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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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2
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Xie L, Merjane J, Bergmann CA, Xu J, Hurtle B, Donnelly CJ. CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603231. [PMID: 39026766 PMCID: PMC11257528 DOI: 10.1101/2024.07.12.603231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Given the mounting evidence implicating TDP-43 dysfunction in several neurodegenerative diseases, there is a pressing need to establish accessible tools to sense and quantify TDP-43 loss-of-function (LOF). These tools are crucial for assessing potential disease contributors and exploring therapeutic candidates in TDP-43 proteinopathies. Here, we develop a sensitive and accurate real-time sensor for TDP-43 LOF: the CUTS (CFTR UNC13A TDP-43 Loss-of-Function) system. This system combines previously reported cryptic exons regulated by TDP-43 with a reporter, enabling the tracking of TDP-43 LOF through live microscopy and RNA/protein-based assays. We demonstrate CUTS' effectiveness in detecting LOF caused by TDP-43 mislocalization and RNA binding dysfunction, and pathological aggregation. Our results highlight the sensitivity and accuracy of the CUTS system in detecting and quantifying TDP-43 LOF, opening avenues to explore unknown TDP-43 interactions that regulate its function. In addition, by replacing the fluorescent tag in the CUTS system with the coding sequence for TDP-43, we show significant recovery of its function under TDP-43 LOF conditions, highlighting CUTS' potential for self-regulating gene therapy applications. In summary, CUTS represents a versatile platform for evaluating TDP-43 LOF in real-time and advancing gene-replacement therapies in neurodegenerative diseases associated with TDP-43 dysfunction. Highlights CUTS is a cryptic exon RNA biosensor enabling real-time detection of TDP-43 loss of splicing function.CUTS exhibits a significant linear relationship with TDP-43 loss.CUTS can deliver an autoregulated gene payload in response to TDP-43 loss-of-function.TDP-43 homotypic phase transitions induce loss of splicing function via CUTS detection.
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3
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Dykstra MM, Weskamp K, Gómez NB, Waksmacki J, Tank E, Glineburg MR, Snyder A, Pinarbasi E, Bekier M, Li X, Bai J, Shahzad S, Nedumaran J, Wieland C, Stewart C, Willey S, Grotewold N, McBride J, Moran JJ, Suryakumar AV, Lucas M, Tessier P, Ward M, Todd P, Barmada SJ. TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601776. [PMID: 39005384 PMCID: PMC11244999 DOI: 10.1101/2024.07.02.601776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
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, highly 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 byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration in vitro and in vivo 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 provide insight into 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
| | - Kaitlin Weskamp
- Chemistry Department, Nebraska Wesleyan University, Lincoln, NE
| | - Nicolás B. Gómez
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jacob Waksmacki
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Elizabeth Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - M. Rebecca Glineburg
- Biological Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA
| | | | - Emile Pinarbasi
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Neuropathology, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Jen Bai
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | | | - Juno Nedumaran
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Clare Wieland
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Corey Stewart
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Sydney Willey
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Nikolas Grotewold
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jonathon McBride
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI
| | - John J. Moran
- Atlanta Pediatric Research Alliance, Emory University, Atlanta, GA
| | | | - Michael Lucas
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | - Peter Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | | | - Peter Todd
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Veterans Affairs Medical Center, Ann Arbor, MI
| | - Sami J. Barmada
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
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4
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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024:BST20231447. [PMID: 38958608 DOI: 10.1042/bst20231447] [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: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
TDP-43 is an abundant and ubiquitously expressed nuclear protein that becomes dysfunctional in a spectrum of neurodegenerative diseases. TDP-43's ability to phase separate and form/enter biomolecular condensates of varying size and composition is critical for its functionality. Despite the high density of phase-separated assemblies in the nucleus and the nuclear abundance of TDP-43, our understanding of the condensate-TDP-43 relationship in this cellular compartment is only emerging. Recent studies have also suggested that misregulation of nuclear TDP-43 condensation is an early event in the neurodegenerative disease amyotrophic lateral sclerosis. This review aims to draw attention to the nuclear facet of functional and aberrant TDP-43 condensation. We will summarise the current knowledge on how TDP-43 containing nuclear condensates form and function and how their homeostasis is affected in disease.
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Affiliation(s)
- Ruaridh Lang
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
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5
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Baghel MS, Burns GD, Tsapatsis M, Mallika AP, Cruz ALF, Cao T, Chen XK, Rosa IDL, Marx SR, Ye Y, Sun S, Li T, Wong PC. Depletion of TDP-43 exacerbates tauopathy-dependent brain atrophy by sensitizing vulnerable neurons to caspase 3-mediated endoproteolysis of tau in a mouse model of Multiple Etiology Dementia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600814. [PMID: 38979270 PMCID: PMC11230425 DOI: 10.1101/2024.06.26.600814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
TDP-43 proteinopathy, initially disclosed in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), coexists with tauopathy in a variety of neurodegenerative disorders, termed multiple etiology dementias (MEDs), including Alzheimer's Disease (AD). While such co-pathology of TDP-43 is strongly associated with worsened neurodegeneration and steeper cognitive decline, the pathogenic mechanism underlying the exacerbated neuron loss remains elusive. The loss of TDP-43 splicing repression that occurs in presymptomatic ALS-FTD individuals suggests that such early loss could facilitate the pathological conversion of tau to accelerate neuron loss. Here, we report that the loss of TDP-43 repression of cryptic exons in forebrain neurons (CaMKII-CreER;Tardbp f/f mice) is necessary to exacerbate tauopathy-dependent brain atrophy by sensitizing vulnerable neurons to caspase 3-dependent cleavage of endogenous tau to promote tauopathy. Corroborating this finding within the human context, we demonstrate that loss of TDP-43 function in iPSC-derived cortical neurons promotes early cryptic exon inclusion and subsequent caspase 3-mediated endoproteolysis of tau. Using a genetic approach to seed tauopathy in CaMKII-CreER;Tardbp f/f mice by expressing a four-repeat microtubule binding domain of human tau, we show that the amount of tau seed positively correlates with levels of caspase 3-cleaved tau. Importantly, we found that the vulnerability of hippocampal neurons to TDP-43 depletion is dependent on the amount of caspase 3-cleaved tau: from most vulnerable neurons in the CA2/3, followed by those in the dentate gyrus, to the least in CA1. Taken together, our findings strongly support the view that TDP-43 loss-of-function exacerbates tauopathy-dependent brain atrophy by increasing the sensitivity of vulnerable neurons to caspase 3-mediated endoproteolysis of tau, resulting in a greater degree of neurodegeneration in human disorders with co-pathologies of tau and TDP-43. Our work thus discloses novel mechanistic insights and therapeutic targets for human tauopathies harboring co-pathology of TDP-43 and provides a new MED model for testing therapeutic strategies.
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Affiliation(s)
- Meghraj S Baghel
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Grace D Burns
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Margarita Tsapatsis
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Aswathy Peethambaran Mallika
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Anna Lourdes F Cruz
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Tianyu Cao
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Xiaoke K Chen
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Isabel De La Rosa
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Shaelyn R Marx
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Physiology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Neuroscience, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Tong Li
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Philip C Wong
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Neuroscience, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
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Huang WP, Ellis BCS, Hodgson RE, Sanchez Avila A, Kumar V, Rayment J, Moll T, Shelkovnikova TA. Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion. Cell Rep 2024; 43:114421. [PMID: 38941189 DOI: 10.1016/j.celrep.2024.114421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.
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Affiliation(s)
- Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Brittany C S Ellis
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Anna Sanchez Avila
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Vedanth Kumar
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Jessica Rayment
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK.
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7
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Snyder A, Ryan VH, Hawrot J, Lawton S, Ramos DM, Qi YA, Johnson KR, Reed X, Johnson NL, Kollasch AW, Duffy MF, VandeVrede L, Cochran JN, Miller BL, Toro C, Bielekova B, Marks DS, Yokoyama JS, Kwan JY, Cookson MR, Ward ME. An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome. Alzheimers Dement 2024. [PMID: 38923692 DOI: 10.1002/alz.13915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Variants of uncertain significance (VUS) surged with affordable genetic testing, posing challenges for determining pathogenicity. We examine the pathogenicity of a novel VUS P93S in Annexin A11 (ANXA11) - an amyotrophic lateral sclerosis/frontotemporal dementia-associated gene - in a corticobasal syndrome kindred. Established ANXA11 mutations cause ANXA11 aggregation, altered lysosomal-RNA granule co-trafficking, and transactive response DNA binding protein of 43 kDa (TDP-43) mis-localization. METHODS We described the clinical presentation and explored the phenotypic diversity of ANXA11 variants. P93S's effect on ANXA11 function and TDP-43 biology was characterized in induced pluripotent stem cell-derived neurons alongside multiomic neuronal and microglial profiling. RESULTS ANXA11 mutations were linked to corticobasal syndrome cases. P93S led to decreased lysosome colocalization, neuritic RNA, and nuclear TDP-43 with cryptic exon expression. Multiomic microglial signatures implicated immune dysregulation and interferon signaling pathways. DISCUSSION This study establishes ANXA11 P93S pathogenicity, broadens the phenotypic spectrum of ANXA11 mutations, underscores neuronal and microglial dysfunction in ANXA11 pathophysiology, and demonstrates the potential of cellular models to determine variant pathogenicity. HIGHLIGHTS ANXA11 P93S is a pathogenic variant. Corticobasal syndrome is part of the ANXA11 phenotypic spectrum. Hybridization chain reaction fluorescence in situ hybridization (HCR FISH) is a new tool for the detection of cryptic exons due to TDP-43-related loss of splicing regulation. Microglial ANXA11 and related immune pathways are important drivers of disease. Cellular models are powerful tools for adjudicating variants of uncertain significance.
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Affiliation(s)
- Allison Snyder
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - James Hawrot
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Sydney Lawton
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Y Andy Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Kory R Johnson
- Intramural Bioinformatics Core, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicholas L Johnson
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
- DataTecnica LLC, Washington, District of Columbia, USA
| | - Aaron W Kollasch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Megan F Duffy
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Lawren VandeVrede
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | | | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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8
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Zhang N, Westerhaus A, Wilson M, Wang E, Goff L, Sockanathan S. Physiological regulation of neuronal Wnt activity is essential for TDP-43 localization and function. EMBO J 2024:10.1038/s44318-024-00156-8. [PMID: 38918634 DOI: 10.1038/s44318-024-00156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Nuclear exclusion of the RNA- and DNA-binding protein TDP-43 can induce neurodegeneration in different diseases. Diverse processes have been implicated to influence TDP-43 mislocalization, including disrupted nucleocytoplasmic transport (NCT); however, the physiological pathways that normally ensure TDP-43 nuclear localization are unclear. The six-transmembrane enzyme glycerophosphodiester phosphodiesterase 2 (GDE2 or GDPD5) cleaves the glycosylphosphatidylinositol (GPI) anchor that tethers some proteins to the membrane. Here we show that GDE2 maintains TDP-43 nuclear localization by regulating the dynamics of canonical Wnt signaling. Ablation of GDE2 causes aberrantly sustained Wnt activation in adult neurons, which is sufficient to cause NCT deficits, nuclear pore abnormalities, and TDP-43 nuclear exclusion. Disruption of GDE2 coincides with TDP-43 abnormalities in postmortem tissue from patients with amyotrophic lateral sclerosis (ALS). Further, GDE2 deficits are evident in human neural cell models of ALS, which display erroneous Wnt activation that, when inhibited, increases mRNA levels of genes regulated by TDP-43. Our study identifies GDE2 as a critical physiological regulator of Wnt signaling in adult neurons and highlights Wnt pathway activation as an unappreciated mechanism contributing to nucleocytoplasmic transport and TDP-43 abnormalities in disease.
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Affiliation(s)
- Nan Zhang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Anna Westerhaus
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Macey Wilson
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- Department of Cellular Biology, University of Georgia, Biological Sciences 302, 120 Cedar St., Athens, GA, 30602, USA
| | - Ethan Wang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Loyal Goff
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- McKusick-Nathans Department of Genetic Medicine, Kavli Neurodiscovery Institute, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Shanthini Sockanathan
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA.
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9
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Keuss MJ, Harley P, Ryadnov E, Jackson RE, Zanovello M, Wilkins OG, Barattucci S, Mehta PR, Oliveira MG, Parkes JE, Sinha A, Correa-Sánchez AF, Oliver PL, Fisher EM, Schiavo G, Shah M, Burrone J, Fratta P. Loss of TDP-43 induces synaptic dysfunction that is rescued by UNC13A splice-switching ASOs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599684. [PMID: 38979232 PMCID: PMC11230273 DOI: 10.1101/2024.06.20.599684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
TDP-43 loss of function induces multiple splicing changes, including a cryptic exon in the amyotrophic lateral sclerosis and fronto-temporal lobar degeneration risk gene UNC13A, leading to nonsense-mediated decay of UNC13A transcripts and loss of protein. UNC13A is an active zone protein with an integral role in coordinating pre-synaptic function. Here, we show TDP-43 depletion induces a severe reduction in synaptic transmission, leading to an asynchronous pattern of network activity. We demonstrate that these deficits are largely driven by a single cryptic exon in UNC13A. Antisense oligonucleotides targeting the UNC13A cryptic exon robustly rescue UNC13A protein levels and restore normal synaptic function, providing a potential new therapeutic approach for ALS and other TDP-43-related disorders.
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Affiliation(s)
- Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Rachel E. Jackson
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Marcio G. Oliveira
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | | | - Aparna Sinha
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | | | - Peter L. Oliver
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Giampietro Schiavo
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- UK Dementia Research Institute at University College London; London, WC1N 3BG, UK
| | - Mala Shah
- Department of Pharmacology, School of Pharmacy, University College London; London, WC1N 4AX, UK
| | - Juan Burrone
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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10
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Zhang X, Das T, Chao TF, Trinh V, Carmen-Orozco RP, Ling JP, Kalab P, Hayes LR. Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes. iScience 2024; 27:110109. [PMID: 38989321 PMCID: PMC11233918 DOI: 10.1016/j.isci.2024.110109] [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: 11/15/2023] [Revised: 03/22/2024] [Accepted: 05/23/2024] [Indexed: 07/12/2024] Open
Abstract
TDP-43 nuclear clearance and cytoplasmic aggregation are hallmarks of TDP-43 proteinopathies. We recently demonstrated that binding to endogenous nuclear GU-rich RNAs sequesters TDP-43 in the nucleus by restricting its passive nuclear export. Here, we tested the feasibility of synthetic RNA oligonucleotide-mediated augmentation of TDP-43 nuclear localization. Using biochemical assays, we compared the ability of GU-rich oligonucleotides to engage in multivalent, RRM-dependent binding with TDP-43. When transfected into cells, (GU)16 attenuated TDP-43 mislocalization induced by transcriptional blockade or RanGAP1 ablation. Clip34nt and (GU)16 accelerated TDP-43 nuclear re-import after cytoplasmic mislocalization. RNA pulldowns confirmed that multivalent GU-oligonucleotides induced high molecular weight RNP complexes, incorporating TDP-43 and possibly other GU-binding proteins. Transfected GU-repeat oligos disrupted TDP-43 cryptic exon repression, likely by diverting TDP-43 from endogenous RNAs, except for Clip34nt that contains interspersed A and C. Thus, exogenous multivalent GU-RNAs can promote TDP-43 nuclear localization, though pure GU-repeat motifs impair TDP-43 function.
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Affiliation(s)
- Xi Zhang
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tanuza Das
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tiffany F. Chao
- Johns Hopkins University Whiting School of Engineering, Baltiomre, MD 21218, USA
| | - Vickie Trinh
- 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
| | - Petr Kalab
- Johns Hopkins University Whiting School of Engineering, Baltiomre, MD 21218, USA
| | - Lindsey R. Hayes
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Brain Science Institute, Baltimore, MD 21205, USA
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11
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Wang H, Zeng R. Aberrant protein aggregation in amyotrophic lateral sclerosis. J Neurol 2024:10.1007/s00415-024-12485-z. [PMID: 38869826 DOI: 10.1007/s00415-024-12485-z] [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: 03/12/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease. As its pathological mechanisms are not well understood, there are no efficient therapeutics for it at present. While it is highly heterogenous both etiologically and clinically, it has a common salient hallmark, i.e., aberrant protein aggregation (APA). The upstream pathogenesis and the downstream effects of APA in ALS are sophisticated and the investigation of this pathology would be of consequence for understanding ALS. In this paper, the pathomechanism of APA in ALS and the candidate treatment strategies for it are discussed.
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Affiliation(s)
- Huaixiu Wang
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China.
- Beijing Ai-Si-Kang Medical Technology Co. Ltd., No. 18 11th St Economical & Technological Development Zone, Beijing, 100176, China.
| | - Rong Zeng
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China
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12
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Carmen-Orozco RP, Tsao W, Ye Y, Sinha IR, Chang K, Trinh VT, Chung W, Bowden K, Troncoso JC, Blackshaw S, Hayes LR, Sun S, Wong PC, Ling JP. Elevated nuclear TDP-43 induces constitutive exon skipping. Mol Neurodegener 2024; 19:45. [PMID: 38853250 PMCID: PMC11163724 DOI: 10.1186/s13024-024-00732-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/20/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Cytoplasmic inclusions and loss of nuclear TDP-43 are key pathological features found in several neurodegenerative disorders, suggesting both gain- and loss-of-function mechanisms of disease. To study gain-of-function, TDP-43 overexpression has been used to generate in vitro and in vivo model systems. METHODS We analyzed RNA-seq datasets from mouse and human neurons overexpressing TDP-43 to explore species specific splicing patterns. We explored the dynamics between TDP-43 levels and exon repression in vitro. Furthermore we analyzed human brain samples and publicly available RNA datasets to explore the relationship between exon repression and disease. RESULTS Our study shows that excessive levels of nuclear TDP-43 protein lead to constitutive exon skipping that is largely species-specific. Furthermore, while aberrant exon skipping is detected in some human brains, it is not correlated with disease, unlike the incorporation of cryptic exons that occurs after loss of TDP-43. CONCLUSIONS Our findings emphasize the need for caution in interpreting TDP-43 overexpression data and stress the importance of controlling for exon skipping when generating models of TDP-43 proteinopathy.
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Affiliation(s)
- Rogger P Carmen-Orozco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Tsao
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Irika R Sinha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Vickie T Trinh
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Chung
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kyra Bowden
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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13
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Caldi Gomes L, Hänzelmann S, Hausmann F, Khatri R, Oller S, Parvaz M, Tzeplaeff L, Pasetto L, Gebelin M, Ebbing M, Holzapfel C, Columbro SF, Scozzari S, Knöferle J, Cordts I, Demleitner AF, Deschauer M, Dufke C, Sturm M, Zhou Q, Zelina P, Sudria-Lopez E, Haack TB, Streb S, Kuzma-Kozakiewicz M, Edbauer D, Pasterkamp RJ, Laczko E, Rehrauer H, Schlapbach R, Carapito C, Bonetto V, Bonn S, Lingor P. Multiomic ALS signatures highlight subclusters and sex differences suggesting the MAPK pathway as therapeutic target. Nat Commun 2024; 15:4893. [PMID: 38849340 PMCID: PMC11161513 DOI: 10.1038/s41467-024-49196-y] [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: 08/03/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating motor neuron disease and lacks effective disease-modifying treatments. This study utilizes a comprehensive multiomic approach to investigate the early and sex-specific molecular mechanisms underlying ALS. By analyzing the prefrontal cortex of 51 patients with sporadic ALS and 50 control subjects, alongside four transgenic mouse models (C9orf72-, SOD1-, TDP-43-, and FUS-ALS), we have uncovered significant molecular alterations associated with the disease. Here, we show that males exhibit more pronounced changes in molecular pathways compared to females. Our integrated analysis of transcriptomes, (phospho)proteomes, and miRNAomes also identified distinct ALS subclusters in humans, characterized by variations in immune response, extracellular matrix composition, mitochondrial function, and RNA processing. The molecular signatures of human subclusters were reflected in specific mouse models. Our study highlighted the mitogen-activated protein kinase (MAPK) pathway as an early disease mechanism. We further demonstrate that trametinib, a MAPK inhibitor, has potential therapeutic benefits in vitro and in vivo, particularly in females, suggesting a direction for developing targeted ALS treatments.
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Affiliation(s)
- Lucas Caldi Gomes
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Sonja Hänzelmann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Hausmann
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sergio Oller
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mojan Parvaz
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Tzeplaeff
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Laura Pasetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marie Gebelin
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Melanie Ebbing
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Constantin Holzapfel
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Serena Scozzari
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Johanna Knöferle
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Isabell Cordts
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Antonia F Demleitner
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Marcus Deschauer
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Pavol Zelina
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emma Sudria-Lopez
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Sebastian Streb
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), München, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Endre Laczko
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, Infrastructure Nationale de Protéomique, Strasbourg, France
| | - Valentina Bonetto
- Research Center for ALS, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Stefan Bonn
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Paul Lingor
- Technical University of Munich, School of Medicine, rechts der Isar Hospital, Clinical Department of Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), München, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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14
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Costantino I, Meng A, Ravits J. Alternatively spliced ELAVL3 cryptic exon 4a causes ELAVL3 downregulation in ALS TDP-43 proteinopathy. Acta Neuropathol 2024; 147:93. [PMID: 38814471 PMCID: PMC11139733 DOI: 10.1007/s00401-024-02732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Affiliation(s)
- Isabel Costantino
- Department of Neurosciences, ALS Translational Research, University of California San Diego, La Jolla, CA, USA
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alex Meng
- Department of Neurosciences, ALS Translational Research, University of California San Diego, La Jolla, CA, USA
| | - John Ravits
- Department of Neurosciences, ALS Translational Research, University of California San Diego, La Jolla, CA, USA.
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15
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Bradford D, Rodgers KE. Advancements and challenges in amyotrophic lateral sclerosis. Front Neurosci 2024; 18:1401706. [PMID: 38846716 PMCID: PMC11155303 DOI: 10.3389/fnins.2024.1401706] [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: 03/15/2024] [Accepted: 05/03/2024] [Indexed: 06/09/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) continues to pose a significant challenge due to the disease complexity and heterogeneous manifestations. Despite recent drug approvals, there remains a critical need for the development of more effective therapies. This review explores the underlying mechanisms involved; including neuroinflammation, glutamate mediated excitotoxicity, mitochondrial dysfunction, and hypermetabolism, and how researchers are trying to develop novel drugs to target these pathways. While progress has been made, the unmet need of ALS patients highlights the urgency for continued research and resource allocation in the pursuit of effective treatments.
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Affiliation(s)
| | - Kathleen E. Rodgers
- Department of Medical Pharmacology, Center for Innovation in Brain Science, University of Arizona College of Medicine, Tucson, AZ, United States
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16
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Al-Chalabi A, Andrews J, Farhan S. Recent advances in the genetics of familial and sporadic ALS. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:49-74. [PMID: 38802182 DOI: 10.1016/bs.irn.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
ALS shows complex genetic inheritance patterns. In about 5% to 10% of cases, there is a family history of ALS or a related condition such as frontotemporal dementia in a first or second degree relative, and for about 80% of such people a pathogenic gene variant can be identified. Such variants are also seen in people with no family history because of factor influencing the expression of genes, such as age. Genetic susceptibility factors also contribute to risk, and the heritability of ALS is between 40% and 60%. The genetic variants influencing ALS risk include single base changes, repeat expansions, copy number variants, and others. Here we review what is known of the genetic landscape and architecture of ALS.
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Affiliation(s)
- Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom.
| | - Jinsy Andrews
- Department of Neurology, Columbia University, New York, NY, United States
| | - Sali Farhan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montreal, QC, Canada; Department of Human Genetics, Montreal Neurological Institute-Hospital, Montreal, QC, Canada
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17
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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00739-7. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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18
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Koike Y. Molecular mechanisms linking loss of TDP-43 function to amyotrophic lateral sclerosis/frontotemporal dementia-related genes. Neurosci Res 2024:S0168-0102(24)00063-4. [PMID: 38723906 DOI: 10.1016/j.neures.2024.05.001] [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: 03/08/2024] [Revised: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by nuclear depletion and cytoplasmic aggregation of TAR DNA-binding protein-43 (TDP-43). TDP-43 plays a key role in regulating the splicing of numerous genes, including TARDBP. This review aims to delineate two aspects of ALS/FTD pathogenesis associated with TDP-43 function. First, we provide novel mechanistic insights into the splicing of UNC13A, a TDP-43 target gene. Single nucleotide polymorphisms (SNPs) in UNC13A are the most common risk factors for ALS/FTD. We found that TDP-43 represses "cryptic exon" inclusion during UNC13A RNA splicing. A risk-associated SNP in this exon results in increased RNA levels of UNC13A retaining the cryptic exon. Second, we described the perturbation of the TDP-43 autoregulatory mechanism caused by age-related DNA demethylation. Aging is a major risk factor for sporadic ALS/FTD. Typically, TDP-43 levels are regulated via alternative splicing of TARDBP mRNA. We hypothesized that TARDBP methylation is altered by aging, thereby disrupting TDP-43 autoregulation. We found that demethylation reduces the efficiency of alternative splicing and increases TARDBP mRNA levels. Moreover, we demonstrated that, with aging, this region is demethylated in the human motor cortex and is associated with the early onset of ALS.
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Affiliation(s)
- Yuka Koike
- Department of Molecular Neuroscience, Brain Research Institute, Niigata University, Japan.
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19
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Xin J, Huang S, Wen J, Li Y, Li A, Satyanarayanan SK, Yao X, Su H. Drug Screening and Validation Targeting TDP-43 Proteinopathy for Amyotrophic Lateral Sclerosis. Aging Dis 2024:AD.2024.0440. [PMID: 38739934 DOI: 10.14336/ad.2024.0440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) stands as a rare, yet severely debilitating disorder marked by the deterioration of motor neurons (MNs) within the brain and spinal cord, which is accompanied by degenerated corticobulbar/corticospinal tracts and denervation in skeletal muscles. Despite ongoing research efforts, ALS remains incurable, attributed to its intricate pathogenic mechanisms. A notable feature in the pathology of ALS is the prevalence of TAR DNA-binding protein 43 (TDP-43) proteinopathy, detected in approximately 97% of ALS cases, underscoring its significance in the disease's progression. As a result, strategies targeting the aberrant TDP-43 protein have garnered attention as a potential avenue for ALS therapy. This review delves into the existing drug screening systems aimed at TDP-43 proteinopathy and the models employed for drug efficacy validation. It also explores the hurdles encountered in the quest to develop potent medications against TDP-43 proteinopathy, offering insights into the intricacies of drug discovery and development for ALS. Through this comprehensive analysis, the review sheds light on the critical aspects of identifying and advancing therapeutic solutions for ALS.
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Affiliation(s)
- Jiaqi Xin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Sen Huang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Jing Wen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yunhao Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ang Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Senthil Kumaran Satyanarayanan
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong Science Park, Hong Kong, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Huanxing Su
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
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20
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Zibold J, Lessard LER, Picard F, da Silva LG, Zadorozhna Y, Streichenberger N, Belotti E, Osseni A, Emerit A, Errazuriz-Cerda E, Michel-Calemard L, Menassa R, Coudert L, Wiessner M, Stucka R, Klopstock T, Simonetti F, Hutten S, Nonaka T, Hasegawa M, Strom TM, Bernard E, Ollagnon E, Urtizberea A, Dormann D, Petiot P, Schaeffer L, Senderek J, Leblanc P. The new missense G376V-TDP-43 variant induces late-onset distal myopathy but not amyotrophic lateral sclerosis. Brain 2024; 147:1768-1783. [PMID: 38079474 PMCID: PMC11068115 DOI: 10.1093/brain/awad410] [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: 07/06/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 05/04/2024] Open
Abstract
TAR DNA binding protein of 43 kDa (TDP-43)-positive inclusions in neurons are a hallmark of several neurodegenerative diseases including familial amyotrophic lateral sclerosis (fALS) caused by pathogenic TARDBP variants as well as more common non-Mendelian sporadic ALS (sALS). Here we report a G376V-TDP-43 missense variant in the C-terminal prion-like domain of the protein in two French families affected by an autosomal dominant myopathy but not fulfilling diagnostic criteria for ALS. Patients from both families presented with progressive weakness and atrophy of distal muscles, starting in their fifth to seventh decade. Muscle biopsies revealed a degenerative myopathy characterized by accumulation of rimmed (autophagic) vacuoles, disruption of sarcomere integrity and severe myofibrillar disorganization. The G376V variant altered a highly conserved amino acid residue and was absent in databases on human genome variation. Variant pathogenicity was supported by in silico analyses and functional studies. The G376V mutant increased the formation of cytoplasmic TDP-43 condensates in cell culture models, promoted assembly into high molecular weight oligomers and aggregates in vitro, and altered morphology of TDP-43 condensates arising from phase separation. Moreover, the variant led to the formation of cytoplasmic TDP-43 condensates in patient-derived myoblasts and induced abnormal mRNA splicing in patient muscle tissue. The identification of individuals with TDP-43-related myopathy, but not ALS, implies that TARDBP missense variants may have more pleiotropic effects than previously anticipated and support a primary role for TDP-43 in skeletal muscle pathophysiology. We propose to include TARDBP screening in the genetic work-up of patients with late-onset distal myopathy. Further research is warranted to examine the precise pathogenic mechanisms of TARDBP variants causing either a neurodegenerative or myopathic phenotype.
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Affiliation(s)
- Julia Zibold
- Friedrich-Baur Institute at the Department of Neurology, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Lola E R Lessard
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
- Service d’Electroneuromyographie et de pathologies neuromusculaires, Hôpital Neurologique Pierre Wertheimer, Hospices Civils de Lyon, 69677 Bron, France
| | - Flavien Picard
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | - Lara Gruijs da Silva
- Johannes Gutenberg University (JGU), Faculty of Biology, Institute of Molecular Physiology, 55128 Mainz, Germany
- Graduate School of Systemic Neurosciences (GSN), LMU BioCenter, Department Biology II Neurobiology, 82152 Planegg-Martinsried, Germany
- Center for Anatomy, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Yelyzaveta Zadorozhna
- Johannes Gutenberg University (JGU), Faculty of Biology, Institute of Molecular Physiology, 55128 Mainz, Germany
- International PhD Programme (IPP) of the Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Nathalie Streichenberger
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
- Département d’Anatomo-Pathologie, Groupement Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France
| | - Edwige Belotti
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | - Alexis Osseni
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | - Andréa Emerit
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | | | - Laurence Michel-Calemard
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
- Service Biochimie et Biologie Moléculaire, Centre de biologie et pathologie Est, Hospices civils de Lyon, 69677 Bron, France
| | - Rita Menassa
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
- Service Biochimie et Biologie Moléculaire, Centre de biologie et pathologie Est, Hospices civils de Lyon, 69677 Bron, France
| | - Laurent Coudert
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | - Manuela Wiessner
- Friedrich-Baur Institute at the Department of Neurology, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Rolf Stucka
- Friedrich-Baur Institute at the Department of Neurology, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur Institute at the Department of Neurology, University Hospital, LMU Munich, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich Site, 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Francesca Simonetti
- Johannes Gutenberg University (JGU), Faculty of Biology, Institute of Molecular Physiology, 55128 Mainz, Germany
- Graduate School of Systemic Neurosciences (GSN), LMU BioCenter, Department Biology II Neurobiology, 82152 Planegg-Martinsried, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich Site, 81377 Munich, Germany
| | - Saskia Hutten
- Johannes Gutenberg University (JGU), Faculty of Biology, Institute of Molecular Physiology, 55128 Mainz, Germany
| | - Takashi Nonaka
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Tim M Strom
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany
| | - Emilien Bernard
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
- Service d’Electroneuromyographie et de pathologies neuromusculaires, Hôpital Neurologique Pierre Wertheimer, Hospices Civils de Lyon, 69677 Bron, France
| | - Elisabeth Ollagnon
- Service de Génétique, Neurogénétique et Médecine Prédictive, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, 69004 Lyon, France
| | - Andoni Urtizberea
- Centre de Référence Neuromusculaire, Hôpital Marin—APHP, 64701 Hendaye, France
| | - Dorothee Dormann
- Johannes Gutenberg University (JGU), Faculty of Biology, Institute of Molecular Physiology, 55128 Mainz, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Laurent Schaeffer
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
| | - Jan Senderek
- Friedrich-Baur Institute at the Department of Neurology, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Pascal Leblanc
- Faculté de Médecine Rockefeller, Institut NeuroMyoGène-PGNM, Université Claude Bernard Lyon, 69008 Lyon, France
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21
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Smith DM, Aggarwal G, Niehoff ML, Jones SA, Banerjee S, Farr SA, Nguyen AD. Biochemical, Biomarker, and Behavioral Characterization of the Grn R493X Mouse Model of Frontotemporal Dementia. Mol Neurobiol 2024:10.1007/s12035-024-04190-9. [PMID: 38696065 DOI: 10.1007/s12035-024-04190-9] [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: 06/07/2023] [Accepted: 04/17/2024] [Indexed: 05/14/2024]
Abstract
Heterozygous loss-of-function mutations in the progranulin gene (GRN) are a major cause of frontotemporal dementia due to progranulin haploinsufficiency; complete deficiency of progranulin causes neuronal ceroid lipofuscinosis. Several progranulin-deficient mouse models have been generated, including both knockout mice and knockin mice harboring a common patient mutation (R493X). However, the GrnR493X mouse model has not been characterized completely. Additionally, while homozygous GrnR493X and Grn knockout mice have been extensively studied, data from heterozygous mice is still limited. Here, we performed more in-depth characterization of heterozygous and homozygous GrnR493X knockin mice, which includes biochemical assessments, behavioral studies, and analysis of fluid biomarkers. In the brains of homozygous GrnR493X mice, we found increased phosphorylated TDP-43 along with increased expression of lysosomal genes, markers of microgliosis and astrogliosis, pro-inflammatory cytokines, and complement factors. Heterozygous GrnR493X mice did not have increased TDP-43 phosphorylation but did exhibit limited increases in lysosomal and inflammatory gene expression. Behavioral studies found social and emotional deficits in GrnR493X mice that mirror those observed in Grn knockout mouse models, as well as impairment in memory and executive function. Overall, the GrnR493X knockin mouse model closely phenocopies Grn knockout models. Lastly, in contrast to homozygous knockin mice, heterozygous GrnR493X mice do not have elevated levels of fluid biomarkers previously identified in humans, including neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) in both plasma and CSF. These results may help to inform pre-clinical studies that use this Grn knockin mouse model and other Grn knockout models.
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Affiliation(s)
- Denise M Smith
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA
| | - Geetika Aggarwal
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA
| | - Michael L Niehoff
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Veterans Affairs Medical Center, St. Louis, USA
| | - Spencer A Jones
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA
| | - Subhashis Banerjee
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA
| | - Susan A Farr
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA
- Veterans Affairs Medical Center, St. Louis, USA
| | - Andrew D Nguyen
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, USA.
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, USA.
- Institute for Translational Neuroscience, Saint Louis University, St. Louis, USA.
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22
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Udine E, DeJesus-Hernandez M, Tian S, das Neves SP, Crook R, Finch NA, Baker MC, Pottier C, Graff-Radford NR, Boeve BF, Petersen RC, Knopman DS, Josephs KA, Oskarsson B, Da Mesquita S, Petrucelli L, Gendron TF, Dickson DW, Rademakers R, van Blitterswijk M. Abundant transcriptomic alterations in the human cerebellum of patients with a C9orf72 repeat expansion. Acta Neuropathol 2024; 147:73. [PMID: 38641715 PMCID: PMC11031479 DOI: 10.1007/s00401-024-02720-2] [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: 10/26/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The most prominent genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) is a repeat expansion in the gene C9orf72. Importantly, the transcriptomic consequences of the C9orf72 repeat expansion remain largely unclear. Here, we used short-read RNA sequencing (RNAseq) to profile the cerebellar transcriptome, detecting alterations in patients with a C9orf72 repeat expansion. We focused on the cerebellum, since key C9orf72-related pathologies are abundant in this neuroanatomical region, yet TDP-43 pathology and neuronal loss are minimal. Consistent with previous work, we showed a reduction in the expression of the C9orf72 gene and an elevation in homeobox genes, when comparing patients with the expansion to both patients without the C9orf72 repeat expansion and control subjects. Interestingly, we identified more than 1000 alternative splicing events, including 4 in genes previously associated with ALS and/or FTLD. We also found an increase of cryptic splicing in C9orf72 patients compared to patients without the expansion and controls. Furthermore, we demonstrated that the expression level of select RNA-binding proteins is associated with cryptic splice junction inclusion. Overall, this study explores the presence of widespread transcriptomic changes in the cerebellum, a region not confounded by severe neurodegeneration, in post-mortem tissue from C9orf72 patients.
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Affiliation(s)
- Evan Udine
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Richard Crook
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | | | | | | | | | | | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Sandro Da Mesquita
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA.
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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23
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Ke YD, van Hummel A, Au C, Chan G, Lee WS, van der Hoven J, Przybyla M, Deng Y, Sabale M, Morey N, Bertz J, Feiten A, Ippati S, Stevens CH, Yang S, Gladbach A, Haass NK, Kril JJ, Blair IP, Delerue F, Ittner LM. Targeting 14-3-3θ-mediated TDP-43 pathology in amyotrophic lateral sclerosis and frontotemporal dementia mice. Neuron 2024; 112:1249-1264.e8. [PMID: 38366598 DOI: 10.1016/j.neuron.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by cytoplasmic deposition of the nuclear TAR-binding protein 43 (TDP-43). Although cytoplasmic re-localization of TDP-43 is a key event in the pathogenesis of ALS/FTD, the underlying mechanisms remain unknown. Here, we identified a non-canonical interaction between 14-3-3θ and TDP-43, which regulates nuclear-cytoplasmic shuttling. Neuronal 14-3-3θ levels were increased in sporadic ALS and FTD with TDP-43 pathology. Pathogenic TDP-43 showed increased interaction with 14-3-3θ, resulting in cytoplasmic accumulation, insolubility, phosphorylation, and fragmentation of TDP-43, resembling pathological changes in disease. Harnessing this increased affinity of 14-3-3θ for pathogenic TDP-43, we devised a gene therapy vector targeting TDP-43 pathology, which mitigated functional deficits and neurodegeneration in different ALS/FTD mouse models expressing mutant or non-mutant TDP-43, including when already symptomatic at the time of treatment. Our study identified 14-3-3θ as a mediator of cytoplasmic TDP-43 localization with implications for ALS/FTD pathogenesis and therapy.
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Affiliation(s)
- Yazi D Ke
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Annika van Hummel
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol Au
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Gabriella Chan
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wei Siang Lee
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Julia van der Hoven
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Magdalena Przybyla
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yuanyuan Deng
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Miheer Sabale
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle Morey
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Josefine Bertz
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Astrid Feiten
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Stefania Ippati
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Claire H Stevens
- School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Shu Yang
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amadeus Gladbach
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nikolas K Haass
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Jillian J Kril
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Ian P Blair
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Fabien Delerue
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Lars M Ittner
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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24
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Wang X, Hu Y, Xu R. The pathogenic mechanism of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis. Neural Regen Res 2024; 19:800-806. [PMID: 37843214 PMCID: PMC10664110 DOI: 10.4103/1673-5374.382233] [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: 03/13/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 10/17/2023] Open
Abstract
The onset of amyotrophic lateral sclerosis is usually characterized by focal death of both upper and/or lower motor neurons occurring in the motor cortex, basal ganglia, brainstem, and spinal cord, and commonly involves the muscles of the upper and/or lower extremities, and the muscles of the bulbar and/or respiratory regions. However, as the disease progresses, it affects the adjacent body regions, leading to generalized muscle weakness, occasionally along with memory, cognitive, behavioral, and language impairments; respiratory dysfunction occurs at the final stage of the disease. The disease has a complicated pathophysiology and currently, only riluzole, edaravone, and phenylbutyrate/taurursodiol are licensed to treat amyotrophic lateral sclerosis in many industrialized countries. The TAR DNA-binding protein 43 inclusions are observed in 97% of those diagnosed with amyotrophic lateral sclerosis. This review provides a preliminary overview of the potential effects of TAR DNA-binding protein 43 in the pathogenesis of amyotrophic lateral sclerosis, including the abnormalities in nucleoplasmic transport, RNA function, post-translational modification, liquid-liquid phase separation, stress granules, mitochondrial dysfunction, oxidative stress, axonal transport, protein quality control system, and non-cellular autonomous functions (e.g., glial cell functions and prion-like propagation).
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Affiliation(s)
- Xinxin Wang
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Yushu Hu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
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25
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Godoy-Corchuelo JM, Ali Z, Brito Armas JM, Martins-Bach AB, García-Toledo I, Fernández-Beltrán LC, López-Carbonero JI, Bascuñana P, Spring S, Jimenez-Coca I, Muñoz de Bustillo Alfaro RA, Sánchez-Barrena MJ, Nair RR, Nieman BJ, Lerch JP, Miller KL, Ozdinler HP, Fisher EMC, Cunningham TJ, Acevedo-Arozena A, Corrochano S. TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43. Neurobiol Dis 2024; 193:106437. [PMID: 38367882 PMCID: PMC10988218 DOI: 10.1016/j.nbd.2024.106437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
TDP-43 pathology is found in several neurodegenerative disorders, collectively referred to as "TDP-43 proteinopathies". Aggregates of TDP-43 are present in the brains and spinal cords of >97% of amyotrophic lateral sclerosis (ALS), and in brains of ∼50% of frontotemporal dementia (FTD) patients. While mutations in the TDP-43 gene (TARDBP) are usually associated with ALS, many clinical reports have linked these mutations to cognitive impairments and/or FTD, but also to other neurodegenerative disorders including Parkinsonism (PD) or progressive supranuclear palsy (PSP). TDP-43 is a ubiquitously expressed, highly conserved RNA-binding protein that is involved in many cellular processes, mainly RNA metabolism. To investigate systemic pathological mechanisms in TDP-43 proteinopathies, aiming to capture the pleiotropic effects of TDP-43 mutations, we have further characterised a mouse model carrying a point mutation (M323K) within the endogenous Tardbp gene. Homozygous mutant mice developed cognitive and behavioural deficits as early as 3 months of age. This was coupled with significant brain structural abnormalities, mainly in the cortex, hippocampus, and white matter fibres, together with progressive cortical interneuron degeneration and neuroinflammation. At the motor level, progressive phenotypes appeared around 6 months of age. Thus, cognitive phenotypes appeared to be of a developmental origin with a mild associated progressive neurodegeneration, while the motor and neuromuscular phenotypes seemed neurodegenerative, underlined by a progressive loss of upper and lower motor neurons as well as distal denervation. This is accompanied by progressive elevated TDP-43 protein and mRNA levels in cortex and spinal cord of homozygous mutant mice from 3 months of age, together with increased cytoplasmic TDP-43 mislocalisation in cortex, hippocampus, hypothalamus, and spinal cord at 12 months of age. In conclusion, we find that Tardbp M323K homozygous mutant mice model many aspects of human TDP-43 proteinopathies, evidencing a dual role for TDP-43 in brain morphogenesis as well as in the maintenance of the motor system, making them an ideal in vivo model system to study the complex biology of TDP-43.
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Affiliation(s)
- Juan M Godoy-Corchuelo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Zeinab Ali
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; MRC Harwell Institute, Oxfordshire, UK
| | - Jose M Brito Armas
- Unidad de Investigación, Hospital Universitario de Canarias, ITB-ULL and CIBERNED, La Laguna, Spain
| | | | - Irene García-Toledo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Luis C Fernández-Beltrán
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan I López-Carbonero
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Pablo Bascuñana
- Brain Mapping Group, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Shoshana Spring
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Irene Jimenez-Coca
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | | | - Maria J Sánchez-Barrena
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Remya R Nair
- MRC Harwell Institute, Oxfordshire, UK; Nucleic Acid Therapy Accelerator (NATA), Harwell Campus, Oxfordshire, UK
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jason P Lerch
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Hande P Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, and UCL Queen Square Motor Neuron Disease Centre, UCL, Institute of Neurology, London, UK
| | - Thomas J Cunningham
- MRC Harwell Institute, Oxfordshire, UK; MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, UK
| | - Abraham Acevedo-Arozena
- Unidad de Investigación, Hospital Universitario de Canarias, ITB-ULL and CIBERNED, La Laguna, Spain.
| | - Silvia Corrochano
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; MRC Harwell Institute, Oxfordshire, UK.
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26
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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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27
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Sinha IR, Sandal PS, Burns GD, Mallika AP, Irwin KE, Cruz ALF, Wang V, Rodríguez JL, Wong PC, Ling JP. Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587011. [PMID: 38585725 PMCID: PMC10996699 DOI: 10.1101/2024.03.27.587011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.
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Affiliation(s)
- Irika R Sinha
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Parker S Sandal
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Grace D Burns
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Katherine E Irwin
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Anna Lourdes F Cruz
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vania Wang
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Philip C Wong
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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28
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Calliari A, Daughrity LM, Albagli EA, Castellanos Otero P, Yue M, Jansen-West K, Islam NN, Caulfield T, Rawlinson B, DeTure M, Cook C, Graff-Radford NR, Day GS, Boeve BF, Knopman DS, Petersen RC, Josephs KA, Oskarsson B, Gitler AD, Dickson DW, Gendron TF, Prudencio M, Ward ME, Zhang YJ, Petrucelli L. HDGFL2 cryptic proteins report presence of TDP-43 pathology in neurodegenerative diseases. Mol Neurodegener 2024; 19:29. [PMID: 38539264 PMCID: PMC10967196 DOI: 10.1186/s13024-024-00718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
This letter demonstrates the potential of novel cryptic proteins resulting from TAR DNA-binding protein 43 (TDP-43) dysfunction as markers of TDP-43 pathology in neurodegenerative diseases.
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Affiliation(s)
- Anna Calliari
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Ellen A Albagli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Naeyma N Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | - Gregory S Day
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | | | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA.
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA.
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29
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Salaikumaran M, Gopal PP. Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders. ACS Chem Neurosci 2024; 15:1096-1109. [PMID: 38466778 PMCID: PMC10959110 DOI: 10.1021/acschemneuro.3c00659] [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: 10/12/2023] [Revised: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
TDP-43, an essential RNA/DNA-binding protein, is central to the pathology of neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Pathological mislocalization and aggregation of TDP-43 disrupt RNA splicing, mRNA stability, and mRNA transport, thereby impairing neuronal function and survival. The formation of amyloid-like TDP-43 filaments is largely facilitated by the destabilization of an α-helical segment within the disordered C-terminal region. In this study, we hypothesized that preventing the destabilization of the α-helical domain could potentially halt the growth of these pathological filaments. To explore this, we utilized a range of in silico techniques to design and evaluate peptide-based therapeutics that bind to pathological TDP-43 amyloid-like filament crystal structures and resist β sheet conversion. Our computational approaches, including biophysical and secondary structure property prediction, molecular docking, 3D structure prediction, and molecular dynamics simulations, were used to assess the structure, stability, and binding affinity of these peptides in relation to pathological TDP-43 filaments. The results of our in silico analyses identified a selection of promising peptides which displayed a stable α-helical structure, exhibited an increased number of intramolecular hydrogen bonds within the helical domain, and demonstrated high binding affinities for pathological TDP-43 amyloid-like filaments. Molecular dynamics simulations provided further support for the structural and thermodynamic stability of these peptides, as they exhibited lower root-mean-square deviation and more favorable free energy landscapes over 300 ns. These findings establish α-helical propensity peptides as potential lead molecules for the development of novel therapeutics against TDP-43 aggregation. This structure-based computational approach for the rational design of peptide inhibitors opens a new direction in the search for effective interventions for ALS, FTD, and other related neurodegenerative diseases. The peptides identified as the most promising candidates in this study are currently subject to further testing and validation through both in vitro and in vivo experiments.
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Affiliation(s)
- Muthu
Raj Salaikumaran
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Pallavi P. Gopal
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Program
in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, Connecticut 06520-8055, United States
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30
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Krus KL, Benitez AM, Strickland A, Milbrandt J, Bloom AJ, DiAntonio A. Reduced STMN2 and pathogenic TDP-43, two hallmarks of ALS, synergize to accelerate motor decline in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585052. [PMID: 38562780 PMCID: PMC10983882 DOI: 10.1101/2024.03.19.585052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pathological TDP-43 loss from the nucleus and cytoplasmic aggregation occurs in almost all cases of ALS and half of frontotemporal dementia patients. Stathmin2 (Stmn2) is a key target of TDP-43 regulation and aberrantly spliced Stmn2 mRNA is found in patients with ALS, frontotemporal dementia, and Alzheimer's Disease. STMN2 participates in the axon injury response and its depletion in vivo partially replicates ALS-like symptoms including progressive motor deficits and distal NMJ denervation. The interaction between STMN2 loss and TDP-43 dysfunction has not been studied in mice because TDP-43 regulates human but not murine Stmn2 splicing. Therefore, we generated trans-heterozygous mice that lack one functional copy of Stmn2 and express one mutant TDP-43Q331K knock-in allele to investigate whether reduced STMN2 function exacerbates TDP-43-dependent pathology. Indeed, we observe synergy between these two alleles, resulting in an early onset, progressive motor deficit. Surprisingly, this behavioral defect is not accompanied by detectable neuropathology in the brain, spinal cord, peripheral nerves or at neuromuscular junctions (NMJs). However, the trans-heterozygous mice exhibit abnormal mitochondrial morphology in their distal axons and NMJs. As both STMN2 and TDP-43 affect mitochondrial dynamics, and neuronal mitochondrial dysfunction is a cardinal feature of many neurodegenerative diseases, this abnormality likely contributes to the observed motor deficit. These findings demonstrate that partial loss of STMN2 significantly exacerbates TDP-43-associated phenotypes, suggesting that STMN2 restoration could ameliorate TDP-43 related disease before the onset of degeneration.
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Affiliation(s)
- Kelsey L. Krus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Ana Morales Benitez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
| | - Amy Strickland
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - A. Joseph Bloom
- Department of Genetics, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States, 63110
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, United States, 63110
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31
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Spence H, Waldron FM, Saleeb RS, Brown AL, Rifai OM, Gilodi M, Read F, Roberts K, Milne G, Wilkinson D, O'Shaughnessy J, Pastore A, Fratta P, Shneider N, Tartaglia GG, Zacco E, Horrocks MH, Gregory JM. RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS. Acta Neuropathol 2024; 147:50. [PMID: 38443601 PMCID: PMC10914926 DOI: 10.1007/s00401-024-02705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
TDP-43 is an aggregation-prone protein which accumulates in the hallmark pathological inclusions of amyotrophic lateral sclerosis (ALS). However, the analysis of deeply phenotyped human post-mortem samples has shown that TDP-43 aggregation, revealed by standard antibody methods, correlates poorly with symptom manifestation. Recent identification of cryptic-splicing events, such as the detection of Stathmin-2 (STMN-2) cryptic exons, are providing evidence implicating TDP-43 loss-of-function as a potential driving pathomechanism but the temporal nature of TDP-43 loss and its relation to the disease process and clinical phenotype is not known. To address these outstanding questions, we used a novel RNA aptamer, TDP-43APT, to detect TDP-43 pathology and used single molecule in situ hybridization to sensitively reveal TDP-43 loss-of-function and applied these in a deeply phenotyped human post-mortem tissue cohort. We demonstrate that TDP-43APT identifies pathological TDP-43, detecting aggregation events that cannot be detected by classical antibody stains. We show that nuclear TDP-43 pathology is an early event, occurring prior to cytoplasmic accumulation and is associated with loss-of-function measured by coincident STMN-2 cryptic splicing pathology. Crucially, we show that these pathological features of TDP-43 loss-of-function precede the clinical inflection point and are not required for region specific clinical manifestation. Furthermore, we demonstrate that gain-of-function in the form of extensive cytoplasmic accumulation, but not loss-of-function, is the primary molecular correlate of clinical manifestation. Taken together, our findings demonstrate implications for early diagnostics as the presence of STMN-2 cryptic exons and early TDP-43 aggregation events could be detected prior to symptom onset, holding promise for early intervention in ALS.
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Affiliation(s)
- Holly Spence
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Fergal M Waldron
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Rebecca S Saleeb
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Olivia M Rifai
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Martina Gilodi
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Fiona Read
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kristine Roberts
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK
| | - Gillian Milne
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Debbie Wilkinson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Judi O'Shaughnessy
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | | | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Neil Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | | | - Elsa Zacco
- RNA System Biology Lab, Instituto Italiano di Tecnologia, Genoa, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Jenna M Gregory
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.
- Department of Pathology, NHS Grampian Tissue Biorepository, Aberdeen, UK.
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32
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Mori F, Yasui H, Miki Y, Kon T, Arai A, Kurotaki H, Tomiyama M, Wakabayashi K. Colocalization of TDP-43 and stress granules at the early stage of TDP-43 aggregation in amyotrophic lateral sclerosis. Brain Pathol 2024; 34:e13215. [PMID: 37793650 PMCID: PMC10901621 DOI: 10.1111/bpa.13215] [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: 07/26/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
TDP-43 aggregates (skeins and round inclusions [RIs]) are frequent histopathological features of amyotrophic lateral sclerosis (ALS). We have shown that diffuse punctate cytoplasmic staining (DPCS) is the earliest pathologic manifestation of TDP-43 in ALS, corresponding to nonfibrillar TDP-43 located in the rough endoplasmic reticulum. Previous in vitro studies have suggested that TDP-43 inclusions may be derived from stress granules (SGs). Therefore, we investigated the involvement of SGs in the formation of TDP-43 inclusions. Formalin-fixed spinal cords of six ALS patients with a disease duration of less than 1 year (short duration), eight patients with a disease duration of 2-5 years (standard duration), and five normal controls were subjected to histopathological examination using antibodies against an SG marker, HuR. In normal controls, the cytoplasm of anterior horn cells was diffusely HuR-positive. In short-duration and standard-duration ALS, the number of HuR-positive anterior horn cells was significantly decreased relative to the controls. DPCS and RIs were more frequent in short-duration ALS than in standard-duration ALS. The majority of DPCS areas and a small proportion of RIs, but not skeins, were positive for HuR. Immunoelectron microscopy showed that ribosome-like granular structures in DPCS areas and RIs were labeled with anti-HuR, whereas skeins were not. These findings suggest that colocalization of TDP-43 and SGs occurs at the early stage of TDP-43 aggregation.
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Affiliation(s)
- Fumiaki Mori
- Department of NeuropathologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
| | - Hina Yasui
- Department of NeuropathologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
| | - Yasuo Miki
- Department of NeuropathologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
| | - Tomoya Kon
- Department of NeurologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
| | - Akira Arai
- Department of NeurologyAomori Prefectural Central HospitalAomoriJapan
| | | | - Masahiko Tomiyama
- Department of NeurologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
| | - Koichi Wakabayashi
- Department of NeuropathologyInstitute of Brain Science, Hirosaki University Graduate School of MedicineHirosakiJapan
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33
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Gomez N, Hsieh C, Li X, Dykstra M, Waksmacki J, Altheim C, Bechar Y, Klim J, Zaepfel B, Rothstein J, Tank EE, Barmada SJ. Counter-regulation of RNA stability by UPF1 and TDP43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578310. [PMID: 38352350 PMCID: PMC10862862 DOI: 10.1101/2024.01.31.578310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
RNA quality control is crucial for proper regulation of gene expression. Disruption of nonsense mediated mRNA decay (NMD), the primary RNA decay pathway responsible for the degradation of transcripts containing premature termination codons (PTCs), can disrupt development and lead to multiple diseases in humans and other animals. Similarly, therapies targeting NMD may have applications in hematological, neoplastic and neurological disorders. As such, tools capable of accurately quantifying NMD status could be invaluable for investigations of disease pathogenesis and biomarker identification. Toward this end, we assemble, validate, and apply a next-generation sequencing approach (NMDq) for identifying and measuring the abundance of PTC-containing transcripts. After validating NMDq performance and confirming its utility for tracking RNA surveillance, we apply it to determine pathway activity in two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) characterized by RNA misprocessing and abnormal RNA stability. Despite the genetic and pathologic evidence implicating dysfunctional RNA metabolism, and NMD in particular, in these conditions, we detected no significant differences in PTC-encoding transcripts in ALS models or disease. Contrary to expectations, overexpression of the master NMD regulator UPF1 had little effect on the clearance of transcripts with PTCs, but rather restored RNA homeostasis through differential use and decay of alternatively poly-adenylated isoforms. Together, these data suggest that canonical NMD is not a significant contributor to ALS/FTD pathogenesis, and that UPF1 promotes neuronal survival by regulating transcripts with abnormally long 3'UTRs.
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34
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang YJ, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Kargbo-Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Sacramento EK, Shah SI, Nalls MA, Colón-Mercado JM, Reyes JF, Ryan VH, Nelson MP, Cook CN, Li Z, Screven L, Kwan JY, Mehta PR, Zanovello M, Hallegger M, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff NP, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Reich DS, Rohrer JD, Malaspina A, Dickson DW, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162. [PMID: 38277467 DOI: 10.1126/scitranslmed.adg7162] [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: 01/17/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Kargbo-Hill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Kelmer Sacramento
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jennifer M Colón-Mercado
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Martina Hallegger
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jernej Ule
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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35
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Chung M, Carter EK, Veire AM, Dammer EB, Chang J, Duong DM, Raj N, Bassell GJ, Glass JD, Gendron TF, Nelson PT, Levey AI, Seyfried NT, McEachin ZT. Cryptic exon inclusion is a molecular signature of LATE-NC in aging brains. Acta Neuropathol 2024; 147:29. [PMID: 38308693 PMCID: PMC10838224 DOI: 10.1007/s00401-023-02671-0] [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: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/17/2023] [Indexed: 02/05/2024]
Abstract
The aggregation, mislocalization, and phosphorylation of TDP-43 are pathologic hallmarks of several neurodegenerative diseases and provide a defining criterion for the neuropathologic diagnosis of Limbic-predominant Age-related TDP-43 Encephalopathy (LATE). LATE neuropathologic changes (LATE-NC) are often comorbid with other neurodegenerative pathologies including Alzheimer's disease neuropathologic changes (ADNC). We examined whether TDP-43 regulated cryptic exons accumulate in the hippocampus of neuropathologically confirmed LATE-NC cases. We found that several cryptic RNAs are robustly expressed in LATE-NC cases with or without comorbid ADNC and correlate with pTDP-43 abundance; however, the accumulation of cryptic RNAs is more robust in LATE-NC with comorbid ADNC. Additionally, cryptic RNAs can robustly distinguish LATE-NC from healthy controls and AD cases. These findings expand our current understanding and provide novel potential biomarkers for LATE pathogenesis.
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Affiliation(s)
- Mingee Chung
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - E Kathleen Carter
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Austin M Veire
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Jianjun Chang
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nisha Raj
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Jonathan D Glass
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center On Aging, University of Kentucky, Lexington, KY, 40536, USA
| | - Allan I Levey
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA.
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
| | - Zachary T McEachin
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA.
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
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36
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Hruska-Plochan M, Wiersma VI, Betz KM, Mallona I, Ronchi S, Maniecka Z, Hock EM, Tantardini E, Laferriere F, Sahadevan S, Hoop V, Delvendahl I, Pérez-Berlanga M, Gatta B, Panatta M, van der Bourg A, Bohaciakova D, Sharma P, De Vos L, Frontzek K, Aguzzi A, Lashley T, Robinson MD, Karayannis T, Mueller M, Hierlemann A, Polymenidou M. A model of human neural networks reveals NPTX2 pathology in ALS and FTLD. Nature 2024; 626:1073-1083. [PMID: 38355792 PMCID: PMC10901740 DOI: 10.1038/s41586-024-07042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms2-5 that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors6. Single-cell transcriptomics and comparison to independent neural stem cells7 showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids8. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3' untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity.
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Affiliation(s)
| | - Vera I Wiersma
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Katharina M Betz
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Izaskun Mallona
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Silvia Ronchi
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- MaxWell Biosystems AG, Zurich, Switzerland
| | - Zuzanna Maniecka
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Eva-Maria Hock
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Elena Tantardini
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Florent Laferriere
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Sonu Sahadevan
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Vanessa Hoop
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Igor Delvendahl
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Beatrice Gatta
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Martina Panatta
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | | | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University Brno, Brno, Czech Republic
| | - Puneet Sharma
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- NCCR RNA and Disease Technology Platform, Bern, Switzerland
| | - Laura De Vos
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological diseases, Department of Movement Disorders, UCL Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Martin Mueller
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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37
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Dos Passos PM, Hemamali EH, Mamede LD, Hayes LR, Ayala YM. RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention. PLoS Biol 2024; 22:e3002527. [PMID: 38422113 DOI: 10.1371/journal.pbio.3002527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
TDP-43 is an essential RNA-binding protein strongly implicated in the pathogenesis of neurodegenerative disorders characterized by cytoplasmic aggregates and loss of nuclear TDP-43. The protein shuttles between nucleus and cytoplasm, yet maintaining predominantly nuclear TDP-43 localization is important for TDP-43 function and for inhibiting cytoplasmic aggregation. We previously demonstrated that specific RNA binding mediates TDP-43 self-assembly and biomolecular condensation, requiring multivalent interactions via N- and C-terminal domains. Here, we show that these complexes play a key role in TDP-43 nuclear retention. TDP-43 forms macromolecular complexes with a wide range of size distribution in cells and we find that defects in RNA binding or inter-domain interactions, including phase separation, impair the assembly of the largest species. Our findings suggest that recruitment into these macromolecular complexes prevents cytoplasmic egress of TDP-43 in a size-dependent manner. Our observations uncover fundamental mechanisms controlling TDP-43 cellular homeostasis, whereby regulation of RNA-mediated self-assembly modulates TDP-43 nucleocytoplasmic distribution. Moreover, these findings highlight pathways that may be implicated in TDP-43 proteinopathies and identify potential therapeutic targets.
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Affiliation(s)
- Patricia M Dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Erandika H Hemamali
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lohany D Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yuna M Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
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38
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Khan M, Chen XXL, Dias M, Santos JR, Kour S, You J, van Bruggen R, Youssef MMM, Wan YW, Liu Z, Rosenfeld JA, Tan Q, Pandey UB, Yalamanchili HK, Park J. MATR3 pathogenic variants differentially impair its cryptic splicing repression function. FEBS Lett 2024; 598:415-436. [PMID: 38320753 DOI: 10.1002/1873-3468.14806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Matrin-3 (MATR3) is an RNA-binding protein implicated in neurodegenerative and neurodevelopmental diseases. However, little is known regarding the role of MATR3 in cryptic splicing within the context of functional genes and how disease-associated variants impact this function. We show that loss of MATR3 leads to cryptic exon inclusion in many transcripts. We reveal that ALS-linked S85C pathogenic variant reduces MATR3 solubility but does not impair RNA binding. In parallel, we report a novel neurodevelopmental disease-associated M548T variant, located in the RRM2 domain, which reduces protein solubility and impairs RNA binding and cryptic splicing repression functions of MATR3. Altogether, our research identifies cryptic events within functional genes and demonstrates how disease-associated variants impact MATR3 cryptic splicing repression function.
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Affiliation(s)
- Mashiat Khan
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Xiao Xiao Lily Chen
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Michelle Dias
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jhune Rizsan Santos
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Justin You
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Rebekah van Bruggen
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Mohieldin M M Youssef
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Qiumin Tan
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeehye Park
- Department of Molecular Genetics, University of Toronto, Canada
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
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39
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Irwin KE, Jasin P, Braunstein KE, Sinha IR, Garret MA, Bowden KD, Chang K, Troncoso JC, Moghekar A, Oh ES, Raitcheva D, Bartlett D, Miller T, Berry JD, Traynor BJ, Ling JP, Wong PC. A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS-FTD. Nat Med 2024; 30:382-393. [PMID: 38278991 PMCID: PMC10878965 DOI: 10.1038/s41591-023-02788-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects loss of function of TDP-43, and thus detection of proteins containing cryptic exon-encoded neoepitopes in cerebrospinal fluid (CSF) or blood could reveal the earliest stages of TDP-43 dysregulation in patients. Here we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in ALS-FTD, including in presymptomatic C9orf72 mutation carriers. Cryptic hepatoma-derived growth factor-like protein 2 (HDGFL2) accumulates in CSF at significantly higher levels in familial ALS-FTD and sporadic ALS compared with controls and is elevated earlier than neurofilament light and phosphorylated neurofilament heavy chain protein levels in familial disease. Cryptic HDGFL2 can also be detected in blood of individuals with ALS-FTD, including in presymptomatic C9orf72 mutation carriers, and accumulates at levels highly correlated with those in CSF. Our findings indicate that loss of TDP-43 cryptic splicing repression occurs early in disease progression, even presymptomatically, and that detection of the HDGFL2 cryptic neoepitope serves as a potential diagnostic biomarker for ALS, which should facilitate patient recruitment and measurement of target engagement in clinical trials.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Pei Jasin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | - Irika R Sinha
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Mark A Garret
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Kyra D Bowden
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Esther S Oh
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD, USA
| | | | | | - Timothy Miller
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- National Institute of Neurological Disorders, National Institutes of Health, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, USA.
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40
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Arribas V, Onetti Y, Ramiro-Pareta M, Villacampa P, Beck H, Alberola M, Esteve-Codina A, Merkel A, Sperandio M, Martínez-Estrada OM, Schmid B, Montanez E. Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation. JCI Insight 2024; 9:e177819. [PMID: 38300714 PMCID: PMC11143933 DOI: 10.1172/jci.insight.177819] [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: 11/20/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA-binding protein that regulates gene expression, and its malfunction in neurons has been causally associated with multiple neurodegenerative disorders. Although progress has been made in understanding the functions of TDP-43 in neurons, little is known about its roles in endothelial cells (ECs), angiogenesis, and vascular function. Using inducible EC-specific TDP-43-KO mice, we showed that TDP-43 is required for sprouting angiogenesis, vascular barrier integrity, and blood vessel stability. Postnatal EC-specific deletion of TDP-43 led to retinal hypovascularization due to defects in vessel sprouting associated with reduced EC proliferation and migration. In mature blood vessels, loss of TDP-43 disrupted the blood-brain barrier and triggered vascular degeneration. These vascular defects were associated with an inflammatory response in the CNS with activation of microglia and astrocytes. Mechanistically, deletion of TDP-43 disrupted the fibronectin matrix around sprouting vessels and reduced β-catenin signaling in ECs. Together, our results indicate that TDP-43 is essential for the formation of a stable and mature vasculature.
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Affiliation(s)
- Víctor Arribas
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Yara Onetti
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Marina Ramiro-Pareta
- Celltec-UB, Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, and
- Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Pilar Villacampa
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Heike Beck
- Walter Brendel Centre of Experimental Medicine, Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Mariona Alberola
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Angelika Merkel
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Markus Sperandio
- Walter Brendel Centre of Experimental Medicine, Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Ofelia M. Martínez-Estrada
- Celltec-UB, Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, and
- Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Bettina Schmid
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Eloi Montanez
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
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41
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Irwin KE, Sheth U, Wong PC, Gendron TF. Fluid biomarkers for amyotrophic lateral sclerosis: a review. Mol Neurodegener 2024; 19:9. [PMID: 38267984 PMCID: PMC10809579 DOI: 10.1186/s13024-023-00685-6] [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: 08/28/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of upper and lower motor neurons. Presently, three FDA-approved drugs are available to help slow functional decline for patients with ALS, but no cure yet exists. With an average life expectancy of only two to five years after diagnosis, there is a clear need for biomarkers to improve the care of patients with ALS and to expedite ALS treatment development. Here, we provide a review of the efforts made towards identifying diagnostic, prognostic, susceptibility/risk, and response fluid biomarkers with the intent to facilitate a more rapid and accurate ALS diagnosis, to better predict prognosis, to improve clinical trial design, and to inform interpretation of clinical trial results. Over the course of 20 + years, several promising fluid biomarker candidates for ALS have emerged. These will be discussed, as will the exciting new strategies being explored for ALS biomarker discovery and development.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, 21205, USA
| | - Udit Sheth
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, 21205, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, 21205, USA.
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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42
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Guise AJ, Misal SA, Carson R, Chu JH, Boekweg H, Van Der Watt D, Welsh NC, Truong T, Liang Y, Xu S, Benedetto G, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. Cell Rep 2024; 43:113636. [PMID: 38183652 PMCID: PMC10926001 DOI: 10.1016/j.celrep.2023.113636] [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: 06/07/2023] [Revised: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024] Open
Abstract
A limitation of conventional bulk-tissue proteome studies in amyotrophic lateral sclerosis (ALS) is the confounding of motor neuron (MN) signals by admixed non-MN proteins. Here, we leverage laser capture microdissection and nanoPOTS single-cell mass spectrometry-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control tissues. In a follow-up analysis, we examine the impact of stratification of MNs based on cytoplasmic transactive response DNA-binding protein 43 (TDP-43)+ inclusion pathology on the profiles of 2,238 proteins. We report extensive overlap in differentially abundant proteins identified in ALS MNs with or without overt TDP-43 pathology, suggesting early and sustained dysregulation of cellular respiration, mRNA splicing, translation, and vesicular transport in ALS. Together, these data provide insights into proteome-level changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein dynamics in human neurologic diseases.
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Affiliation(s)
| | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | - Hannah Boekweg
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | | | | | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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43
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Bryce-Smith S, Brown AL, Mehta PR, Mattedi F, Mikheenko A, Barattucci S, Zanovello M, Dattilo D, Yome M, Hill SE, Qi YA, Wilkins OG, Sun K, Ryadnov E, Wan Y, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Ward M, Secrier M, Fratta P. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576625. [PMID: 38313254 PMCID: PMC10836071 DOI: 10.1101/2024.01.22.576625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Francesca Mattedi
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dario Dattilo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Yome
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E. Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yue A. Qi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Kai Sun
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Yixuan Wan
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Jose Norberto S. Vargas
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicol Birsa
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
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44
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Zeng Y, Lovchykova A, Akiyama T, Liu C, Guo C, Jawahar VM, Sianto O, Calliari A, Prudencio M, Dickson DW, Petrucelli L, Gitler AD. TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575730. [PMID: 38328059 PMCID: PMC10849503 DOI: 10.1101/2024.01.22.575730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B) and providing evidence that alternative polyadenylation is a new facet of TDP-43 pathology.
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Affiliation(s)
- Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Caiwei Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vidhya Maheswari Jawahar
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Odilia Sianto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Calliari
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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45
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Zhu L, Deng F, Bai D, Hou J, Jia Q, Zhang C, Ou K, Li S, Li XJ, Yin P. Loss of TDP-43 mediates severe neurotoxicity by suppressing PJA1 gene transcription in the monkey brain. Cell Mol Life Sci 2024; 81:16. [PMID: 38194085 PMCID: PMC11072099 DOI: 10.1007/s00018-023-05066-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
The nuclear loss and cytoplasmic accumulation of TDP-43 (TAR DNA/RNA binding protein 43) are pathological hallmarks of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previously, we reported that the primate-specific cleavage of TDP-43 accounts for its cytoplasmic mislocalization in patients' brains. This prompted us to investigate further whether and how the loss of nuclear TDP-43 mediates neuropathology in primate brain. In this study, we report that TDP-43 knockdown at the similar effectiveness, induces more damage to neuronal cells in the monkey brain than rodent mouse. Importantly, the loss of TDP-43 suppresses the E3 ubiquitin ligase PJA1 expression in the monkey brain at transcriptional level, but yields an opposite upregulation of PJA1 in the mouse brain. This distinct effect is due to the species-dependent binding of nuclear TDP-43 to the unique promoter sequences of the PJA1 genes. Further analyses reveal that the reduction of PJA1 accelerates neurotoxicity, whereas overexpressing PJA1 diminishes neuronal cell death by the TDP-43 knockdown in vivo. Our findings not only uncover a novel primate-specific neurotoxic contribution to the loss of function theory of TDP-43 proteinopathy, but also underscore a potential therapeutic approach of PJA1 to the loss of nuclear TDP-43.
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Affiliation(s)
- Longhong Zhu
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Fuyu Deng
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Dazhang Bai
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, 637000, China
- Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, 637000, China
| | - Junqi Hou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Qingqing Jia
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Chen Zhang
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Kaili Ou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
| | - Peng Yin
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
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46
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Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JPWE, Denomy C, Hutchinson C, Abidullah HM, Austin Hammond S, Pastushok L, Vizeacoumar FS, Levin MC. hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nat Commun 2024; 15:356. [PMID: 38191621 PMCID: PMC10774274 DOI: 10.1038/s41467-023-44658-1] [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: 06/23/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.
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Affiliation(s)
- Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Yulian Ding
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
- Division of Biomedical Engineering, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Joseph-Patrick W E Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Connor Denomy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Hashim M Abidullah
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Landon Pastushok
- Advanced Diagnostics Research Laboratory, Department of Pathology and Lab Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada.
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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47
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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48
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Harley P, Kerins C, Gatt A, Neves G, Riccio F, Machado CB, Cheesbrough A, R'Bibo L, Burrone J, Lieberam I. Aberrant axon initial segment plasticity and intrinsic excitability of ALS hiPSC motor neurons. Cell Rep 2023; 42:113509. [PMID: 38019651 DOI: 10.1016/j.celrep.2023.113509] [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: 05/04/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Dysregulated neuronal excitability is a hallmark of amyotrophic lateral sclerosis (ALS). We sought to investigate how functional changes to the axon initial segment (AIS), the site of action potential generation, could impact neuronal excitability in ALS human induced pluripotent stem cell (hiPSC) motor neurons. We find that early TDP-43 and C9orf72 hiPSC motor neurons show an increase in the length of the AIS and impaired activity-dependent AIS plasticity that is linked to abnormal homeostatic regulation of neuronal activity and intrinsic hyperexcitability. In turn, these hyperactive neurons drive increased spontaneous myofiber contractions of in vitro hiPSC motor units. In contrast, late hiPSC and postmortem ALS motor neurons show AIS shortening, and hiPSC motor neurons progress to hypoexcitability. At a molecular level, aberrant expression of the AIS master scaffolding protein ankyrin-G and AIS-specific voltage-gated sodium channels mirror these dynamic changes in AIS function and excitability. Our results point toward the AIS as an important site of dysfunction in ALS motor neurons.
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Affiliation(s)
- Peter Harley
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK; UCL Queen Square Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Caoimhe Kerins
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK; Centre for Craniofacial & Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Ariana Gatt
- Queen Square Brain Bank, Department of Neurodegenerative Disease, Institute of Neurology, University College London, London WC1N 1PJ, UK
| | - Guilherme Neves
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK
| | - Federica Riccio
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK
| | - Carolina Barcellos Machado
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK
| | - Aimee Cheesbrough
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK
| | - Lea R'Bibo
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK
| | - Juan Burrone
- Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, Kings College London, London SE1 1UL, UK.
| | - Ivo Lieberam
- Centre for Gene Therapy & Regenerative Medicine, Kings College London, London SE1 9RT, UK; Centre for Developmental Neurobiology, Kings College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, Kings College London, London SE1 1UL, UK.
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49
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Chang K, Ling JP, Redding-Ochoa J, An Y, Li L, Dean SA, Blanchard TG, Pylyukh T, Barrett A, Irwin KE, Moghekar A, Resnick SM, Wong PC, Troncoso JC. Loss of TDP-43 splicing repression occurs early in the aging population and is associated with Alzheimer's disease neuropathologic changes and cognitive decline. Acta Neuropathol 2023; 147:4. [PMID: 38133681 DOI: 10.1007/s00401-023-02653-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
LATE-NC, the neuropathologic changes of limbic-predominant age-related TAR DNA-binding protein 43 kDa (TDP-43) encephalopathy are frequently associated with Alzheimer's disease (AD) and cognitive impairment in older adults. The association of TDP-43 proteinopathy with AD neuropathologic changes (ADNC) and its impact on specific cognitive domains are not fully understood and whether loss of TDP-43 function occurs early in the aging brain remains unknown. Here, using a large set of autopsies from the Baltimore Longitudinal Study of Aging (BLSA) and another younger cohort, we were able to study brains from subjects 21-109 years of age. Examination of these brains show that loss of TDP-43 splicing repression, as judged by TDP-43 nuclear clearance and expression of a cryptic exon in HDGFL2, first occurs during the 6th decade, preceding by a decade the appearance of TDP-43+ neuronal cytoplasmic inclusions (NCIs). We corroborated this observation using a monoclonal antibody to demonstrate a cryptic exon-encoded neoepitope within HDGFL2 in neurons exhibiting nuclear clearance of TDP-43. TDP-43 nuclear clearance is associated with increased burden of tau pathology. Age at death, female sex, high CERAD neuritic plaque score, and high Braak neurofibrillary stage significantly increase the odds of LATE-NC. Faster rates of cognitive decline on verbal memory (California Verbal Learning Test immediate recall), visuospatial ability (Card Rotations Test), mental status (MMSE) and semantic fluency (Category Fluency Test) were associated with LATE-NC. Notably, the effects of LATE-NC on verbal memory and visuospatial ability are independent of ADNC. However, the effects of TDP-43 nuclear clearance in absence of NCI on the longitudinal trajectories and levels of cognitive measures are not significant. These results establish that loss of TDP-43 splicing repression is an early event occurring in the aging population during the development of TDP-43 proteinopathy and is associated with increased tau pathology. Furthermore, LATE-NC correlates with high levels of ADNC but also has an impact on specific memory and visuospatial functions in aging that is independent of AD.
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Affiliation(s)
- Koping Chang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, 100225, Taiwan
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ling Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Office of the Chief Medical Examiner, State of Maryland, Baltimore, MD, 21223, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Stephanie A Dean
- Office of the Chief Medical Examiner, State of Maryland, Baltimore, MD, 21223, USA
| | - Thomas G Blanchard
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tatiana Pylyukh
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alexander Barrett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Katherine E Irwin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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50
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Cheemala A, Kimble AL, Tyburski JD, Leclair NK, Zuberi AR, Murphy M, Jellison ER, Reese B, Hu X, Lutz CM, Yan R, Murphy PA. Loss of Endothelial TDP-43 Leads to Blood Brain Barrier Defects in Mouse Models of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571184. [PMID: 38168388 PMCID: PMC10760101 DOI: 10.1101/2023.12.13.571184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Loss of nuclear TDP-43 occurs in a wide range of neurodegenerative diseases, and specific mutations in the TARDBP gene that encodes the protein are linked to familial Frontal Temporal Lobar Dementia (FTD), and Amyotrophic Lateral Sclerosis (ALS). Although the focus has been on neuronal cell dysfunction caused by TDP-43 variants, TARDBP mRNA transcripts are expressed at similar levels in brain endothelial cells (ECs). Since increased permeability across the blood brain barrier (BBB) precedes cognitive decline, we postulated that altered functions of TDP-43 in ECs contributes to BBB dysfunction in neurodegenerative disease. To test this hypothesis, we examined EC function and BBB properties in mice with either knock-in mutations found in ALS/FTLD patients (TARDBPG348C and GRNR493X) or EC-specific deletion of TDP-43 throughout the endothelium (Cdh5(PAC)CreERT2; Tardbpff) or restricted to brain endothelium (Slco1c1(BAC)CreERT2; Tardbpff). We found that TARDBPG348C mice exhibited increased permeability to 3kDa Texas Red dextran and NHS-biotin, relative to their littermate controls, which could be recapitulated in cultured brain ECs from these mice. Nuclear levels of TDP-43 were reduced in vitro and in vivo in ECs from TARDBPG348C mice. This coincided with a reduction in junctional proteins VE-cadherin, claudin-5 and ZO-1 in isolated ECs, supporting a cell autonomous effect on barrier function through a loss of nuclear TDP-43. We further examined two models of Tardbp deletion in ECs, and found that the loss of TDP-43 throughout the endothelium led to systemic endothelial activation and permeability. Deletion specifically within the brain endothelium acutely increased BBB permeability, and eventually led to hallmarks of FTD, including fibrin deposition, microglial and astrocyte activation, and behavioral defects. Together, these data show that TDP-43 dysfunction specifically within brain ECs would contribute to the BBB defects observed early in the progression of ALS/FTLD.
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Affiliation(s)
- Ashok Cheemala
- Center for Vascular Biology, University of Connecticut Medical School, Farmington, CT
| | - Amy L Kimble
- Center for Vascular Biology, University of Connecticut Medical School, Farmington, CT
| | - Jordan D Tyburski
- Center for Vascular Biology, University of Connecticut Medical School, Farmington, CT
| | - Nathan K Leclair
- MD/PhD Program, University of Connecticut School of Medicine, Farmington, CT
| | - Aamir R Zuberi
- Rare Disease Translational Center and Technology Evaluation and Development Laboratory, The Jackson Laboratory, Bar Harbor, ME
| | - Melissa Murphy
- Center for Vascular Biology, University of Connecticut Medical School, Farmington, CT
| | - Evan R Jellison
- Department of Immunology, University of Connecticut Medical School, Farmington, CT
| | - Bo Reese
- Center for Genome Innovation, University of Connecticut, Storrs, CT
| | - Xiangyou Hu
- Department of Neuroscience, University of Connecticut Medical School, Farmington, CT
| | - Cathleen M Lutz
- Rare Disease Translational Center and Technology Evaluation and Development Laboratory, The Jackson Laboratory, Bar Harbor, ME
| | - Riqiang Yan
- Department of Neuroscience, University of Connecticut Medical School, Farmington, CT
| | - Patrick A Murphy
- Center for Vascular Biology, University of Connecticut Medical School, Farmington, CT
- Department of Immunology, University of Connecticut Medical School, Farmington, CT
- Department of Neuroscience, University of Connecticut Medical School, Farmington, CT
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