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Armas JMB, Taoro-González L, Fisher EMC, Acevedo-Arozena A. Challenges of modelling TDP-43 pathology in mice. Mamm Genome 2025:10.1007/s00335-025-10131-1. [PMID: 40301152 DOI: 10.1007/s00335-025-10131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Accepted: 04/17/2025] [Indexed: 05/01/2025]
Abstract
TDP-43 is a normally nuclear RNA binding protein that under pathological conditions may be excluded from the nucleus and deposited in the cytoplasm in the form of insoluble polyubiquitinated and polyphosphorylated inclusions. This nuclear exclusion coupled with cytoplasmic accumulation is called TDP-43 pathology and contributes to a range of disorders collectively known as TDP-43 proteinopathies. These include the great majority of amyotrophic lateral sclerosis (ALS) cases, all limbic-predominant age-related TDP-43 encephalopathy (LATE), as well as up to 50% of frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD) cases. Thus, TDP-43 pathology is a common feature underlying a wide range of neurodegenerative conditions. However, modelling it has proven to be challenging, particularly generating models with concomitant TDP-43 loss of nuclear function and cytoplasmic inclusions. Here, focussing exclusively on mice, we discuss TDP-43 genetic models in terms of the presence of TDP-43 pathology, and we consider other models with TDP-43 pathology due to mutations in disparate genes. We also consider manipulations aimed at producing TDP-43 pathology, and we look at potential strategies to develop new, much needed models to address the many outstanding questions regarding how and why TDP-43 protein leaves the nucleus and accumulates in the cytoplasm, causing downstream dysfunction and devastating disease.
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Affiliation(s)
- José Miguel Brito Armas
- Unidad de Investigación Hospital Universitario de Canarias, Instituto de Investigación Sanitaria de Canarias, CIBERNED and ITB-ULL, Tenerife, Spain
| | - Lucas Taoro-González
- Unidad de Investigación Hospital Universitario de Canarias, Instituto de Investigación Sanitaria de Canarias, CIBERNED and ITB-ULL, Tenerife, Spain
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases and Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK.
| | - Abraham Acevedo-Arozena
- Unidad de Investigación Hospital Universitario de Canarias, Instituto de Investigación Sanitaria de Canarias, CIBERNED and ITB-ULL, Tenerife, Spain.
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2
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Dykstra MM, Weskamp K, Gómez NB, Waksmacki J, Tank E, Glineburg MR, Snyder A, Pinarbasi E, Bekier M, Li X, Miller MR, Bai J, Shahzad S, Nedumaran N, Wieland C, Stewart C, Willey S, Grotewold N, McBride J, Moran JJ, Suryakumar AV, Lucas M, Tessier PM, Ward M, Todd PK, Barmada SJ. TDP43 autoregulation gives rise to dominant negative isoforms that are tightly controlled by transcriptional and post-translational mechanisms. Cell Rep 2025; 44:115113. [PMID: 39792557 PMCID: PMC11848802 DOI: 10.1016/j.celrep.2024.115113] [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: 07/09/2024] [Revised: 11/06/2024] [Accepted: 12/04/2024] [Indexed: 01/12/2025] Open
Abstract
The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a by-product of TDP43 autoregulation and cleared by nonsense-mediated RNA decay (NMD). sTDP43-encoding transcripts that escape NMD are rapidly degraded post-translationally via the proteasome and macroautophagy. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA-binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and underscore the consequences of aberrant sTDP43 accumulation in disease.
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Affiliation(s)
- Megan M Dykstra
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Kaitlin Weskamp
- Chemistry Department, Nebraska Wesleyan University, Lincoln, NE, USA
| | - Nicolás B Gómez
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Jacob Waksmacki
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - M Rebecca Glineburg
- Biological Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | | | - Emile Pinarbasi
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA; Neuropathology, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Morgan R Miller
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Jen Bai
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Shameena Shahzad
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Neha Nedumaran
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Clare Wieland
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Corey Stewart
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Sydney Willey
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Nikolas Grotewold
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Jonathon McBride
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - John J Moran
- Atlanta Pediatric Research Alliance, Emory University, Atlanta, GA, USA
| | | | - Michael Lucas
- Departments of Chemical Engineering and Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Peter M Tessier
- Departments of Chemical Engineering and Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Michael Ward
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, USA
| | - Peter K Todd
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Department of Neurology, University of Michigan, Ann Arbor, MI, USA; Veterans Affairs Medical Center, Ann Arbor, MI, USA
| | - Sami J Barmada
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
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3
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Xu B, Lei X, Yang Y, Yu J, Chen J, Xu Z, Ye K, Zhang J. Peripheral proteinopathy in neurodegenerative diseases. Transl Neurodegener 2025; 14:2. [PMID: 39819742 PMCID: PMC11737199 DOI: 10.1186/s40035-024-00461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 12/17/2024] [Indexed: 01/19/2025] Open
Abstract
Proteinopathies in neurology typically refer to pathological changes in proteins associated with neurological diseases, such as the aggregation of amyloid β and Tau in Alzheimer's disease, α-synuclein in Parkinson's disease and multiple system atrophy, and TAR DNA-binding protein 43 in amyotrophic lateral sclerosis and frontotemporal dementia. Interestingly, these proteins are also commonly found in peripheral tissues, raising important questions about their roles in neurological disorders. Multiple studies have shown that peripherally derived pathological proteins not only travel to the brain through various routes, aggravating brain pathology, but also contribute significantly to peripheral dysfunction, highlighting their crucial impact on neurological diseases. Investigating how these peripherally derived proteins influence the progression of neurological disorders could open new horizons for achieving early diagnosis and treatment. This review summarizes the distribution, transportation pathways, and pathogenic mechanisms of several neurodegenerative disease-related pathological proteins in the periphery, proposing that targeting these peripheral pathological proteins could be a promising strategy for preventing and managing neurological diseases.
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Affiliation(s)
- Bin Xu
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Xia Lei
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Ying Yang
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Jiayi Yu
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
- School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310002, China
| | - Jun Chen
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Zhi Xu
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
- School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310002, China
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Faculty of Life and Health Sciences, Shenzhen University of Advanced Technology (SUAT), Shenzhen, 518055, China
| | - Jing Zhang
- Department of Pathology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China.
- National Human Brain Bank for Health and Disease, Zhejiang University, Hangzhou, 310012, China.
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4
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Ketabforoush A, Faghihi F, Azedi F, Ariaei A, Habibi MA, Khalili M, Ashtiani BH, Joghataei MT, Arnold WD. Sodium Phenylbutyrate and Tauroursodeoxycholic Acid: A Story of Hope Turned to Disappointment in Amyotrophic Lateral Sclerosis Treatment. Clin Drug Investig 2024; 44:495-512. [PMID: 38909349 DOI: 10.1007/s40261-024-01371-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2024] [Indexed: 06/24/2024]
Abstract
The absence of a definitive cure for amyotrophic lateral sclerosis (ALS) emphasizes the crucial need to explore new and improved treatment approaches for this fatal, progressive, and disabling neurodegenerative disorder. As at the end of 2023, five treatments - riluzole, edaravone, dextromethorphan hydrobromide + quinidine sulfate (DHQ), tofersen, and sodium phenylbutyrate-tauroursodeoxycholic acid (PB-TUDCA) - were FDA approved for the treatment of patients with ALS. Among them PB-TUDCA has been shown to impact DNA processing impairments, mitochondria dysfunction, endoplasmic reticulum stress, oxidative stress, and pathologic folded protein agglomeration defects, which have been associated with ALS pathophysiology. The Phase 2 CENTAUR trial demonstrated significant impact of PB-TUDCA on the ALS Functional Rating Scale-Revised (ALSFRS-R) risk of death, hospitalization, and the need for tracheostomy or permanent assisted ventilation in patients with ALS based on post hoc analyses. More recently, contrasting with the CENTAUR trial results, results from the Phase 3 PHOENIX trial (NCT05021536) showed no change in ALSFRS-R total score at 48 weeks. Consequently, the sponsor company initiated the process with the US FDA and Health Canada to voluntarily withdraw the marketing authorizations for PB-TUDCA. In the present article, we review ALS pathophysiology, with a focus on PB-TUDCA's proposed mechanisms of action and recent clinical trial results and discuss the implications of conflicting trial data for ALS and other neurological disorders.
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Affiliation(s)
- Arsh Ketabforoush
- NextGen Precision Health, University of Missouri, 1030 Hitt St., Columbia, MO, 65211, USA
- Department of Physical Medicine and Rehabilitation, University of Missouri, Columbia, MO, USA
| | - Faezeh Faghihi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Azedi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Armin Ariaei
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohamad Amin Habibi
- Clinical Research Development Center, Shahid Beheshti Hospital, Qom University of Medical Sciences, Qom, Iran
| | - Maryam Khalili
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahram Haghi Ashtiani
- Department of Neurology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghi Joghataei
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - W David Arnold
- NextGen Precision Health, University of Missouri, 1030 Hitt St., Columbia, MO, 65211, USA.
- Department of Physical Medicine and Rehabilitation, University of Missouri, Columbia, MO, USA.
- Department of Neurology, University of Missouri, Columbia, MO, USA.
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, USA.
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5
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Watanabe S, Amporndanai K, Awais R, Latham C, Awais M, O'Neill PM, Yamanaka K, Hasnain SS. Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement. Sci Rep 2024; 14:12118. [PMID: 38802492 PMCID: PMC11130262 DOI: 10.1038/s41598-024-62903-5] [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: 02/14/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) selectively affects motor neurons. SOD1 is the first causative gene to be identified for ALS and accounts for at least 20% of the familial (fALS) and up to 4% of sporadic (sALS) cases globally with some geographical variability. The destabilisation of the SOD1 dimer is a key driving force in fALS and sALS. Protein aggregation resulting from the destabilised SOD1 is arrested by the clinical drug ebselen and its analogues (MR6-8-2 and MR6-26-2) by redeeming the stability of the SOD1 dimer. The in vitro target engagement of these compounds is demonstrated using the bimolecular fluorescence complementation assay with protein-ligand binding directly visualised by co-crystallography in G93A SOD1. MR6-26-2 offers neuroprotection slowing disease onset of SOD1G93A mice by approximately 15 days. It also protected neuromuscular junction from muscle denervation in SOD1G93A mice clearly indicating functional improvement.
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Affiliation(s)
- Seiji Watanabe
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8601, Japan
| | - Kangsa Amporndanai
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, M0polecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Raheela Awais
- School of Life Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Caroline Latham
- School of Life Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Muhammad Awais
- Department of Molecular and Clinical Cancer Medicine, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GE, UK
| | - Paul M O'Neill
- Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 7ZD, UK.
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8601, Japan.
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, M0polecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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6
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Wang T, Sobue A, Watanabe S, Komine O, Saido TC, Saito T, Yamanaka K. Dimethyl fumarate improves cognitive impairment and neuroinflammation in mice with Alzheimer's disease. J Neuroinflammation 2024; 21:55. [PMID: 38383481 PMCID: PMC10882778 DOI: 10.1186/s12974-024-03046-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Neuroinflammation substantially contributes to the pathology of Alzheimer's disease (AD), the most common form of dementia. Studies have reported that nuclear factor erythroid 2-related factor 2 (Nrf2) attenuates neuroinflammation in the mouse models of neurodegenerative diseases, however, the detailed mechanism remains unclear. METHODS The effects of dimethyl fumarate (DMF), a clinically used drug to activate the Nrf2 pathway, on neuroinflammation were analyzed in primary astrocytes and AppNL-G-F (App-KI) mice. The cognitive function and behavior of DMF-administrated App-KI mice were evaluated. For the gene expression analysis, microglia and astrocytes were directly isolated from the mouse cerebral cortex by magnetic-activated cell sorting, followed by quantitative PCR. RESULTS DMF treatment activated some Nrf2 target genes and inhibited the expression of proinflammatory markers in primary astrocytes. Moreover, chronic oral administration of DMF attenuated neuroinflammation, particularly in astrocytes, and reversed cognitive dysfunction presumably by activating the Nrf2-dependent pathway in App-KI mice. Furthermore, DMF administration inhibited the expression of STAT3/C3 and C3 receptor in astrocytes and microglia isolated from App-KI mice, respectively, suggesting that the astrocyte-microglia crosstalk is involved in neuroinflammation in mice with AD. CONCLUSION The activation of astrocytic Nrf2 signaling confers neuroprotection in mice with AD by controlling neuroinflammation, particularly by regulating astrocytic C3-STAT3 signaling. Furthermore, our study has implications for the repositioning of DMF as a drug for AD treatment.
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Affiliation(s)
- Ting Wang
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan
- Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Akira Sobue
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan.
- Medical Interactive Research and Academia Industry Collaboration Center, Research Institute of Environmental Medicine, Nagoya University, Aichi, Japan.
| | - Seiji Watanabe
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan
| | - Okiru Komine
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
| | - Takashi Saito
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Aichi, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, 464-8601, Japan.
- Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Aichi, Japan.
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Aichi, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Aichi, Japan.
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7
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Watanabe S, Murata Y, Oka Y, Oiwa K, Horiuchi M, Iguchi Y, Komine O, Sobue A, Katsuno M, Ogi T, Yamanaka K. Mitochondria-associated membrane collapse impairs TBK1-mediated proteostatic stress response in ALS. Proc Natl Acad Sci U S A 2023; 120:e2315347120. [PMID: 37967220 PMCID: PMC10666035 DOI: 10.1073/pnas.2315347120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023] Open
Abstract
The organelle contact site of the endoplasmic reticulum and mitochondria, known as the mitochondria-associated membrane (MAM), is a multifunctional microdomain in cellular homeostasis. We previously reported that MAM disruption is a common pathological feature in amyotrophic lateral sclerosis (ALS); however, the precise role of MAM in ALS was uncovered. Here, we show that the MAM is essential for TANK-binding kinase 1 (TBK1) activation under proteostatic stress conditions. A MAM-specific E3 ubiquitin ligase, autocrine motility factor receptor, ubiquitinated nascent proteins to activate TBK1 at the MAM, which results in ribosomal protein degradation. MAM or TBK1 deficiency under proteostatic stress conditions resulted in increased cellular vulnerability in vitro and motor impairment in vivo. Thus, MAM disruption exacerbates proteostatic stress via TBK1 inactivation in ALS. Our study has revealed a proteostatic mechanism mediated by the MAM-TBK1 axis, highlighting the physiological importance of the organelle contact sites.
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Affiliation(s)
- Seiji Watanabe
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Yuri Murata
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Kotaro Oiwa
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mai Horiuchi
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Yohei Iguchi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Okiru Komine
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Akira Sobue
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Medical Interactive Research and Academia Industry Collaboration Center, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Glyco-core Research, Nagoya University, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Institute for Glyco-core Research, Nagoya University, Nagoya, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Institute for Glyco-core Research, Nagoya University, Nagoya, Japan
- Center for One Medicine Innovative Translational Research, Nagoya University, Nagoya, Japan
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8
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Patni D, Jha SK. Thermodynamic modulation of folding and aggregation energy landscape by DNA binding of functional domains of TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140916. [PMID: 37061152 DOI: 10.1016/j.bbapap.2023.140916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 04/17/2023]
Abstract
TDP-43 is a vital nucleic acid binding protein which forms stress-induced aberrant aggregates in around 97% cases of ALS, a fatal neurodegenerative disease. The functional tandem RRM domain of the protein (TDP-43tRRM) has been shown to undergo amyloid-like aggregation under stress in a pH-dependent fashion. However, the underlying thermodynamic and molecular basis of aggregation and how the energy landscape of folding, stability, and aggregation are coupled and modulated by nucleic acid binding is poorly understood. Here, we show that the pH stress thermodynamically destabilizes the native protein and systematically populates the unfolded-like aggregation-prone molecules which leads to amyloid-like aggregation. We observed that specific DNA binding inhibits aggregation and populates native-like compact monomeric state even under low-pH stress as measured by circular dichroism, ANS binding, size exclusion chromatography, and transmission electron microscopy. We show that DNA-binding thermodynamically stabilizes and populates the native state even under stress and reduces the population of unfolded-like aggregation-prone molecules which leads to systematic aggregation inhibition. Our results suggest that thermodynamic modulation of the folding and aggregation energy landscape by nucleic-acid-like molecules could be a promising approach for effective therapeutic intervention in TDP-43-associated proteinopathies.
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Affiliation(s)
- Divya Patni
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Hashimoto K, Watanabe S, Akutsu M, Muraki N, Kamishina H, Furukawa Y, Yamanaka K. Intrinsic structural vulnerability in the hydrophobic core induces species-specific aggregation of canine SOD1 with degenerative myelopathy-linked E40K mutation. J Biol Chem 2023:104798. [PMID: 37156398 DOI: 10.1016/j.jbc.2023.104798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
Canine degenerative myelopathy (DM), a fatal neurodegenerative disease in dogs, shares clinical and genetic features with amyotrophic lateral sclerosis (ALS), a human motor neuron disease. Mutations in the SOD1 gene encoding Cu/Zn superoxide dismutase (SOD1) cause canine DM and a subset of inherited human ALS. The most frequent DM causative mutation is homozygous E40K mutation which induces the aggregation of canine SOD1 but not of human SOD1. However, the mechanism through which canine E40K mutation induces species-specific aggregation of SOD1 remains unknown. By screening human/canine chimeric SOD1s, we identified that the humanized mutation of the 117th residue (M117L), encoded by exon 4, significantly reduced aggregation propensity of canine SOD1E40K. Conversely, introducing a mutation of leucine 117 to methionine, a residue homologous to canine, promoted E40K-dependent aggregation in human SOD1. M117L mutation improved protein stability and reduced cytotoxicity of canine SOD1E40K. Furthermore, crystal structural analysis of canine SOD1 proteins revealed that M117L increased the packing within the hydrophobic core of the β-barrel structure, contributing to the increased protein stability. Our findings indicate that the structural vulnerability derived intrinsically from Met 117 in the hydrophobic core of the β-barrel structure induces E40K-dependent species-specific aggregation in canine SOD1.
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Affiliation(s)
- Kei Hashimoto
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Seiji Watanabe
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Masato Akutsu
- Department of Chemistry, Keio University, Yokohama, Kanagawa, Japan
| | - Norifumi Muraki
- Department of Chemistry, Keio University, Yokohama, Kanagawa, Japan
| | - Hiroaki Kamishina
- Life Science Research Center, Gifu University, Gifu, Japan; Kyoto AR Advanced Veterinary Medical Center, Kyoto, Japan
| | | | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan; Institute for Glyco-core Research (iGCORE), Nagoya University, Aichi, Japan; Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
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10
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Sato T, Oda K, Sakai S, Kato R, Yamamori S, Itakura M, Kodera Y, Nishizawa M, Sasaoka T, Onodera O, Yokoyama M. Importance of the Q/N-rich segment for protein stability of endogenous mouse TDP-43. Sci Rep 2022; 12:14923. [PMID: 36056157 PMCID: PMC9440050 DOI: 10.1038/s41598-022-19153-0] [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: 11/25/2021] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
TAR DNA-binding protein 43 kDa (TDP-43), a nuclear protein, plays an important role in the molecular pathogenesis of amyotrophic lateral sclerosis (ALS). The long-disordered C-terminal region (CTR) of TDP-43 is known to be aggregation-prone and a hotspot for ALS mutations, so elucidation of the physiological function of CTR will provide insights into the pathogenesis of ALS. The CTR has two Gly, aromatic, and Ser-rich (GaroS) segments and an amyloidogenic core divided into a hydrophobic patch (HP) and a Gln/Asn (Q/N)-rich segment. Although TDP-43 lacking the CTR is known to be unstable, as observed in knock-in mice, it is unclear which of these segments contributes to the stability of TDP-43. Here, we generated 12 mouse lines lacking the various sub-regions of CTR by genome editing and compared the embryonic lethality of homozygotes, and protein and mRNA expression levels of TDP-43. We demonstrated the functional diversity of the four segments of CTR, finding that the presence of the Q/N-rich segment greatly restored the protein stability of TDP-43. In addition, we found that the second GaroS deletion did not affect protein stability and mouse development.
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Affiliation(s)
- Toshiya Sato
- Department of Laboratory Animal Science, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan. .,Center for Genetic Studies of Integrated Biological Functions, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan. .,Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.
| | - Kanako Oda
- Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Seiko Sakai
- Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Rika Kato
- Center for Genetic Studies of Integrated Biological Functions, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan
| | - Saori Yamamori
- Department of Biochemistry, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan
| | - Makoto Itakura
- Department of Biochemistry, Kitasato University School of Medicine, Sagamihara, 252-0374, Japan
| | - Yoshio Kodera
- Department of Physics, Kitasato University School of Science, Sagamihara, 252-0373, Japan
| | - Masatoyo Nishizawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.,Department of Nursing, Niigata University of Health and Welfare, Niigata, 950-3198, Japan
| | - Toshikuni Sasaoka
- Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Minesuke Yokoyama
- Department of Comparative and Experimental Medicine, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.,Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
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11
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The pathogenesis of amyotrophic lateral sclerosis: Mitochondrial dysfunction, protein misfolding and epigenetics. Brain Res 2022; 1786:147904. [PMID: 35390335 DOI: 10.1016/j.brainres.2022.147904] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with multiple complex mechanisms involved. Among them, mitochondrial dysfunction plays an important role in ALS. Multiple studies have shown that mitochondria are closely associated with reactive oxygen species production and oxidative stress and exhibit different functional states in different genetic backgrounds. In this review we explored the roles of Ca2+, autophagy, mitochondrial quality control in the regulation of mitochondrial homeostasis and their relationship with ALS. In addition, we also summarized and analyzed the roles of protein misfolding and abnormal aggregation in the pathogenesis of ALS. Moreover, we also discussed how epigenetic mechanisms such as DNA methylation and protein post-translational modification affect initiation and progression of ALS. Nevertheless, existing events still cannot fully explain the pathogenesis of ALS at present, more studies are required to explore pathological mechanisms of ALS.
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12
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Todd TW, Petrucelli L. Modelling amyotrophic lateral sclerosis in rodents. Nat Rev Neurosci 2022; 23:231-251. [PMID: 35260846 DOI: 10.1038/s41583-022-00564-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
The efficient study of human disease requires the proper tools, one of the most crucial of which is an accurate animal model that faithfully recapitulates the human condition. The study of amyotrophic lateral sclerosis (ALS) is no exception. Although the majority of ALS cases are considered sporadic, most animal models of this disease rely on genetic mutations identified in familial cases. Over the past decade, the number of genes associated with ALS has risen dramatically and, with each new genetic variant, there is a drive to develop associated animal models. Rodent models are of particular importance as they allow for the study of ALS in the context of a living mammal with a comparable CNS. Such models not only help to verify the pathogenicity of novel mutations but also provide critical insight into disease mechanisms and are crucial for the testing of new therapeutics. In this Review, we aim to summarize the full spectrum of ALS rodent models developed to date.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA.
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13
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Yang C, Qiao T, Yu J, Wang H, Guo Y, Salameh J, Metterville J, Parsi S, Yusuf I, Brown RH, Cai H, Xu Z. Low-level overexpression of wild type TDP-43 causes late-onset, progressive neurodegeneration and paralysis in mice. PLoS One 2022; 17:e0255710. [PMID: 35113871 PMCID: PMC8812852 DOI: 10.1371/journal.pone.0255710] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Modestly increased expression of transactive response DNA binding protein (TDP-43) gene have been reported in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neuromuscular diseases. However, whether this modest elevation triggers neurodegeneration is not known. Although high levels of TDP-43 overexpression have been modeled in mice and shown to cause early death, models with low-level overexpression that mimic the human condition have not been established. In this study, transgenic mice overexpressing wild type TDP-43 at less than 60% above the endogenous CNS levels were constructed, and their phenotypes analyzed by a variety of techniques, including biochemical, molecular, histological, behavioral techniques and electromyography. The TDP-43 transgene was expressed in neurons, astrocytes, and oligodendrocytes in the cortex and predominantly in astrocytes and oligodendrocytes in the spinal cord. The mice developed a reproducible progressive weakness ending in paralysis in mid-life. Detailed analysis showed ~30% loss of large pyramidal neurons in the layer V motor cortex; in the spinal cord, severe demyelination was accompanied by oligodendrocyte injury, protein aggregation, astrogliosis and microgliosis, and elevation of neuroinflammation. Surprisingly, there was no loss of lower motor neurons in the lumbar spinal cord despite the complete paralysis of the hindlimbs. However, denervation was detected at the neuromuscular junction. These results demonstrate that low-level TDP-43 overexpression can cause diverse aspects of ALS, including late-onset and progressive motor dysfunction, neuroinflammation, and neurodegeneration. Our findings suggest that persistent modest elevations in TDP-43 expression can lead to ALS and other neurological disorders involving TDP-43 proteinopathy. Because of the predictable and progressive clinical paralytic phenotype, this transgenic mouse model will be useful in preclinical trial of therapeutics targeting neurological disorders associated with elevated levels of TDP-43.
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Affiliation(s)
- Chunxing Yang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Tao Qiao
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jia Yu
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Hongyan Wang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Yansu Guo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Johnny Salameh
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jake Metterville
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sepideh Parsi
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Issa Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- RNA Therapeutic Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Neuroscience Program, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Huaibin Cai
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- RNA Therapeutic Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Neuroscience Program, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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14
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LncRNAs LCETRL3 and LCETRL4 at chromosome 4q12 diminish EGFR-TKIs efficiency in NSCLC through stabilizing TDP43 and EIF2S1. Signal Transduct Target Ther 2022; 7:30. [PMID: 35095099 PMCID: PMC8801511 DOI: 10.1038/s41392-021-00847-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/13/2021] [Accepted: 12/01/2021] [Indexed: 02/06/2023] Open
Abstract
Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are effective targeted therapy drugs for advanced non-small cell lung cancer (NSCLC) patients carrying sensitized EGFR mutations. The rapid development of EGFR-TKIs resistance represents a major clinical challenge for managing NSCLC. The chromosome 4q12 is the first genome-wide association study (GWAS)-reported locus associated with progression-free survival (PFS) of NSCLC patients treated with EGFR-TKIs. However, the biological significance of the noncoding transcripts at 4q12 in NSCLC remains elusive. In the present study, we identified two 4q12 long noncoding RNAs (lncRNAs) LCETRL3 and LCETRL4 which could significantly dimmish EGFR-TKIs efficiency. In line with their oncogenic role, evidently higher LCETRL3 and LCETRL4 levels were observed in NSCLC tissues as compared with normal specimens. Importantly, lncRNA LCETRL3 can interact with oncoprotein TDP43 and inhibit ubiquitination and degradation of TDP43. Similarly, lncRNA LCETRL4 can bind and stabilize oncoprotein EIF2S1 through reducing ubiquitin-proteasome degradation of EIF2S1. In particular, elevated levels of LCETRL3 or LCETRL4 in NSCLC cells resulted in stabilization of TDP43 or EIF2S1, increased levels of NOTCH1 or phosphorylated PDK1, activated AKT signaling and, thus, EGFR-TKIs resistance. Taken together, our data revealed a novel model that integrates two lncRNAs transcribed from the 4q12 locus into the regulation of EGFR-TKIs resistance in NSCLC. These findings shed new light on the importance of functionally annotating lncRNAs in the GWAS loci and provided insights to declare novel druggable targets, i.e., lncRNAs, which may unlock the therapeutic potential of EGFR-TKIs resistant NSCLC in the clinic.
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15
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Gao J, Wang L, Ren X, Dunn JR, Peters A, Miyagi M, Fujioka H, Zhao F, Askwith C, Liang J, Wang X. Translational regulation in the brain by TDP-43 phase separation. J Cell Biol 2021; 220:e202101019. [PMID: 34427634 PMCID: PMC8404466 DOI: 10.1083/jcb.202101019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/03/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
The in vivo physiological function of liquid-liquid phase separation (LLPS) that governs non-membrane-bound structures remains elusive. Among LLPS-prone proteins, TAR DNA-binding protein of 43 kD (TDP-43) is under intense investigation because of its close association with neurological disorders. Here, we generated mice expressing endogenous LLPS-deficient murine TDP-43. LLPS-deficient TDP-43 mice demonstrate impaired neuronal function and behavioral abnormalities specifically related to brain function. Brain neurons of these mice, however, did not show TDP-43 proteinopathy or neurodegeneration. Instead, the global rate of protein synthesis was found to be greatly enhanced by TDP-43 LLPS loss. Mechanistically, TDP-43 LLPS ablation increased its association with PABPC4, RPS6, RPL7, and other translational factors. The physical interactions between TDP-43 and translational factors relies on a motif, the deletion of which abolished the impact of LLPS-deficient TDP-43 on translation. Our findings show a specific physiological role for TDP-43 LLPS in the regulation of brain function and uncover an intriguing novel molecular mechanism of translational control by LLPS.
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Affiliation(s)
- Ju Gao
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Luwen Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Xiaojia Ren
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Justin R. Dunn
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Ariele Peters
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Hisashi Fujioka
- Electron Microscopy Core Facility, Case Western Reserve University, Cleveland, OH
| | - Fangli Zhao
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Candice Askwith
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Jingjing Liang
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Xinglong Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
- Department of Pathology, Case Western Reserve University, Cleveland, OH
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16
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Chhangani D, Martín-Peña A, Rincon-Limas DE. Molecular, functional, and pathological aspects of TDP-43 fragmentation. iScience 2021; 24:102459. [PMID: 34013172 PMCID: PMC8113996 DOI: 10.1016/j.isci.2021.102459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transactive response DNA binding protein 43 (TDP-43) is a DNA/RNA binding protein involved in transcriptional regulation and RNA processing. It is linked to sporadic and familial amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 is predominantly nuclear, but it translocates to the cytoplasm under pathological conditions. Cytoplasmic accumulation, phosphorylation, ubiquitination and truncation of TDP-43 are the main hallmarks of TDP-43 proteinopathies. Among these processes, the pathways leading to TDP-43 fragmentation remain poorly understood. We review here the molecular and biochemical properties of several TDP-43 fragments, the mechanisms and factors mediating their production, and their potential role in disease progression. We also address the presence of TDP-43 C-terminal fragments in several neurological disorders, including Alzheimer's disease, and highlight their respective implications. Finally, we discuss features of animal models expressing TDP-43 fragments as well as recent therapeutic strategies to approach TDP-43 truncation.
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Affiliation(s)
- Deepak Chhangani
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA
| | - Alfonso Martín-Peña
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32611, USA.,Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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17
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Hou L, Xie J, Wu Y, Wang J, Duan A, Ao Y, Liu X, Yu X, Yan H, Perreault J, Li S. Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. BMC Genomics 2021; 22:164. [PMID: 33750298 PMCID: PMC7941889 DOI: 10.1186/s12864-021-07474-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 11/12/2022] Open
Abstract
Background Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge. Results Here, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins. Conclusions By searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07474-9.
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Affiliation(s)
- Lijuan Hou
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jin Xie
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaoyao Wu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jiaojiao Wang
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Anqi Duan
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaqi Ao
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Xuejiao Liu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Xinmei Yu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Hui Yan
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jonathan Perreault
- INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval, Québec, H7V1B7, Canada
| | - Sanshu Li
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China.
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18
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Aggresome formation and liquid-liquid phase separation independently induce cytoplasmic aggregation of TAR DNA-binding protein 43. Cell Death Dis 2020; 11:909. [PMID: 33097688 PMCID: PMC7585435 DOI: 10.1038/s41419-020-03116-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Cytoplasmic inclusion of TAR DNA-binding protein 43 (TDP-43) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and a subtype of frontotemporal lobar degeneration (FTLD). Recent studies have suggested that the formation of cytoplasmic TDP-43 aggregates is dependent on a liquid-liquid phase separation (LLPS) mechanism. However, it is unclear whether TDP-43 pathology is induced through a single intracellular mechanism such as LLPS. To identify intracellular mechanisms responsible for TDP-43 aggregation, we established a TDP-43 aggregation screening system using a cultured neuronal cell line stably expressing EGFP-fused TDP-43 and a mammalian expression library of the inherited ALS/FTLD causative genes, and performed a screening. We found that microtubule-related proteins (MRPs) and RNA-binding proteins (RBPs) co-aggregated with TDP-43. MRPs and RBPs sequestered TDP-43 into the cytoplasmic aggregates through distinct mechanisms, such as microtubules and LLPS, respectively. The MRPs-induced TDP-43 aggregates were co-localized with aggresomal markers and dependent on histone deacetylase 6 (HDAC6), suggesting that aggresome formation induced the co-aggregation. However, the MRPs-induced aggregates were not affected by 1,6-hexanediol, an LLPS inhibitor. On the other hand, the RBPs-induced TDP-43 aggregates were sensitive to 1,6-hexanediol, but not dependent on microtubules or HDAC6. In sporadic ALS patients, approximately half of skein-like TDP-43 inclusions were co-localized with HDAC6, but round and granular type inclusion were not. Moreover, HDAC6-positive and HDAC6-negative inclusions were found in the same ALS patient, suggesting that the two distinct pathways are both involved in TDP-43 pathology. Our findings suggest that at least two distinct pathways (i.e., aggresome formation and LLPS) are involved in inducing the TDP-43 pathologies.
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19
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Gois AM, Mendonça DMF, Freire MAM, Santos JR. IN VITRO AND IN VIVO MODELS OF AMYOTROPHIC LATERAL SCLEROSIS: AN UPDATED OVERVIEW. Brain Res Bull 2020; 159:32-43. [PMID: 32247802 DOI: 10.1016/j.brainresbull.2020.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/04/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper motor neurons (UMN) and lower motor neurons (LMN). Disease affects people all over the world and is more prevalent in men. Patients with ALS develop extensive muscle wasting, paralysis and ultimately death, with a median survival of usually fewer than five years after disease onset. ALS may be sporadic (sALS, 90%) or familial (fALS, 10%). The large majority of fALS cases are associated with genetic alterations, which are mainly related to the genes SOD1, TDP-43, FUS, and C9ORF72. In vitro and in vivo models have helped elucidate ALS etiology and pathogenesis, as well as its molecular, cellular, and physiological mechanisms. Many studies in cell cultures and animal models, such as Caenorhabditis elegans, Drosophila melanogaster, zebrafish, rodents, and non-human primates have been performed to clarify the relationship of these genes to ALS disease. However, there are inherent limitations to consider when using experimental models. In this review, we provide an updated overview of the most used in vitro and in vivo studies that have contributed to a better understanding of the different ALS pathogenic mechanisms.
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Affiliation(s)
- Auderlan M Gois
- Behavioral and Evolutionary Neurobiology Laboratory, Department of Biosciences, Federal University of Sergipe, Itabaiana, SE, Brazil
| | - Deise M F Mendonça
- Laboratory of Neurobiology of Degenerative Diseases of the Nervous System, Department of Biosciences, Federal University of Sergipe, Itabaiana, SE, Brazil
| | - Marco Aurelio M Freire
- Postgraduation Program in Health and Society, Faculty of Health Sciences, University of the State of Rio Grande do Norte, Mossoró, RN, Brazil
| | - Jose R Santos
- Behavioral and Evolutionary Neurobiology Laboratory, Department of Biosciences, Federal University of Sergipe, Itabaiana, SE, Brazil.
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20
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Watanabe S, Oiwa K, Murata Y, Komine O, Sobue A, Endo F, Takahashi E, Yamanaka K. ALS-linked TDP-43 M337V knock-in mice exhibit splicing deregulation without neurodegeneration. Mol Brain 2020; 13:8. [PMID: 31959210 PMCID: PMC6971932 DOI: 10.1186/s13041-020-0550-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/12/2020] [Indexed: 11/10/2022] Open
Abstract
Abnormal accumulation of TAR DNA-binding protein 43 (TDP-43), a DNA/RNA binding protein, is a pathological signature of amyotrophic lateral sclerosis (ALS). Missense mutations in the TARDBP gene are also found in inherited and sporadic ALS, indicating that dysfunction in TDP-43 is causative for ALS. To model TDP-43-linked ALS in rodents, we generated TDP-43 knock-in mice with inherited ALS patient-derived TDP-43M337V mutation. Homozygous TDP-43M337V mice developed normally without exhibiting detectable motor dysfunction and neurodegeneration. However, splicing of mRNAs regulated by TDP-43 was deregulated in the spinal cords of TDP-43M337V mice. Together with the recently reported TDP-43 knock-in mice with ALS-linked mutations, our finding indicates that ALS patient-derived mutations in the TARDBP gene at a carboxyl-terminal domain of TDP-43 may cause a gain of splicing function by TDP-43, however, were insufficient to induce robust neurodegeneration in mice.
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Affiliation(s)
- Seiji Watanabe
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Kotaro Oiwa
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya University, Nagoya, Aichi, 466-8550, Japan
| | - Yuri Murata
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Okiru Komine
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Akira Sobue
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Fumito Endo
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan.,Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Eiki Takahashi
- Support Unit for Animal Resources Development, Research Resource Division, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, 464-8601, Japan. .,Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan.
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