 16:815765. [PMID: 35185458 PMCID: PMC8851062 DOI: 10.3389/fnins.2022.815765] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/03/2022] [Indexed: 01/02/2023] Open
Abstract
TAR DNA-binding protein 43, mostly referred to as TDP-43 (encoded by the TARDBP gene) is strongly linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). From the identification of TDP-43 positive aggregates in the brains and spinal cords of ALS/FTD patients, to a genetic link between TARBDP mutations and the development of TDP-43 pathology in ALS, there is strong evidence indicating that TDP-43 plays a pivotal role in the process of neuronal degeneration. What this role is, however, remains to be determined with evidence ranging from gain of toxic properties through the formation of cytotoxic aggregates, to an inability to perform its normal functions due to nuclear depletion. To add to an already complex subject, recent studies highlight a role for TDP-43 in muscle physiology and disease. We here review the biophysical, biochemical, cellular and tissue-specific properties of TDP-43 in the context of neurodegeneration and have a look at the nascent stream of evidence that positions TDP-43 in a myogenic context. By integrating the neurogenic and myogenic pathological roles of TDP-43 we provide a more comprehensive and encompassing view of the role and mechanisms associated with TDP-43 across the various cell types of the motor system, all the way from brain to limbs.
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Affiliation(s)
- Lauren Versluys
- Department Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Pedro Ervilha Pereira
- Department Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nika Schuermans
- Department Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Boel De Paepe
- Department of Neurology and Neuromuscular Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jan L. De Bleecker
- Department of Neurology and Neuromuscular Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Bogaert
- Department Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bart Dermaut
- Department Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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42
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TDP-43 pathology: from noxious assembly to therapeutic removal. Prog Neurobiol 2022; 211:102229. [DOI: 10.1016/j.pneurobio.2022.102229] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
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43
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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44
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Corbet GA, Wheeler JR, Parker R, Weskamp K. TDP43 ribonucleoprotein granules: physiologic function to pathologic aggregates. RNA Biol 2021; 18:128-138. [PMID: 34412568 DOI: 10.1080/15476286.2021.1963099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Ribonucleoprotein (RNP) assemblies are ubiquitous in eukaryotic cells and have functions throughout RNA transcription, splicing, and stability. Of the RNA-binding proteins that form RNPs, TAR DNA-binding protein of 43 kD (TDP43) is of particular interest due to its essential nature and its association with disease. TDP43 plays critical roles in RNA metabolism, many of which require its recruitment to RNP granules such as stress granules, myo-granules, and neuronal transport granules. Moreover, the presence of cytoplasmic TDP43-positive inclusions is a pathological hallmark of several neurodegenerative diseases. Despite the pervasiveness of TDP43 aggregates, TDP43 mutations are exceedingly rare, suggesting that aggregation may be linked to dysregulation of TDP43 function. Oligomerization is a part of normal TDP43 function; thus, it is of interest to understand what triggers the irreversible aggregation that is seen in disease. Herein, we examine TDP43 functions, particularly in RNP granules, and the mechanisms which may explain pathological TDP43 aggregation.
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Affiliation(s)
- Giulia Ada Corbet
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | | | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Department of Chemistry, Howard Hughes Medical Institute, Chevy Chase, MD, USA
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45
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Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project. J Clin Med 2021; 10:jcm10153394. [PMID: 34362180 PMCID: PMC8348602 DOI: 10.3390/jcm10153394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 12/25/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS's mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large difference in ALS onset among different populations. In this study, we addressed this issue with a bioinformatics approach, using the United Kingdom Biobank (UKBB) and the European 1000 Genomes Project (1KG) in order to analyze the most ALS-representative single nucleotide polymorphisms (SNPs) that differ for minor allele frequency (MAF) between the United Kingdom population and some European populations including Finnish in Finland, Iberian population in Spain, and Tuscans in Italy. We found 84 SNPs associated with 46 genes that are involved in different pathways including: "Ca2+ activated K+ channels", "cGMP effects", "Nitric oxide stimulates guanylate cyclase", "Proton/oligopeptide cotransporters", and "Signaling by MAPK mutants". In addition, we revealed that 83% of the 84 SNPs can alter transcription factor-motives binding sites of 224 genes implicated in "Regulation of beta-cell development", "Transcription-al regulation by RUNX3", "Transcriptional regulation of pluripotent stem cells", and "FOXO-mediated transcription of cell death genes". In conclusion, the genes and pathways analyzed could explain the cause of the difference of ALS onset.
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46
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Zaepfel BL, Rothstein JD. RNA Is a Double-Edged Sword in ALS Pathogenesis. Front Cell Neurosci 2021; 15:708181. [PMID: 34349625 PMCID: PMC8326408 DOI: 10.3389/fncel.2021.708181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease that affects upper and lower motor neurons. Familial ALS accounts for a small subset of cases (<10-15%) and is caused by dominant mutations in one of more than 10 known genes. Multiple genes have been causally or pathologically linked to both ALS and frontotemporal dementia (FTD). Many of these genes encode RNA-binding proteins, so the role of dysregulated RNA metabolism in neurodegeneration is being actively investigated. In addition to defects in RNA metabolism, recent studies provide emerging evidence into how RNA itself can contribute to the degeneration of both motor and cortical neurons. In this review, we discuss the roles of altered RNA metabolism and RNA-mediated toxicity in the context of TARDBP, FUS, and C9ORF72 mutations. Specifically, we focus on recent studies that describe toxic RNA as the potential initiator of disease, disease-associated defects in specific RNA metabolism pathways, as well as how RNA-based approaches can be used as potential therapies. Altogether, we highlight the importance of RNA-based investigations into the molecular progression of ALS, as well as the need for RNA-dependent structural studies of disease-linked RNA-binding proteins to identify clear therapeutic targets.
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Affiliation(s)
- Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Molecular Biology and Genetics Department, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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47
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Lin LTW, Razzaq A, Di Gregorio SE, Hong S, Charles B, Lopes MH, Beraldo F, Prado VF, Prado MAM, Duennwald ML. Hsp90 and its co-chaperone Sti1 control TDP-43 misfolding and toxicity. FASEB J 2021; 35:e21594. [PMID: 33908654 DOI: 10.1096/fj.202002645r] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/14/2022]
Abstract
Protein misfolding is a central feature of most neurodegenerative diseases. Molecular chaperones can modulate the toxicity associated with protein misfolding, but it remains elusive which molecular chaperones and co-chaperones interact with specific misfolded proteins. TDP-43 misfolding and inclusion formation are a hallmark of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Using yeast and mammalian neuronal cells we find that Hsp90 and its co-chaperone Sti1 have the capacity to alter TDP-43 misfolding, inclusion formation, aggregation, and cellular toxicity. Our data also demonstrate that impaired Hsp90 function sensitizes cells to TDP-43 toxicity and that Sti1 specifically interacts with and strongly modulates TDP-43 toxicity in a dose-dependent manner. Our study thus uncovers a previously unrecognized tie between Hsp90, Sti1, TDP-43 misfolding, and cellular toxicity.
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Affiliation(s)
- Lilian Tsai-Wei Lin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Abdul Razzaq
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Sonja E Di Gregorio
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Soojie Hong
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Brendan Charles
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Marilene H Lopes
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Flavio Beraldo
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Vania F Prado
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Marco A M Prado
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Martin L Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
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48
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Duran-Aniotz C, Orellana P, Leon Rodriguez T, Henriquez F, Cabello V, Aguirre-Pinto MF, Escobedo T, Takada LT, Pina-Escudero SD, Lopez O, Yokoyama JS, Ibanez A, Parra MA, Slachevsky A. Systematic Review: Genetic, Neuroimaging, and Fluids Biomarkers for Frontotemporal Dementia Across Latin America Countries. Front Neurol 2021; 12:663407. [PMID: 34248820 PMCID: PMC8263937 DOI: 10.3389/fneur.2021.663407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Frontotemporal dementia (FTD) includes a group of clinically, genetically, and pathologically heterogeneous neurodegenerative disorders, affecting the fronto-insular-temporal regions of the brain. Clinically, FTD is characterized by progressive deficits in behavior, executive function, and language and its diagnosis relies mainly on the clinical expertise of the physician/consensus group and the use of neuropsychological tests and/or structural/functional neuroimaging, depending on local availability. The modest correlation between clinical findings and FTD neuropathology makes the diagnosis difficult using clinical criteria and often leads to underdiagnosis or misdiagnosis, primarily due to lack of recognition or awareness of FTD as a disease and symptom overlap with psychiatric disorders. Despite advances in understanding the underlying neuropathology of FTD, accurate and sensitive diagnosis for this disease is still lacking. One of the major challenges is to improve diagnosis in FTD patients as early as possible. In this context, biomarkers have emerged as useful methods to provide and/or complement clinical diagnosis for this complex syndrome, although more evidence is needed to incorporate most of them into clinical practice. However, most biomarker studies have been performed using North American or European populations, with little representation of the Latin American and the Caribbean (LAC) region. In the LAC region, there are additional challenges, particularly the lack of awareness and knowledge about FTD, even in specialists. Also, LAC genetic heritage and cultures are complex, and both likely influence clinical presentations and may modify baseline biomarker levels. Even more, due to diagnostic delay, the clinical presentation might be further complicated by both neurological and psychiatric comorbidity, such as vascular brain damage, substance abuse, mood disorders, among others. This systematic review provides a brief update and an overview of the current knowledge on genetic, neuroimaging, and fluid biomarkers for FTD in LAC countries. Our review highlights the need for extensive research on biomarkers in FTD in LAC to contribute to a more comprehensive understanding of the disease and its associated biomarkers. Dementia research is certainly reduced in the LAC region, highlighting an urgent need for harmonized, innovative, and cross-regional studies with a global perspective across multiple areas of dementia knowledge.
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Affiliation(s)
- Claudia Duran-Aniotz
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| | - Paulina Orellana
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| | - Tomas Leon Rodriguez
- Trinity College, Global Brain Health Institute, Dublin, Ireland
- Memory and Neuropsychiatric Clinic (CMYN) Neurology Department, Hospital del Salvador and Faculty of Medicine, University of Chile, Santiago, Chile
| | - Fernando Henriquez
- Neuropsychology and Clinical Neuroscience Laboratory (LANNEC), Physiopathology Department - Institute of Biomedical Sciences (ICBM), Neuroscience and East Neuroscience Departments, Faculty of Medicine, University of Chile, Santiago, Chile
- Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Chile
| | - Victoria Cabello
- Neuropsychology and Clinical Neuroscience Laboratory (LANNEC), Physiopathology Department - Institute of Biomedical Sciences (ICBM), Neuroscience and East Neuroscience Departments, Faculty of Medicine, University of Chile, Santiago, Chile
- Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Chile
| | | | - Tamara Escobedo
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| | - Leonel T. Takada
- Cognitive and Behavioral Neurology Unit - Department of Neurology, University of São Paulo, São Paulo, Brazil
| | - Stefanie D. Pina-Escudero
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, United States
- UCSF Department of Neurology, Memory and Aging Center, UCSF, San Francisco, CA, United States
| | - Oscar Lopez
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer S. Yokoyama
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, United States
- UCSF Department of Neurology, Memory and Aging Center, UCSF, San Francisco, CA, United States
| | - Agustin Ibanez
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
- Trinity College, Global Brain Health Institute, Dublin, Ireland
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, United States
- Cognitive Neuroscience Center (CNC), Universidad de San Andrés, & National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Mario A. Parra
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, United Kingdom
| | - Andrea Slachevsky
- Memory and Neuropsychiatric Clinic (CMYN) Neurology Department, Hospital del Salvador and Faculty of Medicine, University of Chile, Santiago, Chile
- Neuropsychology and Clinical Neuroscience Laboratory (LANNEC), Physiopathology Department - Institute of Biomedical Sciences (ICBM), Neuroscience and East Neuroscience Departments, Faculty of Medicine, University of Chile, Santiago, Chile
- Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Chile
- Cognitive and Behavioral Neurology Unit - Department of Neurology, University of São Paulo, São Paulo, Brazil
- Department of Neurology and Psychiatry, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
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49
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Zgórzyńska E, Krawczyk K, Bełdzińska P, Walczewska A. Molecular basis of proteinopathies: Etiopathology
of dementia and motor disorders. POSTEP HIG MED DOSW 2021. [DOI: 10.5604/01.3001.0014.9513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neurodegenerative diseases are one of the most important medical and social problems affecting
elderly people, the percentage of which is significantly increasing in the total world population.
The cause of these diseases is the destruction of neurons by protein aggregates that form pathological
deposits in neurons, glial cells and in the intercellular space. Proteins whose molecules
are easily destabilized by point mutations or endogenous processes are alpha-synuclein (ASN),
tau and TDP-43. Pathological forms of these proteins form characteristic aggregates, which accumulate
in the neurons and are the cause of various forms of dementia and motor disorders.
The most common causes of dementia are tauopathies. In primary tauopathies, which include
progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), Pick’s disease (PiD), and
frontotemporal dementia (FTD), modified tau molecules disrupt axonal transport and protein
distribution in neurons. Ultimately, the helical filaments and neurofibrillary tangles of tau lead to
neuron death in various structures of the brain. In Alzheimer’s disease hyperphosphorylated tau tangles along with β amyloid plaques are responsible for the degeneration of the hippocampus,
entorhinal cortex and amygdala. The most prevalent synucleinopathies are Parkinson’s disease,
multiple system atrophy (MSA) and dementia with Lewy bodies, where there is a degeneration of
neurons in the extrapyramidal tracts or, as in MSA, autonomic nerves. TDP-43 inclusions in the
cytoplasm cause the degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) and
in one of the frontotemporal dementia variant (FTLD-TDP). In this work ASN, tau and TDP-43
structures are described, as well as the genetic and sporadic factors that lead to the destabilization
of molecules, their aggregation and incorrect distribution in neurons, which are the causes
of neurodegenerative diseases.
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Affiliation(s)
| | - Klaudia Krawczyk
- Zakład Interakcji Międzykomórkowych, Uniwersytet Medyczny w Łodzi
| | | | - Anna Walczewska
- Zakład Interakcji Międzykomórkowych, Uniwersytet Medyczny w Łodzi
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50
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Akbari Dilmaghani N, Hussen BM, Nateghinia S, Taheri M, Ghafouri-Fard S. Emerging role of microRNAs in the pathogenesis of amyotrophic lateral sclerosis. Metab Brain Dis 2021; 36:737-749. [PMID: 33604874 DOI: 10.1007/s11011-021-00697-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a deadly motor neuron disease (MND) and the most frequent MND in adults. ALS is recognized by degenerative alterations in both upper and lower motor neurons. This disorder is classified to familial and sporadic classes. Disease-causing mutations in SOD1, C9ORF72, FUS, and TARDBP have been recognized in familial ALS cases. However, in spite of conduction of several genetic association studies, heritable genetic risk elements in sporadic have not been identified completely. Several miRNAs have been dysregulated in the serum samples or brain tissues of ALS patients. Moreover, a number of miRNAs have been suggested as putative biomarkers for sporadic ALS. In the current manuscript, we review of miRNAs in the development of ALS.
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Affiliation(s)
- Nader Akbari Dilmaghani
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Pharmacognosy Department, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Saeedeh Nateghinia
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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